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revision 1.1942 by jmc, Tue Nov 19 22:16:45 2013 UTC revision 1.2054 by jmc, Wed Aug 27 03:03:27 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o verification:
8      - new experiment testing OBCS and DIC pkgs, using params & output from
9        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
10        passage: take OBCS from the last year of a 2 yrs simulation and initial
11        conditions from t=1.yr while keeping the same forcing.
12    o model/src:
13      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
14        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
15    o pkg/diagnostics (Stats-Diags):
16      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
17        a) refine region where stats are computed, excluding where arrhFac=0 ;
18        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
19        c) extend regional stats over the region edges (for U or V pt location).
20    o pkg/gchem:
21      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
22        pkg/dic is currently changing/updating ptracers values beyond the OB).
23    o verification (hs94):
24      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
25        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
26        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
27        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
28    o pkg/ptracers:
29      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
30        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
31      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
32        with AB-2 code (so that it get tested).
33    o model/src:
34      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
35        with AB-2 code (previously only available with AB-3 code).
36        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
37        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
38        there, by calling CYCLE_AB_TRACER).
39    o pkg/generic_advdiff:
40      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
41        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
42        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
43        S/R temp/salt/ptracers_integrate.F
44    o model/src & pkg/ptracers:
45      - remove common block variables gT,gS (in DYNVARS.h), except when
46         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
47      - remove common block variable gPtr.
48    o model/src & pkgs:
49      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
50         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
51         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
52         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
53      + change accordingly all calling S/R.
54      - use local temperature/salinity/ptracer tendency array (without bi,bj)
55        in S/R temp/salt/ptracers_integrate.F
56    o pkg/seaice:
57      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
58        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
59      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
60        in seaice_lsr
61      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
62        in s/r seaice_lsr_calc_coeffs
63    o pkg/mdsio:
64      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
65        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
66        too long (e.g., > MAX_LEN_FNAM/2 )
67    
68    checkpoint65b (2014/08/12)
69    o pkg/matrix:
70      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
71    o model/src:
72      - fix initialisation of geothermalFile; compile geothermal-flux code in
73        natl_box verification experiment.
74    o model/src & pkg/down_slope:
75      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
76      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
77        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
78        results at machine truncation level: update output of experiments
79        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
80    o pkg/diagnostics (Stats-Diags):
81      - do not cumulate the full volume when DIAGNOSTICS_FILL is
82        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
83        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
84        times (but Min,Max and StD are still wrong).
85    o model/src:
86      - add geothermal flux forcing: read in ini_forcing.F as time-constant
87        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
88    o model/src:
89      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
90        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
91        arrays are already updated while adjustments (filters, conv.adjustment) are
92        still applied later, in S/R TRACERS_CORRECTION_STEP.
93    o model/src:
94      - store in common bloc array "rhoInSitu" the virtual potential temperature
95        anomaly that is used to compute geopotential: this make the atmos code
96        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
97    o pkg/seaice/seaice_lsr.F
98      - rename integer variable ilcall to ipass (that's what it is called
99        in the residual diagnostics
100      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
101        default) for improved non-linear convergence of the first few steps
102      - adjust a few comments and add new ones to explain some of the store
103        directives
104    o pkg/generic_advdiff (& ptracers):
105      - re-work the code to check for valid advection scheme and for minimum
106        size of overlap (now stored in local common bloc in gad_advscheme.F)
107    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
108      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
109      - add an auxilliary variable "bet" and fix store directives and keys in
110        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
111        less exact gradients in my tests); but there are still
112        recomputation warning (although gradients are sort of OK), when
113        SEAICE_LSR_VECTORIZE is not defined, so this flag and
114        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
115      - update verification experiments lab_sea.
116      - change some comments in S/R seaice_calc_viscosities
117    o model/src:
118      - if staggerTimeStep=T, always apply exchange to velocity field in
119        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
120        (independent of using multi-dim advection or not); no effect on FWD run
121        but affects AD results (at machine truncation level): update output of
122        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
123        and isomip (oad: 12.d).
124    o pkg/generic_advdiff:
125      - stop if doAB_onGtGs is set to FALSE but ignored
126      - refine warning related to stability of tracer time-stepping
127        regarding internal wave dynamics.
128      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
129        on staggerTimeStep & implicitIntGravWave (will now get a warning
130        if potentially unstable).
131    o pkg/kl10:
132      - add new pkg "kl10" for mixing due to internal wave breaking, from
133        http://www.sciencedirect.com/science/article/pii/S1463500310000144
134        (contribution from Jody Klymak), tested in verification experiment
135        verification/internal_wave/input.kl10/
136    o isomip experiment:
137      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
138        (input.htd) and update the output.
139    o cd_code experiments:
140      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
141        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
142        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
143        update the corresponding output.
144    o pkg/seaice:
145      - reduce the number of include files and store directives in
146        S/R seaice_lsr_tridiagu/v
147      - change the order of loops in one case in S/R seaice_lsr_tridiagv
148        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
149        get rid off one store directive (a TAF bug?)
150      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
151        S/R seaice_lsr_tridiagv to change the loop range for consistency
152      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
153      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
154        S/R seaice_lsr_tridiagu/v (requires update of
155        offline_exf_seaice/input.dyn_jfnk)
156    
157    checkpoint65a (2014/07/27)
158    o model/src:
159      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
160        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
161        (topo in p-coords, ice-shelf in z-coords); update output of experiments
162        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
163    o model/src:
164      - collect momentum forcing tendency into local 2-D array (passed as argument
165        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
166        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
167        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
168      - collect T & S forcing tendency into local 2-D array (passed as argument to
169        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
170        affects results at machine truncation level (e.g., ocean: if using
171        SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)
172        moist correction due to vertical advection).
173      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
174        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
175        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
176        obcs_ctrl (ad & fwd grd @ 12 & 7).
177    o pkg/ptracers & diagnostics:
178      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
179        title (to avoid some unexpected truncation); sort out ptracers diags units.
180      - collect ptracer forcing tendency into local 2-D array (passed as argument
181        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
182    
183    checkpoint65 (2014/07/18)
184    o pkg/fizhi:
185      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
186        affects results at machine truncation level. Update output of experiments
187        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
188    o pkg/seaice: more clean up
189      - rename TAF common block tapes to be more consistent and remove
190        unnecessary duplicates
191      - add store directives to remove more recomputations, but use smaller
192        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
193        The idea behind this flag is to reduce the memory footprint when the
194        adjoint of the LSR is not required. As of now, defining the flag
195        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
196        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
197        For experiment offline_exf_seaice, this means on a linux box with gfortran
198        nearly a factor of 10 (but keep in mind there is mostly seaice code in
199        this experiment):
200        > size mitgcmuv_ad
201        text    data        bss     dec        hex  
202        5100659 1216  220458952  225560827  d71c8fb
203        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
204        but only a moderate increase of 36% for global_ocean.cs32x15:
205        text    data        bss     dec        hex
206        6695027 1648 1014578664 1021275339 3cdf6ccb
207        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
208      - note: there are still recomputations in global_ocean.cs32x15 and
209        offline_exf_seaice and the gradient agreement changes (gets a
210        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
211      - in general, the AD gradients still are wrong
212    o OpenAD
213      - clean up code_oad/ directories somewhat by moving files
214        dontCompile, dontTransform, keepOriginal to OAD_support/
215    o model/src:
216      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
217        (not currently tested): add dissipation terms before NLFS rescaling of
218        tendencies (previously done after).
219    o pkg/diagnostics:
220      - write stats-diags in ascii file with more digits (same as in monitor).
221    o pkg/down_slope:
222      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
223        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
224    o model/src:
225      - new file "apply_forcing.F" containing all the code previously in
226        external_forcing.F, but with new argument list: pass, as new argument,
227        the current level tendency array to update (instead of a direct update
228        of the common bloc array). Change the corresponding calls.
229      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
230        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
231    o pkg/seaice/seaice_lsr, a little bit of clean up
232      - rearrange some code blocks, so that now all calculations for
233        setting up the right-hand-sides done within one single block
234        (I find that easier to read and understand)
235      - rearrange freedrift-code to reduce the number of ifdefs
236      - adjust some indentations and comments
237    
238    checkpoint64z (2014/07/10)
239    o model/src and several pkgs:
240      - change argument list of all S/R called from external_forcing.F and
241        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
242        to pass, as argument, the current level tendency array to update
243        (instead of a direct update of the common bloc array).
244      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
245      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
246    o pkg/seaice/seaice_lsr.F
247      - always initialize local arrays in seaice_lsr_tridiagu/v
248      - add more local tapes to seaice_lsr_tridiagu/v
249      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
250        keep it in bi/bj loop; this seems to be essential
251      - gradients are still wrong but only by 4-7 orders of magnitude
252        instead of 15 orders of magnitude, lab_sea improves a little
253    o pkg/seaice
254      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
255        generates unnecessary code in seaice_lsr_ad
256      - add more store directives in seaice_lsr to avoid unnecessary code
257        in seaice_lsr_ad
258      - exclude some residual computations in seaice_lsr when
259        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
260        in seaice_lsr_ad
261      - add more storing, a new tape (model/src/the_main_loop.F) and
262        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
263        and klockey should be checked by a specialist)
264      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
265        and update lab_sea after previous changes in pkg/seaice below
266    o pkg/autodiff:
267      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
268        viscFacInAd : run time parameters allowing for adjoint switches
269        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
270    o pkg/ecco:
271      - introduce cost_gencost_boxmean.F that computes a box mean
272        temperature (for use in adjoint sensitivity studies).
273    o model/src/set_defaults.F : initialize viscFacAdj to 1.
274    o pkg/mom_common/mom_calc_visc.F:
275      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
276    o pkg/seaice/seaice_summary.F:
277      - statement for SEAICEadjMODE now in autodiff_readparms.F
278    o pkg/seaice:
279      - remove some store directives and add new ones in an effort to get
280        finally rid off the recomputation warnings. This is successful
281        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
282        defined (i.e. no extensive recomputation warnings left), but there
283        are still too many recomputations on the solver iteration level
284      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
285      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
286        SEAICE_SIZE.h
287      - add a store directive in S/R seaice_calc_viscosities
288    o pkg/seaice (ITD code):
289      - fix definition of Hlimit for multi-threaded case
290      - use double precision arithmetic to compute Hlimit: this affects results;
291        update output of experiment seaice_itd.
292    o replace content of verification/seaice_itd
293      - instead of a 1D column use the configuration of offline_exf_seaice
294        to test the ice thickness distribution code with ridging
295      - this is a first shot at this experiment
296      - change of some defaults of ridging parameters SEAICEhStar (from
297        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
298        and lot of new comments.
299    
300    checkpoint64y (2014/06/20)
301    o pkg/seaice/seaice_reg_ridge.F:
302      - modify the regularization of very small volumes of ice; only check
303        total volume HEFF, and do not apply correction to individual ice
304        classes because that leads to funny patterns in the heat and fw-fluxes
305        into the ocean. Adjust seaice_itd/results/output.txt
306      - replace nITD by SEAICE_multDim in loop-ranges
307    o pkg/exf:
308      - add code to process the case field period = -12. with UV interpolation.
309      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
310        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
311    o verification/global_with_exf:
312      - switch all fields period to -12. (was previously untested) in input/data.exf
313        (but keep secondary test ".yearly" unchanged); update the reference output.
314    o pkg/cal:
315      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
316    o pkg/exf:
317      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
318        to replace logical switch "exf_verbose"
319      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
320    o pkg/sbo:
321      - update from Katherine Quinn: evaluate mass directly from density and SSH
322        (budget using Finite Volume method) instead of from bottom pressure.
323      - allow testreport to collect few selected SBO output ; tested in exp.
324        global_ocean.90x40x15 (after updating the results, to include SBO output).
325      - fix some multi-threading issues (in output part).
326    o model/src & most packages:
327      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
328      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
329        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
330        "data.{pkg}" exist ; and leave the S/R (return) just after.
331      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
332        + call LAND_READPARMS from packages_readparms.F
333    o pkg/seaice:
334      - remove code that resets useThSice in S/R seaice_readparms and
335        replace it by a warning in S/R seaice_check
336      - remove parameter MULTDIM, replace with nITD and runtime
337        parameter SEAICE_multDim (still hard-wired to nITD if
338        SEAICE_ITD is defined)
339    
340    checkpoint64x (2014/05/24)
341    o verification/lab_sea:
342      - update adjoint and TLM output following changes to pkg/salt_plume
343      - un-do the update after putting back local recip_Cp in few places.
344    o pkg/salt_plume: modifications by An Nguyen:
345      - add capability to do brine rejection (salt-plume) as function of
346        volume+tracers (instead of only salinity tracer).
347      - conserve volume by exchanging volume from each kLev to above to
348        accommodate in-coming brine volume
349      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
350      - switch KPP surf buoyancy due to brine forcing to 3-d
351        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
352      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
353      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
354        in East/West Arctic.
355    o pkg/sbo:
356      - incorporate modifications from Katherine Quinn to enable the use of sbo
357        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
358        output for future testreport verification (unfinished).
359    o pkg/atm_phys:
360      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
361        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
362        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
363    o pkg/seaice
364      seaice_calc_ice_strength.F: modify expression to avoid divisions
365        (affects truncation)
366      seaice_do_ridging.F: clean up the insectarium
367      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
368      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
369      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
370      - add some debugging information and error messages (warnings)
371    o model/src: modifications relatd to atmosphere p*:
372      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
373      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
374        of vertical profile tRef in geopotential background and anomaly.
375      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
376        and pkg/atm_phys.
377      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
378        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
379    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
380    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
381        not used right now, but can be used in BGC packages to fix conservation.
382    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
383        other packages too.
384    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
385        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
386    o model/src:
387      - since we have several heat capacity (even in model/src), define "recip_Cp"
388        as local variable (no longer in common block) to avoid any confusion.
389      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
390    o pkg/exf:
391      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
392        air density as function of air Temp, Humidity and atm pressure.
393    
394    checkpoint64w (2014/05/02)
395    o verification:
396      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
397        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
398        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
399        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
400        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
401    o model/src: for atmosphere in p* coords:
402      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
403      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
404        but not yet activated.
405    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
406      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
407      - this changes the results (but not for any verification experiment, because
408        none tests this), but avoids having an extra field in the restart files
409    o pkg/seaice: remove global variable TICE (not needed)
410      - replace by TICES or local variable where necessary (cost_seaice_test,
411        seaice_diagnostics_state)
412      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
413      - use specific read/write routines for reading and writing individual leves
414        of a multilevel field
415    o pkg/ctrl & model/inc:
416      - move additional anomaly fields of control vars (related to options:
417         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
418        from DYNVARS.h into new header file: CTRL_FIELDS.h
419    o pkg/seaice: some small modifications to the ridging code
420      - make fw2ObyRidge a global variable and add the freshwater flux to
421        seaice_growth
422      - pass actual thickness from seaice_prepare_ridging, so that it is
423        computed only in one place and compute it in the same way as in
424        seaice_growth
425      - initialise more fields in seaice_do_ridging that where cause floating
426        point exceptions over land
427    o pkg/seaice: preparations for ridging code and first real ridging code
428      - move most of "PART 1" of S/R seaice_growth into a new and separate
429        S/R seaice_reg_ridge that will both regularize the state variable after
430        advection call the actual ridging routine;
431      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
432        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
433      - remove ridging code from seaice_advdiff
434      - clean up remaining part 1 of seaice_growth in an attempt to make it
435        more readable (this is probably subjective)
436      - call seaice_itd_redist once in the initialisation phase to have the initial
437        conditions in the correct category
438      - finally: add new ridging routine for ITD code
439    
440    checkpoint64v (2014/04/11)
441    o pkg/ecco:
442      - add runtime parameters mdt[start,end]date[1,2]
443      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
444    o pkg/seaice:
445      - make deltaC a global variable, so that it can be used in ridging code
446      - first step towards ridging: introduce new routines that compute
447        ice strength based on ridging parameters
448      - add diagnostic for HSNOWITD
449      - add opnWtrFrac as a global variable (required for ridging scheme)
450    o pkg/salt_plume + pkg/seaice/seaice_growth.F
451      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
452        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
453    o verification/hs94.1x64x5:
454      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
455      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
456    o autodiff:
457      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
458        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
459        For now, only in pkgs used in verification/hs94.1x64x5.
460      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
461        which are specific to TAF/TAMC).
462      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
463        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
464        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
465      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
466        building mitgcmuv_ad (make adAll).
467    o pkg/ecco:
468      - cost_gencost_seaicev4.F:
469         reformulate proxy cost as function of sst and local param SEAICE_freeze
470         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
471      - add stop statement if old names siv4-[sst,vol] are used
472      - add snapshots + cost reports for atmospheric longwave
473      - remove factor 0.1 in front of wtau[u,v]
474      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
475         ALLOW_TMI_SST_COST_CONTRIBUTION
476    o pkg/atm_phys:
477      - add some diagnostics for Short-wave and for convection S/R.
478    o pkg/seaice/seaice_growth:
479      - fix a bug in the lateral melt parameterization for SEAICE_ITD
480        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
481      - rearrange loop order for better vector code in the same code block
482      - rewrite the floeDiameter formula to have fewer divisions
483      -  (miraculously) none of this changes the results of seaice_itd
484    o pkg/smooth:
485      - move param smooth2Ddiffnbt to pkg/ecco
486    o pkg/salt_plume:
487      - salt_plume_frac.F:
488         clean up local param names
489         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
490    o pkg/rw:
491      - add RS version of S/R READ_MFLDS_LEV.
492    o pkg/streamice:
493      - fix the restart test by writing/reading pickup_streamice files.
494    o pkg/seaice:
495      - refine checks for jfnk-related parameters
496      - comment out if statement with SEAICEuseIMEX parameter as long as there
497        is no IMEX code to avoid confusion and surprises
498    
499    checkpoint64u (2014/03/07)
500    o verification/MLAdjust:
501      - rename secondary test suffix:
502         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
503         0.leithD -> AhFlxF  + switch to flux-form
504         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
505         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
506    o pkg/mom_vecinv:
507      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
508        to be before mom_calc_visc.F)
509      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
510      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
511        this is simpler for the adjoint and for diagnostics.
512    o model/src + pkg/momentum:
513      - add input files for  2-D additional Western and Southern cell-edge wall
514         (e.g., to add "thin-wall" where it is =1).
515      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
516        using 2nd hFacZ that is computed from initial (fix domain) hFac
517      - known limitations of thin wall implementation: not yet coded for sigma
518        coords; not working with CD-scheme neither.
519    o pkg/seaice:
520      - rename recently introduced parameters from (wrong name) AB to
521        BDF (backward difference time discretisation)
522      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
523    o tools/adjoint_options:
524      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
525    
526    checkpoint64t (2014/02/01)
527    o pkg/ecco
528      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
529        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
530      - replace hard-coded record number and period which only work for monthly
531        with read-in runtime param that works for other periods (month,day,year)
532    o pkg/thsice
533      - corrected store directive fixes thsice adjoint gradient checks
534    o genmake2 & testreport:
535      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
536        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
537        Update testreport accordingly. No need to set "export OPENAD=true"
538        in adjoint_options/adjoint_oad anymore (will be removed later).
539    o pkg/shelfice:
540      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
541        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
542        so that surface forcing applies to k=kSurf if using pkg/shelfice.
543    o pkg/ctrl, pkg/grdchk, pkg/ecco:
544      - Changes to make GENARR more modular (i.e. invisible if not used)
545    o model/src/temp_integrate.F and salt_integrate.F
546      - re-include store directives that were removed on Dec 27th.
547    o model/src/external_forcing_surf.F
548      - add storage directives for EmPmR and PmEpR to avoid recomputation of
549        seaice_model in the adjoint that is problematic when seaice_model is
550        turned off in the adjoint. The resolved issue dated back to July when
551        EXTERNAL_FORCING_SURF call was moved.
552        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
553    o pkg/exf/exf_check.F
554      - fix a small bug again (originally found by Wentao Liu, now found again)
555      - streamline error output
556    o pkg/streamice and aim_v23:
557      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
558        Apple's /usr/bin/cpp knows what to do:
559        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
560        Target: x86_64-apple-darwin13.0.0
561    
562    checkpoint64s (2014/01/05)
563    o tools/adjoint_options:
564      - switch to fastopt.net TAF server (instead of default fastopt.de) for
565        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
566    o model/src:
567      - remove some unnecessary TAF storage directives in forward_step.F and
568        in dynamics.F (note: not always removed by TAF, e.g., double storage
569        of kappaRU,kappaRV in former version of dynamics.F).
570    o model/src & pkg/ptracers:
571      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
572        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
573        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
574      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
575      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
576      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
577    o useSingleCpuInput separates single-CPU input from single-CPU output;
578        for now only implemented for in exf_interp_read.F
579    o verification/advect_xy:
580      - fix missing EXCH call in local version of ini_salt.F and update output.
581    o momentum diagnostics:
582      - fix which deltaT is used in Total-Tendency diagnostics.
583      - fix typo in diagnostics for momentum tendency from AB.
584    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
585        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
586    
587    checkpoint64r (2013/12/08)
588    o verification/*/results:
589      - Update reference output of experiments that were passing with just 13 digits
590         (make it easier to detect future changes in results)
591    o model/src & pkg/ptracers:
592      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
593        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
594        to inside ptracers_integrate.F ; remove ptracers_advection.F
595    o coupling interface pkgs:
596        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
597      - change the config check to test the agreement of Ocean Depth
598        with ATM land/sea mask (instead of ATM orography);
599      - send to coupler the number of coupler time-steps to do for this run:
600        this allows to check for consistency and don't need anymore to be
601        specified in parameter file "data";
602      in coupler:
603      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
604      - improve report to log-file of config setting (pass log-file unit to few S/R)
605    o pkg/compon_communic:
606      - add coupling send/receive for non-tiled integer vector;
607      - add S/R to check and stop if any proc has an error (similar to
608        eesupp/src/stop_if_error.F but single thread and across Comm_World).
609    o pkg/exch2:
610      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
611        through list of all tiles my proc owns.
612    o model/src:
613      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
614        from rTrans) to simplify dependencies (no need to store rTrans anymore in
615        calling S/R); this affects AD results at machine truncation level:
616        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
617        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
618    o tools/build_options:
619      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
620    o coupling interface pkgs:
621        [compon_communic, atm_compon_interf & ocn_compon_interf]
622      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
623        to each S/R that needs it; remove un-used variables.
624      - change component tile registration (cpl_register.F in both compon_interf
625        and mitcomponent_tile_register.F) to pass the full list of tiles
626        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
627      - with pkg/exch2: adopt the same convention used for I/O to define mapping
628        towards coupler global array (unless W2_useE2ioLayOut=F):
629         a) can now use different tiling between atm & ocn comp.
630         b) no needs to modify the run-Off map when changing tiling (was needed
631            even if using the same tiling between atm & ocn).
632         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
633            full land tiles); not yet tested.
634      - check for valid mapping from comp. tile to coupler global array
635      - improve report of tile registration results to log file.
636    o pkg/exch2:
637      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
638        tile-registration (CPL_REGISTER);
639      - activate (un-comment) definition and setting of "W2_tileIndex" list to
640        store the local bi,bj indices of each tile;
641      - also print bi,bj in local report to log file;
642      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
643        Jun 2009 modif of pkg/exch2).
644    o testing on baudelaire:
645      - run 2 tests at a time: no significant slow down (since enough cpu) and
646        get the full set of test done earlier
647      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
648  o model/src/thermodynamics.F and routines called from it:  o model/src/thermodynamics.F and routines called from it:
649    - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &    - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
650      gmredi_calc_wflow.F) to update eulerian velocity (input) into residual      gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
# Line 23  o model/src/thermodynamics.F and routine Line 664  o model/src/thermodynamics.F and routine
664    - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,    - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
665      global_ocean.90x40x15, tutorial_global_oce_biogeo and      global_ocean.90x40x15, tutorial_global_oce_biogeo and
666      tutorial_tracer_adjsens (+ TLM output).      tutorial_tracer_adjsens (+ TLM output).
667  o toolm/OAD_support and (verification/*/) code_oad:  o tools/OAD_support and (verification/*/) code_oad:
668    - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to    - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
669      module conversion ; remove unneeded CPP_EEOPTIONS.h.      module conversion ; remove unneeded CPP_EEOPTIONS.h.
670    - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard    - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
671      version (closer to model/incCPP_OPTIONS.h).      version (closer to model/inc/CPP_OPTIONS.h).
672  o model/src:  o model/src:
673    - remove parameter "useOldFreezing" from PARAMS.h and push it to the    - remove parameter "useOldFreezing" from PARAMS.h and push it to the
674      retired list of parameters (routine FREEZE has been replace by surface      retired list of parameters (routine FREEZE has been replace by surface
# Line 47  o verification: Line 688  o verification:
688  o pkg/cost:  o pkg/cost:
689    - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL    - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
690      (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:      (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
691      o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL      o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
692        cannot be applied to var in common block).        cannot be applied to var in common block).
693      o allows to get results independent of tile-per-proc setting (if using      o allows to get results independent of tile-per-proc setting (if using
694        slower GLOBAL_SUM_SEND_RECV option).        slower GLOBAL_SUM_SEND_RECV option).
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