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revision 1.1881 by m_bates, Tue Jun 18 21:30:33 2013 UTC revision 1.2047 by jmc, Thu Aug 14 19:56:30 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 model/src & pkgs:
8      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
9         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
10         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
11         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
12      + change accordingly all calling S/R.
13      - use local temperature/salinity/ptracer tendency array (without bi,bj)
14        in S/R temp/salt/ptracers_integrate.F
15    o pkg/seaice:
16      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
17        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
18      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
19        in seaice_lsr
20      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
21        in s/r seaice_lsr_calc_coeffs
22    o pkg/mdsio:
23      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
24        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
25        too long (e.g., > MAX_LEN_FNAM/2 )
26    
27    checkpoint65b (2014/08/12)
28    o pkg/matrix:
29      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
30    o model/src:
31      - fix initialisation of geothermalFile; compile geothermal-flux code in
32        natl_box verification experiment.
33    o model/src & pkg/down_slope:
34      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
35      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
36        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
37        results at machine truncation level: update output of experiments
38        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
39    o pkg/diagnostics (Stats-Diags):
40      - do not cumulate the full volume when DIAGNOSTICS_FILL is
41        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
42        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
43        times (but Min,Max and StD are still wrong).
44    o model/src:
45      - add geothermal flux forcing: read in ini_forcing.F as time-constant
46        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
47    o model/src:
48      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
49        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
50        arrays are already updated while adjustments (filters, conv.adjustment) are
51        still applied later, in S/R TRACERS_CORRECTION_STEP.
52    o model/src:
53      - store in common bloc array "rhoInSitu" the virtual potential temperature
54        anomaly that is used to compute geopotential: this make the atmos code
55        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
56    o pkg/seaice/seaice_lsr.F
57      - rename integer variable ilcall to ipass (that's what it is called
58        in the residual diagnostics
59      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
60        default) for improved non-linear convergence of the first few steps
61      - adjust a few comments and add new ones to explain some of the store
62        directives
63    o pkg/generic_advdiff (& ptracers):
64      - re-work the code to check for valid advection scheme and for minimum
65        size of overlap (now stored in local common bloc in gad_advscheme.F)
66    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
67      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
68      - add an auxilliary variable "bet" and fix store directives and keys in
69        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
70        less exact gradients in my tests); but there are still
71        recomputation warning (although gradients are sort of OK), when
72        SEAICE_LSR_VECTORIZE is not defined, so this flag and
73        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
74      - update verification experiments lab_sea.
75      - change some comments in S/R seaice_calc_viscosities
76    o model/src:
77      - if staggerTimeStep=T, always apply exchange to velocity field in
78        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
79        (independent of using multi-dim advection or not); no effect on FWD run
80        but affects AD results (at machine truncation level): update output of
81        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
82        and isomip (oad: 12.d).
83    o pkg/generic_advdiff:
84      - stop if doAB_onGtGs is set to FALSE but ignored
85      - refine warning related to stability of tracer time-stepping
86        regarding internal wave dynamics.
87      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
88        on staggerTimeStep & implicitIntGravWave (will now get a warning
89        if potentially unstable).
90    o pkg/kl10:
91      - add new pkg "kl10" for mixing due to internal wave breaking, from
92        http://www.sciencedirect.com/science/article/pii/S1463500310000144
93        (contribution from Jody Klymak), tested in verification experiment
94        verification/internal_wave/input.kl10/
95    o isomip experiment:
96      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
97        (input.htd) and update the output.
98    o cd_code experiments:
99      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
100        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
101        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
102        update the corresponding output.
103    o pkg/seaice:
104      - reduce the number of include files and store directives in
105        S/R seaice_lsr_tridiagu/v
106      - change the order of loops in one case in S/R seaice_lsr_tridiagv
107        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
108        get rid off one store directive (a TAF bug?)
109      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
110        S/R seaice_lsr_tridiagv to change the loop range for consistency
111      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
112      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
113        S/R seaice_lsr_tridiagu/v (requires update of
114        offline_exf_seaice/input.dyn_jfnk)
115    
116    checkpoint65a (2014/07/27)
117    o model/src:
118      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
119        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
120        (topo in p-coords, ice-shelf in z-coords); update output of experiments
121        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
122    o model/src:
123      - collect momentum forcing tendency into local 2-D array (passed as argument
124        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
125        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
126        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
127      - collect T & S forcing tendency into local 2-D array (passed as argument to
128        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
129        affects results at machine truncation level (e.g., ocean: if using
130        SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)
131        moist correction due to vertical advection).
132      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
133        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
134        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
135        obcs_ctrl (ad & fwd grd @ 12 & 7).
136    o pkg/ptracers & diagnostics:
137      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
138        title (to avoid some unexpected truncation); sort out ptracers diags units.
139      - collect ptracer forcing tendency into local 2-D array (passed as argument
140        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
141    
142    checkpoint65 (2014/07/18)
143    o pkg/fizhi:
144      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
145        affects results at machine truncation level. Update output of experiments
146        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
147    o pkg/seaice: more clean up
148      - rename TAF common block tapes to be more consistent and remove
149        unnecessary duplicates
150      - add store directives to remove more recomputations, but use smaller
151        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
152        The idea behind this flag is to reduce the memory footprint when the
153        adjoint of the LSR is not required. As of now, defining the flag
154        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
155        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
156        For experiment offline_exf_seaice, this means on a linux box with gfortran
157        nearly a factor of 10 (but keep in mind there is mostly seaice code in
158        this experiment):
159        > size mitgcmuv_ad
160        text    data        bss     dec        hex  
161        5100659 1216  220458952  225560827  d71c8fb
162        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
163        but only a moderate increase of 36% for global_ocean.cs32x15:
164        text    data        bss     dec        hex
165        6695027 1648 1014578664 1021275339 3cdf6ccb
166        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
167      - note: there are still recomputations in global_ocean.cs32x15 and
168        offline_exf_seaice and the gradient agreement changes (gets a
169        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
170      - in general, the AD gradients still are wrong
171    o OpenAD
172      - clean up code_oad/ directories somewhat by moving files
173        dontCompile, dontTransform, keepOriginal to OAD_support/
174    o model/src:
175      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
176        (not currently tested): add dissipation terms before NLFS rescaling of
177        tendencies (previously done after).
178    o pkg/diagnostics:
179      - write stats-diags in ascii file with more digits (same as in monitor).
180    o pkg/down_slope:
181      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
182        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
183    o model/src:
184      - new file "apply_forcing.F" containing all the code previously in
185        external_forcing.F, but with new argument list: pass, as new argument,
186        the current level tendency array to update (instead of a direct update
187        of the common bloc array). Change the corresponding calls.
188      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
189        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
190    o pkg/seaice/seaice_lsr, a little bit of clean up
191      - rearrange some code blocks, so that now all calculations for
192        setting up the right-hand-sides done within one single block
193        (I find that easier to read and understand)
194      - rearrange freedrift-code to reduce the number of ifdefs
195      - adjust some indentations and comments
196    
197    checkpoint64z (2014/07/10)
198    o model/src and several pkgs:
199      - change argument list of all S/R called from external_forcing.F and
200        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
201        to pass, as argument, the current level tendency array to update
202        (instead of a direct update of the common bloc array).
203      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
204      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
205    o pkg/seaice/seaice_lsr.F
206      - always initialize local arrays in seaice_lsr_tridiagu/v
207      - add more local tapes to seaice_lsr_tridiagu/v
208      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
209        keep it in bi/bj loop; this seems to be essential
210      - gradients are still wrong but only by 4-7 orders of magnitude
211        instead of 15 orders of magnitude, lab_sea improves a little
212    o pkg/seaice
213      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
214        generates unnecessary code in seaice_lsr_ad
215      - add more store directives in seaice_lsr to avoid unnecessary code
216        in seaice_lsr_ad
217      - exclude some residual computations in seaice_lsr when
218        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
219        in seaice_lsr_ad
220      - add more storing, a new tape (model/src/the_main_loop.F) and
221        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
222        and klockey should be checked by a specialist)
223      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
224        and update lab_sea after previous changes in pkg/seaice below
225    o pkg/autodiff:
226      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
227        viscFacInAd : run time parameters allowing for adjoint switches
228        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
229    o pkg/ecco:
230      - introduce cost_gencost_boxmean.F that computes a box mean
231        temperature (for use in adjoint sensitivity studies).
232    o model/src/set_defaults.F : initialize viscFacAdj to 1.
233    o pkg/mom_common/mom_calc_visc.F:
234      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
235    o pkg/seaice/seaice_summary.F:
236      - statement for SEAICEadjMODE now in autodiff_readparms.F
237    o pkg/seaice:
238      - remove some store directives and add new ones in an effort to get
239        finally rid off the recomputation warnings. This is successful
240        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
241        defined (i.e. no extensive recomputation warnings left), but there
242        are still too many recomputations on the solver iteration level
243      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
244      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
245        SEAICE_SIZE.h
246      - add a store directive in S/R seaice_calc_viscosities
247    o pkg/seaice (ITD code):
248      - fix definition of Hlimit for multi-threaded case
249      - use double precision arithmetic to compute Hlimit: this affects results;
250        update output of experiment seaice_itd.
251    o replace content of verification/seaice_itd
252      - instead of a 1D column use the configuration of offline_exf_seaice
253        to test the ice thickness distribution code with ridging
254      - this is a first shot at this experiment
255      - change of some defaults of ridging parameters SEAICEhStar (from
256        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
257        and lot of new comments.
258    
259    checkpoint64y (2014/06/20)
260    o pkg/seaice/seaice_reg_ridge.F:
261      - modify the regularization of very small volumes of ice; only check
262        total volume HEFF, and do not apply correction to individual ice
263        classes because that leads to funny patterns in the heat and fw-fluxes
264        into the ocean. Adjust seaice_itd/results/output.txt
265      - replace nITD by SEAICE_multDim in loop-ranges
266    o pkg/exf:
267      - add code to process the case field period = -12. with UV interpolation.
268      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
269        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
270    o verification/global_with_exf:
271      - switch all fields period to -12. (was previously untested) in input/data.exf
272        (but keep secondary test ".yearly" unchanged); update the reference output.
273    o pkg/cal:
274      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
275    o pkg/exf:
276      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
277        to replace logical switch "exf_verbose"
278      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
279    o pkg/sbo:
280      - update from Katherine Quinn: evaluate mass directly from density and SSH
281        (budget using Finite Volume method) instead of from bottom pressure.
282      - allow testreport to collect few selected SBO output ; tested in exp.
283        global_ocean.90x40x15 (after updating the results, to include SBO output).
284      - fix some multi-threading issues (in output part).
285    o model/src & most packages:
286      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
287      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
288        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
289        "data.{pkg}" exist ; and leave the S/R (return) just after.
290      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
291        + call LAND_READPARMS from packages_readparms.F
292    o pkg/seaice:
293      - remove code that resets useThSice in S/R seaice_readparms and
294        replace it by a warning in S/R seaice_check
295      - remove parameter MULTDIM, replace with nITD and runtime
296        parameter SEAICE_multDim (still hard-wired to nITD if
297        SEAICE_ITD is defined)
298    
299    checkpoint64x (2014/05/24)
300    o verification/lab_sea:
301      - update adjoint and TLM output following changes to pkg/salt_plume
302      - un-do the update after putting back local recip_Cp in few places.
303    o pkg/salt_plume: modifications by An Nguyen:
304      - add capability to do brine rejection (salt-plume) as function of
305        volume+tracers (instead of only salinity tracer).
306      - conserve volume by exchanging volume from each kLev to above to
307        accommodate in-coming brine volume
308      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
309      - switch KPP surf buoyancy due to brine forcing to 3-d
310        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
311      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
312      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
313        in East/West Arctic.
314    o pkg/sbo:
315      - incorporate modifications from Katherine Quinn to enable the use of sbo
316        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
317        output for future testreport verification (unfinished).
318    o pkg/atm_phys:
319      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
320        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
321        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
322    o pkg/seaice
323      seaice_calc_ice_strength.F: modify expression to avoid divisions
324        (affects truncation)
325      seaice_do_ridging.F: clean up the insectarium
326      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
327      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
328      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
329      - add some debugging information and error messages (warnings)
330    o model/src: modifications relatd to atmosphere p*:
331      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
332      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
333        of vertical profile tRef in geopotential background and anomaly.
334      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
335        and pkg/atm_phys.
336      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
337        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
338    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
339    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
340        not used right now, but can be used in BGC packages to fix conservation.
341    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
342        other packages too.
343    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
344        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
345    o model/src:
346      - since we have several heat capacity (even in model/src), define "recip_Cp"
347        as local variable (no longer in common block) to avoid any confusion.
348      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
349    o pkg/exf:
350      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
351        air density as function of air Temp, Humidity and atm pressure.
352    
353    checkpoint64w (2014/05/02)
354    o verification:
355      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
356        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
357        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
358        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
359        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
360    o model/src: for atmosphere in p* coords:
361      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
362      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
363        but not yet activated.
364    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
365      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
366      - this changes the results (but not for any verification experiment, because
367        none tests this), but avoids having an extra field in the restart files
368    o pkg/seaice: remove global variable TICE (not needed)
369      - replace by TICES or local variable where necessary (cost_seaice_test,
370        seaice_diagnostics_state)
371      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
372      - use specific read/write routines for reading and writing individual leves
373        of a multilevel field
374    o pkg/ctrl & model/inc:
375      - move additional anomaly fields of control vars (related to options:
376         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
377        from DYNVARS.h into new header file: CTRL_FIELDS.h
378    o pkg/seaice: some small modifications to the ridging code
379      - make fw2ObyRidge a global variable and add the freshwater flux to
380        seaice_growth
381      - pass actual thickness from seaice_prepare_ridging, so that it is
382        computed only in one place and compute it in the same way as in
383        seaice_growth
384      - initialise more fields in seaice_do_ridging that where cause floating
385        point exceptions over land
386    o pkg/seaice: preparations for ridging code and first real ridging code
387      - move most of "PART 1" of S/R seaice_growth into a new and separate
388        S/R seaice_reg_ridge that will both regularize the state variable after
389        advection call the actual ridging routine;
390      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
391        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
392      - remove ridging code from seaice_advdiff
393      - clean up remaining part 1 of seaice_growth in an attempt to make it
394        more readable (this is probably subjective)
395      - call seaice_itd_redist once in the initialisation phase to have the initial
396        conditions in the correct category
397      - finally: add new ridging routine for ITD code
398    
399    checkpoint64v (2014/04/11)
400    o pkg/ecco:
401      - add runtime parameters mdt[start,end]date[1,2]
402      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
403    o pkg/seaice:
404      - make deltaC a global variable, so that it can be used in ridging code
405      - first step towards ridging: introduce new routines that compute
406        ice strength based on ridging parameters
407      - add diagnostic for HSNOWITD
408      - add opnWtrFrac as a global variable (required for ridging scheme)
409    o pkg/salt_plume + pkg/seaice/seaice_growth.F
410      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
411        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
412    o verification/hs94.1x64x5:
413      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
414      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
415    o autodiff:
416      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
417        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
418        For now, only in pkgs used in verification/hs94.1x64x5.
419      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
420        which are specific to TAF/TAMC).
421      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
422        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
423        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
424      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
425        building mitgcmuv_ad (make adAll).
426    o pkg/ecco:
427      - cost_gencost_seaicev4.F:
428         reformulate proxy cost as function of sst and local param SEAICE_freeze
429         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
430      - add stop statement if old names siv4-[sst,vol] are used
431      - add snapshots + cost reports for atmospheric longwave
432      - remove factor 0.1 in front of wtau[u,v]
433      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
434         ALLOW_TMI_SST_COST_CONTRIBUTION
435    o pkg/atm_phys:
436      - add some diagnostics for Short-wave and for convection S/R.
437    o pkg/seaice/seaice_growth:
438      - fix a bug in the lateral melt parameterization for SEAICE_ITD
439        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
440      - rearrange loop order for better vector code in the same code block
441      - rewrite the floeDiameter formula to have fewer divisions
442      -  (miraculously) none of this changes the results of seaice_itd
443    o pkg/smooth:
444      - move param smooth2Ddiffnbt to pkg/ecco
445    o pkg/salt_plume:
446      - salt_plume_frac.F:
447         clean up local param names
448         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
449    o pkg/rw:
450      - add RS version of S/R READ_MFLDS_LEV.
451    o pkg/streamice:
452      - fix the restart test by writing/reading pickup_streamice files.
453    o pkg/seaice:
454      - refine checks for jfnk-related parameters
455      - comment out if statement with SEAICEuseIMEX parameter as long as there
456        is no IMEX code to avoid confusion and surprises
457    
458    checkpoint64u (2014/03/07)
459    o verification/MLAdjust:
460      - rename secondary test suffix:
461         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
462         0.leithD -> AhFlxF  + switch to flux-form
463         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
464         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
465    o pkg/mom_vecinv:
466      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
467        to be before mom_calc_visc.F)
468      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
469      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
470        this is simpler for the adjoint and for diagnostics.
471    o model/src + pkg/momentum:
472      - add input files for  2-D additional Western and Southern cell-edge wall
473         (e.g., to add "thin-wall" where it is =1).
474      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
475        using 2nd hFacZ that is computed from initial (fix domain) hFac
476      - known limitations of thin wall implementation: not yet coded for sigma
477        coords; not working with CD-scheme neither.
478    o pkg/seaice:
479      - rename recently introduced parameters from (wrong name) AB to
480        BDF (backward difference time discretisation)
481      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
482    o tools/adjoint_options:
483      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
484    
485    checkpoint64t (2014/02/01)
486    o pkg/ecco
487      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
488        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
489      - replace hard-coded record number and period which only work for monthly
490        with read-in runtime param that works for other periods (month,day,year)
491    o pkg/thsice
492      - corrected store directive fixes thsice adjoint gradient checks
493    o genmake2 & testreport:
494      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
495        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
496        Update testreport accordingly. No need to set "export OPENAD=true"
497        in adjoint_options/adjoint_oad anymore (will be removed later).
498    o pkg/shelfice:
499      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
500        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
501        so that surface forcing applies to k=kSurf if using pkg/shelfice.
502    o pkg/ctrl, pkg/grdchk, pkg/ecco:
503      - Changes to make GENARR more modular (i.e. invisible if not used)
504    o model/src/temp_integrate.F and salt_integrate.F
505      - re-include store directives that were removed on Dec 27th.
506    o model/src/external_forcing_surf.F
507      - add storage directives for EmPmR and PmEpR to avoid recomputation of
508        seaice_model in the adjoint that is problematic when seaice_model is
509        turned off in the adjoint. The resolved issue dated back to July when
510        EXTERNAL_FORCING_SURF call was moved.
511        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
512    o pkg/exf/exf_check.F
513      - fix a small bug again (originally found by Wentao Liu, now found again)
514      - streamline error output
515    o pkg/streamice and aim_v23:
516      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
517        Apple's /usr/bin/cpp knows what to do:
518        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
519        Target: x86_64-apple-darwin13.0.0
520    
521    checkpoint64s (2014/01/05)
522    o tools/adjoint_options:
523      - switch to fastopt.net TAF server (instead of default fastopt.de) for
524        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
525    o model/src:
526      - remove some unnecessary TAF storage directives in forward_step.F and
527        in dynamics.F (note: not always removed by TAF, e.g., double storage
528        of kappaRU,kappaRV in former version of dynamics.F).
529    o model/src & pkg/ptracers:
530      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
531        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
532        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
533      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
534      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
535      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
536    o useSingleCpuInput separates single-CPU input from single-CPU output;
537        for now only implemented for in exf_interp_read.F
538    o verification/advect_xy:
539      - fix missing EXCH call in local version of ini_salt.F and update output.
540    o momentum diagnostics:
541      - fix which deltaT is used in Total-Tendency diagnostics.
542      - fix typo in diagnostics for momentum tendency from AB.
543    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
544        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
545    
546    checkpoint64r (2013/12/08)
547    o verification/*/results:
548      - Update reference output of experiments that were passing with just 13 digits
549         (make it easier to detect future changes in results)
550    o model/src & pkg/ptracers:
551      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
552        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
553        to inside ptracers_integrate.F ; remove ptracers_advection.F
554    o coupling interface pkgs:
555        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
556      - change the config check to test the agreement of Ocean Depth
557        with ATM land/sea mask (instead of ATM orography);
558      - send to coupler the number of coupler time-steps to do for this run:
559        this allows to check for consistency and don't need anymore to be
560        specified in parameter file "data";
561      in coupler:
562      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
563      - improve report to log-file of config setting (pass log-file unit to few S/R)
564    o pkg/compon_communic:
565      - add coupling send/receive for non-tiled integer vector;
566      - add S/R to check and stop if any proc has an error (similar to
567        eesupp/src/stop_if_error.F but single thread and across Comm_World).
568    o pkg/exch2:
569      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
570        through list of all tiles my proc owns.
571    o model/src:
572      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
573        from rTrans) to simplify dependencies (no need to store rTrans anymore in
574        calling S/R); this affects AD results at machine truncation level:
575        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
576        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
577    o tools/build_options:
578      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
579    o coupling interface pkgs:
580        [compon_communic, atm_compon_interf & ocn_compon_interf]
581      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
582        to each S/R that needs it; remove un-used variables.
583      - change component tile registration (cpl_register.F in both compon_interf
584        and mitcomponent_tile_register.F) to pass the full list of tiles
585        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
586      - with pkg/exch2: adopt the same convention used for I/O to define mapping
587        towards coupler global array (unless W2_useE2ioLayOut=F):
588         a) can now use different tiling between atm & ocn comp.
589         b) no needs to modify the run-Off map when changing tiling (was needed
590            even if using the same tiling between atm & ocn).
591         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
592            full land tiles); not yet tested.
593      - check for valid mapping from comp. tile to coupler global array
594      - improve report of tile registration results to log file.
595    o pkg/exch2:
596      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
597        tile-registration (CPL_REGISTER);
598      - activate (un-comment) definition and setting of "W2_tileIndex" list to
599        store the local bi,bj indices of each tile;
600      - also print bi,bj in local report to log file;
601      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
602        Jun 2009 modif of pkg/exch2).
603    o testing on baudelaire:
604      - run 2 tests at a time: no significant slow down (since enough cpu) and
605        get the full set of test done earlier
606      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
607    o model/src/thermodynamics.F and routines called from it:
608      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
609        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
610        velocity (outp) by adding bolus velocity.
611      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
612        mass transport from velocity + lateral grid cell area
613      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
614      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
615     in thermodynamics.F
616      - remove k from thermodynamics.F and move it to temp_integrate.F
617        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
618        loop).
619      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
620        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
621        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
622        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
623      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
624        global_ocean.90x40x15, tutorial_global_oce_biogeo and
625        tutorial_tracer_adjsens (+ TLM output).
626    o tools/OAD_support and (verification/*/) code_oad:
627      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
628        module conversion ; remove unneeded CPP_EEOPTIONS.h.
629      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
630        version (closer to model/inc/CPP_OPTIONS.h).
631    o model/src:
632      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
633        retired list of parameters (routine FREEZE has been replace by surface
634        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
635    o pkg/gmredi:
636      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
637        velocity (same scheme but affects machine truncation) for GM_AdvForm.
638      - update output of FWD experiments: front_relax.bvp,
639        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
640    
641    checkpoint64q (2013/11/17)
642    o verification:
643      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
644        tutorial_global_oce_biogeo and global_ocean.90x40x15.
645      - generate new output (growth & melt) for seaice_itd experiment after
646        updating the input pickup_seaice files (previously wrong).
647    o pkg/cost:
648      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
649        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
650        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
651          cannot be applied to var in common block).
652        o allows to get results independent of tile-per-proc setting (if using
653          slower GLOBAL_SUM_SEND_RECV option).
654      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
655        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
656        forward gradients: update output).
657      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
658        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
659    o pkg/mom_common:
660      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
661        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
662        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
663        ensure that all field value that are used are set.
664    o tutorial_deep_convection (smag3d):
665      - add missing scaling in mom_calc_smag_3d.F;
666      - set smag3D_coeff in input.smag3d such that results do not change.
667    o pkg/dic:
668      - change dic_cost.F to compute cost on each tile first and then apply
669        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
670        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
671      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
672    o eesupp/src & pkg/mdsio:
673      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
674        (from pkg/mdsio) since they are no longer used for tape IO.
675      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
676        (+ keep a copy in pkg/atm_ocn_coupler).
677    o verification/isomip:
678      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
679    o tools/build_options:
680      - optfile linux_amd64_ifort11, fast (no ieee) case:
681        to get a working restart for all experiments, add "-fp-model source"
682        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
683    
684    checkpoint64p (2013/10/20)
685    o pkg/autodiff:
686      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
687        criteria, return to simple (default) tape IO format.
688    o pkg/mdsio (+ eesupp/src):
689      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
690        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
691      - fix globalFile and singleCpuIO options using simpler global mapping.
692      - new pairs of scatter/gather vector S/R (one for each type, generated from
693        template) corresponding to simpler global mapping.
694      - adread_write.F: switch to new S/R (but leave old calls commented) and write
695        to globalFile when parameter globalFiles is set to True.
696      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
697    o pkg/autodiff:
698      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
699        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
700        missing, just add a STOP if array type do not match.
701    o pkg/exf:
702      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
703         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
704         and rename array obsSIce to exf_iceFraction.
705    o tutorial_deep_convection:
706      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
707        for now all in this exp. code dir.
708      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
709        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
710    o eesupp/src:
711      - added SINGLE_DISK_IO option because reading of parameter files on
712        very large number of processors did not work with existing set-up
713    
714    checkpoint64o (2013/09/25)
715    o pkg/atm_phys & atm_compon_interf:
716      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
717    o tools/build_options:
718      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
719        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
720        remove CPP setting (was identical to genmake2 default).
721    o pkg/gmredi & model/src: Some updating and work done on the residual model.
722      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
723      - fixed up the calculation of the eddy stress and how it is added to the
724        external forcing via taueddy_external_forcing.F
725      - at the moment, it is very experimental and only works with the variable eddy
726        diffusivity calculated in gmredi_k3d.F
727    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
728        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
729    o testreport (& tools/do_tst_2+2):
730      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
731    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
732      - remove CPP='cpp -traditional -P' (this is genmake2 default)
733      - add switch (for big setups) to use 'medium' memory-model (but leave it
734        commented out for now). Note: needed with FC 19 to compile big setups.
735    o pkg/atm_compon_interf:
736      - regroup per field origin (model & pkgs) the coupling storage routines
737         (which accumalate in time each coupling field)
738      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
739        update accordingly + simplify aim_do_physics.F
740    
741    checkpoint64n (2013/08/26)
742    o pkg/bbl:
743      - update formulation to reduce dispersion of tracer properties in bbl
744      - replaced horizontal and vertical transport parameters with velocities
745      - changes results for verification/global_with_exf.yearly
746    o verification/halfpipe_streamice:
747      - change to matrix construction; update both Fwd & AD output.
748    o verification/tutorial_tracer_adjsens:
749      - OpenAD test: switch to vector-invariant momentum since fluxform with
750        rStar causes problems with OpenAD; update output.
751    o tools:
752      - genmake2: define a common prefix for all temp-file names ; move them
753        to local /tmp disk (but would be easy to move them back);
754      - xmakedepend: apply the same switch for temp-files.
755    o pkg/offline:
756      - changes for use with rStar (NLFS): assume that we continue to provide
757        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
758        output files) and apply r* scaling at each time-step (function of the time
759        varying Eta field); use normal pickup files (needed for restart with NLFS).
760    o adjoint with OpenAD:
761      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
762        package openad.  This package has to be compiled for all runs with OpenAD
763        instead of specifying code_oad_all as a modification directory.
764      - link the fortran templates from tools/OAD_support to the build directory
765        for preprocessing to avoid conflicts between different setups compiled
766        simultaneously and simplify cleanup.
767    o pkg/exf:
768      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
769        main model or other pkgs are exchanged in EXF_MAPFIELDS).
770    o model/src:
771      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
772        (similar to do_fields_blocking_exchanges.F).
773    o tools/genmake2:
774      - remove TAF output src code just before calling staf (when not doing a fresh
775        built, will stop if things go wrong with staf).
776      - fix target "adobj" (left from TAF version-2 transition)
777    o pkg/diagnostics:
778      - add a parameter to track the status of pkg/diagnostics activation;
779        this replace/extend the use of logical param "settingDiags" (to check
780        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
781        New S/R to print error message and stop when pkgStatus is not right.
782      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
783    
784    checkpoint64m (2013/08/13)
785    o model/inc:
786      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
787        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
788    o pkg/kpp & aim_v23:
789      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
790    o pkg/seaice:
791      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
792        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
793      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
794    o eesupp/src:
795      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
796        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
797    o switch to TAF version-2:
798      - add flow directives to "freeze" naming convention for ad-routines that
799        are used in I/O routines of adjoint state and associated common blocks
800        that are used in adcommon.h (backward compatible with version-1)
801      - update all ad-optfiles (in tools/adjoint_options + few local to some
802        verification exp) to switch to latest TAF version (currently 2.5.5);
803        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
804        out except for diva).
805      - the major change with TAF version-2 is that both the differentiated
806        routines and the forward routines (new) are returned as part of the TAF
807        output source code. Update genmake2 accordingly.
808      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
809        with version-2 when compared to TLM or FWD gradient); other experiments
810        output show minor changes (machine truncation level); update the few AD &
811        TLM output with 12 matching digits only (some prior to version-2 switch).
812    
813    checkpoint64l (2013/08/05)
814    o model/src:
815      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
816      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
817        when using TAF but only if using OpenAD.
818    o pkg/mom_common+fluxform+vecinv:
819      - always set horiz. viscosity arrays to background value before calling
820        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
821        only when using variable horiz. viscosity (useVariableVisc=T);
822      - simplify mom_vecinv.F (only 1 block for momViscosity).
823    o pkg/mom_common: variable horiz. viscosity in NH code
824      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
825        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
826      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
827        useBiharmonicVisc & useVariableVisc.
828      - fix old bug (already in 1rst implementation of variable horizontal viscosity
829        in calc_gw.F, version 1.27, 2006/06/20):
830        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
831        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
832      - change background horiz viscosity in vertical momentum (gW) to always be
833        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
834        any type of variable viscosity, e.g., viscAh/4Grid)
835      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
836        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
837        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
838        default viscAh,viscA4 is zero).
839    o model/src:
840      - extend length of drC & recip_drC from Nr to Nr+1.
841    o Divided Adjoint (DIVA) with MPI:
842      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
843      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
844        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
845    
846    checkpoint64k (2013/07/23)
847    o tools/OAD_support:
848      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
849        and remove it from genmake2.
850    o tools/build_options:
851      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
852        MPI_HEADER_FILES list (let genmake2 find the missing headers)
853    o verification/halfpipe_streamice:
854      - change to driving stress formulation; update both Fwd & AD output.
855    o tools/genmake2 and Divided Adjoint with MPI:
856      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
857      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
858      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
859        Makefile, which is set by genmake2, and check which mpi-headers are needed.
860        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
861      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
862    o testreport:
863      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
864        perform additional runs (number of additional runs is "add_DIVA_runs" taken
865        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
866    o verification/lab_sea (AD test):
867      - change to test Divided Adjoint Run in this set-up (both standard AD test
868        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
869    o pkg atm_ & ocn_compon_interf:
870      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
871        staggerTimeStep implementation) and disable (retired) corresponding
872        parameter.
873    o pkg/offline:
874      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
875      - add S/R OFFLINE_CHECK to print offline parameter summary
876        and stop if loading a file that is not used;
877      - enable to calculate GMRedi tensor, KPP mixing and convective index
878        when the corresponding file(s) is/are not specified (but pkg is used).
879      - comment out resetting of monitorFreq (to endTime) since it still useful
880        for monitoring CFL numbers and checking offline fields.
881    o OpenAD:
882      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
883        smaller standard output) and generate new (smaller) output (on baudelaire
884        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
885    o model/src:
886      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
887        (where external_forcing_adjust was called) and change list of arguments;
888      - merge external_forcing_adjust.F into external_forcing_surf.F
889      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
890        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
891        previously in file "balance_relax.F", now removed); remove corresponding
892        arrays in FFIELDS.h.
893      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
894        a hack for getting back surfaceForcingS (loaded from file) when using
895        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
896      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
897        (was getting only 11 digits for AD-grad, due to different truncation
898         error in AD code).
899    
900    checkpoint64j (2013/07/04)
901    o pkg/offline:
902      - to enable the use of other features with pkg offline (e.g., obcs),
903        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
904      - comment out "allowFreezing" (now active) in 2 offline testing exp.
905    o pkg/exf ALLOW_RUNOFTEMP
906      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
907      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
908      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
909    o pkg/atm_phys:
910      - allows to add some damping on uVel,vVel (strength only function of k).
911    o verification, ad-tests:
912      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
913        global_ocean_ebm and offline_exf_seaice.thsice.
914    o verification/halfpipe_streamice:
915      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
916        flux input boundary conditions to be ignored; a fix for this bug changed
917        verification results for forward test.
918      - add adjoint test.
919    o pkg/ptracers:
920      - allow to restart without SOM pickup (resetting SOM to zero).
921    o pkg/gmredi:
922      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
923      - It uses mixing length theory and suppression by steering level effects to
924        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
925        to JPO, for more details).
926      - It also uses the diffusivity to calculate an eddy induced streamfunction
927        based on a PV closure (rather than a buoyancy closure as in GM).
928      - New files added to pkg/gmredi:
929        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
930          induced overturning streamfunction (called from gmredi_calc_tensor)
931        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
932          for use in gmredi_k3d
933        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
934          the eddy diffusivity
935    
936  checkpoint64i (2013/06/18)  checkpoint64i (2013/06/18)
937  o pkg/cheapaml:  o pkg/cheapaml:
# Line 40  o pkg/cfc: Line 968  o pkg/cfc:
968      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
969    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
970    - new routine to print summary of CFC params and check for consistency.    - new routine to print summary of CFC params and check for consistency.
971    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
972      similar to thsice_advdiff.
973      Note that for the B-grid case the routine parameters uc/vc are overwritten.
974  o pkg/cfc:  o pkg/cfc:
975    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
976      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
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