| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
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| 7 |
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| 8 |
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o pkg/ctrl : |
| 9 |
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- introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, |
| 10 |
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ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) |
| 11 |
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- re-activate ctrl_summary (call in ctrl_init.F) |
| 12 |
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o pkg/ctrl/ctrl_cost_gen.F : |
| 13 |
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- rename ctrl_cost_gen2d input parameters {wmean_gen,wgen,genmask} |
| 14 |
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as {xx_gen_wmean,xx_gen_weight,xx_gen_mask} |
| 15 |
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- add ctrl_cost_gen3d for ARR3D (ctrl_cost_gen2d is for ARR2D,TIM2D) |
| 16 |
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o pkg/ctrl/CTRL_GENARR.h : |
| 17 |
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- add objf_genarr2d, num_genarr2d, mult_genarr2d |
| 18 |
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- add objf_genarr3d, num_genarr3d, mult_genarr3d |
| 19 |
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- add wgenarr2d, wgenarr3d |
| 20 |
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o pkg/ctrl/ctrl_readparms.F : |
| 21 |
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- add mult_genarr2d,mult_genarr3d in namelist |
| 22 |
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o pkg/ctrl_map_ini_genarr.F : |
| 23 |
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- bug fixes |
| 24 |
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o pkg/ctrl/ctrl_cost_driver.F : |
| 25 |
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- remove un-necessary cal.h, fix CCP brackets, remove un-necessary |
| 26 |
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myiter, mytime, add return |
| 27 |
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o pkg/ctrl/ctrl_cost_gen.F : |
| 28 |
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- fix CCP brackets, remove un-necessary myiter, mytime |
| 29 |
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o pkg/ecco : |
| 30 |
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- remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) |
| 31 |
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- remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) |
| 32 |
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- update cost_forcing_gen calls in cost_forcing.F |
| 33 |
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- update cost_genctrl call in ecco_cost_driver.F |
| 34 |
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- update ecco_ad_diff.list accordingly |
| 35 |
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o pkg/ctrl : |
| 36 |
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- add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) |
| 37 |
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- add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) |
| 38 |
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- update ctrl_ad_diff.list accordingly |
| 39 |
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|
| 40 |
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checkpoint65d (2014/09/15) |
| 41 |
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o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : |
| 42 |
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- add xx_genarr2d_bounds,xx_genarr3d_bounds, |
| 43 |
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xx_genarr2d_numsmooth, xx_genarr3d_numsmooth |
| 44 |
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o pkg/ctrl/ctrl_map_ini_genarr.F : |
| 45 |
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- remove compilation failure |
| 46 |
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- replace hard coded example |
| 47 |
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- use ctrl_map_ini_gen2D, 3D |
| 48 |
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o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : |
| 49 |
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- on/off switch based upon xx_genarr2d_weight,3d |
| 50 |
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o src/packages_init_variables.F : |
| 51 |
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- regroup pkg/estimation calls |
| 52 |
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- remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
| 53 |
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(moved to ctrl_init_variables) |
| 54 |
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o cost/cost_init_varia.F : |
| 55 |
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- remove ecco_cost_init_varia |
| 56 |
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(moved to ecco_init_varia) |
| 57 |
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o ctrl/ctrl_init_variables.F : |
| 58 |
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- add CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
| 59 |
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- add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI |
| 60 |
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o ctrl/ctrl_map_ini.F : |
| 61 |
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- remove ctrl_map_ini_genarr, seaice_ctrl_map_ini |
| 62 |
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(moved to ctrl_init_variables) |
| 63 |
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o ctrl/ctrl_map_ini_ecco.F : |
| 64 |
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- remove ECCO_PHYS (mv to ecco_init_varia) |
| 65 |
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- remove seaice_ctrl_map_ini (mv to ctrl_init_variables) |
| 66 |
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o ecco/ecco_ad_diff.list : |
| 67 |
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- add ecco_init_varia.f |
| 68 |
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o ecco/ecco_init_varia.F |
| 69 |
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- new routine |
| 70 |
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o pkg/streamice: |
| 71 |
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- move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F |
| 72 |
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to streamice_init_fixed.F ; fix setting of STREAMICEisOn. |
| 73 |
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- from model/src, only call pkg/streamice routines if useStreamIce is TRUE. |
| 74 |
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o pkg/generic_advdiff: |
| 75 |
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- fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. |
| 76 |
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o pkg/exf: |
| 77 |
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- exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, |
| 78 |
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xxg_precip capability |
| 79 |
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- exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch |
| 80 |
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o pkg/ctrl: |
| 81 |
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- ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d |
| 82 |
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o model/src/load_fields_driver.F : |
| 83 |
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- move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING |
| 84 |
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so xx_gentim2d can be applied to e.g. exf fields in a timely manner. |
| 85 |
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o OpenAD verification experiments: |
| 86 |
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- Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h |
| 87 |
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in src files (to enable to skip the ECCO_CPPOPTIONS.h); |
| 88 |
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for now, only in pkgs used in OpenAD verification experiments. |
| 89 |
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- Change all except one (halfpipe_streamice) OpenAD experiments to use pkg |
| 90 |
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specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) |
| 91 |
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instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). |
| 92 |
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This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. |
| 93 |
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o OpenAD verification tests: |
| 94 |
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- finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); |
| 95 |
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- finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for |
| 96 |
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tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. |
| 97 |
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- leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) |
| 98 |
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and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). |
| 99 |
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o model/src & generic_advdiff: |
| 100 |
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- change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S |
| 101 |
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forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model |
| 102 |
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dynamics requires valid tracer forcing only over tile interior but, for |
| 103 |
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some diagnostics, may need to extend it over 1 point in tile halo region. |
| 104 |
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- in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid |
| 105 |
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tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max |
| 106 |
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setting in temp/salt/ptracer_integrate.F |
| 107 |
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o pkg/dic: |
| 108 |
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- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
| 109 |
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gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
| 110 |
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in gchem_forcing_sep.F |
| 111 |
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o pkg/autodiff & obcs: |
| 112 |
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- add storage of current OB values for U & V (was already done for T & S). |
| 113 |
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|
| 114 |
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checkpoint65c (2014/08/30) |
| 115 |
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o pkg/dic: |
| 116 |
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- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
| 117 |
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and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
| 118 |
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AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
| 119 |
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o verification: |
| 120 |
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- new experiment testing OBCS and DIC pkgs, using params & output from |
| 121 |
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tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
| 122 |
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passage: take OBCS from the last year of a 2 yrs simulation and initial |
| 123 |
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conditions from t=1.yr while keeping the same forcing. |
| 124 |
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o model/src: |
| 125 |
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- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
| 126 |
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(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
| 127 |
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o pkg/diagnostics (Stats-Diags): |
| 128 |
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- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
| 129 |
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a) refine region where stats are computed, excluding where arrhFac=0 ; |
| 130 |
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b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
| 131 |
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c) extend regional stats over the region edges (for U or V pt location). |
| 132 |
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o pkg/gchem: |
| 133 |
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- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
| 134 |
|
pkg/dic is currently changing/updating ptracers values beyond the OB). |
| 135 |
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o verification (hs94): |
| 136 |
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- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
| 137 |
|
bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
| 138 |
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hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
| 139 |
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apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
| 140 |
|
o pkg/ptracers: |
| 141 |
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- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
| 142 |
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switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
| 143 |
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- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
| 144 |
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with AB-2 code (so that it get tested). |
| 145 |
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o model/src: |
| 146 |
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- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
| 147 |
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with AB-2 code (previously only available with AB-3 code). |
| 148 |
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Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
| 149 |
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to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
| 150 |
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there, by calling CYCLE_AB_TRACER). |
| 151 |
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o pkg/generic_advdiff: |
| 152 |
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- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
| 153 |
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GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
| 154 |
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+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
| 155 |
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S/R temp/salt/ptracers_integrate.F |
| 156 |
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o model/src & pkg/ptracers: |
| 157 |
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- remove common block variables gT,gS (in DYNVARS.h), except when |
| 158 |
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USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
| 159 |
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- remove common block variable gPtr. |
| 160 |
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o model/src & pkgs: |
| 161 |
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- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
| 162 |
|
ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
| 163 |
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IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
| 164 |
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GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
| 165 |
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+ change accordingly all calling S/R. |
| 166 |
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- use local temperature/salinity/ptracer tendency array (without bi,bj) |
| 167 |
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in S/R temp/salt/ptracers_integrate.F |
| 168 |
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o pkg/seaice: |
| 169 |
|
- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
| 170 |
|
to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
| 171 |
|
- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
| 172 |
|
in seaice_lsr |
| 173 |
|
- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
| 174 |
|
in s/r seaice_lsr_calc_coeffs |
| 175 |
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o pkg/mdsio: |
| 176 |
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- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
| 177 |
|
(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
| 178 |
|
too long (e.g., > MAX_LEN_FNAM/2 ) |
| 179 |
|
|
| 180 |
|
checkpoint65b (2014/08/12) |
| 181 |
|
o pkg/matrix: |
| 182 |
|
- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
| 183 |
|
o model/src: |
| 184 |
|
- fix initialisation of geothermalFile; compile geothermal-flux code in |
| 185 |
|
natl_box verification experiment. |
| 186 |
|
o model/src & pkg/down_slope: |
| 187 |
|
- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
| 188 |
|
- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
| 189 |
|
field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
| 190 |
|
results at machine truncation level: update output of experiments |
| 191 |
|
global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
| 192 |
|
o pkg/diagnostics (Stats-Diags): |
| 193 |
|
- do not cumulate the full volume when DIAGNOSTICS_FILL is |
| 194 |
|
called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
| 195 |
|
This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
| 196 |
|
times (but Min,Max and StD are still wrong). |
| 197 |
|
o model/src: |
| 198 |
|
- add geothermal flux forcing: read in ini_forcing.F as time-constant |
| 199 |
|
field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
| 200 |
|
o model/src: |
| 201 |
|
- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
| 202 |
|
_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
| 203 |
|
arrays are already updated while adjustments (filters, conv.adjustment) are |
| 204 |
|
still applied later, in S/R TRACERS_CORRECTION_STEP. |
| 205 |
|
o model/src: |
| 206 |
|
- store in common bloc array "rhoInSitu" the virtual potential temperature |
| 207 |
|
anomaly that is used to compute geopotential: this make the atmos code |
| 208 |
|
more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
| 209 |
|
o pkg/seaice/seaice_lsr.F |
| 210 |
|
- rename integer variable ilcall to ipass (that's what it is called |
| 211 |
|
in the residual diagnostics |
| 212 |
|
- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
| 213 |
|
default) for improved non-linear convergence of the first few steps |
| 214 |
|
- adjust a few comments and add new ones to explain some of the store |
| 215 |
|
directives |
| 216 |
|
o pkg/generic_advdiff (& ptracers): |
| 217 |
|
- re-work the code to check for valid advection scheme and for minimum |
| 218 |
|
size of overlap (now stored in local common bloc in gad_advscheme.F) |
| 219 |
|
o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
| 220 |
|
- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
| 221 |
|
- add an auxilliary variable "bet" and fix store directives and keys in |
| 222 |
|
seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
| 223 |
|
less exact gradients in my tests); but there are still |
| 224 |
|
recomputation warning (although gradients are sort of OK), when |
| 225 |
|
SEAICE_LSR_VECTORIZE is not defined, so this flag and |
| 226 |
|
SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
| 227 |
|
- update verification experiments lab_sea. |
| 228 |
|
- change some comments in S/R seaice_calc_viscosities |
| 229 |
|
o model/src: |
| 230 |
|
- if staggerTimeStep=T, always apply exchange to velocity field in |
| 231 |
|
do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
| 232 |
|
(independent of using multi-dim advection or not); no effect on FWD run |
| 233 |
|
but affects AD results (at machine truncation level): update output of |
| 234 |
|
experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
| 235 |
|
and isomip (oad: 12.d). |
| 236 |
|
o pkg/generic_advdiff: |
| 237 |
|
- stop if doAB_onGtGs is set to FALSE but ignored |
| 238 |
|
- refine warning related to stability of tracer time-stepping |
| 239 |
|
regarding internal wave dynamics. |
| 240 |
|
- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
| 241 |
|
on staggerTimeStep & implicitIntGravWave (will now get a warning |
| 242 |
|
if potentially unstable). |
| 243 |
|
o pkg/kl10: |
| 244 |
|
- add new pkg "kl10" for mixing due to internal wave breaking, from |
| 245 |
|
http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
| 246 |
|
(contribution from Jody Klymak), tested in verification experiment |
| 247 |
|
verification/internal_wave/input.kl10/ |
| 248 |
|
o isomip experiment: |
| 249 |
|
- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
| 250 |
|
(input.htd) and update the output. |
| 251 |
|
o cd_code experiments: |
| 252 |
|
- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
| 253 |
|
#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
| 254 |
|
global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
| 255 |
|
update the corresponding output. |
| 256 |
|
o pkg/seaice: |
| 257 |
|
- reduce the number of include files and store directives in |
| 258 |
|
S/R seaice_lsr_tridiagu/v |
| 259 |
|
- change the order of loops in one case in S/R seaice_lsr_tridiagv |
| 260 |
|
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
| 261 |
|
get rid off one store directive (a TAF bug?) |
| 262 |
|
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
| 263 |
|
S/R seaice_lsr_tridiagv to change the loop range for consistency |
| 264 |
|
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
| 265 |
|
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
| 266 |
|
S/R seaice_lsr_tridiagu/v (requires update of |
| 267 |
|
offline_exf_seaice/input.dyn_jfnk) |
| 268 |
|
|
| 269 |
|
checkpoint65a (2014/07/27) |
| 270 |
|
o model/src: |
| 271 |
|
- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
| 272 |
|
surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
| 273 |
|
(topo in p-coords, ice-shelf in z-coords); update output of experiments |
| 274 |
|
tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
| 275 |
|
o model/src: |
| 276 |
|
- collect momentum forcing tendency into local 2-D array (passed as argument |
| 277 |
|
to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
| 278 |
|
parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
| 279 |
|
affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
| 280 |
|
- collect T & S forcing tendency into local 2-D array (passed as argument to |
| 281 |
|
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
| 282 |
|
affects results at machine truncation level (e.g., ocean: if using |
| 283 |
|
SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
| 284 |
|
correction due to vertical advection). |
| 285 |
|
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
| 286 |
|
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
| 287 |
|
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
| 288 |
|
obcs_ctrl (ad & fwd grd @ 12 & 7). |
| 289 |
|
o pkg/ptracers & diagnostics: |
| 290 |
|
- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
| 291 |
|
title (to avoid some unexpected truncation); sort out ptracers diags units. |
| 292 |
|
- collect ptracer forcing tendency into local 2-D array (passed as argument |
| 293 |
|
to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
| 294 |
|
|
| 295 |
|
checkpoint65 (2014/07/18) |
| 296 |
|
o pkg/fizhi: |
| 297 |
|
- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
| 298 |
|
affects results at machine truncation level. Update output of experiments |
| 299 |
|
fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). |
| 300 |
|
o pkg/seaice: more clean up |
| 301 |
|
- rename TAF common block tapes to be more consistent and remove |
| 302 |
|
unnecessary duplicates |
| 303 |
|
- add store directives to remove more recomputations, but use smaller |
| 304 |
|
tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. |
| 305 |
|
The idea behind this flag is to reduce the memory footprint when the |
| 306 |
|
adjoint of the LSR is not required. As of now, defining the flag |
| 307 |
|
SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by |
| 308 |
|
a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). |
| 309 |
|
For experiment offline_exf_seaice, this means on a linux box with gfortran |
| 310 |
|
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
| 311 |
|
this experiment): |
| 312 |
|
> size mitgcmuv_ad |
| 313 |
|
text data bss dec hex |
| 314 |
|
5100659 1216 220458952 225560827 d71c8fb |
| 315 |
|
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
| 316 |
|
but only a moderate increase of 36% for global_ocean.cs32x15: |
| 317 |
|
text data bss dec hex |
| 318 |
|
6695027 1648 1014578664 1021275339 3cdf6ccb |
| 319 |
|
6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER) |
| 320 |
|
- note: there are still recomputations in global_ocean.cs32x15 and |
| 321 |
|
offline_exf_seaice and the gradient agreement changes (gets a |
| 322 |
|
little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) |
| 323 |
|
- in general, the AD gradients still are wrong |
| 324 |
|
o OpenAD |
| 325 |
|
- clean up code_oad/ directories somewhat by moving files |
| 326 |
|
dontCompile, dontTransform, keepOriginal to OAD_support/ |
| 327 |
|
o model/src: |
| 328 |
|
- using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F |
| 329 |
|
(not currently tested): add dissipation terms before NLFS rescaling of |
| 330 |
|
tendencies (previously done after). |
| 331 |
|
o pkg/diagnostics: |
| 332 |
|
- write stats-diags in ascii file with more digits (same as in monitor). |
| 333 |
|
o pkg/down_slope: |
| 334 |
|
- drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with |
| 335 |
|
NLFS (not tested), use new recip_hFac value in order to conserve tracer. |
| 336 |
|
o model/src: |
| 337 |
|
- new file "apply_forcing.F" containing all the code previously in |
| 338 |
|
external_forcing.F, but with new argument list: pass, as new argument, |
| 339 |
|
the current level tendency array to update (instead of a direct update |
| 340 |
|
of the common bloc array). Change the corresponding calls. |
| 341 |
|
- add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use |
| 342 |
|
EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility). |
| 343 |
|
o pkg/seaice/seaice_lsr, a little bit of clean up |
| 344 |
|
- rearrange some code blocks, so that now all calculations for |
| 345 |
|
setting up the right-hand-sides done within one single block |
| 346 |
|
(I find that easier to read and understand) |
| 347 |
|
- rearrange freedrift-code to reduce the number of ifdefs |
| 348 |
|
- adjust some indentations and comments |
| 349 |
|
|
| 350 |
|
checkpoint64z (2014/07/10) |
| 351 |
|
o model/src and several pkgs: |
| 352 |
|
- change argument list of all S/R called from external_forcing.F and |
| 353 |
|
called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F) |
| 354 |
|
to pass, as argument, the current level tendency array to update |
| 355 |
|
(instead of a direct update of the common bloc array). |
| 356 |
|
- change also (in the same way) argument list of PTRACERS_APPLY_FORCING; |
| 357 |
|
- rename taueddy_external_forcing.f to taueddy_tendency_apply.F |
| 358 |
|
o pkg/seaice/seaice_lsr.F |
| 359 |
|
- always initialize local arrays in seaice_lsr_tridiagu/v |
| 360 |
|
- add more local tapes to seaice_lsr_tridiagu/v |
| 361 |
|
- move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but |
| 362 |
|
keep it in bi/bj loop; this seems to be essential |
| 363 |
|
- gradients are still wrong but only by 4-7 orders of magnitude |
| 364 |
|
instead of 15 orders of magnitude, lab_sea improves a little |
| 365 |
|
o pkg/seaice |
| 366 |
|
- (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that |
| 367 |
|
generates unnecessary code in seaice_lsr_ad |
| 368 |
|
- add more store directives in seaice_lsr to avoid unnecessary code |
| 369 |
|
in seaice_lsr_ad |
| 370 |
|
- exclude some residual computations in seaice_lsr when |
| 371 |
|
ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code |
| 372 |
|
in seaice_lsr_ad |
| 373 |
|
- add more storing, a new tape (model/src/the_main_loop.F) and |
| 374 |
|
another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey |
| 375 |
|
and klockey should be checked by a specialist) |
| 376 |
|
- modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER ) |
| 377 |
|
and update lab_sea after previous changes in pkg/seaice below |
| 378 |
|
o pkg/autodiff: |
| 379 |
|
- introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and |
| 380 |
|
viscFacInAd : run time parameters allowing for adjoint switches |
| 381 |
|
note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F |
| 382 |
|
o pkg/ecco: |
| 383 |
|
- introduce cost_gencost_boxmean.F that computes a box mean |
| 384 |
|
temperature (for use in adjoint sensitivity studies). |
| 385 |
|
o model/src/set_defaults.F : initialize viscFacAdj to 1. |
| 386 |
|
o pkg/mom_common/mom_calc_visc.F: |
| 387 |
|
- ifdef ALLOW_AUTODIFF then include viscFacAdj factor. |
| 388 |
|
o pkg/seaice/seaice_summary.F: |
| 389 |
|
- statement for SEAICEadjMODE now in autodiff_readparms.F |
| 390 |
|
o pkg/seaice: |
| 391 |
|
- remove some store directives and add new ones in an effort to get |
| 392 |
|
finally rid off the recomputation warnings. This is successful |
| 393 |
|
when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are |
| 394 |
|
defined (i.e. no extensive recomputation warnings left), but there |
| 395 |
|
are still too many recomputations on the solver iteration level |
| 396 |
|
- define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h |
| 397 |
|
- move definition of MPSEUDOTIMESTEPS into TAMC-block in |
| 398 |
|
SEAICE_SIZE.h |
| 399 |
|
- add a store directive in S/R seaice_calc_viscosities |
| 400 |
|
o pkg/seaice (ITD code): |
| 401 |
|
- fix definition of Hlimit for multi-threaded case |
| 402 |
|
- use double precision arithmetic to compute Hlimit: this affects results; |
| 403 |
|
update output of experiment seaice_itd. |
| 404 |
|
o replace content of verification/seaice_itd |
| 405 |
|
- instead of a 1D column use the configuration of offline_exf_seaice |
| 406 |
|
to test the ice thickness distribution code with ridging |
| 407 |
|
- this is a first shot at this experiment |
| 408 |
|
- change of some defaults of ridging parameters SEAICEhStar (from |
| 409 |
|
100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F |
| 410 |
|
and lot of new comments. |
| 411 |
|
|
| 412 |
|
checkpoint64y (2014/06/20) |
| 413 |
|
o pkg/seaice/seaice_reg_ridge.F: |
| 414 |
|
- modify the regularization of very small volumes of ice; only check |
| 415 |
|
total volume HEFF, and do not apply correction to individual ice |
| 416 |
|
classes because that leads to funny patterns in the heat and fw-fluxes |
| 417 |
|
into the ocean. Adjust seaice_itd/results/output.txt |
| 418 |
|
- replace nITD by SEAICE_multDim in loop-ranges |
| 419 |
|
o pkg/exf: |
| 420 |
|
- add code to process the case field period = -12. with UV interpolation. |
| 421 |
|
- move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec |
| 422 |
|
into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F) |
| 423 |
|
o verification/global_with_exf: |
| 424 |
|
- switch all fields period to -12. (was previously untested) in input/data.exf |
| 425 |
|
(but keep secondary test ".yearly" unchanged); update the reference output. |
| 426 |
|
o pkg/cal: |
| 427 |
|
- new calendar type "noLeapYear" for 365 days calendar without any leap year. |
| 428 |
|
o pkg/exf: |
| 429 |
|
- new integer parameter "exf_debugLev" (default set to main model debugLevel) |
| 430 |
|
to replace logical switch "exf_verbose" |
| 431 |
|
- report in STDOUT when loading a new record (if exf_debugLev >= 3) |
| 432 |
|
o pkg/sbo: |
| 433 |
|
- update from Katherine Quinn: evaluate mass directly from density and SSH |
| 434 |
|
(budget using Finite Volume method) instead of from bottom pressure. |
| 435 |
|
- allow testreport to collect few selected SBO output ; tested in exp. |
| 436 |
|
global_ocean.90x40x15 (after updating the results, to include SBO output). |
| 437 |
|
- fix some multi-threading issues (in output part). |
| 438 |
|
o model/src & most packages: |
| 439 |
|
- always call {PKG}_READPARMS even if corresponding use{PKG}=F; |
| 440 |
|
- in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R |
| 441 |
|
PACKAGES_UNUSED_MSG to print a weak warning when parameter file |
| 442 |
|
"data.{pkg}" exist ; and leave the S/R (return) just after. |
| 443 |
|
- more standard LAND pkg interface (land_init_fixed.F, land_check.F). |
| 444 |
|
+ call LAND_READPARMS from packages_readparms.F |
| 445 |
|
o pkg/seaice: |
| 446 |
|
- remove code that resets useThSice in S/R seaice_readparms and |
| 447 |
|
replace it by a warning in S/R seaice_check |
| 448 |
|
- remove parameter MULTDIM, replace with nITD and runtime |
| 449 |
|
parameter SEAICE_multDim (still hard-wired to nITD if |
| 450 |
|
SEAICE_ITD is defined) |
| 451 |
|
|
| 452 |
|
checkpoint64x (2014/05/24) |
| 453 |
|
o verification/lab_sea: |
| 454 |
|
- update adjoint and TLM output following changes to pkg/salt_plume |
| 455 |
|
- un-do the update after putting back local recip_Cp in few places. |
| 456 |
|
o pkg/salt_plume: modifications by An Nguyen: |
| 457 |
|
- add capability to do brine rejection (salt-plume) as function of |
| 458 |
|
volume+tracers (instead of only salinity tracer). |
| 459 |
|
- conserve volume by exchanging volume from each kLev to above to |
| 460 |
|
accommodate in-coming brine volume |
| 461 |
|
- store surface and klev exchanged fraction + volume in 4 new 3-d arrays |
| 462 |
|
- switch KPP surf buoyancy due to brine forcing to 3-d |
| 463 |
|
(3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume) |
| 464 |
|
- add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t |
| 465 |
|
- unrelatedly, also add ad-hoc capability to vary salt_plume scheme |
| 466 |
|
in East/West Arctic. |
| 467 |
|
o pkg/sbo: |
| 468 |
|
- incorporate modifications from Katherine Quinn to enable the use of sbo |
| 469 |
|
pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like |
| 470 |
|
output for future testreport verification (unfinished). |
| 471 |
|
o pkg/atm_phys: |
| 472 |
|
- change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R: |
| 473 |
|
skip the reseting of t_ref & q_ref to initial t & q ; this preserve the |
| 474 |
|
output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics. |
| 475 |
|
o pkg/seaice |
| 476 |
|
seaice_calc_ice_strength.F: modify expression to avoid divisions |
| 477 |
|
(affects truncation) |
| 478 |
|
seaice_do_ridging.F: clean up the insectarium |
| 479 |
|
- fix a bug that was compensated by areaScaling (-> remove areaScaling code) |
| 480 |
|
- added SEAICEsnowFracRidge to redistributed snow (2nd bug) |
| 481 |
|
- set closing/openingRate to zero where no extra iteration is need (3rd bug) |
| 482 |
|
- add some debugging information and error messages (warnings) |
| 483 |
|
o model/src: modifications relatd to atmosphere p*: |
| 484 |
|
- Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F) |
| 485 |
|
- With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead |
| 486 |
|
of vertical profile tRef in geopotential background and anomaly. |
| 487 |
|
- Acount for true p* correction in theta <-> T conversion in pkg/aim_v23 |
| 488 |
|
and pkg/atm_phys. |
| 489 |
|
- Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40, |
| 490 |
|
fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn. |
| 491 |
|
o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt |
| 492 |
|
o pkg/ptracers: compute ptracer source/sink due to linear free surface. |
| 493 |
|
not used right now, but can be used in BGC packages to fix conservation. |
| 494 |
|
o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by |
| 495 |
|
other packages too. |
| 496 |
|
o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by |
| 497 |
|
SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix) |
| 498 |
|
o model/src: |
| 499 |
|
- since we have several heat capacity (even in model/src), define "recip_Cp" |
| 500 |
|
as local variable (no longer in common block) to avoid any confusion. |
| 501 |
|
- add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords). |
| 502 |
|
o pkg/exf: |
| 503 |
|
- from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local |
| 504 |
|
air density as function of air Temp, Humidity and atm pressure. |
| 505 |
|
|
| 506 |
|
checkpoint64w (2014/05/02) |
| 507 |
|
o verification: |
| 508 |
|
- update output_adm.txt files for experiment global_ocean.cs32x15 (seaice & |
| 509 |
|
seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing |
| 510 |
|
code from seaice_growth.F & seaice_advdiff.F to new ridging routines |
| 511 |
|
seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient |
| 512 |
|
(down to 8-7 matching digits for global_ocean and 5-6 for lab_sea). |
| 513 |
|
o model/src: for atmosphere in p* coords: |
| 514 |
|
- store factor rStarFacC**atm_kappa (= pStarFacK) in common block |
| 515 |
|
- implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F), |
| 516 |
|
but not yet activated. |
| 517 |
|
o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation: |
| 518 |
|
- move computation of opnWtrFrac = 1-AREA to before computing ice strength |
| 519 |
|
- this changes the results (but not for any verification experiment, because |
| 520 |
|
none tests this), but avoids having an extra field in the restart files |
| 521 |
|
o pkg/seaice: remove global variable TICE (not needed) |
| 522 |
|
- replace by TICES or local variable where necessary (cost_seaice_test, |
| 523 |
|
seaice_diagnostics_state) |
| 524 |
|
- move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup |
| 525 |
|
- use specific read/write routines for reading and writing individual leves |
| 526 |
|
of a multilevel field |
| 527 |
|
o pkg/ctrl & model/inc: |
| 528 |
|
- move additional anomaly fields of control vars (related to options: |
| 529 |
|
ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL) |
| 530 |
|
from DYNVARS.h into new header file: CTRL_FIELDS.h |
| 531 |
|
o pkg/seaice: some small modifications to the ridging code |
| 532 |
|
- make fw2ObyRidge a global variable and add the freshwater flux to |
| 533 |
|
seaice_growth |
| 534 |
|
- pass actual thickness from seaice_prepare_ridging, so that it is |
| 535 |
|
computed only in one place and compute it in the same way as in |
| 536 |
|
seaice_growth |
| 537 |
|
- initialise more fields in seaice_do_ridging that where cause floating |
| 538 |
|
point exceptions over land |
| 539 |
o pkg/seaice: preparations for ridging code and first real ridging code |
o pkg/seaice: preparations for ridging code and first real ridging code |
| 540 |
- move most of "PART 1" of S/R seaice_growth into a new and separate |
- move most of "PART 1" of S/R seaice_growth into a new and separate |
| 541 |
S/R seaice_reg_ridge that will both regularize the state variable after |
S/R seaice_reg_ridge that will both regularize the state variable after |
| 542 |
advection call the actual ridging routine; |
advection call the actual ridging routine; |
| 543 |
- requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG, |
- requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG, |
| 544 |
d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust; |
d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust; |
| 545 |
- remove ridging code from seaice_advdiff |
- remove ridging code from seaice_advdiff |
| 546 |
- clean up remaining part 1 of seaice_growth in an attempt to make it |
- clean up remaining part 1 of seaice_growth in an attempt to make it |
| 547 |
more readable (this is probably subjective) |
more readable (this is probably subjective) |
| 548 |
- call seaice_itd_redist once in the initialisation phase to have the initial |
- call seaice_itd_redist once in the initialisation phase to have the initial |
| 549 |
conditions in the correct category |
conditions in the correct category |
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