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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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checkpoint65g (2014/11/19) |
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o pkg/diagnostcis: |
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- add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param |
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o pkg/my82,pp81,kl10: |
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- fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D |
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field diffKr as background diffusivity to set minimum diffusivity value. |
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o pkg/seaice: |
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- add new parameter SEAICEuseEVPrev (for revisited EVP by |
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Bouillon et al 2013) |
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- add SEAICE_evpAlpha/Beta to namelist |
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- modify seaice_evp code to able to use SEAICEuseEVPrev. These changes |
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involve trivial re-ordering of divisions/multiplications that should not |
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have any effects, but ... they do change the results of lab_sea.hb87 so |
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that only 2 digits of agreement remain, in line with the general |
21 |
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instability/fragility of the evp-code. For now, I do not care and just |
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update the verification experiment |
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o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc) |
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- remove xx_genarr2d_numsmooth etc |
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- use xx_genarr2d_preproc etc instead |
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- carry out smooth_correl2D at initialization stage rather than during |
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time stepping. |
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- get smoothOpNb from xx_gentim2d_preproc |
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o global_oce_cs32 : |
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- add test of generic ecco capabilities. |
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o pkg/exf/exf_getsurfacefluxes.F : |
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- add to tmpUE/tmpVN rather than re-initializing them (conventional behavior). |
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o pkg/ctrl,ecco : |
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- omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED |
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is defined. |
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o pkg/seaice: add diagnostics for Delta (deformation parameter) |
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o model/src: |
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- when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical |
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diffusivity (background) is specified but ignored. |
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o verification: |
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- in testreport, convert hostname to lower case for default output dir name |
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o model, pkg : add useCTRL, useECCO parameters (on/off run time switch). |
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o pkg/dic: add modifications from Hajoon: |
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- add iron sedimentation flux function of the flux of PO4 out of bottom layer |
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- light attenuation: add self-shading effect by climatological Chlorophyll |
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(read from file). |
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o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also |
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compiles when SEAICE_ALLOW_DYNAMICS is undefined |
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o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
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AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
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ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
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approach where CPP_OPTIONS.h includes an omnipotent |
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ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
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o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
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ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
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o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
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to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
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(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
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o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
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add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
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- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
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- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
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- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
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o pkg/ctrl,ecco,exf : |
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- remove variables associated with NON-generic costs, |
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unless ECCO_CTRL_DEPRECATED is defined. |
67 |
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- remove NON-generic NON-obcs controls, |
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unless ECCO_CTRL_DEPRECATED is defined. |
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o pkg/ctrl : added ctrl_local_params.h |
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o pkg/ecco : added ecco_local_params.h |
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o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
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experiments, which will progressively be removed once the |
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experiments are revised to use only generic controls/costs. |
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|
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checkpoint65f (2014/10/13) |
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o pkg/ctrl, ecco, seaice : minor changes in headers |
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o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
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cost function and control capabilities added since checkpoint65c. |
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o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
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o pkg/ecco: increase modularity and improve logic |
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- ecco_toolbox.F (new) : basic operations that are often used, |
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including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk, |
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ecco_addcost, ecco_add, ecco_div, ecco_readbar. |
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- cost_gencal.F (new) : determine filnames and records. |
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- cost_genread.F, cost_generic.F : condense code using ecco_toolbox. |
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- cost_generic.F : use spzeroloc rather than hard-coded -9999, |
87 |
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and exploit the above functions leading to more compact code. |
88 |
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- cost_genread.F : rm un-necessary arguments, re-arrange args order. |
89 |
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- ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj, |
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using_ers, using_gfo, using_mdt is now only defined within gencost) |
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o pkg/ecco: extend generic cost capabilities |
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- pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost |
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capabilities via gencost_preproc (+ _c,_i,_r related params), |
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gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod, |
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gencost_outputlevel arguments to cost_generic |
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- pkg/ecco/cost_genread.F (new) : interface between cost_generic |
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and active_read, making room for gencost_preproc to take effect. |
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Added preproc code ('climmon') to replace GENERIC_BAR_MONTH. |
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- pkg/ecco/cost_generic.F : |
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compute and store misfit maks*(model-data) in localdif that is |
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then used in cost and for output, output misfit if outlev.GT.0 |
102 |
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- pkg/ecco/cost_averagesfields.F : depend on gencost_barskip |
103 |
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rather gencost_barfile for deciding whether to write barfile |
104 |
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- pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd |
105 |
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- pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from |
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ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip |
107 |
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- pkg/ecco/ecco_summary.F : report gencost variables |
108 |
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- pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs |
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o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA |
110 |
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o pkg/ecco: internal re-organization |
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- resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl |
112 |
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(rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter, |
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mv relevant variables definition from ecco_cost.h to ecco.h, |
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make sure gencost routines only include ecco.h) |
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- throughout : add missing CCP switches, rm unused variables, |
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and rm un-necessary CPP switches |
117 |
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- throughout gencost routines : replace modelstartdate with |
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gencost_startdate when needed |
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- cost_bp_read.F : use arguments, instead of common blocs |
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so that it can be used also by (new) cost_gencost_bpv4.F |
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- ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0 |
122 |
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- ecco_phys.F : compute etanFull |
123 |
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- ecco_readparms.F : rename using_topex as using_tpj, add |
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bpv4-grace to gencost list, initialize added parameters |
125 |
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- ecco_summary.F : include SIZE.h needed for augmented ecco.h |
126 |
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|
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checkpoint65e (2014/09/28) |
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o pkg/obcs: |
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- replaced the just-added CPP options with run-time variables |
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(see pkg/obcs/OBCS_PARAMS.h for details) |
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o pkg/obcs: |
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- add additional CPP options for sponge boundary layers |
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(see pkg/obcs/OBCS_OPTIONS.h for details) |
134 |
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o pkg/atm_phys: |
135 |
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- implement simple (obliquity only, assuming circular planet orbit) |
136 |
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seasonal cycle for incoming insolation ; used when run-time parameter |
137 |
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"select_incSW" is set to 1 ; by default (=0), uses old unchanged formula. |
138 |
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o pkg/exf, pkg/ecco, pkg/ctrl: |
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- add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets |
140 |
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- activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip |
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- implement gentim2d for xx_tauu, xx_tauv |
142 |
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o pkg/ctrl, pkg/ecco : |
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- fix and complement the generic controls implementation |
144 |
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o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F, |
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pkg/shelfice/shelfice_thermodynamics.F, |
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verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F, |
147 |
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verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F : |
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- add weight in CTRL_GET_GEN calls |
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o pkg/ctrl : |
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- ctrl_get_gen.F : add weight as input parameter, and apply |
151 |
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it directly rather than using smooth_correl2Dw (to be retired). |
152 |
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- ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call |
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o pkg/ctrl : |
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- introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, |
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ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) |
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- re-activate ctrl_summary (call in ctrl_init.F) |
157 |
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o pkg/ctrl/ctrl_cost_gen.F : |
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- fix CCP brackets, remove un-necessary myiter, mytime |
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o pkg/ecco, pkg/ctrl : |
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- remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) |
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- remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) |
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- add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) |
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- add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) |
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|
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checkpoint65d (2014/09/15) |
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o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : |
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- add xx_genarr2d_bounds,xx_genarr3d_bounds, |
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xx_genarr2d_numsmooth, xx_genarr3d_numsmooth |
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o pkg/ctrl/ctrl_map_ini_genarr.F : |
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- remove compilation failure |
171 |
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- replace hard coded example |
172 |
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- use ctrl_map_ini_gen2D, 3D |
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o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : |
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- on/off switch based upon xx_genarr2d_weight,3d |
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o src/packages_init_variables.F : |
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- regroup pkg/estimation calls |
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- remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
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(moved to ctrl_init_variables) |
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o cost/cost_init_varia.F : |
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- remove ecco_cost_init_varia |
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(moved to ecco_init_varia) |
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o ctrl/ctrl_init_variables.F : |
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- add CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
184 |
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- add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI |
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o ctrl/ctrl_map_ini.F : |
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- remove ctrl_map_ini_genarr, seaice_ctrl_map_ini |
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(moved to ctrl_init_variables) |
188 |
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o ctrl/ctrl_map_ini_ecco.F : |
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- remove ECCO_PHYS (mv to ecco_init_varia) |
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- remove seaice_ctrl_map_ini (mv to ctrl_init_variables) |
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o ecco/ecco_ad_diff.list : |
192 |
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- add ecco_init_varia.f |
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o ecco/ecco_init_varia.F |
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- new routine |
195 |
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o pkg/streamice: |
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- move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F |
197 |
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to streamice_init_fixed.F ; fix setting of STREAMICEisOn. |
198 |
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- from model/src, only call pkg/streamice routines if useStreamIce is TRUE. |
199 |
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o pkg/generic_advdiff: |
200 |
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- fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. |
201 |
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o pkg/exf: |
202 |
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- exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, |
203 |
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xxg_precip capability |
204 |
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- exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch |
205 |
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o pkg/ctrl: |
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- ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d |
207 |
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o model/src/load_fields_driver.F : |
208 |
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- move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING |
209 |
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so xx_gentim2d can be applied to e.g. exf fields in a timely manner. |
210 |
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o OpenAD verification experiments: |
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- Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h |
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in src files (to enable to skip the ECCO_CPPOPTIONS.h); |
213 |
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for now, only in pkgs used in OpenAD verification experiments. |
214 |
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- Change all except one (halfpipe_streamice) OpenAD experiments to use pkg |
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specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) |
216 |
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instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). |
217 |
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This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. |
218 |
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o OpenAD verification tests: |
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- finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); |
220 |
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- finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for |
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tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. |
222 |
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- leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) |
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and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). |
224 |
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o model/src & generic_advdiff: |
225 |
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- change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S |
226 |
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forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model |
227 |
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dynamics requires valid tracer forcing only over tile interior but, for |
228 |
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some diagnostics, may need to extend it over 1 point in tile halo region. |
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- in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid |
230 |
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tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max |
231 |
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setting in temp/salt/ptracer_integrate.F |
232 |
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o pkg/dic: |
233 |
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- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
234 |
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gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
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in gchem_forcing_sep.F |
236 |
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o pkg/autodiff & obcs: |
237 |
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- add storage of current OB values for U & V (was already done for T & S). |
238 |
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|
239 |
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checkpoint65c (2014/08/30) |
240 |
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o pkg/dic: |
241 |
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- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
242 |
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and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
243 |
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AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
244 |
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o verification: |
245 |
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- new experiment testing OBCS and DIC pkgs, using params & output from |
246 |
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tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
247 |
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passage: take OBCS from the last year of a 2 yrs simulation and initial |
248 |
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conditions from t=1.yr while keeping the same forcing. |
249 |
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o model/src: |
250 |
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- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
251 |
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(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
252 |
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o pkg/diagnostics (Stats-Diags): |
253 |
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- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
254 |
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a) refine region where stats are computed, excluding where arrhFac=0 ; |
255 |
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b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
256 |
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c) extend regional stats over the region edges (for U or V pt location). |
257 |
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o pkg/gchem: |
258 |
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- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
259 |
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pkg/dic is currently changing/updating ptracers values beyond the OB). |
260 |
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o verification (hs94): |
261 |
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- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
262 |
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bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
263 |
|
hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
264 |
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apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
265 |
o pkg/ptracers: |
o pkg/ptracers: |
266 |
- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
267 |
switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
405 |
- collect T & S forcing tendency into local 2-D array (passed as argument to |
- collect T & S forcing tendency into local 2-D array (passed as argument to |
406 |
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
407 |
affects results at machine truncation level (e.g., ocean: if using |
affects results at machine truncation level (e.g., ocean: if using |
408 |
SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0) |
SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
409 |
moist correction due to vertical advection). |
correction due to vertical advection). |
410 |
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
411 |
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
412 |
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
435 |
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 |
436 |
this experiment): |
this experiment): |
437 |
> size mitgcmuv_ad |
> size mitgcmuv_ad |
438 |
text data bss dec hex |
text data bss dec hex |
439 |
5100659 1216 220458952 225560827 d71c8fb |
5100659 1216 220458952 225560827 d71c8fb |
440 |
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
441 |
but only a moderate increase of 36% for global_ocean.cs32x15: |
but only a moderate increase of 36% for global_ocean.cs32x15: |
442 |
text data bss dec hex |
text data bss dec hex |