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revision 1.1959 by jmc, Fri Jan 17 22:12:57 2014 UTC revision 1.2008 by jmc, Fri Jun 20 13:13:37 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint64y (2014/06/20)
8    o pkg/seaice/seaice_reg_ridge.F:
9      - modify the regularization of very small volumes of ice; only check
10        total volume HEFF, and do not apply correction to individual ice
11        classes because that leads to funny patterns in the heat and fw-fluxes
12        into the ocean. Adjust seaice_itd/results/output.txt
13      - replace nITD by SEAICE_multDim in loop-ranges
14    o pkg/exf:
15      - add code to process the case field period = -12. with UV interpolation.
16      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
17        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
18    o verification/global_with_exf:
19      - switch all fields period to -12. (was previously untested) in input/data.exf
20        (but keep secondary test ".yearly" unchanged); update the reference output.
21    o pkg/cal:
22      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
23    o pkg/exf:
24      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
25        to replace logical switch "exf_verbose"
26      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
27    o pkg/sbo:
28      - update from Katherine Quinn: evaluate mass directly from density and SSH
29        (budget using Finite Volume method) instead of from bottom pressure.
30      - allow testreport to collect few selected SBO output ; tested in exp.
31        global_ocean.90x40x15 (after updating the results, to include SBO output).
32      - fix some multi-threading issues (in output part).
33    o model/src & most packages:
34      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
35      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
36        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
37        "data.{pkg}" exist ; and leave the S/R (return) just after.
38      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
39        + call LAND_READPARMS from packages_readparms.F
40    o pkg/seaice:
41      - remove code that resets useThSice in S/R seaice_readparms and
42        replace it by a warning in S/R seaice_check
43      - remove parameter MULTDIM, replace with nITD and runtime
44        parameter SEAICE_multDim (still hard-wired to nITD if
45        SEAICE_ITD is defined)
46    
47    checkpoint64x (2014/05/24)
48    o verification/lab_sea:
49      - update adjoint and TLM output following changes to pkg/salt_plume
50      - un-do the update after putting back local recip_Cp in few places.
51    o pkg/salt_plume: modifications by An Nguyen:
52      - add capability to do brine rejection (salt-plume) as function of
53        volume+tracers (instead of only salinity tracer).
54      - conserve volume by exchanging volume from each kLev to above to
55        accommodate in-coming brine volume
56      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
57      - switch KPP surf buoyancy due to brine forcing to 3-d
58        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
59      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
60      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
61        in East/West Arctic.
62    o pkg/sbo:
63      - incorporate modifications from Katherine Quinn to enable the use of sbo
64        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
65        output for future testreport verification (unfinished).
66    o pkg/atm_phys:
67      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
68        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
69        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
70    o pkg/seaice
71      seaice_calc_ice_strength.F: modify expression to avoid divisions
72        (affects truncation)
73      seaice_do_ridging.F: clean up the insectarium
74      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
75      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
76      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
77      - add some debugging information and error messages (warnings)
78    o model/src: modifications relatd to atmosphere p*:
79      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
80      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
81        of vertical profile tRef in geopotential background and anomaly.
82      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
83        and pkg/atm_phys.
84      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
85        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
86    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
87    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
88        not used right now, but can be used in BGC packages to fix conservation.
89    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
90        other packages too.
91    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
92        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
93    o model/src:
94      - since we have several heat capacity (even in model/src), define "recip_Cp"
95        as local variable (no longer in common block) to avoid any confusion.
96      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
97    o pkg/exf:
98      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
99        air density as function of air Temp, Humidity and atm pressure.
100    
101    checkpoint64w (2014/05/02)
102    o verification:
103      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
104        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
105        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
106        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
107        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
108    o model/src: for atmosphere in p* coords:
109      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
110      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
111        but not yet activated.
112    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
113      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
114      - this changes the results (but not for any verification experiment, because
115        none tests this), but avoids having an extra field in the restart files
116    o pkg/seaice: remove global variable TICE (not needed)
117      - replace by TICES or local variable where necessary (cost_seaice_test,
118        seaice_diagnostics_state)
119      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
120      - use specific read/write routines for reading and writing individual leves
121        of a multilevel field
122    o pkg/ctrl & model/inc:
123      - move additional anomaly fields of control vars (related to options:
124         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
125        from DYNVARS.h into new header file: CTRL_FIELDS.h
126    o pkg/seaice: some small modifications to the ridging code
127      - make fw2ObyRidge a global variable and add the freshwater flux to
128        seaice_growth
129      - pass actual thickness from seaice_prepare_ridging, so that it is
130        computed only in one place and compute it in the same way as in
131        seaice_growth
132      - initialise more fields in seaice_do_ridging that where cause floating
133        point exceptions over land
134    o pkg/seaice: preparations for ridging code and first real ridging code
135      - move most of "PART 1" of S/R seaice_growth into a new and separate
136        S/R seaice_reg_ridge that will both regularize the state variable after
137        advection call the actual ridging routine;
138      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
139        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
140      - remove ridging code from seaice_advdiff
141      - clean up remaining part 1 of seaice_growth in an attempt to make it
142        more readable (this is probably subjective)
143      - call seaice_itd_redist once in the initialisation phase to have the initial
144        conditions in the correct category
145      - finally: add new ridging routine for ITD code
146    
147    checkpoint64v (2014/04/11)
148    o pkg/ecco:
149      - add runtime parameters mdt[start,end]date[1,2]
150      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
151    o pkg/seaice:
152      - make deltaC a global variable, so that it can be used in ridging code
153      - first step towards ridging: introduce new routines that compute
154        ice strength based on ridging parameters
155      - add diagnostic for HSNOWITD
156      - add opnWtrFrac as a global variable (required for ridging scheme)
157    o pkg/salt_plume + pkg/seaice/seaice_growth.F
158      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
159        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
160    o verification/hs94.1x64x5:
161      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
162      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
163    o autodiff:
164      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
165        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
166        For now, only in pkgs used in verification/hs94.1x64x5.
167      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
168        which are specific to TAF/TAMC).
169      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
170        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
171        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
172      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
173        building mitgcmuv_ad (make adAll).
174    o pkg/ecco:
175      - cost_gencost_seaicev4.F:
176         reformulate proxy cost as function of sst and local param SEAICE_freeze
177         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
178      - add stop statement if old names siv4-[sst,vol] are used
179      - add snapshots + cost reports for atmospheric longwave
180      - remove factor 0.1 in front of wtau[u,v]
181      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
182         ALLOW_TMI_SST_COST_CONTRIBUTION
183    o pkg/atm_phys:
184      - add some diagnostics for Short-wave and for convection S/R.
185    o pkg/seaice/seaice_growth:
186      - fix a bug in the lateral melt parameterization for SEAICE_ITD
187        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
188      - rearrange loop order for better vector code in the same code block
189      - rewrite the floeDiameter formula to have fewer divisions
190      -  (miraculously) none of this changes the results of seaice_itd
191    o pkg/smooth:
192      - move param smooth2Ddiffnbt to pkg/ecco
193    o pkg/salt_plume:
194      - salt_plume_frac.F:
195         clean up local param names
196         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
197    o pkg/rw:
198      - add RS version of S/R READ_MFLDS_LEV.
199    o pkg/streamice:
200      - fix the restart test by writing/reading pickup_streamice files.
201    o pkg/seaice:
202      - refine checks for jfnk-related parameters
203      - comment out if statement with SEAICEuseIMEX parameter as long as there
204        is no IMEX code to avoid confusion and surprises
205    
206    checkpoint64u (2014/03/07)
207    o verification/MLAdjust:
208      - rename secondary test suffix:
209         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
210         0.leithD -> AhFlxF  + switch to flux-form
211         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
212         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
213    o pkg/mom_vecinv:
214      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
215        to be before mom_calc_visc.F)
216      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
217      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
218        this is simpler for the adjoint and for diagnostics.
219    o model/src + pkg/momentum:
220      - add input files for  2-D additional Western and Southern cell-edge wall
221         (e.g., to add "thin-wall" where it is =1).
222      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
223        using 2nd hFacZ that is computed from initial (fix domain) hFac
224      - known limitations of thin wall implementation: not yet coded for sigma
225        coords; not working with CD-scheme neither.
226    o pkg/seaice:
227      - rename recently introduced parameters from (wrong name) AB to
228        BDF (backward difference time discretisation)
229      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
230    o tools/adjoint_options:
231      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
232    
233    checkpoint64t (2014/02/01)
234    o pkg/ecco
235      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
236        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
237      - replace hard-coded record number and period which only work for monthly
238        with read-in runtime param that works for other periods (month,day,year)
239    o pkg/thsice
240      - corrected store directive fixes thsice adjoint gradient checks
241    o genmake2 & testreport:
242      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
243        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
244        Update testreport accordingly. No need to set "export OPENAD=true"
245        in adjoint_options/adjoint_oad anymore (will be removed later).
246  o pkg/shelfice:  o pkg/shelfice:
247    - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,    - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
248      only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F      only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
# Line 156  o verification: Line 395  o verification:
395  o pkg/cost:  o pkg/cost:
396    - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL    - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
397      (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:      (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
398      o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL      o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
399        cannot be applied to var in common block).        cannot be applied to var in common block).
400      o allows to get results independent of tile-per-proc setting (if using      o allows to get results independent of tile-per-proc setting (if using
401        slower GLOBAL_SUM_SEND_RECV option).        slower GLOBAL_SUM_SEND_RECV option).
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