4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
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|
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o pkg/seaice: |
o pkg/ecco: internal re-organization |
8 |
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- resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl |
9 |
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(rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter, |
10 |
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mv relevant variables definition from ecco_cost.h to ecco.h, |
11 |
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make sure gencost routines only include ecco.h) |
12 |
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- throughout : add missing CCP switches, rm unused variables, |
13 |
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and rm un-necessary CPP switches |
14 |
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- throughout gencost routines : replace modelstartdate with |
15 |
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gencost_startdate when needed |
16 |
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- cost_bp_read.F : use arguments, instead of common blocs |
17 |
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so that it can be used also by (new) cost_gencost_bpv4.F |
18 |
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- ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0 |
19 |
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- ecco_phys.F : compute etanFull |
20 |
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- ecco_readparms.F : rename using_topex as using_tpj, add |
21 |
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bpv4-grace to gencost list, initialize added parameters |
22 |
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- ecco_summary.F : include SIZE.h needed for augmented ecco.h |
23 |
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|
24 |
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checkpoint65e (2014/09/28) |
25 |
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o pkg/obcs: |
26 |
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- replaced the just-added CPP options with run-time variables |
27 |
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(see pkg/obcs/OBCS_PARAMS.h for details) |
28 |
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o pkg/obcs: |
29 |
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- add additional CPP options for sponge boundary layers |
30 |
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(see pkg/obcs/OBCS_OPTIONS.h for details) |
31 |
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o pkg/atm_phys: |
32 |
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- implement simple (obliquity only, assuming circular planet orbit) |
33 |
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seasonal cycle for incoming insolation ; used when run-time parameter |
34 |
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"select_incSW" is set to 1 ; by default (=0), uses old unchanged formula. |
35 |
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o pkg/exf, pkg/ecco, pkg/ctrl: |
36 |
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- add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets |
37 |
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- activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip |
38 |
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- implement gentim2d for xx_tauu, xx_tauv |
39 |
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o pkg/ctrl, pkg/ecco : |
40 |
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- fix and complement the generic controls implementation |
41 |
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o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F, |
42 |
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pkg/shelfice/shelfice_thermodynamics.F, |
43 |
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verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F, |
44 |
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verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F : |
45 |
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- add weight in CTRL_GET_GEN calls |
46 |
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o pkg/ctrl : |
47 |
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- ctrl_get_gen.F : add weight as input parameter, and apply |
48 |
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it directly rather than using smooth_correl2Dw (to be retired). |
49 |
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- ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call |
50 |
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o pkg/ctrl : |
51 |
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- introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, |
52 |
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ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) |
53 |
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- re-activate ctrl_summary (call in ctrl_init.F) |
54 |
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o pkg/ctrl/ctrl_cost_gen.F : |
55 |
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- fix CCP brackets, remove un-necessary myiter, mytime |
56 |
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o pkg/ecco, pkg/ctrl : |
57 |
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- remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) |
58 |
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- remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) |
59 |
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- add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) |
60 |
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- add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) |
61 |
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|
62 |
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checkpoint65d (2014/09/15) |
63 |
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o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : |
64 |
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- add xx_genarr2d_bounds,xx_genarr3d_bounds, |
65 |
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xx_genarr2d_numsmooth, xx_genarr3d_numsmooth |
66 |
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o pkg/ctrl/ctrl_map_ini_genarr.F : |
67 |
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- remove compilation failure |
68 |
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- replace hard coded example |
69 |
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- use ctrl_map_ini_gen2D, 3D |
70 |
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o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : |
71 |
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- on/off switch based upon xx_genarr2d_weight,3d |
72 |
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o src/packages_init_variables.F : |
73 |
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- regroup pkg/estimation calls |
74 |
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- remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
75 |
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(moved to ctrl_init_variables) |
76 |
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o cost/cost_init_varia.F : |
77 |
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- remove ecco_cost_init_varia |
78 |
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(moved to ecco_init_varia) |
79 |
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o ctrl/ctrl_init_variables.F : |
80 |
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- add CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
81 |
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- add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI |
82 |
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o ctrl/ctrl_map_ini.F : |
83 |
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- remove ctrl_map_ini_genarr, seaice_ctrl_map_ini |
84 |
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(moved to ctrl_init_variables) |
85 |
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o ctrl/ctrl_map_ini_ecco.F : |
86 |
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- remove ECCO_PHYS (mv to ecco_init_varia) |
87 |
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- remove seaice_ctrl_map_ini (mv to ctrl_init_variables) |
88 |
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o ecco/ecco_ad_diff.list : |
89 |
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- add ecco_init_varia.f |
90 |
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o ecco/ecco_init_varia.F |
91 |
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- new routine |
92 |
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o pkg/streamice: |
93 |
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- move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F |
94 |
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to streamice_init_fixed.F ; fix setting of STREAMICEisOn. |
95 |
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- from model/src, only call pkg/streamice routines if useStreamIce is TRUE. |
96 |
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o pkg/generic_advdiff: |
97 |
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- fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. |
98 |
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o pkg/exf: |
99 |
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- exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, |
100 |
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xxg_precip capability |
101 |
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- exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch |
102 |
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o pkg/ctrl: |
103 |
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- ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d |
104 |
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o model/src/load_fields_driver.F : |
105 |
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- move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING |
106 |
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so xx_gentim2d can be applied to e.g. exf fields in a timely manner. |
107 |
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o OpenAD verification experiments: |
108 |
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- Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h |
109 |
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in src files (to enable to skip the ECCO_CPPOPTIONS.h); |
110 |
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for now, only in pkgs used in OpenAD verification experiments. |
111 |
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- Change all except one (halfpipe_streamice) OpenAD experiments to use pkg |
112 |
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specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) |
113 |
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instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). |
114 |
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This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. |
115 |
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o OpenAD verification tests: |
116 |
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- finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); |
117 |
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- finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for |
118 |
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tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. |
119 |
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- leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) |
120 |
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and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). |
121 |
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o model/src & generic_advdiff: |
122 |
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- change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S |
123 |
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forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model |
124 |
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dynamics requires valid tracer forcing only over tile interior but, for |
125 |
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some diagnostics, may need to extend it over 1 point in tile halo region. |
126 |
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- in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid |
127 |
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tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max |
128 |
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setting in temp/salt/ptracer_integrate.F |
129 |
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o pkg/dic: |
130 |
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- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
131 |
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gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
132 |
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in gchem_forcing_sep.F |
133 |
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o pkg/autodiff & obcs: |
134 |
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- add storage of current OB values for U & V (was already done for T & S). |
135 |
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|
136 |
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checkpoint65c (2014/08/30) |
137 |
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o pkg/dic: |
138 |
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- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
139 |
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and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
140 |
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AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
141 |
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o verification: |
142 |
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- new experiment testing OBCS and DIC pkgs, using params & output from |
143 |
|
tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
144 |
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passage: take OBCS from the last year of a 2 yrs simulation and initial |
145 |
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conditions from t=1.yr while keeping the same forcing. |
146 |
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o model/src: |
147 |
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- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
148 |
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(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
149 |
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o pkg/diagnostics (Stats-Diags): |
150 |
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- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
151 |
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a) refine region where stats are computed, excluding where arrhFac=0 ; |
152 |
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b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
153 |
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c) extend regional stats over the region edges (for U or V pt location). |
154 |
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o pkg/gchem: |
155 |
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- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
156 |
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pkg/dic is currently changing/updating ptracers values beyond the OB). |
157 |
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o verification (hs94): |
158 |
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- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
159 |
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bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
160 |
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hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
161 |
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apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
162 |
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o pkg/ptracers: |
163 |
|
- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
164 |
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switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
165 |
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- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
166 |
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with AB-2 code (so that it get tested). |
167 |
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o model/src: |
168 |
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- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
169 |
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with AB-2 code (previously only available with AB-3 code). |
170 |
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Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
171 |
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to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
172 |
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there, by calling CYCLE_AB_TRACER). |
173 |
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o pkg/generic_advdiff: |
174 |
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- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
175 |
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GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
176 |
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+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
177 |
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S/R temp/salt/ptracers_integrate.F |
178 |
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o model/src & pkg/ptracers: |
179 |
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- remove common block variables gT,gS (in DYNVARS.h), except when |
180 |
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USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
181 |
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- remove common block variable gPtr. |
182 |
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o model/src & pkgs: |
183 |
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- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
184 |
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ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
185 |
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IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
186 |
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GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
187 |
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+ change accordingly all calling S/R. |
188 |
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- use local temperature/salinity/ptracer tendency array (without bi,bj) |
189 |
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in S/R temp/salt/ptracers_integrate.F |
190 |
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o pkg/seaice: |
191 |
|
- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
192 |
|
to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
193 |
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- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
194 |
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in seaice_lsr |
195 |
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- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
196 |
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in s/r seaice_lsr_calc_coeffs |
197 |
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o pkg/mdsio: |
198 |
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- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
199 |
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(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
200 |
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too long (e.g., > MAX_LEN_FNAM/2 ) |
201 |
|
|
202 |
|
checkpoint65b (2014/08/12) |
203 |
|
o pkg/matrix: |
204 |
|
- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
205 |
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o model/src: |
206 |
|
- fix initialisation of geothermalFile; compile geothermal-flux code in |
207 |
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natl_box verification experiment. |
208 |
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o model/src & pkg/down_slope: |
209 |
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- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
210 |
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- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
211 |
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field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
212 |
|
results at machine truncation level: update output of experiments |
213 |
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global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
214 |
|
o pkg/diagnostics (Stats-Diags): |
215 |
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- do not cumulate the full volume when DIAGNOSTICS_FILL is |
216 |
|
called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
217 |
|
This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
218 |
|
times (but Min,Max and StD are still wrong). |
219 |
|
o model/src: |
220 |
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- add geothermal flux forcing: read in ini_forcing.F as time-constant |
221 |
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field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
222 |
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o model/src: |
223 |
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- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
224 |
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_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
225 |
|
arrays are already updated while adjustments (filters, conv.adjustment) are |
226 |
|
still applied later, in S/R TRACERS_CORRECTION_STEP. |
227 |
|
o model/src: |
228 |
|
- store in common bloc array "rhoInSitu" the virtual potential temperature |
229 |
|
anomaly that is used to compute geopotential: this make the atmos code |
230 |
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more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
231 |
|
o pkg/seaice/seaice_lsr.F |
232 |
|
- rename integer variable ilcall to ipass (that's what it is called |
233 |
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in the residual diagnostics |
234 |
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- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
235 |
|
default) for improved non-linear convergence of the first few steps |
236 |
|
- adjust a few comments and add new ones to explain some of the store |
237 |
|
directives |
238 |
|
o pkg/generic_advdiff (& ptracers): |
239 |
|
- re-work the code to check for valid advection scheme and for minimum |
240 |
|
size of overlap (now stored in local common bloc in gad_advscheme.F) |
241 |
|
o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
242 |
|
- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
243 |
|
- add an auxilliary variable "bet" and fix store directives and keys in |
244 |
|
seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
245 |
|
less exact gradients in my tests); but there are still |
246 |
|
recomputation warning (although gradients are sort of OK), when |
247 |
|
SEAICE_LSR_VECTORIZE is not defined, so this flag and |
248 |
|
SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
249 |
|
- update verification experiments lab_sea. |
250 |
|
- change some comments in S/R seaice_calc_viscosities |
251 |
|
o model/src: |
252 |
|
- if staggerTimeStep=T, always apply exchange to velocity field in |
253 |
|
do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
254 |
|
(independent of using multi-dim advection or not); no effect on FWD run |
255 |
|
but affects AD results (at machine truncation level): update output of |
256 |
|
experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
257 |
|
and isomip (oad: 12.d). |
258 |
|
o pkg/generic_advdiff: |
259 |
|
- stop if doAB_onGtGs is set to FALSE but ignored |
260 |
|
- refine warning related to stability of tracer time-stepping |
261 |
|
regarding internal wave dynamics. |
262 |
|
- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
263 |
|
on staggerTimeStep & implicitIntGravWave (will now get a warning |
264 |
|
if potentially unstable). |
265 |
|
o pkg/kl10: |
266 |
|
- add new pkg "kl10" for mixing due to internal wave breaking, from |
267 |
|
http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
268 |
|
(contribution from Jody Klymak), tested in verification experiment |
269 |
|
verification/internal_wave/input.kl10/ |
270 |
|
o isomip experiment: |
271 |
|
- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
272 |
|
(input.htd) and update the output. |
273 |
|
o cd_code experiments: |
274 |
|
- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
275 |
|
#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
276 |
|
global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
277 |
|
update the corresponding output. |
278 |
|
o pkg/seaice: |
279 |
- reduce the number of include files and store directives in |
- reduce the number of include files and store directives in |
280 |
S/R seaice_lsr_tridiagu/v |
S/R seaice_lsr_tridiagu/v |
281 |
- change the order of loops in one case in S/R seaice_lsr_tridiagv |
- change the order of loops in one case in S/R seaice_lsr_tridiagv |
282 |
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
283 |
get rid off one store directive (a TAF bug?) |
get rid off one store directive (a TAF bug?) |
284 |
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
285 |
S/R seaice_lsr_tridiagv to change the loop range for consistency |
S/R seaice_lsr_tridiagv to change the loop range for consistency |
286 |
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
287 |
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
288 |
S/R seaice_lsr_tridiagu/v (requires update of |
S/R seaice_lsr_tridiagu/v (requires update of |
289 |
offline_exf_seaice/input.dyn_jfnk) |
offline_exf_seaice/input.dyn_jfnk) |
290 |
|
|
291 |
checkpoint65a (2014/07/27) |
checkpoint65a (2014/07/27) |
292 |
o model/src: |
o model/src: |
302 |
- 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 |
303 |
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. |
304 |
affects results at machine truncation level (e.g., ocean: if using |
affects results at machine truncation level (e.g., ocean: if using |
305 |
SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0) |
SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
306 |
moist correction due to vertical advection). |
correction due to vertical advection). |
307 |
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
308 |
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
309 |
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |