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revision 1.1973 by atn, Sat Apr 5 22:51:52 2014 UTC revision 1.2019 by jmc, Thu Jul 10 00:24:24 2014 UTC
# Line 3  $Name$ Line 3  $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6  <<<<<<< tag-index  
7  o pkg/salt_plume:  o model/src and several pkgs:
8    - salt_plume_frac.F:    - change argument list of all S/R called from external_forcing.F and
9       clean up local param names      called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
10       reformulate (1-frac) to frac; original 1-frac was based on swfrac code      to pass, as argument, the current level tendency array to update
11        (instead of a direct update of the common bloc array).
12      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
13      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
14    o pkg/seaice/seaice_lsr.F
15      - always initialize local arrays in seaice_lsr_tridiagu/v
16      - add more local tapes to seaice_lsr_tridiagu/v
17      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
18        keep it in bi/bj loop; this seems to be essential
19      - gradients are still wrong but only by 4-7 orders of magnitude
20        instead of 15 orders of magnitude, lab_sea improves a little
21    o pkg/seaice
22      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
23        generates unnecessary code in seaice_lsr_ad
24      - add more store directives in seaice_lsr to avoid unnecessary code
25        in seaice_lsr_ad
26      - exclude some residual computations in seaice_lsr when
27        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
28        in seaice_lsr_ad
29      - add more storing, a new tape (model/src/the_main_loop.F) and
30        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
31        and klockey should be checked by a specialist)
32      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
33        and update lab_sea after previous changes in pkg/seaice below
34    o pkg/autodiff:
35      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
36        viscFacInAd : run time parameters allowing for adjoint switches
37        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
38  o pkg/ecco:  o pkg/ecco:
39    - cost_gencost_seaicev4.F:    - introduce cost_gencost_boxmean.F that computes a box mean
40       reformulate proxy cost as function of sst and local param SEAICE_freeze      temperature (for use in adjoint sensitivity studies).
41       change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]  o model/src/set_defaults.F : initialize viscFacAdj to 1.
42    - add stop statement if old names siv4-[sst,vol] are used  o pkg/mom_common/mom_calc_visc.F:
43    - add snapshots + cost reports for atmospheric longwave    - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
44    - remove factor 0.1 in front of wtau[u,v]  o pkg/seaice/seaice_summary.F:
45    - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with    - statement for SEAICEadjMODE now in autodiff_readparms.F
46       ALLOW_TMI_SST_COST_CONTRIBUTION  o pkg/seaice:
47  o pkg/smooth:    - remove some store directives and add new ones in an effort to get
48    - move param smooth2Ddiffnbt to pkg/ecco      finally rid off the recomputation warnings. This is successful
49  =======      when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
50        defined (i.e. no extensive recomputation warnings left), but there
51        are still too many recomputations on the solver iteration level
52      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
53      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
54        SEAICE_SIZE.h
55      - add a store directive in S/R seaice_calc_viscosities
56    o pkg/seaice (ITD code):
57      - fix definition of Hlimit for multi-threaded case
58      - use double precision arithmetic to compute Hlimit: this affects results;
59        update output of experiment seaice_itd.
60    o replace content of verification/seaice_itd
61      - instead of a 1D column use the configuration of offline_exf_seaice
62        to test the ice thickness distribution code with ridging
63      - this is a first shot at this experiment
64      - change of some defaults of ridging parameters SEAICEhStar (from
65        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
66        and lot of new comments.
67    
68    checkpoint64y (2014/06/20)
69    o pkg/seaice/seaice_reg_ridge.F:
70      - modify the regularization of very small volumes of ice; only check
71        total volume HEFF, and do not apply correction to individual ice
72        classes because that leads to funny patterns in the heat and fw-fluxes
73        into the ocean. Adjust seaice_itd/results/output.txt
74      - replace nITD by SEAICE_multDim in loop-ranges
75    o pkg/exf:
76      - add code to process the case field period = -12. with UV interpolation.
77      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
78        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
79    o verification/global_with_exf:
80      - switch all fields period to -12. (was previously untested) in input/data.exf
81        (but keep secondary test ".yearly" unchanged); update the reference output.
82    o pkg/cal:
83      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
84    o pkg/exf:
85      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
86        to replace logical switch "exf_verbose"
87      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
88    o pkg/sbo:
89      - update from Katherine Quinn: evaluate mass directly from density and SSH
90        (budget using Finite Volume method) instead of from bottom pressure.
91      - allow testreport to collect few selected SBO output ; tested in exp.
92        global_ocean.90x40x15 (after updating the results, to include SBO output).
93      - fix some multi-threading issues (in output part).
94    o model/src & most packages:
95      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
96      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
97        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
98        "data.{pkg}" exist ; and leave the S/R (return) just after.
99      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
100        + call LAND_READPARMS from packages_readparms.F
101    o pkg/seaice:
102      - remove code that resets useThSice in S/R seaice_readparms and
103        replace it by a warning in S/R seaice_check
104      - remove parameter MULTDIM, replace with nITD and runtime
105        parameter SEAICE_multDim (still hard-wired to nITD if
106        SEAICE_ITD is defined)
107    
108    checkpoint64x (2014/05/24)
109    o verification/lab_sea:
110      - update adjoint and TLM output following changes to pkg/salt_plume
111      - un-do the update after putting back local recip_Cp in few places.
112    o pkg/salt_plume: modifications by An Nguyen:
113      - add capability to do brine rejection (salt-plume) as function of
114        volume+tracers (instead of only salinity tracer).
115      - conserve volume by exchanging volume from each kLev to above to
116        accommodate in-coming brine volume
117      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
118      - switch KPP surf buoyancy due to brine forcing to 3-d
119        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
120      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
121      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
122        in East/West Arctic.
123    o pkg/sbo:
124      - incorporate modifications from Katherine Quinn to enable the use of sbo
125        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
126        output for future testreport verification (unfinished).
127    o pkg/atm_phys:
128      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
129        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
130        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
131    o pkg/seaice
132      seaice_calc_ice_strength.F: modify expression to avoid divisions
133        (affects truncation)
134      seaice_do_ridging.F: clean up the insectarium
135      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
136      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
137      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
138      - add some debugging information and error messages (warnings)
139    o model/src: modifications relatd to atmosphere p*:
140      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
141      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
142        of vertical profile tRef in geopotential background and anomaly.
143      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
144        and pkg/atm_phys.
145      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
146        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
147    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
148    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
149        not used right now, but can be used in BGC packages to fix conservation.
150    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
151        other packages too.
152    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
153        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
154    o model/src:
155      - since we have several heat capacity (even in model/src), define "recip_Cp"
156        as local variable (no longer in common block) to avoid any confusion.
157      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
158    o pkg/exf:
159      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
160        air density as function of air Temp, Humidity and atm pressure.
161    
162    checkpoint64w (2014/05/02)
163    o verification:
164      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
165        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
166        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
167        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
168        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
169    o model/src: for atmosphere in p* coords:
170      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
171      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
172        but not yet activated.
173    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
174      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
175      - this changes the results (but not for any verification experiment, because
176        none tests this), but avoids having an extra field in the restart files
177    o pkg/seaice: remove global variable TICE (not needed)
178      - replace by TICES or local variable where necessary (cost_seaice_test,
179        seaice_diagnostics_state)
180      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
181      - use specific read/write routines for reading and writing individual leves
182        of a multilevel field
183    o pkg/ctrl & model/inc:
184      - move additional anomaly fields of control vars (related to options:
185         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
186        from DYNVARS.h into new header file: CTRL_FIELDS.h
187    o pkg/seaice: some small modifications to the ridging code
188      - make fw2ObyRidge a global variable and add the freshwater flux to
189        seaice_growth
190      - pass actual thickness from seaice_prepare_ridging, so that it is
191        computed only in one place and compute it in the same way as in
192        seaice_growth
193      - initialise more fields in seaice_do_ridging that where cause floating
194        point exceptions over land
195    o pkg/seaice: preparations for ridging code and first real ridging code
196      - move most of "PART 1" of S/R seaice_growth into a new and separate
197        S/R seaice_reg_ridge that will both regularize the state variable after
198        advection call the actual ridging routine;
199      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
200        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
201      - remove ridging code from seaice_advdiff
202      - clean up remaining part 1 of seaice_growth in an attempt to make it
203        more readable (this is probably subjective)
204      - call seaice_itd_redist once in the initialisation phase to have the initial
205        conditions in the correct category
206      - finally: add new ridging routine for ITD code
207    
208    checkpoint64v (2014/04/11)
209    o pkg/ecco:
210      - add runtime parameters mdt[start,end]date[1,2]
211      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
212    o pkg/seaice:
213      - make deltaC a global variable, so that it can be used in ridging code
214      - first step towards ridging: introduce new routines that compute
215        ice strength based on ridging parameters
216      - add diagnostic for HSNOWITD
217      - add opnWtrFrac as a global variable (required for ridging scheme)
218    o pkg/salt_plume + pkg/seaice/seaice_growth.F
219      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
220        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
221    o verification/hs94.1x64x5:
222      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
223      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
224  o autodiff:  o autodiff:
225    - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,    - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
226      and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)      and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
227      For now, only in pkgs used in verification/hs94.1x64x5.      For now, only in pkgs used in verification/hs94.1x64x5.
228    - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage    - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
229      which are specific to TAF/TAMC).      which are specific to TAF/TAMC).
230    - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:    - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
231      since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad      since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
232      is compiled), this simplifies/reduces which *_OPTIONS.h file to include.      is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
233    - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when    - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
234      building mitgcmuv_ad (make adAll).      building mitgcmuv_ad (make adAll).
235  o pkg/atm_phys:  o pkg/ecco:
236      - cost_gencost_seaicev4.F:
237         reformulate proxy cost as function of sst and local param SEAICE_freeze
238         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
239      - add stop statement if old names siv4-[sst,vol] are used
240      - add snapshots + cost reports for atmospheric longwave
241      - remove factor 0.1 in front of wtau[u,v]
242      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
243         ALLOW_TMI_SST_COST_CONTRIBUTION
244    o pkg/atm_phys:
245    - add some diagnostics for Short-wave and for convection S/R.    - add some diagnostics for Short-wave and for convection S/R.
246  o pkg/seaice/seaice_growth:  o pkg/seaice/seaice_growth:
247    - fix a bug in the lateral melt parameterization for SEAICE_ITD    - fix a bug in the lateral melt parameterization for SEAICE_ITD
248      in seaice_growth; tempFrz needs to be computed inside the i/j-loop      in seaice_growth; tempFrz needs to be computed inside the i/j-loop
249    - rearrange loop order for better vector code in the same code block    - rearrange loop order for better vector code in the same code block
250    - rewrite the floeDiameter formula to have fewer divisions    - rewrite the floeDiameter formula to have fewer divisions
251    -  (miraculously) none of this changes the results of seaice_itd    -  (miraculously) none of this changes the results of seaice_itd
252  >>>>>>> 1.1972  o pkg/smooth:
253      - move param smooth2Ddiffnbt to pkg/ecco
254    o pkg/salt_plume:
255      - salt_plume_frac.F:
256         clean up local param names
257         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
258  o pkg/rw:  o pkg/rw:
259    - add RS version of S/R READ_MFLDS_LEV.    - add RS version of S/R READ_MFLDS_LEV.
260  o pkg/streamice:  o pkg/streamice:
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