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revision 1.1962 by jmc, Sat Feb 1 22:51:56 2014 UTC revision 1.2025 by mlosch, Wed Jul 16 12:03:54 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: more clean up
8      - rename TAF common block tapes to be more consistent and remove
9        unnecessary duplicates
10      - add store directives to remove more recomputations,
11        but use smaller tapes (and adjust keys) when
12        SEAICE_LSR_ADJOINT_ITER is undefined. The idea behind this flag is
13        to reduce the memory footprint when the adjoint of the LSR is not
14        required. As of now, defining the flag SEAICE_LSR_ADJOINT_ITER
15        increase 4 common block tapes for 2D field by a factor of
16        SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). For experiment
17        offline_exf_seaice, this means on a linux box with gfortran nearly
18        a factor of 10 (but keep in mind there is mostly seaice code
19        in this experiment)
20        > size mitgcmuv_ad
21        text    data        bss     dec        hex  
22        5100659 1216  220458952  225560827  d71c8fb
23        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
24        but only a moderate increase of 36% for global_ocean.cs32x15
25        text    data        bss     dec        hex
26        6695027 1648 1014578664 1021275339 3cdf6ccb
27        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
28      - note: there are still recomputations in global_ocean.cs32x15 and
29        the gradient agreement changes (gets a little worse)
30      - in general, the AD gradients still are wrong
31    o OpenAD
32      - clean up code_oad/ directories somewhat by moving files
33        dontCompile, dontTransform, keepOriginal to OAD_support/
34    o model/src:
35      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
36        (not currently tested): add dissipation terms before NLFS rescaling of
37        tendencies (previously done after).
38    o pkg/diagnostics:
39      - write stats-diags in ascii file with more digits (same as in monitor).
40    o pkg/down_slope:
41      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
42        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
43    o model/src:
44      - new file "apply_forcing.F" containing all the code previously in
45        external_forcing.F, but with new argument list: pass, as new argument,
46        the current level tendency array to update (instead of a direct update
47        of the common bloc array). Change the corresponding calls.
48      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
49        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
50    o pkg/seaice/seaice_lsr, a little bit of clean up
51      - rearrange some code blocks, so that now all calculations for
52        setting up the right-hand-sides done within one single block
53        (I find that easier to read and understand)
54      - rearrange freedrift-code to reduce the number of ifdefs
55      - adjust some indentations and comments
56    
57    checkpoint64z (2014/07/10)
58    o model/src and several pkgs:
59      - change argument list of all S/R called from external_forcing.F and
60        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
61        to pass, as argument, the current level tendency array to update
62        (instead of a direct update of the common bloc array).
63      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
64      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
65    o pkg/seaice/seaice_lsr.F
66      - always initialize local arrays in seaice_lsr_tridiagu/v
67      - add more local tapes to seaice_lsr_tridiagu/v
68      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
69        keep it in bi/bj loop; this seems to be essential
70      - gradients are still wrong but only by 4-7 orders of magnitude
71        instead of 15 orders of magnitude, lab_sea improves a little
72    o pkg/seaice
73      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
74        generates unnecessary code in seaice_lsr_ad
75      - add more store directives in seaice_lsr to avoid unnecessary code
76        in seaice_lsr_ad
77      - exclude some residual computations in seaice_lsr when
78        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
79        in seaice_lsr_ad
80      - add more storing, a new tape (model/src/the_main_loop.F) and
81        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
82        and klockey should be checked by a specialist)
83      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
84        and update lab_sea after previous changes in pkg/seaice below
85    o pkg/autodiff:
86      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
87        viscFacInAd : run time parameters allowing for adjoint switches
88        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
89    o pkg/ecco:
90      - introduce cost_gencost_boxmean.F that computes a box mean
91        temperature (for use in adjoint sensitivity studies).
92    o model/src/set_defaults.F : initialize viscFacAdj to 1.
93    o pkg/mom_common/mom_calc_visc.F:
94      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
95    o pkg/seaice/seaice_summary.F:
96      - statement for SEAICEadjMODE now in autodiff_readparms.F
97    o pkg/seaice:
98      - remove some store directives and add new ones in an effort to get
99        finally rid off the recomputation warnings. This is successful
100        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
101        defined (i.e. no extensive recomputation warnings left), but there
102        are still too many recomputations on the solver iteration level
103      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
104      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
105        SEAICE_SIZE.h
106      - add a store directive in S/R seaice_calc_viscosities
107    o pkg/seaice (ITD code):
108      - fix definition of Hlimit for multi-threaded case
109      - use double precision arithmetic to compute Hlimit: this affects results;
110        update output of experiment seaice_itd.
111    o replace content of verification/seaice_itd
112      - instead of a 1D column use the configuration of offline_exf_seaice
113        to test the ice thickness distribution code with ridging
114      - this is a first shot at this experiment
115      - change of some defaults of ridging parameters SEAICEhStar (from
116        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
117        and lot of new comments.
118    
119    checkpoint64y (2014/06/20)
120    o pkg/seaice/seaice_reg_ridge.F:
121      - modify the regularization of very small volumes of ice; only check
122        total volume HEFF, and do not apply correction to individual ice
123        classes because that leads to funny patterns in the heat and fw-fluxes
124        into the ocean. Adjust seaice_itd/results/output.txt
125      - replace nITD by SEAICE_multDim in loop-ranges
126    o pkg/exf:
127      - add code to process the case field period = -12. with UV interpolation.
128      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
129        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
130    o verification/global_with_exf:
131      - switch all fields period to -12. (was previously untested) in input/data.exf
132        (but keep secondary test ".yearly" unchanged); update the reference output.
133    o pkg/cal:
134      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
135    o pkg/exf:
136      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
137        to replace logical switch "exf_verbose"
138      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
139    o pkg/sbo:
140      - update from Katherine Quinn: evaluate mass directly from density and SSH
141        (budget using Finite Volume method) instead of from bottom pressure.
142      - allow testreport to collect few selected SBO output ; tested in exp.
143        global_ocean.90x40x15 (after updating the results, to include SBO output).
144      - fix some multi-threading issues (in output part).
145    o model/src & most packages:
146      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
147      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
148        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
149        "data.{pkg}" exist ; and leave the S/R (return) just after.
150      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
151        + call LAND_READPARMS from packages_readparms.F
152    o pkg/seaice:
153      - remove code that resets useThSice in S/R seaice_readparms and
154        replace it by a warning in S/R seaice_check
155      - remove parameter MULTDIM, replace with nITD and runtime
156        parameter SEAICE_multDim (still hard-wired to nITD if
157        SEAICE_ITD is defined)
158    
159    checkpoint64x (2014/05/24)
160    o verification/lab_sea:
161      - update adjoint and TLM output following changes to pkg/salt_plume
162      - un-do the update after putting back local recip_Cp in few places.
163    o pkg/salt_plume: modifications by An Nguyen:
164      - add capability to do brine rejection (salt-plume) as function of
165        volume+tracers (instead of only salinity tracer).
166      - conserve volume by exchanging volume from each kLev to above to
167        accommodate in-coming brine volume
168      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
169      - switch KPP surf buoyancy due to brine forcing to 3-d
170        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
171      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
172      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
173        in East/West Arctic.
174    o pkg/sbo:
175      - incorporate modifications from Katherine Quinn to enable the use of sbo
176        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
177        output for future testreport verification (unfinished).
178    o pkg/atm_phys:
179      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
180        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
181        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
182    o pkg/seaice
183      seaice_calc_ice_strength.F: modify expression to avoid divisions
184        (affects truncation)
185      seaice_do_ridging.F: clean up the insectarium
186      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
187      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
188      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
189      - add some debugging information and error messages (warnings)
190    o model/src: modifications relatd to atmosphere p*:
191      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
192      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
193        of vertical profile tRef in geopotential background and anomaly.
194      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
195        and pkg/atm_phys.
196      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
197        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
198    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
199    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
200        not used right now, but can be used in BGC packages to fix conservation.
201    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
202        other packages too.
203    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
204        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
205    o model/src:
206      - since we have several heat capacity (even in model/src), define "recip_Cp"
207        as local variable (no longer in common block) to avoid any confusion.
208      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
209    o pkg/exf:
210      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
211        air density as function of air Temp, Humidity and atm pressure.
212    
213    checkpoint64w (2014/05/02)
214    o verification:
215      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
216        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
217        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
218        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
219        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
220    o model/src: for atmosphere in p* coords:
221      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
222      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
223        but not yet activated.
224    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
225      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
226      - this changes the results (but not for any verification experiment, because
227        none tests this), but avoids having an extra field in the restart files
228    o pkg/seaice: remove global variable TICE (not needed)
229      - replace by TICES or local variable where necessary (cost_seaice_test,
230        seaice_diagnostics_state)
231      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
232      - use specific read/write routines for reading and writing individual leves
233        of a multilevel field
234    o pkg/ctrl & model/inc:
235      - move additional anomaly fields of control vars (related to options:
236         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
237        from DYNVARS.h into new header file: CTRL_FIELDS.h
238    o pkg/seaice: some small modifications to the ridging code
239      - make fw2ObyRidge a global variable and add the freshwater flux to
240        seaice_growth
241      - pass actual thickness from seaice_prepare_ridging, so that it is
242        computed only in one place and compute it in the same way as in
243        seaice_growth
244      - initialise more fields in seaice_do_ridging that where cause floating
245        point exceptions over land
246    o pkg/seaice: preparations for ridging code and first real ridging code
247      - move most of "PART 1" of S/R seaice_growth into a new and separate
248        S/R seaice_reg_ridge that will both regularize the state variable after
249        advection call the actual ridging routine;
250      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
251        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
252      - remove ridging code from seaice_advdiff
253      - clean up remaining part 1 of seaice_growth in an attempt to make it
254        more readable (this is probably subjective)
255      - call seaice_itd_redist once in the initialisation phase to have the initial
256        conditions in the correct category
257      - finally: add new ridging routine for ITD code
258    
259    checkpoint64v (2014/04/11)
260    o pkg/ecco:
261      - add runtime parameters mdt[start,end]date[1,2]
262      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
263    o pkg/seaice:
264      - make deltaC a global variable, so that it can be used in ridging code
265      - first step towards ridging: introduce new routines that compute
266        ice strength based on ridging parameters
267      - add diagnostic for HSNOWITD
268      - add opnWtrFrac as a global variable (required for ridging scheme)
269    o pkg/salt_plume + pkg/seaice/seaice_growth.F
270      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
271        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
272    o verification/hs94.1x64x5:
273      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
274      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
275    o autodiff:
276      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
277        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
278        For now, only in pkgs used in verification/hs94.1x64x5.
279      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
280        which are specific to TAF/TAMC).
281      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
282        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
283        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
284      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
285        building mitgcmuv_ad (make adAll).
286    o pkg/ecco:
287      - cost_gencost_seaicev4.F:
288         reformulate proxy cost as function of sst and local param SEAICE_freeze
289         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
290      - add stop statement if old names siv4-[sst,vol] are used
291      - add snapshots + cost reports for atmospheric longwave
292      - remove factor 0.1 in front of wtau[u,v]
293      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
294         ALLOW_TMI_SST_COST_CONTRIBUTION
295    o pkg/atm_phys:
296      - add some diagnostics for Short-wave and for convection S/R.
297    o pkg/seaice/seaice_growth:
298      - fix a bug in the lateral melt parameterization for SEAICE_ITD
299        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
300      - rearrange loop order for better vector code in the same code block
301      - rewrite the floeDiameter formula to have fewer divisions
302      -  (miraculously) none of this changes the results of seaice_itd
303    o pkg/smooth:
304      - move param smooth2Ddiffnbt to pkg/ecco
305    o pkg/salt_plume:
306      - salt_plume_frac.F:
307         clean up local param names
308         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
309    o pkg/rw:
310      - add RS version of S/R READ_MFLDS_LEV.
311    o pkg/streamice:
312      - fix the restart test by writing/reading pickup_streamice files.
313    o pkg/seaice:
314      - refine checks for jfnk-related parameters
315      - comment out if statement with SEAICEuseIMEX parameter as long as there
316        is no IMEX code to avoid confusion and surprises
317    
318    checkpoint64u (2014/03/07)
319    o verification/MLAdjust:
320      - rename secondary test suffix:
321         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
322         0.leithD -> AhFlxF  + switch to flux-form
323         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
324         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
325    o pkg/mom_vecinv:
326      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
327        to be before mom_calc_visc.F)
328      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
329      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
330        this is simpler for the adjoint and for diagnostics.
331    o model/src + pkg/momentum:
332      - add input files for  2-D additional Western and Southern cell-edge wall
333         (e.g., to add "thin-wall" where it is =1).
334      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
335        using 2nd hFacZ that is computed from initial (fix domain) hFac
336      - known limitations of thin wall implementation: not yet coded for sigma
337        coords; not working with CD-scheme neither.
338    o pkg/seaice:
339      - rename recently introduced parameters from (wrong name) AB to
340        BDF (backward difference time discretisation)
341      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
342    o tools/adjoint_options:
343      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
344    
345  checkpoint64t (2014/02/01)  checkpoint64t (2014/02/01)
346    o pkg/ecco
347      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
348        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
349      - replace hard-coded record number and period which only work for monthly
350        with read-in runtime param that works for other periods (month,day,year)
351  o pkg/thsice  o pkg/thsice
352    - corrected store directive fixes thsice adjoint gradient checks    - corrected store directive fixes thsice adjoint gradient checks
353  o genmake2 & testreport:  o genmake2 & testreport:

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