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revision 1.1980 by mlosch, Wed Apr 23 12:42:19 2014 UTC revision 1.2061 by jahn, Fri Sep 12 17:24:38 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 pkg/generic_advdiff:
8      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
9    o pkg/exf :
10      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, xxg_precip capability
11      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
12    o pkg/ctrl :
13      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
14    o model/src/load_fields_driver.F :
15      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
16        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
17    o OpenAD verification experiments:
18      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
19        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
20        for now, only in pkgs used in OpenAD verification experiments.
21      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
22        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
23        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
24        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
25    o OpenAD verification tests:
26      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
27      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
28        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
29      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
30        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
31    o model/src & generic_advdiff:
32      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
33        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
34        dynamics requires valid tracer forcing only over tile interior but, for
35        some diagnostics, may need to extend it over 1 point in tile halo region.
36      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
37        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
38        setting in temp/salt/ptracer_integrate.F
39    o pkg/dic:
40      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
41        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
42        in gchem_forcing_sep.F
43    o pkg/autodiff & obcs:
44      - add storage of current OB values for U & V (was already done for T & S).
45    
46    checkpoint65c (2014/08/30)
47    o pkg/dic:
48      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
49        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
50        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
51    o verification:
52      - new experiment testing OBCS and DIC pkgs, using params & output from
53        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
54        passage: take OBCS from the last year of a 2 yrs simulation and initial
55        conditions from t=1.yr while keeping the same forcing.
56    o model/src:
57      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
58        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
59    o pkg/diagnostics (Stats-Diags):
60      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
61        a) refine region where stats are computed, excluding where arrhFac=0 ;
62        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
63        c) extend regional stats over the region edges (for U or V pt location).
64    o pkg/gchem:
65      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
66        pkg/dic is currently changing/updating ptracers values beyond the OB).
67    o verification (hs94):
68      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
69        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
70        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
71        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
72    o pkg/ptracers:
73      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
74        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
75      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
76        with AB-2 code (so that it get tested).
77    o model/src:
78      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
79        with AB-2 code (previously only available with AB-3 code).
80        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
81        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
82        there, by calling CYCLE_AB_TRACER).
83    o pkg/generic_advdiff:
84      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
85        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
86        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
87        S/R temp/salt/ptracers_integrate.F
88    o model/src & pkg/ptracers:
89      - remove common block variables gT,gS (in DYNVARS.h), except when
90         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
91      - remove common block variable gPtr.
92    o model/src & pkgs:
93      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
94         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
95         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
96         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
97      + change accordingly all calling S/R.
98      - use local temperature/salinity/ptracer tendency array (without bi,bj)
99        in S/R temp/salt/ptracers_integrate.F
100    o pkg/seaice:
101      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
102        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
103      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
104        in seaice_lsr
105      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
106        in s/r seaice_lsr_calc_coeffs
107    o pkg/mdsio:
108      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
109        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
110        too long (e.g., > MAX_LEN_FNAM/2 )
111    
112    checkpoint65b (2014/08/12)
113    o pkg/matrix:
114      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
115    o model/src:
116      - fix initialisation of geothermalFile; compile geothermal-flux code in
117        natl_box verification experiment.
118    o model/src & pkg/down_slope:
119      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
120      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
121        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
122        results at machine truncation level: update output of experiments
123        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
124    o pkg/diagnostics (Stats-Diags):
125      - do not cumulate the full volume when DIAGNOSTICS_FILL is
126        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
127        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
128        times (but Min,Max and StD are still wrong).
129    o model/src:
130      - add geothermal flux forcing: read in ini_forcing.F as time-constant
131        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
132    o model/src:
133      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
134        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
135        arrays are already updated while adjustments (filters, conv.adjustment) are
136        still applied later, in S/R TRACERS_CORRECTION_STEP.
137    o model/src:
138      - store in common bloc array "rhoInSitu" the virtual potential temperature
139        anomaly that is used to compute geopotential: this make the atmos code
140        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
141    o pkg/seaice/seaice_lsr.F
142      - rename integer variable ilcall to ipass (that's what it is called
143        in the residual diagnostics
144      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
145        default) for improved non-linear convergence of the first few steps
146      - adjust a few comments and add new ones to explain some of the store
147        directives
148    o pkg/generic_advdiff (& ptracers):
149      - re-work the code to check for valid advection scheme and for minimum
150        size of overlap (now stored in local common bloc in gad_advscheme.F)
151    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
152      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
153      - add an auxilliary variable "bet" and fix store directives and keys in
154        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
155        less exact gradients in my tests); but there are still
156        recomputation warning (although gradients are sort of OK), when
157        SEAICE_LSR_VECTORIZE is not defined, so this flag and
158        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
159      - update verification experiments lab_sea.
160      - change some comments in S/R seaice_calc_viscosities
161    o model/src:
162      - if staggerTimeStep=T, always apply exchange to velocity field in
163        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
164        (independent of using multi-dim advection or not); no effect on FWD run
165        but affects AD results (at machine truncation level): update output of
166        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
167        and isomip (oad: 12.d).
168    o pkg/generic_advdiff:
169      - stop if doAB_onGtGs is set to FALSE but ignored
170      - refine warning related to stability of tracer time-stepping
171        regarding internal wave dynamics.
172      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
173        on staggerTimeStep & implicitIntGravWave (will now get a warning
174        if potentially unstable).
175    o pkg/kl10:
176      - add new pkg "kl10" for mixing due to internal wave breaking, from
177        http://www.sciencedirect.com/science/article/pii/S1463500310000144
178        (contribution from Jody Klymak), tested in verification experiment
179        verification/internal_wave/input.kl10/
180    o isomip experiment:
181      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
182        (input.htd) and update the output.
183    o cd_code experiments:
184      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
185        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
186        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
187        update the corresponding output.
188    o pkg/seaice:
189      - reduce the number of include files and store directives in
190        S/R seaice_lsr_tridiagu/v
191      - change the order of loops in one case in S/R seaice_lsr_tridiagv
192        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
193        get rid off one store directive (a TAF bug?)
194      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
195        S/R seaice_lsr_tridiagv to change the loop range for consistency
196      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
197      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
198        S/R seaice_lsr_tridiagu/v (requires update of
199        offline_exf_seaice/input.dyn_jfnk)
200    
201    checkpoint65a (2014/07/27)
202    o model/src:
203      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
204        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
205        (topo in p-coords, ice-shelf in z-coords); update output of experiments
206        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
207    o model/src:
208      - collect momentum forcing tendency into local 2-D array (passed as argument
209        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
210        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
211        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
212      - collect T & S forcing tendency into local 2-D array (passed as argument to
213        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
214        affects results at machine truncation level (e.g., ocean: if using
215        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
216        correction due to vertical advection).
217      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
218        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
219        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
220        obcs_ctrl (ad & fwd grd @ 12 & 7).
221    o pkg/ptracers & diagnostics:
222      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
223        title (to avoid some unexpected truncation); sort out ptracers diags units.
224      - collect ptracer forcing tendency into local 2-D array (passed as argument
225        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
226    
227    checkpoint65 (2014/07/18)
228    o pkg/fizhi:
229      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
230        affects results at machine truncation level. Update output of experiments
231        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
232    o pkg/seaice: more clean up
233      - rename TAF common block tapes to be more consistent and remove
234        unnecessary duplicates
235      - add store directives to remove more recomputations, but use smaller
236        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
237        The idea behind this flag is to reduce the memory footprint when the
238        adjoint of the LSR is not required. As of now, defining the flag
239        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
240        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
241        For experiment offline_exf_seaice, this means on a linux box with gfortran
242        nearly a factor of 10 (but keep in mind there is mostly seaice code in
243        this experiment):
244        > size mitgcmuv_ad
245        text    data        bss     dec        hex  
246        5100659 1216  220458952  225560827  d71c8fb
247        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
248        but only a moderate increase of 36% for global_ocean.cs32x15:
249        text    data        bss     dec        hex
250        6695027 1648 1014578664 1021275339 3cdf6ccb
251        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
252      - note: there are still recomputations in global_ocean.cs32x15 and
253        offline_exf_seaice and the gradient agreement changes (gets a
254        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
255      - in general, the AD gradients still are wrong
256    o OpenAD
257      - clean up code_oad/ directories somewhat by moving files
258        dontCompile, dontTransform, keepOriginal to OAD_support/
259    o model/src:
260      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
261        (not currently tested): add dissipation terms before NLFS rescaling of
262        tendencies (previously done after).
263    o pkg/diagnostics:
264      - write stats-diags in ascii file with more digits (same as in monitor).
265    o pkg/down_slope:
266      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
267        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
268    o model/src:
269      - new file "apply_forcing.F" containing all the code previously in
270        external_forcing.F, but with new argument list: pass, as new argument,
271        the current level tendency array to update (instead of a direct update
272        of the common bloc array). Change the corresponding calls.
273      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
274        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
275    o pkg/seaice/seaice_lsr, a little bit of clean up
276      - rearrange some code blocks, so that now all calculations for
277        setting up the right-hand-sides done within one single block
278        (I find that easier to read and understand)
279      - rearrange freedrift-code to reduce the number of ifdefs
280      - adjust some indentations and comments
281    
282    checkpoint64z (2014/07/10)
283    o model/src and several pkgs:
284      - change argument list of all S/R called from external_forcing.F and
285        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
286        to pass, as argument, the current level tendency array to update
287        (instead of a direct update of the common bloc array).
288      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
289      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
290    o pkg/seaice/seaice_lsr.F
291      - always initialize local arrays in seaice_lsr_tridiagu/v
292      - add more local tapes to seaice_lsr_tridiagu/v
293      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
294        keep it in bi/bj loop; this seems to be essential
295      - gradients are still wrong but only by 4-7 orders of magnitude
296        instead of 15 orders of magnitude, lab_sea improves a little
297    o pkg/seaice
298      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
299        generates unnecessary code in seaice_lsr_ad
300      - add more store directives in seaice_lsr to avoid unnecessary code
301        in seaice_lsr_ad
302      - exclude some residual computations in seaice_lsr when
303        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
304        in seaice_lsr_ad
305      - add more storing, a new tape (model/src/the_main_loop.F) and
306        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
307        and klockey should be checked by a specialist)
308      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
309        and update lab_sea after previous changes in pkg/seaice below
310    o pkg/autodiff:
311      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
312        viscFacInAd : run time parameters allowing for adjoint switches
313        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
314    o pkg/ecco:
315      - introduce cost_gencost_boxmean.F that computes a box mean
316        temperature (for use in adjoint sensitivity studies).
317    o model/src/set_defaults.F : initialize viscFacAdj to 1.
318    o pkg/mom_common/mom_calc_visc.F:
319      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
320    o pkg/seaice/seaice_summary.F:
321      - statement for SEAICEadjMODE now in autodiff_readparms.F
322    o pkg/seaice:
323      - remove some store directives and add new ones in an effort to get
324        finally rid off the recomputation warnings. This is successful
325        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
326        defined (i.e. no extensive recomputation warnings left), but there
327        are still too many recomputations on the solver iteration level
328      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
329      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
330        SEAICE_SIZE.h
331      - add a store directive in S/R seaice_calc_viscosities
332    o pkg/seaice (ITD code):
333      - fix definition of Hlimit for multi-threaded case
334      - use double precision arithmetic to compute Hlimit: this affects results;
335        update output of experiment seaice_itd.
336    o replace content of verification/seaice_itd
337      - instead of a 1D column use the configuration of offline_exf_seaice
338        to test the ice thickness distribution code with ridging
339      - this is a first shot at this experiment
340      - change of some defaults of ridging parameters SEAICEhStar (from
341        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
342        and lot of new comments.
343    
344    checkpoint64y (2014/06/20)
345    o pkg/seaice/seaice_reg_ridge.F:
346      - modify the regularization of very small volumes of ice; only check
347        total volume HEFF, and do not apply correction to individual ice
348        classes because that leads to funny patterns in the heat and fw-fluxes
349        into the ocean. Adjust seaice_itd/results/output.txt
350      - replace nITD by SEAICE_multDim in loop-ranges
351    o pkg/exf:
352      - add code to process the case field period = -12. with UV interpolation.
353      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
354        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
355    o verification/global_with_exf:
356      - switch all fields period to -12. (was previously untested) in input/data.exf
357        (but keep secondary test ".yearly" unchanged); update the reference output.
358    o pkg/cal:
359      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
360    o pkg/exf:
361      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
362        to replace logical switch "exf_verbose"
363      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
364    o pkg/sbo:
365      - update from Katherine Quinn: evaluate mass directly from density and SSH
366        (budget using Finite Volume method) instead of from bottom pressure.
367      - allow testreport to collect few selected SBO output ; tested in exp.
368        global_ocean.90x40x15 (after updating the results, to include SBO output).
369      - fix some multi-threading issues (in output part).
370    o model/src & most packages:
371      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
372      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
373        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
374        "data.{pkg}" exist ; and leave the S/R (return) just after.
375      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
376        + call LAND_READPARMS from packages_readparms.F
377    o pkg/seaice:
378      - remove code that resets useThSice in S/R seaice_readparms and
379        replace it by a warning in S/R seaice_check
380      - remove parameter MULTDIM, replace with nITD and runtime
381        parameter SEAICE_multDim (still hard-wired to nITD if
382        SEAICE_ITD is defined)
383    
384    checkpoint64x (2014/05/24)
385    o verification/lab_sea:
386      - update adjoint and TLM output following changes to pkg/salt_plume
387      - un-do the update after putting back local recip_Cp in few places.
388    o pkg/salt_plume: modifications by An Nguyen:
389      - add capability to do brine rejection (salt-plume) as function of
390        volume+tracers (instead of only salinity tracer).
391      - conserve volume by exchanging volume from each kLev to above to
392        accommodate in-coming brine volume
393      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
394      - switch KPP surf buoyancy due to brine forcing to 3-d
395        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
396      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
397      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
398        in East/West Arctic.
399    o pkg/sbo:
400      - incorporate modifications from Katherine Quinn to enable the use of sbo
401        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
402        output for future testreport verification (unfinished).
403    o pkg/atm_phys:
404      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
405        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
406        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
407    o pkg/seaice
408      seaice_calc_ice_strength.F: modify expression to avoid divisions
409        (affects truncation)
410      seaice_do_ridging.F: clean up the insectarium
411      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
412      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
413      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
414      - add some debugging information and error messages (warnings)
415    o model/src: modifications relatd to atmosphere p*:
416      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
417      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
418        of vertical profile tRef in geopotential background and anomaly.
419      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
420        and pkg/atm_phys.
421      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
422        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
423    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
424    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
425        not used right now, but can be used in BGC packages to fix conservation.
426    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
427        other packages too.
428    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
429        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
430    o model/src:
431      - since we have several heat capacity (even in model/src), define "recip_Cp"
432        as local variable (no longer in common block) to avoid any confusion.
433      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
434    o pkg/exf:
435      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
436        air density as function of air Temp, Humidity and atm pressure.
437    
438    checkpoint64w (2014/05/02)
439    o verification:
440      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
441        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
442        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
443        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
444        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
445    o model/src: for atmosphere in p* coords:
446      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
447      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
448        but not yet activated.
449    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
450      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
451      - this changes the results (but not for any verification experiment, because
452        none tests this), but avoids having an extra field in the restart files
453    o pkg/seaice: remove global variable TICE (not needed)
454      - replace by TICES or local variable where necessary (cost_seaice_test,
455        seaice_diagnostics_state)
456      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
457      - use specific read/write routines for reading and writing individual leves
458        of a multilevel field
459    o pkg/ctrl & model/inc:
460      - move additional anomaly fields of control vars (related to options:
461         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
462        from DYNVARS.h into new header file: CTRL_FIELDS.h
463    o pkg/seaice: some small modifications to the ridging code
464      - make fw2ObyRidge a global variable and add the freshwater flux to
465        seaice_growth
466      - pass actual thickness from seaice_prepare_ridging, so that it is
467        computed only in one place and compute it in the same way as in
468        seaice_growth
469      - initialise more fields in seaice_do_ridging that where cause floating
470        point exceptions over land
471  o pkg/seaice: preparations for ridging code and first real ridging code  o pkg/seaice: preparations for ridging code and first real ridging code
472    - move most of "PART 1" of S/R seaice_growth into a new and separate    - move most of "PART 1" of S/R seaice_growth into a new and separate
473      S/R seaice_reg_ridge that will both regularize the state variable after      S/R seaice_reg_ridge that will both regularize the state variable after
474      advection call the actual ridging routine;      advection call the actual ridging routine;
475    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
476      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
477    - remove ridging code from seaice_advdiff    - remove ridging code from seaice_advdiff
478    - clean up remaining part 1 of seaice_growth in an attempt to make it    - clean up remaining part 1 of seaice_growth in an attempt to make it
479      more readable (this is probably subjective)      more readable (this is probably subjective)
480    - call seaice_itd_redist once in the initialisation phase to have the initial    - call seaice_itd_redist once in the initialisation phase to have the initial
481      conditions in the correct category      conditions in the correct category
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