/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.1889 by dimitri, Mon Jul 1 16:55:57 2013 UTC revision 1.2038 by mlosch, Tue Aug 5 12:44:51 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_lsr.F
8      - rename integer variable ilcall to ipass (that's what it is called
9        in the residual diagnostics
10      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
11        default) for improved non-linear convergence of the first few
12        steps
13      - add a few comments and add new ones to explain some of the store
14        directives
15    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
16      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
17      - add an auxilliary variable "bet" and fix store directives and keys in
18        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
19        less exact gradients in my tests); but there are still
20        recomputation warning (although gradients are sort of OK), when
21        SEAICE_LSR_VECTORIZE is not defined, so this flag and
22        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
23      - update verification experiments lab_sea.
24      - change some comments in S/R seaice_calc_viscosities
25    o model/src:
26      - if staggerTimeStep=T, always apply exchange to velocity field in
27        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
28        (independent of using multi-dim advection or not); no effect on FWD run
29        but affects AD results (at machine truncation level): update output of
30        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
31        and isomip (oad: 12.d).
32    o pkg/generic_advdiff:
33      - stop if doAB_onGtGs is set to FALSE but ignored
34      - refine warning related to stability of tracer time-stepping
35        regarding internal wave dynamics.
36      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
37        on staggerTimeStep & implicitIntGravWave (will now get a warning
38        if potentially unstable).
39    o pkg/kl10:
40      - add new pkg "kl10" for mixing due to internal wave breaking, from
41        http://www.sciencedirect.com/science/article/pii/S1463500310000144
42        (contribution from Jody Klymak), tested in verification experiment
43        verification/internal_wave/input.kl10/
44    o isomip experiment:
45      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
46        (input.htd) and update the output.
47    o cd_code experiments:
48      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
49        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
50        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
51        update the corresponding output.
52    o pkg/seaice:
53      - reduce the number of include files and store directives in
54        S/R seaice_lsr_tridiagu/v
55      - change the order of loops in one case in S/R seaice_lsr_tridiagv
56        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
57        get rid off one store directive (a TAF bug?)
58      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
59        S/R seaice_lsr_tridiagv to change the loop range for consistency
60      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
61      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
62        S/R seaice_lsr_tridiagu/v (requires update of
63        offline_exf_seaice/input.dyn_jfnk)
64    
65    checkpoint65a (2014/07/27)
66    o model/src:
67      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
68        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
69        (topo in p-coords, ice-shelf in z-coords); update output of experiments
70        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
71    o model/src:
72      - collect momentum forcing tendency into local 2-D array (passed as argument
73        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
74        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
75        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
76      - collect T & S forcing tendency into local 2-D array (passed as argument to
77        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
78        affects results at machine truncation level (e.g., ocean: if using
79        SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)
80        moist correction due to vertical advection).
81      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
82        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
83        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
84        obcs_ctrl (ad & fwd grd @ 12 & 7).
85    o pkg/ptracers & diagnostics:
86      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
87        title (to avoid some unexpected truncation); sort out ptracers diags units.
88      - collect ptracer forcing tendency into local 2-D array (passed as argument
89        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
90    
91    checkpoint65 (2014/07/18)
92    o pkg/fizhi:
93      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
94        affects results at machine truncation level. Update output of experiments
95        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
96    o pkg/seaice: more clean up
97      - rename TAF common block tapes to be more consistent and remove
98        unnecessary duplicates
99      - add store directives to remove more recomputations, but use smaller
100        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
101        The idea behind this flag is to reduce the memory footprint when the
102        adjoint of the LSR is not required. As of now, defining the flag
103        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
104        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
105        For experiment offline_exf_seaice, this means on a linux box with gfortran
106        nearly a factor of 10 (but keep in mind there is mostly seaice code in
107        this experiment):
108        > size mitgcmuv_ad
109        text    data        bss     dec        hex  
110        5100659 1216  220458952  225560827  d71c8fb
111        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
112        but only a moderate increase of 36% for global_ocean.cs32x15:
113        text    data        bss     dec        hex
114        6695027 1648 1014578664 1021275339 3cdf6ccb
115        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
116      - note: there are still recomputations in global_ocean.cs32x15 and
117        offline_exf_seaice and the gradient agreement changes (gets a
118        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
119      - in general, the AD gradients still are wrong
120    o OpenAD
121      - clean up code_oad/ directories somewhat by moving files
122        dontCompile, dontTransform, keepOriginal to OAD_support/
123    o model/src:
124      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
125        (not currently tested): add dissipation terms before NLFS rescaling of
126        tendencies (previously done after).
127    o pkg/diagnostics:
128      - write stats-diags in ascii file with more digits (same as in monitor).
129    o pkg/down_slope:
130      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
131        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
132    o model/src:
133      - new file "apply_forcing.F" containing all the code previously in
134        external_forcing.F, but with new argument list: pass, as new argument,
135        the current level tendency array to update (instead of a direct update
136        of the common bloc array). Change the corresponding calls.
137      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
138        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
139    o pkg/seaice/seaice_lsr, a little bit of clean up
140      - rearrange some code blocks, so that now all calculations for
141        setting up the right-hand-sides done within one single block
142        (I find that easier to read and understand)
143      - rearrange freedrift-code to reduce the number of ifdefs
144      - adjust some indentations and comments
145    
146    checkpoint64z (2014/07/10)
147    o model/src and several pkgs:
148      - change argument list of all S/R called from external_forcing.F and
149        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
150        to pass, as argument, the current level tendency array to update
151        (instead of a direct update of the common bloc array).
152      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
153      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
154    o pkg/seaice/seaice_lsr.F
155      - always initialize local arrays in seaice_lsr_tridiagu/v
156      - add more local tapes to seaice_lsr_tridiagu/v
157      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
158        keep it in bi/bj loop; this seems to be essential
159      - gradients are still wrong but only by 4-7 orders of magnitude
160        instead of 15 orders of magnitude, lab_sea improves a little
161    o pkg/seaice
162      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
163        generates unnecessary code in seaice_lsr_ad
164      - add more store directives in seaice_lsr to avoid unnecessary code
165        in seaice_lsr_ad
166      - exclude some residual computations in seaice_lsr when
167        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
168        in seaice_lsr_ad
169      - add more storing, a new tape (model/src/the_main_loop.F) and
170        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
171        and klockey should be checked by a specialist)
172      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
173        and update lab_sea after previous changes in pkg/seaice below
174    o pkg/autodiff:
175      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
176        viscFacInAd : run time parameters allowing for adjoint switches
177        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
178    o pkg/ecco:
179      - introduce cost_gencost_boxmean.F that computes a box mean
180        temperature (for use in adjoint sensitivity studies).
181    o model/src/set_defaults.F : initialize viscFacAdj to 1.
182    o pkg/mom_common/mom_calc_visc.F:
183      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
184    o pkg/seaice/seaice_summary.F:
185      - statement for SEAICEadjMODE now in autodiff_readparms.F
186    o pkg/seaice:
187      - remove some store directives and add new ones in an effort to get
188        finally rid off the recomputation warnings. This is successful
189        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
190        defined (i.e. no extensive recomputation warnings left), but there
191        are still too many recomputations on the solver iteration level
192      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
193      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
194        SEAICE_SIZE.h
195      - add a store directive in S/R seaice_calc_viscosities
196    o pkg/seaice (ITD code):
197      - fix definition of Hlimit for multi-threaded case
198      - use double precision arithmetic to compute Hlimit: this affects results;
199        update output of experiment seaice_itd.
200    o replace content of verification/seaice_itd
201      - instead of a 1D column use the configuration of offline_exf_seaice
202        to test the ice thickness distribution code with ridging
203      - this is a first shot at this experiment
204      - change of some defaults of ridging parameters SEAICEhStar (from
205        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
206        and lot of new comments.
207    
208    checkpoint64y (2014/06/20)
209    o pkg/seaice/seaice_reg_ridge.F:
210      - modify the regularization of very small volumes of ice; only check
211        total volume HEFF, and do not apply correction to individual ice
212        classes because that leads to funny patterns in the heat and fw-fluxes
213        into the ocean. Adjust seaice_itd/results/output.txt
214      - replace nITD by SEAICE_multDim in loop-ranges
215    o pkg/exf:
216      - add code to process the case field period = -12. with UV interpolation.
217      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
218        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
219    o verification/global_with_exf:
220      - switch all fields period to -12. (was previously untested) in input/data.exf
221        (but keep secondary test ".yearly" unchanged); update the reference output.
222    o pkg/cal:
223      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
224    o pkg/exf:
225      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
226        to replace logical switch "exf_verbose"
227      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
228    o pkg/sbo:
229      - update from Katherine Quinn: evaluate mass directly from density and SSH
230        (budget using Finite Volume method) instead of from bottom pressure.
231      - allow testreport to collect few selected SBO output ; tested in exp.
232        global_ocean.90x40x15 (after updating the results, to include SBO output).
233      - fix some multi-threading issues (in output part).
234    o model/src & most packages:
235      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
236      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
237        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
238        "data.{pkg}" exist ; and leave the S/R (return) just after.
239      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
240        + call LAND_READPARMS from packages_readparms.F
241    o pkg/seaice:
242      - remove code that resets useThSice in S/R seaice_readparms and
243        replace it by a warning in S/R seaice_check
244      - remove parameter MULTDIM, replace with nITD and runtime
245        parameter SEAICE_multDim (still hard-wired to nITD if
246        SEAICE_ITD is defined)
247    
248    checkpoint64x (2014/05/24)
249    o verification/lab_sea:
250      - update adjoint and TLM output following changes to pkg/salt_plume
251      - un-do the update after putting back local recip_Cp in few places.
252    o pkg/salt_plume: modifications by An Nguyen:
253      - add capability to do brine rejection (salt-plume) as function of
254        volume+tracers (instead of only salinity tracer).
255      - conserve volume by exchanging volume from each kLev to above to
256        accommodate in-coming brine volume
257      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
258      - switch KPP surf buoyancy due to brine forcing to 3-d
259        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
260      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
261      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
262        in East/West Arctic.
263    o pkg/sbo:
264      - incorporate modifications from Katherine Quinn to enable the use of sbo
265        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
266        output for future testreport verification (unfinished).
267    o pkg/atm_phys:
268      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
269        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
270        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
271    o pkg/seaice
272      seaice_calc_ice_strength.F: modify expression to avoid divisions
273        (affects truncation)
274      seaice_do_ridging.F: clean up the insectarium
275      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
276      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
277      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
278      - add some debugging information and error messages (warnings)
279    o model/src: modifications relatd to atmosphere p*:
280      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
281      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
282        of vertical profile tRef in geopotential background and anomaly.
283      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
284        and pkg/atm_phys.
285      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
286        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
287    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
288    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
289        not used right now, but can be used in BGC packages to fix conservation.
290    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
291        other packages too.
292    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
293        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
294    o model/src:
295      - since we have several heat capacity (even in model/src), define "recip_Cp"
296        as local variable (no longer in common block) to avoid any confusion.
297      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
298    o pkg/exf:
299      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
300        air density as function of air Temp, Humidity and atm pressure.
301    
302    checkpoint64w (2014/05/02)
303    o verification:
304      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
305        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
306        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
307        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
308        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
309    o model/src: for atmosphere in p* coords:
310      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
311      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
312        but not yet activated.
313    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
314      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
315      - this changes the results (but not for any verification experiment, because
316        none tests this), but avoids having an extra field in the restart files
317    o pkg/seaice: remove global variable TICE (not needed)
318      - replace by TICES or local variable where necessary (cost_seaice_test,
319        seaice_diagnostics_state)
320      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
321      - use specific read/write routines for reading and writing individual leves
322        of a multilevel field
323    o pkg/ctrl & model/inc:
324      - move additional anomaly fields of control vars (related to options:
325         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
326        from DYNVARS.h into new header file: CTRL_FIELDS.h
327    o pkg/seaice: some small modifications to the ridging code
328      - make fw2ObyRidge a global variable and add the freshwater flux to
329        seaice_growth
330      - pass actual thickness from seaice_prepare_ridging, so that it is
331        computed only in one place and compute it in the same way as in
332        seaice_growth
333      - initialise more fields in seaice_do_ridging that where cause floating
334        point exceptions over land
335    o pkg/seaice: preparations for ridging code and first real ridging code
336      - move most of "PART 1" of S/R seaice_growth into a new and separate
337        S/R seaice_reg_ridge that will both regularize the state variable after
338        advection call the actual ridging routine;
339      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
340        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
341      - remove ridging code from seaice_advdiff
342      - clean up remaining part 1 of seaice_growth in an attempt to make it
343        more readable (this is probably subjective)
344      - call seaice_itd_redist once in the initialisation phase to have the initial
345        conditions in the correct category
346      - finally: add new ridging routine for ITD code
347    
348    checkpoint64v (2014/04/11)
349    o pkg/ecco:
350      - add runtime parameters mdt[start,end]date[1,2]
351      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
352    o pkg/seaice:
353      - make deltaC a global variable, so that it can be used in ridging code
354      - first step towards ridging: introduce new routines that compute
355        ice strength based on ridging parameters
356      - add diagnostic for HSNOWITD
357      - add opnWtrFrac as a global variable (required for ridging scheme)
358    o pkg/salt_plume + pkg/seaice/seaice_growth.F
359      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
360        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
361    o verification/hs94.1x64x5:
362      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
363      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
364    o autodiff:
365      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
366        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
367        For now, only in pkgs used in verification/hs94.1x64x5.
368      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
369        which are specific to TAF/TAMC).
370      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
371        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
372        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
373      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
374        building mitgcmuv_ad (make adAll).
375    o pkg/ecco:
376      - cost_gencost_seaicev4.F:
377         reformulate proxy cost as function of sst and local param SEAICE_freeze
378         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
379      - add stop statement if old names siv4-[sst,vol] are used
380      - add snapshots + cost reports for atmospheric longwave
381      - remove factor 0.1 in front of wtau[u,v]
382      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
383         ALLOW_TMI_SST_COST_CONTRIBUTION
384    o pkg/atm_phys:
385      - add some diagnostics for Short-wave and for convection S/R.
386    o pkg/seaice/seaice_growth:
387      - fix a bug in the lateral melt parameterization for SEAICE_ITD
388        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
389      - rearrange loop order for better vector code in the same code block
390      - rewrite the floeDiameter formula to have fewer divisions
391      -  (miraculously) none of this changes the results of seaice_itd
392    o pkg/smooth:
393      - move param smooth2Ddiffnbt to pkg/ecco
394    o pkg/salt_plume:
395      - salt_plume_frac.F:
396         clean up local param names
397         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
398    o pkg/rw:
399      - add RS version of S/R READ_MFLDS_LEV.
400    o pkg/streamice:
401      - fix the restart test by writing/reading pickup_streamice files.
402    o pkg/seaice:
403      - refine checks for jfnk-related parameters
404      - comment out if statement with SEAICEuseIMEX parameter as long as there
405        is no IMEX code to avoid confusion and surprises
406    
407    checkpoint64u (2014/03/07)
408    o verification/MLAdjust:
409      - rename secondary test suffix:
410         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
411         0.leithD -> AhFlxF  + switch to flux-form
412         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
413         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
414    o pkg/mom_vecinv:
415      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
416        to be before mom_calc_visc.F)
417      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
418      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
419        this is simpler for the adjoint and for diagnostics.
420    o model/src + pkg/momentum:
421      - add input files for  2-D additional Western and Southern cell-edge wall
422         (e.g., to add "thin-wall" where it is =1).
423      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
424        using 2nd hFacZ that is computed from initial (fix domain) hFac
425      - known limitations of thin wall implementation: not yet coded for sigma
426        coords; not working with CD-scheme neither.
427    o pkg/seaice:
428      - rename recently introduced parameters from (wrong name) AB to
429        BDF (backward difference time discretisation)
430      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
431    o tools/adjoint_options:
432      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
433    
434    checkpoint64t (2014/02/01)
435    o pkg/ecco
436      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
437        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
438      - replace hard-coded record number and period which only work for monthly
439        with read-in runtime param that works for other periods (month,day,year)
440    o pkg/thsice
441      - corrected store directive fixes thsice adjoint gradient checks
442    o genmake2 & testreport:
443      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
444        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
445        Update testreport accordingly. No need to set "export OPENAD=true"
446        in adjoint_options/adjoint_oad anymore (will be removed later).
447    o pkg/shelfice:
448      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
449        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
450        so that surface forcing applies to k=kSurf if using pkg/shelfice.
451    o pkg/ctrl, pkg/grdchk, pkg/ecco:
452      - Changes to make GENARR more modular (i.e. invisible if not used)
453    o model/src/temp_integrate.F and salt_integrate.F
454      - re-include store directives that were removed on Dec 27th.
455    o model/src/external_forcing_surf.F
456      - add storage directives for EmPmR and PmEpR to avoid recomputation of
457        seaice_model in the adjoint that is problematic when seaice_model is
458        turned off in the adjoint. The resolved issue dated back to July when
459        EXTERNAL_FORCING_SURF call was moved.
460        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
461    o pkg/exf/exf_check.F
462      - fix a small bug again (originally found by Wentao Liu, now found again)
463      - streamline error output
464    o pkg/streamice and aim_v23:
465      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
466        Apple's /usr/bin/cpp knows what to do:
467        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
468        Target: x86_64-apple-darwin13.0.0
469    
470    checkpoint64s (2014/01/05)
471    o tools/adjoint_options:
472      - switch to fastopt.net TAF server (instead of default fastopt.de) for
473        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
474    o model/src:
475      - remove some unnecessary TAF storage directives in forward_step.F and
476        in dynamics.F (note: not always removed by TAF, e.g., double storage
477        of kappaRU,kappaRV in former version of dynamics.F).
478    o model/src & pkg/ptracers:
479      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
480        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
481        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
482      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
483      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
484      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
485    o useSingleCpuInput separates single-CPU input from single-CPU output;
486        for now only implemented for in exf_interp_read.F
487    o verification/advect_xy:
488      - fix missing EXCH call in local version of ini_salt.F and update output.
489    o momentum diagnostics:
490      - fix which deltaT is used in Total-Tendency diagnostics.
491      - fix typo in diagnostics for momentum tendency from AB.
492    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
493        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
494    
495    checkpoint64r (2013/12/08)
496    o verification/*/results:
497      - Update reference output of experiments that were passing with just 13 digits
498         (make it easier to detect future changes in results)
499    o model/src & pkg/ptracers:
500      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
501        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
502        to inside ptracers_integrate.F ; remove ptracers_advection.F
503    o coupling interface pkgs:
504        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
505      - change the config check to test the agreement of Ocean Depth
506        with ATM land/sea mask (instead of ATM orography);
507      - send to coupler the number of coupler time-steps to do for this run:
508        this allows to check for consistency and don't need anymore to be
509        specified in parameter file "data";
510      in coupler:
511      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
512      - improve report to log-file of config setting (pass log-file unit to few S/R)
513    o pkg/compon_communic:
514      - add coupling send/receive for non-tiled integer vector;
515      - add S/R to check and stop if any proc has an error (similar to
516        eesupp/src/stop_if_error.F but single thread and across Comm_World).
517    o pkg/exch2:
518      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
519        through list of all tiles my proc owns.
520    o model/src:
521      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
522        from rTrans) to simplify dependencies (no need to store rTrans anymore in
523        calling S/R); this affects AD results at machine truncation level:
524        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
525        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
526    o tools/build_options:
527      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
528    o coupling interface pkgs:
529        [compon_communic, atm_compon_interf & ocn_compon_interf]
530      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
531        to each S/R that needs it; remove un-used variables.
532      - change component tile registration (cpl_register.F in both compon_interf
533        and mitcomponent_tile_register.F) to pass the full list of tiles
534        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
535      - with pkg/exch2: adopt the same convention used for I/O to define mapping
536        towards coupler global array (unless W2_useE2ioLayOut=F):
537         a) can now use different tiling between atm & ocn comp.
538         b) no needs to modify the run-Off map when changing tiling (was needed
539            even if using the same tiling between atm & ocn).
540         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
541            full land tiles); not yet tested.
542      - check for valid mapping from comp. tile to coupler global array
543      - improve report of tile registration results to log file.
544    o pkg/exch2:
545      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
546        tile-registration (CPL_REGISTER);
547      - activate (un-comment) definition and setting of "W2_tileIndex" list to
548        store the local bi,bj indices of each tile;
549      - also print bi,bj in local report to log file;
550      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
551        Jun 2009 modif of pkg/exch2).
552    o testing on baudelaire:
553      - run 2 tests at a time: no significant slow down (since enough cpu) and
554        get the full set of test done earlier
555      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
556    o model/src/thermodynamics.F and routines called from it:
557      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
558        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
559        velocity (outp) by adding bolus velocity.
560      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
561        mass transport from velocity + lateral grid cell area
562      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
563      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
564     in thermodynamics.F
565      - remove k from thermodynamics.F and move it to temp_integrate.F
566        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
567        loop).
568      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
569        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
570        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
571        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
572      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
573        global_ocean.90x40x15, tutorial_global_oce_biogeo and
574        tutorial_tracer_adjsens (+ TLM output).
575    o tools/OAD_support and (verification/*/) code_oad:
576      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
577        module conversion ; remove unneeded CPP_EEOPTIONS.h.
578      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
579        version (closer to model/inc/CPP_OPTIONS.h).
580    o model/src:
581      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
582        retired list of parameters (routine FREEZE has been replace by surface
583        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
584    o pkg/gmredi:
585      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
586        velocity (same scheme but affects machine truncation) for GM_AdvForm.
587      - update output of FWD experiments: front_relax.bvp,
588        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
589    
590    checkpoint64q (2013/11/17)
591    o verification:
592      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
593        tutorial_global_oce_biogeo and global_ocean.90x40x15.
594      - generate new output (growth & melt) for seaice_itd experiment after
595        updating the input pickup_seaice files (previously wrong).
596    o pkg/cost:
597      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
598        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
599        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
600          cannot be applied to var in common block).
601        o allows to get results independent of tile-per-proc setting (if using
602          slower GLOBAL_SUM_SEND_RECV option).
603      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
604        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
605        forward gradients: update output).
606      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
607        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
608    o pkg/mom_common:
609      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
610        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
611        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
612        ensure that all field value that are used are set.
613    o tutorial_deep_convection (smag3d):
614      - add missing scaling in mom_calc_smag_3d.F;
615      - set smag3D_coeff in input.smag3d such that results do not change.
616    o pkg/dic:
617      - change dic_cost.F to compute cost on each tile first and then apply
618        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
619        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
620      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
621    o eesupp/src & pkg/mdsio:
622      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
623        (from pkg/mdsio) since they are no longer used for tape IO.
624      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
625        (+ keep a copy in pkg/atm_ocn_coupler).
626    o verification/isomip:
627      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
628    o tools/build_options:
629      - optfile linux_amd64_ifort11, fast (no ieee) case:
630        to get a working restart for all experiments, add "-fp-model source"
631        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
632    
633    checkpoint64p (2013/10/20)
634    o pkg/autodiff:
635      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
636        criteria, return to simple (default) tape IO format.
637    o pkg/mdsio (+ eesupp/src):
638      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
639        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
640      - fix globalFile and singleCpuIO options using simpler global mapping.
641      - new pairs of scatter/gather vector S/R (one for each type, generated from
642        template) corresponding to simpler global mapping.
643      - adread_write.F: switch to new S/R (but leave old calls commented) and write
644        to globalFile when parameter globalFiles is set to True.
645      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
646    o pkg/autodiff:
647      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
648        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
649        missing, just add a STOP if array type do not match.
650    o pkg/exf:
651      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
652         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
653         and rename array obsSIce to exf_iceFraction.
654    o tutorial_deep_convection:
655      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
656        for now all in this exp. code dir.
657      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
658        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
659    o eesupp/src:
660      - added SINGLE_DISK_IO option because reading of parameter files on
661        very large number of processors did not work with existing set-up
662    
663    checkpoint64o (2013/09/25)
664    o pkg/atm_phys & atm_compon_interf:
665      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
666    o tools/build_options:
667      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
668        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
669        remove CPP setting (was identical to genmake2 default).
670    o pkg/gmredi & model/src: Some updating and work done on the residual model.
671      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
672      - fixed up the calculation of the eddy stress and how it is added to the
673        external forcing via taueddy_external_forcing.F
674      - at the moment, it is very experimental and only works with the variable eddy
675        diffusivity calculated in gmredi_k3d.F
676    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
677        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
678    o testreport (& tools/do_tst_2+2):
679      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
680    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
681      - remove CPP='cpp -traditional -P' (this is genmake2 default)
682      - add switch (for big setups) to use 'medium' memory-model (but leave it
683        commented out for now). Note: needed with FC 19 to compile big setups.
684    o pkg/atm_compon_interf:
685      - regroup per field origin (model & pkgs) the coupling storage routines
686         (which accumalate in time each coupling field)
687      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
688        update accordingly + simplify aim_do_physics.F
689    
690    checkpoint64n (2013/08/26)
691    o pkg/bbl:
692      - update formulation to reduce dispersion of tracer properties in bbl
693      - replaced horizontal and vertical transport parameters with velocities
694      - changes results for verification/global_with_exf.yearly
695    o verification/halfpipe_streamice:
696      - change to matrix construction; update both Fwd & AD output.
697    o verification/tutorial_tracer_adjsens:
698      - OpenAD test: switch to vector-invariant momentum since fluxform with
699        rStar causes problems with OpenAD; update output.
700    o tools:
701      - genmake2: define a common prefix for all temp-file names ; move them
702        to local /tmp disk (but would be easy to move them back);
703      - xmakedepend: apply the same switch for temp-files.
704    o pkg/offline:
705      - changes for use with rStar (NLFS): assume that we continue to provide
706        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
707        output files) and apply r* scaling at each time-step (function of the time
708        varying Eta field); use normal pickup files (needed for restart with NLFS).
709    o adjoint with OpenAD:
710      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
711        package openad.  This package has to be compiled for all runs with OpenAD
712        instead of specifying code_oad_all as a modification directory.
713      - link the fortran templates from tools/OAD_support to the build directory
714        for preprocessing to avoid conflicts between different setups compiled
715        simultaneously and simplify cleanup.
716    o pkg/exf:
717      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
718        main model or other pkgs are exchanged in EXF_MAPFIELDS).
719    o model/src:
720      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
721        (similar to do_fields_blocking_exchanges.F).
722    o tools/genmake2:
723      - remove TAF output src code just before calling staf (when not doing a fresh
724        built, will stop if things go wrong with staf).
725      - fix target "adobj" (left from TAF version-2 transition)
726    o pkg/diagnostics:
727      - add a parameter to track the status of pkg/diagnostics activation;
728        this replace/extend the use of logical param "settingDiags" (to check
729        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
730        New S/R to print error message and stop when pkgStatus is not right.
731      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
732    
733    checkpoint64m (2013/08/13)
734    o model/inc:
735      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
736        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
737    o pkg/kpp & aim_v23:
738      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
739    o pkg/seaice:
740      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
741        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
742      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
743    o eesupp/src:
744      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
745        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
746    o switch to TAF version-2:
747      - add flow directives to "freeze" naming convention for ad-routines that
748        are used in I/O routines of adjoint state and associated common blocks
749        that are used in adcommon.h (backward compatible with version-1)
750      - update all ad-optfiles (in tools/adjoint_options + few local to some
751        verification exp) to switch to latest TAF version (currently 2.5.5);
752        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
753        out except for diva).
754      - the major change with TAF version-2 is that both the differentiated
755        routines and the forward routines (new) are returned as part of the TAF
756        output source code. Update genmake2 accordingly.
757      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
758        with version-2 when compared to TLM or FWD gradient); other experiments
759        output show minor changes (machine truncation level); update the few AD &
760        TLM output with 12 matching digits only (some prior to version-2 switch).
761    
762    checkpoint64l (2013/08/05)
763    o model/src:
764      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
765      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
766        when using TAF but only if using OpenAD.
767    o pkg/mom_common+fluxform+vecinv:
768      - always set horiz. viscosity arrays to background value before calling
769        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
770        only when using variable horiz. viscosity (useVariableVisc=T);
771      - simplify mom_vecinv.F (only 1 block for momViscosity).
772    o pkg/mom_common: variable horiz. viscosity in NH code
773      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
774        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
775      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
776        useBiharmonicVisc & useVariableVisc.
777      - fix old bug (already in 1rst implementation of variable horizontal viscosity
778        in calc_gw.F, version 1.27, 2006/06/20):
779        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
780        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
781      - change background horiz viscosity in vertical momentum (gW) to always be
782        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
783        any type of variable viscosity, e.g., viscAh/4Grid)
784      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
785        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
786        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
787        default viscAh,viscA4 is zero).
788    o model/src:
789      - extend length of drC & recip_drC from Nr to Nr+1.
790    o Divided Adjoint (DIVA) with MPI:
791      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
792      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
793        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
794    
795    checkpoint64k (2013/07/23)
796    o tools/OAD_support:
797      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
798        and remove it from genmake2.
799    o tools/build_options:
800      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
801        MPI_HEADER_FILES list (let genmake2 find the missing headers)
802    o verification/halfpipe_streamice:
803      - change to driving stress formulation; update both Fwd & AD output.
804    o tools/genmake2 and Divided Adjoint with MPI:
805      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
806      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
807      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
808        Makefile, which is set by genmake2, and check which mpi-headers are needed.
809        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
810      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
811    o testreport:
812      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
813        perform additional runs (number of additional runs is "add_DIVA_runs" taken
814        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
815    o verification/lab_sea (AD test):
816      - change to test Divided Adjoint Run in this set-up (both standard AD test
817        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
818    o pkg atm_ & ocn_compon_interf:
819      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
820        staggerTimeStep implementation) and disable (retired) corresponding
821        parameter.
822    o pkg/offline:
823      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
824      - add S/R OFFLINE_CHECK to print offline parameter summary
825        and stop if loading a file that is not used;
826      - enable to calculate GMRedi tensor, KPP mixing and convective index
827        when the corresponding file(s) is/are not specified (but pkg is used).
828      - comment out resetting of monitorFreq (to endTime) since it still useful
829        for monitoring CFL numbers and checking offline fields.
830    o OpenAD:
831      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
832        smaller standard output) and generate new (smaller) output (on baudelaire
833        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
834    o model/src:
835      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
836        (where external_forcing_adjust was called) and change list of arguments;
837      - merge external_forcing_adjust.F into external_forcing_surf.F
838      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
839        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
840        previously in file "balance_relax.F", now removed); remove corresponding
841        arrays in FFIELDS.h.
842      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
843        a hack for getting back surfaceForcingS (loaded from file) when using
844        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
845      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
846        (was getting only 11 digits for AD-grad, due to different truncation
847         error in AD code).
848    
849    checkpoint64j (2013/07/04)
850    o pkg/offline:
851      - to enable the use of other features with pkg offline (e.g., obcs),
852        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
853      - comment out "allowFreezing" (now active) in 2 offline testing exp.
854  o pkg/exf ALLOW_RUNOFTEMP  o pkg/exf ALLOW_RUNOFTEMP
855    - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL    - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
856    - added RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice    - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
857    - changes verification/global_ocean.cs32x15/results/output.seaice.txt    - changes verification/global_ocean.cs32x15/results/output.seaice.txt
858  o pkg/atm_phys:  o pkg/atm_phys:
859    - allows to add some damping on uVel,vVel (strength only function of k).    - allows to add some damping on uVel,vVel (strength only function of k).
Legend:
Removed from v.1.1889  
changed lines
  Added in v.1.2038
  ViewVC Help
Powered by ViewVC 1.1.22