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revision 1.1950 by dimitri, Thu Dec 19 01:06:09 2013 UTC revision 1.1998 by heimbach, Wed May 21 12:31:05 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 useSingleCpuInput separates single-CPU input from single-CPU output  o verification/lab_sea:
8  o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the    update adjoint and TLM output following changes to pkg/salt_plume
9    SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8  o pkg/salt_plume: modifications by An Nguyen:
10      - add capability to do brine rejection (salt-plume) as function of
11        volume+tracers (instead of only salinity tracer).
12      - conserve volume by exchanging volume from each kLev to above to
13        accommodate in-coming brine volume
14      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
15      - switch KPP surf buoyancy due to brine forcing to 3-d
16        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
17      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
18      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
19        in East/West Arctic.
20    o pkg/sbo:
21      - incorporate modifications from Katherine Quinn to enable the use of sbo
22        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
23        output for future testreport verification (unfinished).
24    o pkg/atm_phys:
25      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
26        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
27        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
28    o pkg/seaice
29      seaice_calc_ice_strength.F: modify expression to avoid divisions
30        (affects truncation)
31      seaice_do_ridging.F: clean up the insectarium
32      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
33      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
34      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
35      - add some debugging information and error messages (warnings)
36    o model/src: modifications relatd to atmosphere p*:
37      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
38      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
39        of vertical profile tRef in geopotential background and anomaly.
40      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
41        and pkg/atm_phys.
42      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
43        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
44    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
45    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
46        not used right now, but can be used in BGC packages to fix conservation.
47    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
48        other packages too.
49    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
50        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
51    o model/src:
52      - since we have several heat capacity (even in model/src), define "recip_Cp"
53        as local variable (no longer in common block) to avoid any confusion.
54      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
55    o pkg/exf:
56      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
57        air density as function of air Temp, Humidity and atm pressure.
58    
59    checkpoint64w (2014/05/02)
60    o verification:
61      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
62        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
63        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
64        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
65        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
66    o model/src: for atmosphere in p* coords:
67      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
68      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
69        but not yet activated.
70    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
71      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
72      - this changes the results (but not for any verification experiment, because
73        none tests this), but avoids having an extra field in the restart files
74    o pkg/seaice: remove global variable TICE (not needed)
75      - replace by TICES or local variable where necessary (cost_seaice_test,
76        seaice_diagnostics_state)
77      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
78      - use specific read/write routines for reading and writing individual leves
79        of a multilevel field
80    o pkg/ctrl & model/inc:
81      - move additional anomaly fields of control vars (related to options:
82         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
83        from DYNVARS.h into new header file: CTRL_FIELDS.h
84    o pkg/seaice: some small modifications to the ridging code
85      - make fw2ObyRidge a global variable and add the freshwater flux to
86        seaice_growth
87      - pass actual thickness from seaice_prepare_ridging, so that it is
88        computed only in one place and compute it in the same way as in
89        seaice_growth
90      - initialise more fields in seaice_do_ridging that where cause floating
91        point exceptions over land
92    o pkg/seaice: preparations for ridging code and first real ridging code
93      - move most of "PART 1" of S/R seaice_growth into a new and separate
94        S/R seaice_reg_ridge that will both regularize the state variable after
95        advection call the actual ridging routine;
96      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
97        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
98      - remove ridging code from seaice_advdiff
99      - clean up remaining part 1 of seaice_growth in an attempt to make it
100        more readable (this is probably subjective)
101      - call seaice_itd_redist once in the initialisation phase to have the initial
102        conditions in the correct category
103      - finally: add new ridging routine for ITD code
104    
105    checkpoint64v (2014/04/11)
106    o pkg/ecco:
107      - add runtime parameters mdt[start,end]date[1,2]
108      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
109    o pkg/seaice:
110      - make deltaC a global variable, so that it can be used in ridging code
111      - first step towards ridging: introduce new routines that compute
112        ice strength based on ridging parameters
113      - add diagnostic for HSNOWITD
114      - add opnWtrFrac as a global variable (required for ridging scheme)
115    o pkg/salt_plume + pkg/seaice/seaice_growth.F
116      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
117        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
118    o verification/hs94.1x64x5:
119      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
120      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
121    o autodiff:
122      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
123        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
124        For now, only in pkgs used in verification/hs94.1x64x5.
125      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
126        which are specific to TAF/TAMC).
127      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
128        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
129        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
130      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
131        building mitgcmuv_ad (make adAll).
132    o pkg/ecco:
133      - cost_gencost_seaicev4.F:
134         reformulate proxy cost as function of sst and local param SEAICE_freeze
135         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
136      - add stop statement if old names siv4-[sst,vol] are used
137      - add snapshots + cost reports for atmospheric longwave
138      - remove factor 0.1 in front of wtau[u,v]
139      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
140         ALLOW_TMI_SST_COST_CONTRIBUTION
141    o pkg/atm_phys:
142      - add some diagnostics for Short-wave and for convection S/R.
143    o pkg/seaice/seaice_growth:
144      - fix a bug in the lateral melt parameterization for SEAICE_ITD
145        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
146      - rearrange loop order for better vector code in the same code block
147      - rewrite the floeDiameter formula to have fewer divisions
148      -  (miraculously) none of this changes the results of seaice_itd
149    o pkg/smooth:
150      - move param smooth2Ddiffnbt to pkg/ecco
151    o pkg/salt_plume:
152      - salt_plume_frac.F:
153         clean up local param names
154         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
155    o pkg/rw:
156      - add RS version of S/R READ_MFLDS_LEV.
157    o pkg/streamice:
158      - fix the restart test by writing/reading pickup_streamice files.
159    o pkg/seaice:
160      - refine checks for jfnk-related parameters
161      - comment out if statement with SEAICEuseIMEX parameter as long as there
162        is no IMEX code to avoid confusion and surprises
163    
164    checkpoint64u (2014/03/07)
165    o verification/MLAdjust:
166      - rename secondary test suffix:
167         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
168         0.leithD -> AhFlxF  + switch to flux-form
169         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
170         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
171    o pkg/mom_vecinv:
172      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
173        to be before mom_calc_visc.F)
174      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
175      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
176        this is simpler for the adjoint and for diagnostics.
177    o model/src + pkg/momentum:
178      - add input files for  2-D additional Western and Southern cell-edge wall
179         (e.g., to add "thin-wall" where it is =1).
180      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
181        using 2nd hFacZ that is computed from initial (fix domain) hFac
182      - known limitations of thin wall implementation: not yet coded for sigma
183        coords; not working with CD-scheme neither.
184    o pkg/seaice:
185      - rename recently introduced parameters from (wrong name) AB to
186        BDF (backward difference time discretisation)
187      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
188    o tools/adjoint_options:
189      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
190    
191    checkpoint64t (2014/02/01)
192    o pkg/ecco
193      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
194        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
195      - replace hard-coded record number and period which only work for monthly
196        with read-in runtime param that works for other periods (month,day,year)
197    o pkg/thsice
198      - corrected store directive fixes thsice adjoint gradient checks
199    o genmake2 & testreport:
200      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
201        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
202        Update testreport accordingly. No need to set "export OPENAD=true"
203        in adjoint_options/adjoint_oad anymore (will be removed later).
204    o pkg/shelfice:
205      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
206        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
207        so that surface forcing applies to k=kSurf if using pkg/shelfice.
208    o pkg/ctrl, pkg/grdchk, pkg/ecco:
209      - Changes to make GENARR more modular (i.e. invisible if not used)
210    o model/src/temp_integrate.F and salt_integrate.F
211      - re-include store directives that were removed on Dec 27th.
212    o model/src/external_forcing_surf.F
213      - add storage directives for EmPmR and PmEpR to avoid recomputation of
214        seaice_model in the adjoint that is problematic when seaice_model is
215        turned off in the adjoint. The resolved issue dated back to July when
216        EXTERNAL_FORCING_SURF call was moved.
217        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
218    o pkg/exf/exf_check.F
219      - fix a small bug again (originally found by Wentao Liu, now found again)
220      - streamline error output
221    o pkg/streamice and aim_v23:
222      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
223        Apple's /usr/bin/cpp knows what to do:
224        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
225        Target: x86_64-apple-darwin13.0.0
226    
227    checkpoint64s (2014/01/05)
228    o tools/adjoint_options:
229      - switch to fastopt.net TAF server (instead of default fastopt.de) for
230        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
231    o model/src:
232      - remove some unnecessary TAF storage directives in forward_step.F and
233        in dynamics.F (note: not always removed by TAF, e.g., double storage
234        of kappaRU,kappaRV in former version of dynamics.F).
235    o model/src & pkg/ptracers:
236      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
237        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
238        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
239      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
240      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
241      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
242    o useSingleCpuInput separates single-CPU input from single-CPU output;
243        for now only implemented for in exf_interp_read.F
244    o verification/advect_xy:
245      - fix missing EXCH call in local version of ini_salt.F and update output.
246    o momentum diagnostics:
247      - fix which deltaT is used in Total-Tendency diagnostics.
248      - fix typo in diagnostics for momentum tendency from AB.
249    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
250        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
251    
252  checkpoint64r (2013/12/08)  checkpoint64r (2013/12/08)
253  o verification/*/results:  o verification/*/results:
# Line 112  o verification: Line 353  o verification:
353  o pkg/cost:  o pkg/cost:
354    - 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
355      (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:
356      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
357        cannot be applied to var in common block).        cannot be applied to var in common block).
358      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
359        slower GLOBAL_SUM_SEND_RECV option).        slower GLOBAL_SUM_SEND_RECV option).
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