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revision 1.1875 by jmc, Mon Jun 10 03:08:50 2013 UTC revision 1.2058 by jmc, Fri Sep 5 21:18:53 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 model/src & generic_advdiff:
8      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
9        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
10        dynamics requires valid tracer forcing only over tile interior but, for
11        some diagnostics, may need to extend it over 1 point in tile halo region.
12      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
13        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
14        setting in temp/salt/ptracer_integrate.F
15    o pkg/dic:
16      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
17        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
18        in gchem_forcing_sep.F
19    o pkg/autodiff & obcs:
20      - add storage of current OB values for U & V (was already done for T & S).
21    
22    checkpoint65c (2014/08/30)
23    o pkg/dic:
24      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
25        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
26        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
27    o verification:
28      - new experiment testing OBCS and DIC pkgs, using params & output from
29        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
30        passage: take OBCS from the last year of a 2 yrs simulation and initial
31        conditions from t=1.yr while keeping the same forcing.
32    o model/src:
33      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
34        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
35    o pkg/diagnostics (Stats-Diags):
36      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
37        a) refine region where stats are computed, excluding where arrhFac=0 ;
38        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
39        c) extend regional stats over the region edges (for U or V pt location).
40    o pkg/gchem:
41      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
42        pkg/dic is currently changing/updating ptracers values beyond the OB).
43    o verification (hs94):
44      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
45        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
46        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
47        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
48    o pkg/ptracers:
49      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
50        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
51      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
52        with AB-2 code (so that it get tested).
53    o model/src:
54      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
55        with AB-2 code (previously only available with AB-3 code).
56        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
57        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
58        there, by calling CYCLE_AB_TRACER).
59    o pkg/generic_advdiff:
60      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
61        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
62        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
63        S/R temp/salt/ptracers_integrate.F
64    o model/src & pkg/ptracers:
65      - remove common block variables gT,gS (in DYNVARS.h), except when
66         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
67      - remove common block variable gPtr.
68    o model/src & pkgs:
69      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
70         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
71         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
72         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
73      + change accordingly all calling S/R.
74      - use local temperature/salinity/ptracer tendency array (without bi,bj)
75        in S/R temp/salt/ptracers_integrate.F
76    o pkg/seaice:
77      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
78        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
79      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
80        in seaice_lsr
81      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
82        in s/r seaice_lsr_calc_coeffs
83    o pkg/mdsio:
84      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
85        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
86        too long (e.g., > MAX_LEN_FNAM/2 )
87    
88    checkpoint65b (2014/08/12)
89    o pkg/matrix:
90      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
91    o model/src:
92      - fix initialisation of geothermalFile; compile geothermal-flux code in
93        natl_box verification experiment.
94    o model/src & pkg/down_slope:
95      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
96      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
97        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
98        results at machine truncation level: update output of experiments
99        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
100    o pkg/diagnostics (Stats-Diags):
101      - do not cumulate the full volume when DIAGNOSTICS_FILL is
102        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
103        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
104        times (but Min,Max and StD are still wrong).
105    o model/src:
106      - add geothermal flux forcing: read in ini_forcing.F as time-constant
107        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
108    o model/src:
109      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
110        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
111        arrays are already updated while adjustments (filters, conv.adjustment) are
112        still applied later, in S/R TRACERS_CORRECTION_STEP.
113    o model/src:
114      - store in common bloc array "rhoInSitu" the virtual potential temperature
115        anomaly that is used to compute geopotential: this make the atmos code
116        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
117    o pkg/seaice/seaice_lsr.F
118      - rename integer variable ilcall to ipass (that's what it is called
119        in the residual diagnostics
120      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
121        default) for improved non-linear convergence of the first few steps
122      - adjust a few comments and add new ones to explain some of the store
123        directives
124    o pkg/generic_advdiff (& ptracers):
125      - re-work the code to check for valid advection scheme and for minimum
126        size of overlap (now stored in local common bloc in gad_advscheme.F)
127    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
128      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
129      - add an auxilliary variable "bet" and fix store directives and keys in
130        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
131        less exact gradients in my tests); but there are still
132        recomputation warning (although gradients are sort of OK), when
133        SEAICE_LSR_VECTORIZE is not defined, so this flag and
134        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
135      - update verification experiments lab_sea.
136      - change some comments in S/R seaice_calc_viscosities
137    o model/src:
138      - if staggerTimeStep=T, always apply exchange to velocity field in
139        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
140        (independent of using multi-dim advection or not); no effect on FWD run
141        but affects AD results (at machine truncation level): update output of
142        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
143        and isomip (oad: 12.d).
144    o pkg/generic_advdiff:
145      - stop if doAB_onGtGs is set to FALSE but ignored
146      - refine warning related to stability of tracer time-stepping
147        regarding internal wave dynamics.
148      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
149        on staggerTimeStep & implicitIntGravWave (will now get a warning
150        if potentially unstable).
151    o pkg/kl10:
152      - add new pkg "kl10" for mixing due to internal wave breaking, from
153        http://www.sciencedirect.com/science/article/pii/S1463500310000144
154        (contribution from Jody Klymak), tested in verification experiment
155        verification/internal_wave/input.kl10/
156    o isomip experiment:
157      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
158        (input.htd) and update the output.
159    o cd_code experiments:
160      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
161        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
162        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
163        update the corresponding output.
164    o pkg/seaice:
165      - reduce the number of include files and store directives in
166        S/R seaice_lsr_tridiagu/v
167      - change the order of loops in one case in S/R seaice_lsr_tridiagv
168        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
169        get rid off one store directive (a TAF bug?)
170      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
171        S/R seaice_lsr_tridiagv to change the loop range for consistency
172      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
173      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
174        S/R seaice_lsr_tridiagu/v (requires update of
175        offline_exf_seaice/input.dyn_jfnk)
176    
177    checkpoint65a (2014/07/27)
178    o model/src:
179      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
180        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
181        (topo in p-coords, ice-shelf in z-coords); update output of experiments
182        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
183    o model/src:
184      - collect momentum forcing tendency into local 2-D array (passed as argument
185        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
186        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
187        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
188      - collect T & S forcing tendency into local 2-D array (passed as argument to
189        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
190        affects results at machine truncation level (e.g., ocean: if using
191        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
192        correction due to vertical advection).
193      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
194        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
195        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
196        obcs_ctrl (ad & fwd grd @ 12 & 7).
197    o pkg/ptracers & diagnostics:
198      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
199        title (to avoid some unexpected truncation); sort out ptracers diags units.
200      - collect ptracer forcing tendency into local 2-D array (passed as argument
201        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
202    
203    checkpoint65 (2014/07/18)
204    o pkg/fizhi:
205      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
206        affects results at machine truncation level. Update output of experiments
207        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
208    o pkg/seaice: more clean up
209      - rename TAF common block tapes to be more consistent and remove
210        unnecessary duplicates
211      - add store directives to remove more recomputations, but use smaller
212        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
213        The idea behind this flag is to reduce the memory footprint when the
214        adjoint of the LSR is not required. As of now, defining the flag
215        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
216        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
217        For experiment offline_exf_seaice, this means on a linux box with gfortran
218        nearly a factor of 10 (but keep in mind there is mostly seaice code in
219        this experiment):
220        > size mitgcmuv_ad
221        text    data        bss     dec        hex  
222        5100659 1216  220458952  225560827  d71c8fb
223        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
224        but only a moderate increase of 36% for global_ocean.cs32x15:
225        text    data        bss     dec        hex
226        6695027 1648 1014578664 1021275339 3cdf6ccb
227        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
228      - note: there are still recomputations in global_ocean.cs32x15 and
229        offline_exf_seaice and the gradient agreement changes (gets a
230        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
231      - in general, the AD gradients still are wrong
232    o OpenAD
233      - clean up code_oad/ directories somewhat by moving files
234        dontCompile, dontTransform, keepOriginal to OAD_support/
235    o model/src:
236      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
237        (not currently tested): add dissipation terms before NLFS rescaling of
238        tendencies (previously done after).
239    o pkg/diagnostics:
240      - write stats-diags in ascii file with more digits (same as in monitor).
241    o pkg/down_slope:
242      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
243        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
244    o model/src:
245      - new file "apply_forcing.F" containing all the code previously in
246        external_forcing.F, but with new argument list: pass, as new argument,
247        the current level tendency array to update (instead of a direct update
248        of the common bloc array). Change the corresponding calls.
249      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
250        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
251    o pkg/seaice/seaice_lsr, a little bit of clean up
252      - rearrange some code blocks, so that now all calculations for
253        setting up the right-hand-sides done within one single block
254        (I find that easier to read and understand)
255      - rearrange freedrift-code to reduce the number of ifdefs
256      - adjust some indentations and comments
257    
258    checkpoint64z (2014/07/10)
259    o model/src and several pkgs:
260      - change argument list of all S/R called from external_forcing.F and
261        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
262        to pass, as argument, the current level tendency array to update
263        (instead of a direct update of the common bloc array).
264      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
265      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
266    o pkg/seaice/seaice_lsr.F
267      - always initialize local arrays in seaice_lsr_tridiagu/v
268      - add more local tapes to seaice_lsr_tridiagu/v
269      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
270        keep it in bi/bj loop; this seems to be essential
271      - gradients are still wrong but only by 4-7 orders of magnitude
272        instead of 15 orders of magnitude, lab_sea improves a little
273    o pkg/seaice
274      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
275        generates unnecessary code in seaice_lsr_ad
276      - add more store directives in seaice_lsr to avoid unnecessary code
277        in seaice_lsr_ad
278      - exclude some residual computations in seaice_lsr when
279        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
280        in seaice_lsr_ad
281      - add more storing, a new tape (model/src/the_main_loop.F) and
282        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
283        and klockey should be checked by a specialist)
284      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
285        and update lab_sea after previous changes in pkg/seaice below
286    o pkg/autodiff:
287      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
288        viscFacInAd : run time parameters allowing for adjoint switches
289        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
290    o pkg/ecco:
291      - introduce cost_gencost_boxmean.F that computes a box mean
292        temperature (for use in adjoint sensitivity studies).
293    o model/src/set_defaults.F : initialize viscFacAdj to 1.
294    o pkg/mom_common/mom_calc_visc.F:
295      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
296    o pkg/seaice/seaice_summary.F:
297      - statement for SEAICEadjMODE now in autodiff_readparms.F
298    o pkg/seaice:
299      - remove some store directives and add new ones in an effort to get
300        finally rid off the recomputation warnings. This is successful
301        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
302        defined (i.e. no extensive recomputation warnings left), but there
303        are still too many recomputations on the solver iteration level
304      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
305      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
306        SEAICE_SIZE.h
307      - add a store directive in S/R seaice_calc_viscosities
308    o pkg/seaice (ITD code):
309      - fix definition of Hlimit for multi-threaded case
310      - use double precision arithmetic to compute Hlimit: this affects results;
311        update output of experiment seaice_itd.
312    o replace content of verification/seaice_itd
313      - instead of a 1D column use the configuration of offline_exf_seaice
314        to test the ice thickness distribution code with ridging
315      - this is a first shot at this experiment
316      - change of some defaults of ridging parameters SEAICEhStar (from
317        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
318        and lot of new comments.
319    
320    checkpoint64y (2014/06/20)
321    o pkg/seaice/seaice_reg_ridge.F:
322      - modify the regularization of very small volumes of ice; only check
323        total volume HEFF, and do not apply correction to individual ice
324        classes because that leads to funny patterns in the heat and fw-fluxes
325        into the ocean. Adjust seaice_itd/results/output.txt
326      - replace nITD by SEAICE_multDim in loop-ranges
327    o pkg/exf:
328      - add code to process the case field period = -12. with UV interpolation.
329      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
330        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
331    o verification/global_with_exf:
332      - switch all fields period to -12. (was previously untested) in input/data.exf
333        (but keep secondary test ".yearly" unchanged); update the reference output.
334    o pkg/cal:
335      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
336    o pkg/exf:
337      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
338        to replace logical switch "exf_verbose"
339      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
340    o pkg/sbo:
341      - update from Katherine Quinn: evaluate mass directly from density and SSH
342        (budget using Finite Volume method) instead of from bottom pressure.
343      - allow testreport to collect few selected SBO output ; tested in exp.
344        global_ocean.90x40x15 (after updating the results, to include SBO output).
345      - fix some multi-threading issues (in output part).
346    o model/src & most packages:
347      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
348      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
349        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
350        "data.{pkg}" exist ; and leave the S/R (return) just after.
351      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
352        + call LAND_READPARMS from packages_readparms.F
353    o pkg/seaice:
354      - remove code that resets useThSice in S/R seaice_readparms and
355        replace it by a warning in S/R seaice_check
356      - remove parameter MULTDIM, replace with nITD and runtime
357        parameter SEAICE_multDim (still hard-wired to nITD if
358        SEAICE_ITD is defined)
359    
360    checkpoint64x (2014/05/24)
361    o verification/lab_sea:
362      - update adjoint and TLM output following changes to pkg/salt_plume
363      - un-do the update after putting back local recip_Cp in few places.
364    o pkg/salt_plume: modifications by An Nguyen:
365      - add capability to do brine rejection (salt-plume) as function of
366        volume+tracers (instead of only salinity tracer).
367      - conserve volume by exchanging volume from each kLev to above to
368        accommodate in-coming brine volume
369      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
370      - switch KPP surf buoyancy due to brine forcing to 3-d
371        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
372      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
373      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
374        in East/West Arctic.
375    o pkg/sbo:
376      - incorporate modifications from Katherine Quinn to enable the use of sbo
377        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
378        output for future testreport verification (unfinished).
379    o pkg/atm_phys:
380      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
381        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
382        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
383    o pkg/seaice
384      seaice_calc_ice_strength.F: modify expression to avoid divisions
385        (affects truncation)
386      seaice_do_ridging.F: clean up the insectarium
387      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
388      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
389      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
390      - add some debugging information and error messages (warnings)
391    o model/src: modifications relatd to atmosphere p*:
392      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
393      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
394        of vertical profile tRef in geopotential background and anomaly.
395      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
396        and pkg/atm_phys.
397      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
398        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
399    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
400    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
401        not used right now, but can be used in BGC packages to fix conservation.
402    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
403        other packages too.
404    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
405        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
406    o model/src:
407      - since we have several heat capacity (even in model/src), define "recip_Cp"
408        as local variable (no longer in common block) to avoid any confusion.
409      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
410    o pkg/exf:
411      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
412        air density as function of air Temp, Humidity and atm pressure.
413    
414    checkpoint64w (2014/05/02)
415    o verification:
416      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
417        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
418        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
419        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
420        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
421    o model/src: for atmosphere in p* coords:
422      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
423      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
424        but not yet activated.
425    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
426      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
427      - this changes the results (but not for any verification experiment, because
428        none tests this), but avoids having an extra field in the restart files
429    o pkg/seaice: remove global variable TICE (not needed)
430      - replace by TICES or local variable where necessary (cost_seaice_test,
431        seaice_diagnostics_state)
432      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
433      - use specific read/write routines for reading and writing individual leves
434        of a multilevel field
435    o pkg/ctrl & model/inc:
436      - move additional anomaly fields of control vars (related to options:
437         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
438        from DYNVARS.h into new header file: CTRL_FIELDS.h
439    o pkg/seaice: some small modifications to the ridging code
440      - make fw2ObyRidge a global variable and add the freshwater flux to
441        seaice_growth
442      - pass actual thickness from seaice_prepare_ridging, so that it is
443        computed only in one place and compute it in the same way as in
444        seaice_growth
445      - initialise more fields in seaice_do_ridging that where cause floating
446        point exceptions over land
447    o pkg/seaice: preparations for ridging code and first real ridging code
448      - move most of "PART 1" of S/R seaice_growth into a new and separate
449        S/R seaice_reg_ridge that will both regularize the state variable after
450        advection call the actual ridging routine;
451      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
452        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
453      - remove ridging code from seaice_advdiff
454      - clean up remaining part 1 of seaice_growth in an attempt to make it
455        more readable (this is probably subjective)
456      - call seaice_itd_redist once in the initialisation phase to have the initial
457        conditions in the correct category
458      - finally: add new ridging routine for ITD code
459    
460    checkpoint64v (2014/04/11)
461    o pkg/ecco:
462      - add runtime parameters mdt[start,end]date[1,2]
463      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
464    o pkg/seaice:
465      - make deltaC a global variable, so that it can be used in ridging code
466      - first step towards ridging: introduce new routines that compute
467        ice strength based on ridging parameters
468      - add diagnostic for HSNOWITD
469      - add opnWtrFrac as a global variable (required for ridging scheme)
470    o pkg/salt_plume + pkg/seaice/seaice_growth.F
471      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
472        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
473    o verification/hs94.1x64x5:
474      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
475      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
476    o autodiff:
477      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
478        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
479        For now, only in pkgs used in verification/hs94.1x64x5.
480      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
481        which are specific to TAF/TAMC).
482      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
483        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
484        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
485      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
486        building mitgcmuv_ad (make adAll).
487    o pkg/ecco:
488      - cost_gencost_seaicev4.F:
489         reformulate proxy cost as function of sst and local param SEAICE_freeze
490         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
491      - add stop statement if old names siv4-[sst,vol] are used
492      - add snapshots + cost reports for atmospheric longwave
493      - remove factor 0.1 in front of wtau[u,v]
494      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
495         ALLOW_TMI_SST_COST_CONTRIBUTION
496    o pkg/atm_phys:
497      - add some diagnostics for Short-wave and for convection S/R.
498    o pkg/seaice/seaice_growth:
499      - fix a bug in the lateral melt parameterization for SEAICE_ITD
500        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
501      - rearrange loop order for better vector code in the same code block
502      - rewrite the floeDiameter formula to have fewer divisions
503      -  (miraculously) none of this changes the results of seaice_itd
504    o pkg/smooth:
505      - move param smooth2Ddiffnbt to pkg/ecco
506    o pkg/salt_plume:
507      - salt_plume_frac.F:
508         clean up local param names
509         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
510    o pkg/rw:
511      - add RS version of S/R READ_MFLDS_LEV.
512    o pkg/streamice:
513      - fix the restart test by writing/reading pickup_streamice files.
514    o pkg/seaice:
515      - refine checks for jfnk-related parameters
516      - comment out if statement with SEAICEuseIMEX parameter as long as there
517        is no IMEX code to avoid confusion and surprises
518    
519    checkpoint64u (2014/03/07)
520    o verification/MLAdjust:
521      - rename secondary test suffix:
522         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
523         0.leithD -> AhFlxF  + switch to flux-form
524         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
525         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
526    o pkg/mom_vecinv:
527      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
528        to be before mom_calc_visc.F)
529      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
530      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
531        this is simpler for the adjoint and for diagnostics.
532    o model/src + pkg/momentum:
533      - add input files for  2-D additional Western and Southern cell-edge wall
534         (e.g., to add "thin-wall" where it is =1).
535      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
536        using 2nd hFacZ that is computed from initial (fix domain) hFac
537      - known limitations of thin wall implementation: not yet coded for sigma
538        coords; not working with CD-scheme neither.
539    o pkg/seaice:
540      - rename recently introduced parameters from (wrong name) AB to
541        BDF (backward difference time discretisation)
542      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
543    o tools/adjoint_options:
544      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
545    
546    checkpoint64t (2014/02/01)
547    o pkg/ecco
548      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
549        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
550      - replace hard-coded record number and period which only work for monthly
551        with read-in runtime param that works for other periods (month,day,year)
552    o pkg/thsice
553      - corrected store directive fixes thsice adjoint gradient checks
554    o genmake2 & testreport:
555      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
556        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
557        Update testreport accordingly. No need to set "export OPENAD=true"
558        in adjoint_options/adjoint_oad anymore (will be removed later).
559    o pkg/shelfice:
560      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
561        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
562        so that surface forcing applies to k=kSurf if using pkg/shelfice.
563    o pkg/ctrl, pkg/grdchk, pkg/ecco:
564      - Changes to make GENARR more modular (i.e. invisible if not used)
565    o model/src/temp_integrate.F and salt_integrate.F
566      - re-include store directives that were removed on Dec 27th.
567    o model/src/external_forcing_surf.F
568      - add storage directives for EmPmR and PmEpR to avoid recomputation of
569        seaice_model in the adjoint that is problematic when seaice_model is
570        turned off in the adjoint. The resolved issue dated back to July when
571        EXTERNAL_FORCING_SURF call was moved.
572        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
573    o pkg/exf/exf_check.F
574      - fix a small bug again (originally found by Wentao Liu, now found again)
575      - streamline error output
576    o pkg/streamice and aim_v23:
577      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
578        Apple's /usr/bin/cpp knows what to do:
579        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
580        Target: x86_64-apple-darwin13.0.0
581    
582    checkpoint64s (2014/01/05)
583    o tools/adjoint_options:
584      - switch to fastopt.net TAF server (instead of default fastopt.de) for
585        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
586    o model/src:
587      - remove some unnecessary TAF storage directives in forward_step.F and
588        in dynamics.F (note: not always removed by TAF, e.g., double storage
589        of kappaRU,kappaRV in former version of dynamics.F).
590    o model/src & pkg/ptracers:
591      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
592        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
593        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
594      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
595      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
596      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
597    o useSingleCpuInput separates single-CPU input from single-CPU output;
598        for now only implemented for in exf_interp_read.F
599    o verification/advect_xy:
600      - fix missing EXCH call in local version of ini_salt.F and update output.
601    o momentum diagnostics:
602      - fix which deltaT is used in Total-Tendency diagnostics.
603      - fix typo in diagnostics for momentum tendency from AB.
604    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
605        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
606    
607    checkpoint64r (2013/12/08)
608    o verification/*/results:
609      - Update reference output of experiments that were passing with just 13 digits
610         (make it easier to detect future changes in results)
611    o model/src & pkg/ptracers:
612      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
613        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
614        to inside ptracers_integrate.F ; remove ptracers_advection.F
615    o coupling interface pkgs:
616        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
617      - change the config check to test the agreement of Ocean Depth
618        with ATM land/sea mask (instead of ATM orography);
619      - send to coupler the number of coupler time-steps to do for this run:
620        this allows to check for consistency and don't need anymore to be
621        specified in parameter file "data";
622      in coupler:
623      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
624      - improve report to log-file of config setting (pass log-file unit to few S/R)
625    o pkg/compon_communic:
626      - add coupling send/receive for non-tiled integer vector;
627      - add S/R to check and stop if any proc has an error (similar to
628        eesupp/src/stop_if_error.F but single thread and across Comm_World).
629    o pkg/exch2:
630      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
631        through list of all tiles my proc owns.
632    o model/src:
633      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
634        from rTrans) to simplify dependencies (no need to store rTrans anymore in
635        calling S/R); this affects AD results at machine truncation level:
636        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
637        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
638    o tools/build_options:
639      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
640    o coupling interface pkgs:
641        [compon_communic, atm_compon_interf & ocn_compon_interf]
642      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
643        to each S/R that needs it; remove un-used variables.
644      - change component tile registration (cpl_register.F in both compon_interf
645        and mitcomponent_tile_register.F) to pass the full list of tiles
646        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
647      - with pkg/exch2: adopt the same convention used for I/O to define mapping
648        towards coupler global array (unless W2_useE2ioLayOut=F):
649         a) can now use different tiling between atm & ocn comp.
650         b) no needs to modify the run-Off map when changing tiling (was needed
651            even if using the same tiling between atm & ocn).
652         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
653            full land tiles); not yet tested.
654      - check for valid mapping from comp. tile to coupler global array
655      - improve report of tile registration results to log file.
656    o pkg/exch2:
657      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
658        tile-registration (CPL_REGISTER);
659      - activate (un-comment) definition and setting of "W2_tileIndex" list to
660        store the local bi,bj indices of each tile;
661      - also print bi,bj in local report to log file;
662      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
663        Jun 2009 modif of pkg/exch2).
664    o testing on baudelaire:
665      - run 2 tests at a time: no significant slow down (since enough cpu) and
666        get the full set of test done earlier
667      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
668    o model/src/thermodynamics.F and routines called from it:
669      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
670        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
671        velocity (outp) by adding bolus velocity.
672      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
673        mass transport from velocity + lateral grid cell area
674      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
675      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
676     in thermodynamics.F
677      - remove k from thermodynamics.F and move it to temp_integrate.F
678        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
679        loop).
680      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
681        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
682        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
683        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
684      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
685        global_ocean.90x40x15, tutorial_global_oce_biogeo and
686        tutorial_tracer_adjsens (+ TLM output).
687    o tools/OAD_support and (verification/*/) code_oad:
688      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
689        module conversion ; remove unneeded CPP_EEOPTIONS.h.
690      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
691        version (closer to model/inc/CPP_OPTIONS.h).
692    o model/src:
693      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
694        retired list of parameters (routine FREEZE has been replace by surface
695        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
696    o pkg/gmredi:
697      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
698        velocity (same scheme but affects machine truncation) for GM_AdvForm.
699      - update output of FWD experiments: front_relax.bvp,
700        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
701    
702    checkpoint64q (2013/11/17)
703    o verification:
704      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
705        tutorial_global_oce_biogeo and global_ocean.90x40x15.
706      - generate new output (growth & melt) for seaice_itd experiment after
707        updating the input pickup_seaice files (previously wrong).
708    o pkg/cost:
709      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
710        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
711        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
712          cannot be applied to var in common block).
713        o allows to get results independent of tile-per-proc setting (if using
714          slower GLOBAL_SUM_SEND_RECV option).
715      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
716        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
717        forward gradients: update output).
718      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
719        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
720    o pkg/mom_common:
721      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
722        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
723        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
724        ensure that all field value that are used are set.
725    o tutorial_deep_convection (smag3d):
726      - add missing scaling in mom_calc_smag_3d.F;
727      - set smag3D_coeff in input.smag3d such that results do not change.
728    o pkg/dic:
729      - change dic_cost.F to compute cost on each tile first and then apply
730        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
731        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
732      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
733    o eesupp/src & pkg/mdsio:
734      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
735        (from pkg/mdsio) since they are no longer used for tape IO.
736      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
737        (+ keep a copy in pkg/atm_ocn_coupler).
738    o verification/isomip:
739      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
740    o tools/build_options:
741      - optfile linux_amd64_ifort11, fast (no ieee) case:
742        to get a working restart for all experiments, add "-fp-model source"
743        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
744    
745    checkpoint64p (2013/10/20)
746    o pkg/autodiff:
747      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
748        criteria, return to simple (default) tape IO format.
749    o pkg/mdsio (+ eesupp/src):
750      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
751        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
752      - fix globalFile and singleCpuIO options using simpler global mapping.
753      - new pairs of scatter/gather vector S/R (one for each type, generated from
754        template) corresponding to simpler global mapping.
755      - adread_write.F: switch to new S/R (but leave old calls commented) and write
756        to globalFile when parameter globalFiles is set to True.
757      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
758    o pkg/autodiff:
759      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
760        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
761        missing, just add a STOP if array type do not match.
762    o pkg/exf:
763      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
764         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
765         and rename array obsSIce to exf_iceFraction.
766    o tutorial_deep_convection:
767      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
768        for now all in this exp. code dir.
769      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
770        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
771    o eesupp/src:
772      - added SINGLE_DISK_IO option because reading of parameter files on
773        very large number of processors did not work with existing set-up
774    
775    checkpoint64o (2013/09/25)
776    o pkg/atm_phys & atm_compon_interf:
777      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
778    o tools/build_options:
779      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
780        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
781        remove CPP setting (was identical to genmake2 default).
782    o pkg/gmredi & model/src: Some updating and work done on the residual model.
783      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
784      - fixed up the calculation of the eddy stress and how it is added to the
785        external forcing via taueddy_external_forcing.F
786      - at the moment, it is very experimental and only works with the variable eddy
787        diffusivity calculated in gmredi_k3d.F
788    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
789        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
790    o testreport (& tools/do_tst_2+2):
791      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
792    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
793      - remove CPP='cpp -traditional -P' (this is genmake2 default)
794      - add switch (for big setups) to use 'medium' memory-model (but leave it
795        commented out for now). Note: needed with FC 19 to compile big setups.
796    o pkg/atm_compon_interf:
797      - regroup per field origin (model & pkgs) the coupling storage routines
798         (which accumalate in time each coupling field)
799      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
800        update accordingly + simplify aim_do_physics.F
801    
802    checkpoint64n (2013/08/26)
803    o pkg/bbl:
804      - update formulation to reduce dispersion of tracer properties in bbl
805      - replaced horizontal and vertical transport parameters with velocities
806      - changes results for verification/global_with_exf.yearly
807    o verification/halfpipe_streamice:
808      - change to matrix construction; update both Fwd & AD output.
809    o verification/tutorial_tracer_adjsens:
810      - OpenAD test: switch to vector-invariant momentum since fluxform with
811        rStar causes problems with OpenAD; update output.
812    o tools:
813      - genmake2: define a common prefix for all temp-file names ; move them
814        to local /tmp disk (but would be easy to move them back);
815      - xmakedepend: apply the same switch for temp-files.
816    o pkg/offline:
817      - changes for use with rStar (NLFS): assume that we continue to provide
818        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
819        output files) and apply r* scaling at each time-step (function of the time
820        varying Eta field); use normal pickup files (needed for restart with NLFS).
821    o adjoint with OpenAD:
822      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
823        package openad.  This package has to be compiled for all runs with OpenAD
824        instead of specifying code_oad_all as a modification directory.
825      - link the fortran templates from tools/OAD_support to the build directory
826        for preprocessing to avoid conflicts between different setups compiled
827        simultaneously and simplify cleanup.
828    o pkg/exf:
829      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
830        main model or other pkgs are exchanged in EXF_MAPFIELDS).
831    o model/src:
832      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
833        (similar to do_fields_blocking_exchanges.F).
834    o tools/genmake2:
835      - remove TAF output src code just before calling staf (when not doing a fresh
836        built, will stop if things go wrong with staf).
837      - fix target "adobj" (left from TAF version-2 transition)
838    o pkg/diagnostics:
839      - add a parameter to track the status of pkg/diagnostics activation;
840        this replace/extend the use of logical param "settingDiags" (to check
841        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
842        New S/R to print error message and stop when pkgStatus is not right.
843      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
844    
845    checkpoint64m (2013/08/13)
846    o model/inc:
847      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
848        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
849    o pkg/kpp & aim_v23:
850      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
851    o pkg/seaice:
852      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
853        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
854      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
855    o eesupp/src:
856      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
857        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
858    o switch to TAF version-2:
859      - add flow directives to "freeze" naming convention for ad-routines that
860        are used in I/O routines of adjoint state and associated common blocks
861        that are used in adcommon.h (backward compatible with version-1)
862      - update all ad-optfiles (in tools/adjoint_options + few local to some
863        verification exp) to switch to latest TAF version (currently 2.5.5);
864        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
865        out except for diva).
866      - the major change with TAF version-2 is that both the differentiated
867        routines and the forward routines (new) are returned as part of the TAF
868        output source code. Update genmake2 accordingly.
869      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
870        with version-2 when compared to TLM or FWD gradient); other experiments
871        output show minor changes (machine truncation level); update the few AD &
872        TLM output with 12 matching digits only (some prior to version-2 switch).
873    
874    checkpoint64l (2013/08/05)
875    o model/src:
876      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
877      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
878        when using TAF but only if using OpenAD.
879    o pkg/mom_common+fluxform+vecinv:
880      - always set horiz. viscosity arrays to background value before calling
881        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
882        only when using variable horiz. viscosity (useVariableVisc=T);
883      - simplify mom_vecinv.F (only 1 block for momViscosity).
884    o pkg/mom_common: variable horiz. viscosity in NH code
885      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
886        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
887      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
888        useBiharmonicVisc & useVariableVisc.
889      - fix old bug (already in 1rst implementation of variable horizontal viscosity
890        in calc_gw.F, version 1.27, 2006/06/20):
891        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
892        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
893      - change background horiz viscosity in vertical momentum (gW) to always be
894        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
895        any type of variable viscosity, e.g., viscAh/4Grid)
896      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
897        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
898        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
899        default viscAh,viscA4 is zero).
900    o model/src:
901      - extend length of drC & recip_drC from Nr to Nr+1.
902    o Divided Adjoint (DIVA) with MPI:
903      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
904      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
905        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
906    
907    checkpoint64k (2013/07/23)
908    o tools/OAD_support:
909      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
910        and remove it from genmake2.
911    o tools/build_options:
912      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
913        MPI_HEADER_FILES list (let genmake2 find the missing headers)
914    o verification/halfpipe_streamice:
915      - change to driving stress formulation; update both Fwd & AD output.
916    o tools/genmake2 and Divided Adjoint with MPI:
917      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
918      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
919      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
920        Makefile, which is set by genmake2, and check which mpi-headers are needed.
921        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
922      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
923    o testreport:
924      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
925        perform additional runs (number of additional runs is "add_DIVA_runs" taken
926        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
927    o verification/lab_sea (AD test):
928      - change to test Divided Adjoint Run in this set-up (both standard AD test
929        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
930    o pkg atm_ & ocn_compon_interf:
931      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
932        staggerTimeStep implementation) and disable (retired) corresponding
933        parameter.
934    o pkg/offline:
935      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
936      - add S/R OFFLINE_CHECK to print offline parameter summary
937        and stop if loading a file that is not used;
938      - enable to calculate GMRedi tensor, KPP mixing and convective index
939        when the corresponding file(s) is/are not specified (but pkg is used).
940      - comment out resetting of monitorFreq (to endTime) since it still useful
941        for monitoring CFL numbers and checking offline fields.
942    o OpenAD:
943      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
944        smaller standard output) and generate new (smaller) output (on baudelaire
945        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
946    o model/src:
947      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
948        (where external_forcing_adjust was called) and change list of arguments;
949      - merge external_forcing_adjust.F into external_forcing_surf.F
950      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
951        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
952        previously in file "balance_relax.F", now removed); remove corresponding
953        arrays in FFIELDS.h.
954      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
955        a hack for getting back surfaceForcingS (loaded from file) when using
956        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
957      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
958        (was getting only 11 digits for AD-grad, due to different truncation
959         error in AD code).
960    
961    checkpoint64j (2013/07/04)
962    o pkg/offline:
963      - to enable the use of other features with pkg offline (e.g., obcs),
964        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
965      - comment out "allowFreezing" (now active) in 2 offline testing exp.
966    o pkg/exf ALLOW_RUNOFTEMP
967      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
968      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
969      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
970    o pkg/atm_phys:
971      - allows to add some damping on uVel,vVel (strength only function of k).
972    o verification, ad-tests:
973      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
974        global_ocean_ebm and offline_exf_seaice.thsice.
975    o verification/halfpipe_streamice:
976      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
977        flux input boundary conditions to be ignored; a fix for this bug changed
978        verification results for forward test.
979      - add adjoint test.
980    o pkg/ptracers:
981      - allow to restart without SOM pickup (resetting SOM to zero).
982    o pkg/gmredi:
983      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
984      - It uses mixing length theory and suppression by steering level effects to
985        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
986        to JPO, for more details).
987      - It also uses the diffusivity to calculate an eddy induced streamfunction
988        based on a PV closure (rather than a buoyancy closure as in GM).
989      - New files added to pkg/gmredi:
990        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
991          induced overturning streamfunction (called from gmredi_calc_tensor)
992        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
993          for use in gmredi_k3d
994        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
995          the eddy diffusivity
996    
997    checkpoint64i (2013/06/18)
998    o pkg/cheapaml:
999      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
1000        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
1001        with pkg/cheapaml.
1002    o utils/python: add subpackage for cubed sphere function, first example is
1003        simple cs.pcol to plot 2D fields on a map
1004    o pkg/streamice:
1005      - This is a new package in MITgcm, which solves dynamic equations for ice
1006         sheets and ice streams
1007      - At the moment it is independent of atmosphere/ocean dynamics, or any
1008        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
1009        ed that this will change)
1010      - There is a new verification exercise that tests it, halfpipe_streamice,
1011        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
1012        rectangular embayment
1013      - halfpipe_streamice is forward-only for now, will have TAF test soon
1014      - for questions, email dgoldber@mit.edu
1015    o pkg/thsice:
1016      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
1017        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
1018      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
1019         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
1020      - allow precip from pkg/cheapaml to make snow over seaice.
1021  o pkg/cfc:  o pkg/cfc:
1022    - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC    - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
1023    - remove atmos CFC 2-D arrays from common bloc (now local variables)    - remove atmos CFC 2-D arrays from common bloc (now local variables)
# Line 15  o pkg/cfc: Line 1029  o pkg/cfc:
1029      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
1030    - 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
1031    - new routine to print summary of CFC params and check for consistency.    - new routine to print summary of CFC params and check for consistency.
1032    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
1033      similar to thsice_advdiff.
1034      Note that for the B-grid case the routine parameters uc/vc are overwritten.
1035  o pkg/cfc:  o pkg/cfc:
1036    - 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);
1037      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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