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revision 1.2078 by gforget, Mon Oct 6 14:12:28 2014 UTC revision 1.2097 by mlosch, Fri Nov 28 14:19:20 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/autodiff
8      - add extra exchanges in addummy_in_steppging also for mnc output
9    o pkg/seaice:
10      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
11        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
12    o pkg/obcs:
13      - add option to specify domain-connected piece Id along OB though files
14        (for now, only used to diagnose PhiVel; default =1 -> global correction)
15      - modify obcs_diag_balance.F to process each connected-part separately;
16        exclude OB where Id = 0 but keep the full divergence there (-> constant
17        Psi along this portion of OB and all inflow derived from grad(Phi))
18      - add example of OB-conect files in verification/so_box_biogeo/input.
19    o pkg/diagnostics:
20      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
21      a) use non zero matrix element across OB and solve for Phi 1 grid point
22         outside OB (i.e, where tracer OBCS are applied).
23      b) global imbalance of inFlow/outFlow across OB: instead of modifying
24         velocity across OB, spread it uniformly along the OB in the RHS.
25    
26    checkpoint65g (2014/11/19)
27    o pkg/diagnostcis:
28      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
29    o pkg/my82,pp81,kl10:
30      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
31        field diffKr as background diffusivity to set minimum diffusivity value.
32    o pkg/seaice:
33      - add new parameter SEAICEuseEVPrev (for revisited EVP by
34        Bouillon et al 2013)
35      - add SEAICE_evpAlpha/Beta to namelist
36      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
37        involve trivial re-ordering of divisions/multiplications that should not
38        have any effects, but ... they do change the results of lab_sea.hb87 so
39        that only 2 digits of agreement remain, in line with the general
40        instability/fragility of the evp-code. For now, I do not care and just
41        update the verification experiment
42    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
43      - remove xx_genarr2d_numsmooth etc
44      - use xx_genarr2d_preproc etc instead
45      - carry out smooth_correl2D at initialization stage rather than during
46        time stepping.
47      - get smoothOpNb from xx_gentim2d_preproc
48    o global_oce_cs32 :
49      - add test of generic ecco capabilities.
50    o pkg/exf/exf_getsurfacefluxes.F :
51      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
52    o pkg/ctrl,ecco :
53      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
54        is defined.
55    o pkg/seaice: add diagnostics for Delta (deformation parameter)
56    o model/src:
57      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
58        diffusivity (background) is specified but ignored.
59    o verification:
60      - in testreport, convert hostname to lower case for default output dir name
61    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
62    o pkg/dic: add modifications from Hajoon:
63      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
64      - light attenuation: add self-shading effect by climatological Chlorophyll
65        (read from file).
66    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
67        compiles when SEAICE_ALLOW_DYNAMICS is undefined
68    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
69        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
70        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
71        approach where CPP_OPTIONS.h includes an omnipotent
72        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
73    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
74        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
75    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
76        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
77        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
78    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
79      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
80      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
81      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
82      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
83    o pkg/ctrl,ecco,exf :
84      - remove variables associated with NON-generic costs,
85        unless ECCO_CTRL_DEPRECATED is defined.
86      - remove NON-generic NON-obcs controls,
87        unless ECCO_CTRL_DEPRECATED is defined.
88    o pkg/ctrl : added ctrl_local_params.h
89    o pkg/ecco : added ecco_local_params.h
90    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
91        experiments, which will progressively be removed once the
92        experiments are revised to use only generic controls/costs.
93    
94    checkpoint65f (2014/10/13)
95    o pkg/ctrl, ecco, seaice : minor changes in headers
96    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
97        cost function and control capabilities added since checkpoint65c.
98    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
99  o pkg/ecco: increase modularity and improve logic  o pkg/ecco: increase modularity and improve logic
100    - ecco_toolbox.F (new) : basic operations that are often used    - ecco_toolbox.F (new) : basic operations that are often used,
101       (for now, ecco_toolbox.F simply contains function ecco_zero).      including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
102        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
103    - cost_gencal.F (new) : determine filnames and records.    - cost_gencal.F (new) : determine filnames and records.
104    - cost_gendif.F (new) : compute masked model-data difference.    - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
   - cost_genread.F : use ecco_zero to initialize field to 0s.  
105    - cost_generic.F : use spzeroloc rather than hard-coded -9999,    - cost_generic.F : use spzeroloc rather than hard-coded -9999,
106      and exploit the above functions leading to more compact code.      and exploit the above functions leading to more compact code.
107      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
108    - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,    - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
109      using_ers, using_gfo, using_mdt is now only defined within gencost)      using_ers, using_gfo, using_mdt is now only defined within gencost)
110  o pkg/ecco: extend generic cost capabilities  o pkg/ecco: extend generic cost capabilities
111    - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost    - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
112      capabilities via gencost_preproc (+ _c,_i,_r related params),      capabilities via gencost_preproc (+ _c,_i,_r related params),
113      gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,      gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
114      gencost_outputlevel arguments to cost_generic      gencost_outputlevel arguments to cost_generic
115    - pkg/ecco/cost_genread.F (new) : interface between cost_generic    - pkg/ecco/cost_genread.F (new) : interface between cost_generic
# Line 34  o pkg/ecco: extend generic cost capabili Line 127  o pkg/ecco: extend generic cost capabili
127    - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs    - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
128  o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA  o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
129  o pkg/ecco: internal re-organization  o pkg/ecco: internal re-organization
130    - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl    - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
131      (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,      (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
132      mv relevant variables definition from ecco_cost.h to ecco.h,      mv relevant variables definition from ecco_cost.h to ecco.h,
133      make sure gencost routines only include ecco.h)      make sure gencost routines only include ecco.h)
134    - throughout : add missing CCP switches, rm unused variables,    - throughout : add missing CCP switches, rm unused variables,
135      and rm un-necessary CPP switches      and rm un-necessary CPP switches
136    - throughout gencost routines : replace modelstartdate with    - throughout gencost routines : replace modelstartdate with
137      gencost_startdate when needed      gencost_startdate when needed
138    - cost_bp_read.F : use arguments, instead of common blocs    - cost_bp_read.F : use arguments, instead of common blocs
139      so that it can be used also by (new) cost_gencost_bpv4.F      so that it can be used also by (new) cost_gencost_bpv4.F
140    - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0    - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
141    - ecco_phys.F : compute etanFull    - ecco_phys.F : compute etanFull
142    - ecco_readparms.F : rename using_topex as using_tpj, add    - ecco_readparms.F : rename using_topex as using_tpj, add
# Line 361  o pkg/seaice: more clean up Line 454  o pkg/seaice: more clean up
454      nearly a factor of 10 (but keep in mind there is mostly seaice code in      nearly a factor of 10 (but keep in mind there is mostly seaice code in
455      this experiment):      this experiment):
456      > size mitgcmuv_ad      > size mitgcmuv_ad
457      text    data        bss     dec        hex        text    data        bss     dec        hex
458      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
459      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
460      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
461      text    data        bss     dec        hex      text    data        bss     dec        hex
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