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revision 1.1971 by mlosch, Wed Apr 2 15:58:54 2014 UTC revision 1.2052 by jmc, Mon Aug 25 22:12:06 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/seaice/seaice_growth:  o pkg/diagnostics (Stats-Diags):
8      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
9        a) refine region where stats are computed, excluding where arrhFac=0 ;
10        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
11        c) extend regional stats over the region edges (for U or V pt location).
12    o pkg/gchem:
13      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
14        pkg/dic is currently changing/updating ptracers values beyond the OB).
15    o verification (hs94):
16      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
17        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
18        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
19        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
20    o pkg/ptracers:
21      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
22        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
23      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
24        with AB-2 code (so that it get tested).
25    o model/src:
26      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
27        with AB-2 code (previously only available with AB-3 code).
28        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
29        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
30        there, by calling CYCLE_AB_TRACER).
31    o pkg/generic_advdiff:
32      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
33        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
34        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
35        S/R temp/salt/ptracers_integrate.F
36    o model/src & pkg/ptracers:
37      - remove common block variables gT,gS (in DYNVARS.h), except when
38         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
39      - remove common block variable gPtr.
40    o model/src & pkgs:
41      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
42         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
43         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
44         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
45      + change accordingly all calling S/R.
46      - use local temperature/salinity/ptracer tendency array (without bi,bj)
47        in S/R temp/salt/ptracers_integrate.F
48    o pkg/seaice:
49      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
50        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
51      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
52        in seaice_lsr
53      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
54        in s/r seaice_lsr_calc_coeffs
55    o pkg/mdsio:
56      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
57        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
58        too long (e.g., > MAX_LEN_FNAM/2 )
59    
60    checkpoint65b (2014/08/12)
61    o pkg/matrix:
62      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
63    o model/src:
64      - fix initialisation of geothermalFile; compile geothermal-flux code in
65        natl_box verification experiment.
66    o model/src & pkg/down_slope:
67      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
68      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
69        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
70        results at machine truncation level: update output of experiments
71        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
72    o pkg/diagnostics (Stats-Diags):
73      - do not cumulate the full volume when DIAGNOSTICS_FILL is
74        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
75        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
76        times (but Min,Max and StD are still wrong).
77    o model/src:
78      - add geothermal flux forcing: read in ini_forcing.F as time-constant
79        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
80    o model/src:
81      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
82        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
83        arrays are already updated while adjustments (filters, conv.adjustment) are
84        still applied later, in S/R TRACERS_CORRECTION_STEP.
85    o model/src:
86      - store in common bloc array "rhoInSitu" the virtual potential temperature
87        anomaly that is used to compute geopotential: this make the atmos code
88        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
89    o pkg/seaice/seaice_lsr.F
90      - rename integer variable ilcall to ipass (that's what it is called
91        in the residual diagnostics
92      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
93        default) for improved non-linear convergence of the first few steps
94      - adjust a few comments and add new ones to explain some of the store
95        directives
96    o pkg/generic_advdiff (& ptracers):
97      - re-work the code to check for valid advection scheme and for minimum
98        size of overlap (now stored in local common bloc in gad_advscheme.F)
99    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
100      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
101      - add an auxilliary variable "bet" and fix store directives and keys in
102        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
103        less exact gradients in my tests); but there are still
104        recomputation warning (although gradients are sort of OK), when
105        SEAICE_LSR_VECTORIZE is not defined, so this flag and
106        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
107      - update verification experiments lab_sea.
108      - change some comments in S/R seaice_calc_viscosities
109    o model/src:
110      - if staggerTimeStep=T, always apply exchange to velocity field in
111        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
112        (independent of using multi-dim advection or not); no effect on FWD run
113        but affects AD results (at machine truncation level): update output of
114        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
115        and isomip (oad: 12.d).
116    o pkg/generic_advdiff:
117      - stop if doAB_onGtGs is set to FALSE but ignored
118      - refine warning related to stability of tracer time-stepping
119        regarding internal wave dynamics.
120      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
121        on staggerTimeStep & implicitIntGravWave (will now get a warning
122        if potentially unstable).
123    o pkg/kl10:
124      - add new pkg "kl10" for mixing due to internal wave breaking, from
125        http://www.sciencedirect.com/science/article/pii/S1463500310000144
126        (contribution from Jody Klymak), tested in verification experiment
127        verification/internal_wave/input.kl10/
128    o isomip experiment:
129      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
130        (input.htd) and update the output.
131    o cd_code experiments:
132      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
133        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
134        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
135        update the corresponding output.
136    o pkg/seaice:
137      - reduce the number of include files and store directives in
138        S/R seaice_lsr_tridiagu/v
139      - change the order of loops in one case in S/R seaice_lsr_tridiagv
140        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
141        get rid off one store directive (a TAF bug?)
142      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
143        S/R seaice_lsr_tridiagv to change the loop range for consistency
144      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
145      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
146        S/R seaice_lsr_tridiagu/v (requires update of
147        offline_exf_seaice/input.dyn_jfnk)
148    
149    checkpoint65a (2014/07/27)
150    o model/src:
151      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
152        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
153        (topo in p-coords, ice-shelf in z-coords); update output of experiments
154        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
155    o model/src:
156      - collect momentum forcing tendency into local 2-D array (passed as argument
157        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
158        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
159        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
160      - collect T & S forcing tendency into local 2-D array (passed as argument to
161        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
162        affects results at machine truncation level (e.g., ocean: if using
163        SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)
164        moist correction due to vertical advection).
165      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
166        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
167        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
168        obcs_ctrl (ad & fwd grd @ 12 & 7).
169    o pkg/ptracers & diagnostics:
170      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
171        title (to avoid some unexpected truncation); sort out ptracers diags units.
172      - collect ptracer forcing tendency into local 2-D array (passed as argument
173        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
174    
175    checkpoint65 (2014/07/18)
176    o pkg/fizhi:
177      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
178        affects results at machine truncation level. Update output of experiments
179        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
180    o pkg/seaice: more clean up
181      - rename TAF common block tapes to be more consistent and remove
182        unnecessary duplicates
183      - add store directives to remove more recomputations, but use smaller
184        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
185        The idea behind this flag is to reduce the memory footprint when the
186        adjoint of the LSR is not required. As of now, defining the flag
187        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
188        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
189        For experiment offline_exf_seaice, this means on a linux box with gfortran
190        nearly a factor of 10 (but keep in mind there is mostly seaice code in
191        this experiment):
192        > size mitgcmuv_ad
193        text    data        bss     dec        hex  
194        5100659 1216  220458952  225560827  d71c8fb
195        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
196        but only a moderate increase of 36% for global_ocean.cs32x15:
197        text    data        bss     dec        hex
198        6695027 1648 1014578664 1021275339 3cdf6ccb
199        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
200      - note: there are still recomputations in global_ocean.cs32x15 and
201        offline_exf_seaice and the gradient agreement changes (gets a
202        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
203      - in general, the AD gradients still are wrong
204    o OpenAD
205      - clean up code_oad/ directories somewhat by moving files
206        dontCompile, dontTransform, keepOriginal to OAD_support/
207    o model/src:
208      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
209        (not currently tested): add dissipation terms before NLFS rescaling of
210        tendencies (previously done after).
211    o pkg/diagnostics:
212      - write stats-diags in ascii file with more digits (same as in monitor).
213    o pkg/down_slope:
214      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
215        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
216    o model/src:
217      - new file "apply_forcing.F" containing all the code previously in
218        external_forcing.F, but with new argument list: pass, as new argument,
219        the current level tendency array to update (instead of a direct update
220        of the common bloc array). Change the corresponding calls.
221      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
222        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
223    o pkg/seaice/seaice_lsr, a little bit of clean up
224      - rearrange some code blocks, so that now all calculations for
225        setting up the right-hand-sides done within one single block
226        (I find that easier to read and understand)
227      - rearrange freedrift-code to reduce the number of ifdefs
228      - adjust some indentations and comments
229    
230    checkpoint64z (2014/07/10)
231    o model/src and several pkgs:
232      - change argument list of all S/R called from external_forcing.F and
233        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
234        to pass, as argument, the current level tendency array to update
235        (instead of a direct update of the common bloc array).
236      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
237      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
238    o pkg/seaice/seaice_lsr.F
239      - always initialize local arrays in seaice_lsr_tridiagu/v
240      - add more local tapes to seaice_lsr_tridiagu/v
241      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
242        keep it in bi/bj loop; this seems to be essential
243      - gradients are still wrong but only by 4-7 orders of magnitude
244        instead of 15 orders of magnitude, lab_sea improves a little
245    o pkg/seaice
246      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
247        generates unnecessary code in seaice_lsr_ad
248      - add more store directives in seaice_lsr to avoid unnecessary code
249        in seaice_lsr_ad
250      - exclude some residual computations in seaice_lsr when
251        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
252        in seaice_lsr_ad
253      - add more storing, a new tape (model/src/the_main_loop.F) and
254        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
255        and klockey should be checked by a specialist)
256      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
257        and update lab_sea after previous changes in pkg/seaice below
258    o pkg/autodiff:
259      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
260        viscFacInAd : run time parameters allowing for adjoint switches
261        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
262    o pkg/ecco:
263      - introduce cost_gencost_boxmean.F that computes a box mean
264        temperature (for use in adjoint sensitivity studies).
265    o model/src/set_defaults.F : initialize viscFacAdj to 1.
266    o pkg/mom_common/mom_calc_visc.F:
267      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
268    o pkg/seaice/seaice_summary.F:
269      - statement for SEAICEadjMODE now in autodiff_readparms.F
270    o pkg/seaice:
271      - remove some store directives and add new ones in an effort to get
272        finally rid off the recomputation warnings. This is successful
273        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
274        defined (i.e. no extensive recomputation warnings left), but there
275        are still too many recomputations on the solver iteration level
276      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
277      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
278        SEAICE_SIZE.h
279      - add a store directive in S/R seaice_calc_viscosities
280    o pkg/seaice (ITD code):
281      - fix definition of Hlimit for multi-threaded case
282      - use double precision arithmetic to compute Hlimit: this affects results;
283        update output of experiment seaice_itd.
284    o replace content of verification/seaice_itd
285      - instead of a 1D column use the configuration of offline_exf_seaice
286        to test the ice thickness distribution code with ridging
287      - this is a first shot at this experiment
288      - change of some defaults of ridging parameters SEAICEhStar (from
289        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
290        and lot of new comments.
291    
292    checkpoint64y (2014/06/20)
293    o pkg/seaice/seaice_reg_ridge.F:
294      - modify the regularization of very small volumes of ice; only check
295        total volume HEFF, and do not apply correction to individual ice
296        classes because that leads to funny patterns in the heat and fw-fluxes
297        into the ocean. Adjust seaice_itd/results/output.txt
298      - replace nITD by SEAICE_multDim in loop-ranges
299    o pkg/exf:
300      - add code to process the case field period = -12. with UV interpolation.
301      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
302        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
303    o verification/global_with_exf:
304      - switch all fields period to -12. (was previously untested) in input/data.exf
305        (but keep secondary test ".yearly" unchanged); update the reference output.
306    o pkg/cal:
307      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
308    o pkg/exf:
309      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
310        to replace logical switch "exf_verbose"
311      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
312    o pkg/sbo:
313      - update from Katherine Quinn: evaluate mass directly from density and SSH
314        (budget using Finite Volume method) instead of from bottom pressure.
315      - allow testreport to collect few selected SBO output ; tested in exp.
316        global_ocean.90x40x15 (after updating the results, to include SBO output).
317      - fix some multi-threading issues (in output part).
318    o model/src & most packages:
319      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
320      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
321        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
322        "data.{pkg}" exist ; and leave the S/R (return) just after.
323      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
324        + call LAND_READPARMS from packages_readparms.F
325    o pkg/seaice:
326      - remove code that resets useThSice in S/R seaice_readparms and
327        replace it by a warning in S/R seaice_check
328      - remove parameter MULTDIM, replace with nITD and runtime
329        parameter SEAICE_multDim (still hard-wired to nITD if
330        SEAICE_ITD is defined)
331    
332    checkpoint64x (2014/05/24)
333    o verification/lab_sea:
334      - update adjoint and TLM output following changes to pkg/salt_plume
335      - un-do the update after putting back local recip_Cp in few places.
336    o pkg/salt_plume: modifications by An Nguyen:
337      - add capability to do brine rejection (salt-plume) as function of
338        volume+tracers (instead of only salinity tracer).
339      - conserve volume by exchanging volume from each kLev to above to
340        accommodate in-coming brine volume
341      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
342      - switch KPP surf buoyancy due to brine forcing to 3-d
343        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
344      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
345      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
346        in East/West Arctic.
347    o pkg/sbo:
348      - incorporate modifications from Katherine Quinn to enable the use of sbo
349        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
350        output for future testreport verification (unfinished).
351    o pkg/atm_phys:
352      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
353        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
354        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
355    o pkg/seaice
356      seaice_calc_ice_strength.F: modify expression to avoid divisions
357        (affects truncation)
358      seaice_do_ridging.F: clean up the insectarium
359      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
360      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
361      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
362      - add some debugging information and error messages (warnings)
363    o model/src: modifications relatd to atmosphere p*:
364      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
365      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
366        of vertical profile tRef in geopotential background and anomaly.
367      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
368        and pkg/atm_phys.
369      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
370        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
371    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
372    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
373        not used right now, but can be used in BGC packages to fix conservation.
374    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
375        other packages too.
376    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
377        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
378    o model/src:
379      - since we have several heat capacity (even in model/src), define "recip_Cp"
380        as local variable (no longer in common block) to avoid any confusion.
381      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
382    o pkg/exf:
383      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
384        air density as function of air Temp, Humidity and atm pressure.
385    
386    checkpoint64w (2014/05/02)
387    o verification:
388      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
389        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
390        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
391        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
392        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
393    o model/src: for atmosphere in p* coords:
394      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
395      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
396        but not yet activated.
397    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
398      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
399      - this changes the results (but not for any verification experiment, because
400        none tests this), but avoids having an extra field in the restart files
401    o pkg/seaice: remove global variable TICE (not needed)
402      - replace by TICES or local variable where necessary (cost_seaice_test,
403        seaice_diagnostics_state)
404      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
405      - use specific read/write routines for reading and writing individual leves
406        of a multilevel field
407    o pkg/ctrl & model/inc:
408      - move additional anomaly fields of control vars (related to options:
409         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
410        from DYNVARS.h into new header file: CTRL_FIELDS.h
411    o pkg/seaice: some small modifications to the ridging code
412      - make fw2ObyRidge a global variable and add the freshwater flux to
413        seaice_growth
414      - pass actual thickness from seaice_prepare_ridging, so that it is
415        computed only in one place and compute it in the same way as in
416        seaice_growth
417      - initialise more fields in seaice_do_ridging that where cause floating
418        point exceptions over land
419    o pkg/seaice: preparations for ridging code and first real ridging code
420      - move most of "PART 1" of S/R seaice_growth into a new and separate
421        S/R seaice_reg_ridge that will both regularize the state variable after
422        advection call the actual ridging routine;
423      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
424        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
425      - remove ridging code from seaice_advdiff
426      - clean up remaining part 1 of seaice_growth in an attempt to make it
427        more readable (this is probably subjective)
428      - call seaice_itd_redist once in the initialisation phase to have the initial
429        conditions in the correct category
430      - finally: add new ridging routine for ITD code
431    
432    checkpoint64v (2014/04/11)
433    o pkg/ecco:
434      - add runtime parameters mdt[start,end]date[1,2]
435      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
436    o pkg/seaice:
437      - make deltaC a global variable, so that it can be used in ridging code
438      - first step towards ridging: introduce new routines that compute
439        ice strength based on ridging parameters
440      - add diagnostic for HSNOWITD
441      - add opnWtrFrac as a global variable (required for ridging scheme)
442    o pkg/salt_plume + pkg/seaice/seaice_growth.F
443      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
444        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
445    o verification/hs94.1x64x5:
446      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
447      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
448    o autodiff:
449      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
450        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
451        For now, only in pkgs used in verification/hs94.1x64x5.
452      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
453        which are specific to TAF/TAMC).
454      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
455        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
456        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
457      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
458        building mitgcmuv_ad (make adAll).
459    o pkg/ecco:
460      - cost_gencost_seaicev4.F:
461         reformulate proxy cost as function of sst and local param SEAICE_freeze
462         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
463      - add stop statement if old names siv4-[sst,vol] are used
464      - add snapshots + cost reports for atmospheric longwave
465      - remove factor 0.1 in front of wtau[u,v]
466      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
467         ALLOW_TMI_SST_COST_CONTRIBUTION
468    o pkg/atm_phys:
469      - add some diagnostics for Short-wave and for convection S/R.
470    o pkg/seaice/seaice_growth:
471    - fix a bug in the lateral melt parameterization for SEAICE_ITD    - fix a bug in the lateral melt parameterization for SEAICE_ITD
472      in seaice_growth; tempFrz needs to be computed inside the i/j-loop      in seaice_growth; tempFrz needs to be computed inside the i/j-loop
473    - rearrange loop order for better vector code in the same code block    - rearrange loop order for better vector code in the same code block
474    - rewrite the floeDiameter formula to have fewer divisions    - rewrite the floeDiameter formula to have fewer divisions
475    -  (miraculously) none of this changes the results of seaice_itd    -  (miraculously) none of this changes the results of seaice_itd
476    o pkg/smooth:
477      - move param smooth2Ddiffnbt to pkg/ecco
478    o pkg/salt_plume:
479      - salt_plume_frac.F:
480         clean up local param names
481         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
482  o pkg/rw:  o pkg/rw:
483    - add RS version of S/R READ_MFLDS_LEV.    - add RS version of S/R READ_MFLDS_LEV.
484  o pkg/streamice:  o pkg/streamice:
# Line 47  o tools/adjoint_options: Line 516  o tools/adjoint_options:
516    - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")    - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
517    
518  checkpoint64t (2014/02/01)  checkpoint64t (2014/02/01)
519    o pkg/ecco
520      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
521        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
522      - replace hard-coded record number and period which only work for monthly
523        with read-in runtime param that works for other periods (month,day,year)
524  o pkg/thsice  o pkg/thsice
525    - corrected store directive fixes thsice adjoint gradient checks    - corrected store directive fixes thsice adjoint gradient checks
526  o genmake2 & testreport:  o genmake2 & testreport:
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