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revision 1.1943 by jmc, Wed Nov 27 22:53:37 2013 UTC revision 1.2042 by jmc, Thu Aug 7 21:07:11 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o model/src:
8      - add geothermal flux forcing: read in ini_forcing.F as time-constant
9        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
10    o model/src:
11      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
12        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
13        arrays are already updated while adjustments (filters, conv.adjustment) are
14        still applied later, in S/R TRACERS_CORRECTION_STEP.
15    o model/src:
16      - store in common bloc array "rhoInSitu" the virtual potential temperature
17        anomaly that is used to compute geopotential: this make the atmos code
18        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
19    o pkg/seaice/seaice_lsr.F
20      - rename integer variable ilcall to ipass (that's what it is called
21        in the residual diagnostics
22      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
23        default) for improved non-linear convergence of the first few steps
24      - adjust a few comments and add new ones to explain some of the store
25        directives
26    o pkg/generic_advdiff (& ptracers):
27      - re-work the code to check for valid advection scheme and for minimum
28        size of overlap (now stored in local common bloc in gad_advscheme.F)
29    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
30      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
31      - add an auxilliary variable "bet" and fix store directives and keys in
32        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
33        less exact gradients in my tests); but there are still
34        recomputation warning (although gradients are sort of OK), when
35        SEAICE_LSR_VECTORIZE is not defined, so this flag and
36        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
37      - update verification experiments lab_sea.
38      - change some comments in S/R seaice_calc_viscosities
39    o model/src:
40      - if staggerTimeStep=T, always apply exchange to velocity field in
41        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
42        (independent of using multi-dim advection or not); no effect on FWD run
43        but affects AD results (at machine truncation level): update output of
44        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
45        and isomip (oad: 12.d).
46    o pkg/generic_advdiff:
47      - stop if doAB_onGtGs is set to FALSE but ignored
48      - refine warning related to stability of tracer time-stepping
49        regarding internal wave dynamics.
50      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
51        on staggerTimeStep & implicitIntGravWave (will now get a warning
52        if potentially unstable).
53    o pkg/kl10:
54      - add new pkg "kl10" for mixing due to internal wave breaking, from
55        http://www.sciencedirect.com/science/article/pii/S1463500310000144
56        (contribution from Jody Klymak), tested in verification experiment
57        verification/internal_wave/input.kl10/
58    o isomip experiment:
59      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
60        (input.htd) and update the output.
61    o cd_code experiments:
62      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
63        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
64        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
65        update the corresponding output.
66    o pkg/seaice:
67      - reduce the number of include files and store directives in
68        S/R seaice_lsr_tridiagu/v
69      - change the order of loops in one case in S/R seaice_lsr_tridiagv
70        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
71        get rid off one store directive (a TAF bug?)
72      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
73        S/R seaice_lsr_tridiagv to change the loop range for consistency
74      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
75      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
76        S/R seaice_lsr_tridiagu/v (requires update of
77        offline_exf_seaice/input.dyn_jfnk)
78    
79    checkpoint65a (2014/07/27)
80    o model/src:
81      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
82        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
83        (topo in p-coords, ice-shelf in z-coords); update output of experiments
84        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
85    o model/src:
86      - collect momentum forcing tendency into local 2-D array (passed as argument
87        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
88        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
89        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
90      - collect T & S forcing tendency into local 2-D array (passed as argument to
91        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
92        affects results at machine truncation level (e.g., ocean: if using
93        SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)
94        moist correction due to vertical advection).
95      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
96        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
97        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
98        obcs_ctrl (ad & fwd grd @ 12 & 7).
99    o pkg/ptracers & diagnostics:
100      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
101        title (to avoid some unexpected truncation); sort out ptracers diags units.
102      - collect ptracer forcing tendency into local 2-D array (passed as argument
103        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
104    
105    checkpoint65 (2014/07/18)
106    o pkg/fizhi:
107      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
108        affects results at machine truncation level. Update output of experiments
109        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
110    o pkg/seaice: more clean up
111      - rename TAF common block tapes to be more consistent and remove
112        unnecessary duplicates
113      - add store directives to remove more recomputations, but use smaller
114        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
115        The idea behind this flag is to reduce the memory footprint when the
116        adjoint of the LSR is not required. As of now, defining the flag
117        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
118        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
119        For experiment offline_exf_seaice, this means on a linux box with gfortran
120        nearly a factor of 10 (but keep in mind there is mostly seaice code in
121        this experiment):
122        > size mitgcmuv_ad
123        text    data        bss     dec        hex  
124        5100659 1216  220458952  225560827  d71c8fb
125        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
126        but only a moderate increase of 36% for global_ocean.cs32x15:
127        text    data        bss     dec        hex
128        6695027 1648 1014578664 1021275339 3cdf6ccb
129        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
130      - note: there are still recomputations in global_ocean.cs32x15 and
131        offline_exf_seaice and the gradient agreement changes (gets a
132        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
133      - in general, the AD gradients still are wrong
134    o OpenAD
135      - clean up code_oad/ directories somewhat by moving files
136        dontCompile, dontTransform, keepOriginal to OAD_support/
137    o model/src:
138      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
139        (not currently tested): add dissipation terms before NLFS rescaling of
140        tendencies (previously done after).
141    o pkg/diagnostics:
142      - write stats-diags in ascii file with more digits (same as in monitor).
143    o pkg/down_slope:
144      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
145        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
146    o model/src:
147      - new file "apply_forcing.F" containing all the code previously in
148        external_forcing.F, but with new argument list: pass, as new argument,
149        the current level tendency array to update (instead of a direct update
150        of the common bloc array). Change the corresponding calls.
151      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
152        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
153    o pkg/seaice/seaice_lsr, a little bit of clean up
154      - rearrange some code blocks, so that now all calculations for
155        setting up the right-hand-sides done within one single block
156        (I find that easier to read and understand)
157      - rearrange freedrift-code to reduce the number of ifdefs
158      - adjust some indentations and comments
159    
160    checkpoint64z (2014/07/10)
161    o model/src and several pkgs:
162      - change argument list of all S/R called from external_forcing.F and
163        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
164        to pass, as argument, the current level tendency array to update
165        (instead of a direct update of the common bloc array).
166      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
167      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
168    o pkg/seaice/seaice_lsr.F
169      - always initialize local arrays in seaice_lsr_tridiagu/v
170      - add more local tapes to seaice_lsr_tridiagu/v
171      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
172        keep it in bi/bj loop; this seems to be essential
173      - gradients are still wrong but only by 4-7 orders of magnitude
174        instead of 15 orders of magnitude, lab_sea improves a little
175    o pkg/seaice
176      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
177        generates unnecessary code in seaice_lsr_ad
178      - add more store directives in seaice_lsr to avoid unnecessary code
179        in seaice_lsr_ad
180      - exclude some residual computations in seaice_lsr when
181        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
182        in seaice_lsr_ad
183      - add more storing, a new tape (model/src/the_main_loop.F) and
184        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
185        and klockey should be checked by a specialist)
186      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
187        and update lab_sea after previous changes in pkg/seaice below
188    o pkg/autodiff:
189      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
190        viscFacInAd : run time parameters allowing for adjoint switches
191        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
192    o pkg/ecco:
193      - introduce cost_gencost_boxmean.F that computes a box mean
194        temperature (for use in adjoint sensitivity studies).
195    o model/src/set_defaults.F : initialize viscFacAdj to 1.
196    o pkg/mom_common/mom_calc_visc.F:
197      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
198    o pkg/seaice/seaice_summary.F:
199      - statement for SEAICEadjMODE now in autodiff_readparms.F
200    o pkg/seaice:
201      - remove some store directives and add new ones in an effort to get
202        finally rid off the recomputation warnings. This is successful
203        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
204        defined (i.e. no extensive recomputation warnings left), but there
205        are still too many recomputations on the solver iteration level
206      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
207      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
208        SEAICE_SIZE.h
209      - add a store directive in S/R seaice_calc_viscosities
210    o pkg/seaice (ITD code):
211      - fix definition of Hlimit for multi-threaded case
212      - use double precision arithmetic to compute Hlimit: this affects results;
213        update output of experiment seaice_itd.
214    o replace content of verification/seaice_itd
215      - instead of a 1D column use the configuration of offline_exf_seaice
216        to test the ice thickness distribution code with ridging
217      - this is a first shot at this experiment
218      - change of some defaults of ridging parameters SEAICEhStar (from
219        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
220        and lot of new comments.
221    
222    checkpoint64y (2014/06/20)
223    o pkg/seaice/seaice_reg_ridge.F:
224      - modify the regularization of very small volumes of ice; only check
225        total volume HEFF, and do not apply correction to individual ice
226        classes because that leads to funny patterns in the heat and fw-fluxes
227        into the ocean. Adjust seaice_itd/results/output.txt
228      - replace nITD by SEAICE_multDim in loop-ranges
229    o pkg/exf:
230      - add code to process the case field period = -12. with UV interpolation.
231      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
232        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
233    o verification/global_with_exf:
234      - switch all fields period to -12. (was previously untested) in input/data.exf
235        (but keep secondary test ".yearly" unchanged); update the reference output.
236    o pkg/cal:
237      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
238    o pkg/exf:
239      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
240        to replace logical switch "exf_verbose"
241      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
242    o pkg/sbo:
243      - update from Katherine Quinn: evaluate mass directly from density and SSH
244        (budget using Finite Volume method) instead of from bottom pressure.
245      - allow testreport to collect few selected SBO output ; tested in exp.
246        global_ocean.90x40x15 (after updating the results, to include SBO output).
247      - fix some multi-threading issues (in output part).
248    o model/src & most packages:
249      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
250      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
251        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
252        "data.{pkg}" exist ; and leave the S/R (return) just after.
253      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
254        + call LAND_READPARMS from packages_readparms.F
255    o pkg/seaice:
256      - remove code that resets useThSice in S/R seaice_readparms and
257        replace it by a warning in S/R seaice_check
258      - remove parameter MULTDIM, replace with nITD and runtime
259        parameter SEAICE_multDim (still hard-wired to nITD if
260        SEAICE_ITD is defined)
261    
262    checkpoint64x (2014/05/24)
263    o verification/lab_sea:
264      - update adjoint and TLM output following changes to pkg/salt_plume
265      - un-do the update after putting back local recip_Cp in few places.
266    o pkg/salt_plume: modifications by An Nguyen:
267      - add capability to do brine rejection (salt-plume) as function of
268        volume+tracers (instead of only salinity tracer).
269      - conserve volume by exchanging volume from each kLev to above to
270        accommodate in-coming brine volume
271      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
272      - switch KPP surf buoyancy due to brine forcing to 3-d
273        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
274      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
275      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
276        in East/West Arctic.
277    o pkg/sbo:
278      - incorporate modifications from Katherine Quinn to enable the use of sbo
279        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
280        output for future testreport verification (unfinished).
281    o pkg/atm_phys:
282      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
283        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
284        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
285    o pkg/seaice
286      seaice_calc_ice_strength.F: modify expression to avoid divisions
287        (affects truncation)
288      seaice_do_ridging.F: clean up the insectarium
289      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
290      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
291      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
292      - add some debugging information and error messages (warnings)
293    o model/src: modifications relatd to atmosphere p*:
294      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
295      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
296        of vertical profile tRef in geopotential background and anomaly.
297      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
298        and pkg/atm_phys.
299      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
300        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
301    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
302    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
303        not used right now, but can be used in BGC packages to fix conservation.
304    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
305        other packages too.
306    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
307        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
308    o model/src:
309      - since we have several heat capacity (even in model/src), define "recip_Cp"
310        as local variable (no longer in common block) to avoid any confusion.
311      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
312    o pkg/exf:
313      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
314        air density as function of air Temp, Humidity and atm pressure.
315    
316    checkpoint64w (2014/05/02)
317    o verification:
318      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
319        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
320        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
321        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
322        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
323    o model/src: for atmosphere in p* coords:
324      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
325      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
326        but not yet activated.
327    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
328      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
329      - this changes the results (but not for any verification experiment, because
330        none tests this), but avoids having an extra field in the restart files
331    o pkg/seaice: remove global variable TICE (not needed)
332      - replace by TICES or local variable where necessary (cost_seaice_test,
333        seaice_diagnostics_state)
334      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
335      - use specific read/write routines for reading and writing individual leves
336        of a multilevel field
337    o pkg/ctrl & model/inc:
338      - move additional anomaly fields of control vars (related to options:
339         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
340        from DYNVARS.h into new header file: CTRL_FIELDS.h
341    o pkg/seaice: some small modifications to the ridging code
342      - make fw2ObyRidge a global variable and add the freshwater flux to
343        seaice_growth
344      - pass actual thickness from seaice_prepare_ridging, so that it is
345        computed only in one place and compute it in the same way as in
346        seaice_growth
347      - initialise more fields in seaice_do_ridging that where cause floating
348        point exceptions over land
349    o pkg/seaice: preparations for ridging code and first real ridging code
350      - move most of "PART 1" of S/R seaice_growth into a new and separate
351        S/R seaice_reg_ridge that will both regularize the state variable after
352        advection call the actual ridging routine;
353      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
354        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
355      - remove ridging code from seaice_advdiff
356      - clean up remaining part 1 of seaice_growth in an attempt to make it
357        more readable (this is probably subjective)
358      - call seaice_itd_redist once in the initialisation phase to have the initial
359        conditions in the correct category
360      - finally: add new ridging routine for ITD code
361    
362    checkpoint64v (2014/04/11)
363    o pkg/ecco:
364      - add runtime parameters mdt[start,end]date[1,2]
365      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
366    o pkg/seaice:
367      - make deltaC a global variable, so that it can be used in ridging code
368      - first step towards ridging: introduce new routines that compute
369        ice strength based on ridging parameters
370      - add diagnostic for HSNOWITD
371      - add opnWtrFrac as a global variable (required for ridging scheme)
372    o pkg/salt_plume + pkg/seaice/seaice_growth.F
373      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
374        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
375    o verification/hs94.1x64x5:
376      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
377      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
378    o autodiff:
379      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
380        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
381        For now, only in pkgs used in verification/hs94.1x64x5.
382      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
383        which are specific to TAF/TAMC).
384      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
385        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
386        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
387      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
388        building mitgcmuv_ad (make adAll).
389    o pkg/ecco:
390      - cost_gencost_seaicev4.F:
391         reformulate proxy cost as function of sst and local param SEAICE_freeze
392         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
393      - add stop statement if old names siv4-[sst,vol] are used
394      - add snapshots + cost reports for atmospheric longwave
395      - remove factor 0.1 in front of wtau[u,v]
396      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
397         ALLOW_TMI_SST_COST_CONTRIBUTION
398    o pkg/atm_phys:
399      - add some diagnostics for Short-wave and for convection S/R.
400    o pkg/seaice/seaice_growth:
401      - fix a bug in the lateral melt parameterization for SEAICE_ITD
402        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
403      - rearrange loop order for better vector code in the same code block
404      - rewrite the floeDiameter formula to have fewer divisions
405      -  (miraculously) none of this changes the results of seaice_itd
406    o pkg/smooth:
407      - move param smooth2Ddiffnbt to pkg/ecco
408    o pkg/salt_plume:
409      - salt_plume_frac.F:
410         clean up local param names
411         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
412    o pkg/rw:
413      - add RS version of S/R READ_MFLDS_LEV.
414    o pkg/streamice:
415      - fix the restart test by writing/reading pickup_streamice files.
416    o pkg/seaice:
417      - refine checks for jfnk-related parameters
418      - comment out if statement with SEAICEuseIMEX parameter as long as there
419        is no IMEX code to avoid confusion and surprises
420    
421    checkpoint64u (2014/03/07)
422    o verification/MLAdjust:
423      - rename secondary test suffix:
424         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
425         0.leithD -> AhFlxF  + switch to flux-form
426         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
427         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
428    o pkg/mom_vecinv:
429      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
430        to be before mom_calc_visc.F)
431      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
432      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
433        this is simpler for the adjoint and for diagnostics.
434    o model/src + pkg/momentum:
435      - add input files for  2-D additional Western and Southern cell-edge wall
436         (e.g., to add "thin-wall" where it is =1).
437      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
438        using 2nd hFacZ that is computed from initial (fix domain) hFac
439      - known limitations of thin wall implementation: not yet coded for sigma
440        coords; not working with CD-scheme neither.
441    o pkg/seaice:
442      - rename recently introduced parameters from (wrong name) AB to
443        BDF (backward difference time discretisation)
444      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
445    o tools/adjoint_options:
446      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
447    
448    checkpoint64t (2014/02/01)
449    o pkg/ecco
450      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
451        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
452      - replace hard-coded record number and period which only work for monthly
453        with read-in runtime param that works for other periods (month,day,year)
454    o pkg/thsice
455      - corrected store directive fixes thsice adjoint gradient checks
456    o genmake2 & testreport:
457      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
458        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
459        Update testreport accordingly. No need to set "export OPENAD=true"
460        in adjoint_options/adjoint_oad anymore (will be removed later).
461    o pkg/shelfice:
462      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
463        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
464        so that surface forcing applies to k=kSurf if using pkg/shelfice.
465    o pkg/ctrl, pkg/grdchk, pkg/ecco:
466      - Changes to make GENARR more modular (i.e. invisible if not used)
467    o model/src/temp_integrate.F and salt_integrate.F
468      - re-include store directives that were removed on Dec 27th.
469    o model/src/external_forcing_surf.F
470      - add storage directives for EmPmR and PmEpR to avoid recomputation of
471        seaice_model in the adjoint that is problematic when seaice_model is
472        turned off in the adjoint. The resolved issue dated back to July when
473        EXTERNAL_FORCING_SURF call was moved.
474        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
475    o pkg/exf/exf_check.F
476      - fix a small bug again (originally found by Wentao Liu, now found again)
477      - streamline error output
478    o pkg/streamice and aim_v23:
479      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
480        Apple's /usr/bin/cpp knows what to do:
481        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
482        Target: x86_64-apple-darwin13.0.0
483    
484    checkpoint64s (2014/01/05)
485    o tools/adjoint_options:
486      - switch to fastopt.net TAF server (instead of default fastopt.de) for
487        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
488    o model/src:
489      - remove some unnecessary TAF storage directives in forward_step.F and
490        in dynamics.F (note: not always removed by TAF, e.g., double storage
491        of kappaRU,kappaRV in former version of dynamics.F).
492    o model/src & pkg/ptracers:
493      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
494        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
495        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
496      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
497      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
498      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
499    o useSingleCpuInput separates single-CPU input from single-CPU output;
500        for now only implemented for in exf_interp_read.F
501    o verification/advect_xy:
502      - fix missing EXCH call in local version of ini_salt.F and update output.
503    o momentum diagnostics:
504      - fix which deltaT is used in Total-Tendency diagnostics.
505      - fix typo in diagnostics for momentum tendency from AB.
506    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
507        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
508    
509    checkpoint64r (2013/12/08)
510    o verification/*/results:
511      - Update reference output of experiments that were passing with just 13 digits
512         (make it easier to detect future changes in results)
513    o model/src & pkg/ptracers:
514      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
515        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
516        to inside ptracers_integrate.F ; remove ptracers_advection.F
517    o coupling interface pkgs:
518        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
519      - change the config check to test the agreement of Ocean Depth
520        with ATM land/sea mask (instead of ATM orography);
521      - send to coupler the number of coupler time-steps to do for this run:
522        this allows to check for consistency and don't need anymore to be
523        specified in parameter file "data";
524      in coupler:
525      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
526      - improve report to log-file of config setting (pass log-file unit to few S/R)
527    o pkg/compon_communic:
528      - add coupling send/receive for non-tiled integer vector;
529      - add S/R to check and stop if any proc has an error (similar to
530        eesupp/src/stop_if_error.F but single thread and across Comm_World).
531    o pkg/exch2:
532      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
533        through list of all tiles my proc owns.
534    o model/src:
535      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
536        from rTrans) to simplify dependencies (no need to store rTrans anymore in
537        calling S/R); this affects AD results at machine truncation level:
538        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
539        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
540  o tools/build_options:  o tools/build_options:
541    - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran    - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
542  o coupling interface pkgs:  o coupling interface pkgs:
# Line 77  o verification: Line 610  o verification:
610  o pkg/cost:  o pkg/cost:
611    - 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
612      (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:
613      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
614        cannot be applied to var in common block).        cannot be applied to var in common block).
615      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
616        slower GLOBAL_SUM_SEND_RECV option).        slower GLOBAL_SUM_SEND_RECV option).
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