4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
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7 |
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o pkg/atm_phys: |
8 |
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- implement simple (obliquity only, assuming circular planet orbit) |
9 |
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seasonal cycle for incoming insolation ; used when run-time parameter |
10 |
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"select_incSW" is set to 1 ; by default (=0), uses old unchanged formula. |
11 |
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o pkg/exf/exf_getffields.F : |
12 |
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add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets |
13 |
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and activate gentim2d for xx_atemp, xx_aqh, xx_swdown, xx_lwdown, xx_precip |
14 |
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o pkg/exf/exf_getsurfacefluxes.F : |
15 |
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implement gentim2d for xx_tauu, xx_tauv |
16 |
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and add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets. |
17 |
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o pkg/ecco/cost_forcing.F, cost_hyd.F, cost_internal_params.F : |
18 |
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add .NOT.ctrlUseGen exclusive brackets -- ctrl_cost_driver |
19 |
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is used instead when ctrlUseGen is .TRUE. |
20 |
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o pkg/ecco/ecco_cost_final.F : print f_genarr3d to stdout |
21 |
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o pkg/ctrl/ctrl_cost_driver.F : add ctrl_cost_gen3d loop |
22 |
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o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F, |
23 |
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pkg/shelfice/shelfice_thermodynamics.F, |
24 |
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verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F, |
25 |
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verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F : |
26 |
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- add weight in CTRL_GET_GEN calls |
27 |
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o pkg/ctrl : |
28 |
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- ctrl_get_gen.F : add weight as input parameter, and apply |
29 |
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it directly rather than using smooth_correl2Dw (to be retired). |
30 |
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- ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call |
31 |
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o pkg/ctrl : |
32 |
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- CTRL_GENARR.h : add xx_gentim2d_numsmooth |
33 |
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- ctrl_cost_driver.F : bug fix (iarr, not 1) |
34 |
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- ctrl_init.F : bug fix (missing iarr) |
35 |
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- ctrl_readparms.F : add xx_gentim2d_numsmooth, improve numsmooth defaults |
36 |
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- ctrl_summary.F : improved report of controls settings |
37 |
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o pkg/ecco/ecco_cost_final.F : add genarr2d, genarr3d cost contributions |
38 |
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o pkg/ctrl : |
39 |
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- introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, |
40 |
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ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) |
41 |
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- re-activate ctrl_summary (call in ctrl_init.F) |
42 |
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o pkg/ctrl/ctrl_cost_gen.F : |
43 |
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- rename ctrl_cost_gen2d input parameters {wmean_gen,wgen,genmask} |
44 |
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as {xx_gen_wmean,xx_gen_weight,xx_gen_mask} |
45 |
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- add ctrl_cost_gen3d for ARR3D (ctrl_cost_gen2d is for ARR2D,TIM2D) |
46 |
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o pkg/ctrl/CTRL_GENARR.h : |
47 |
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- add objf_genarr2d, num_genarr2d, mult_genarr2d |
48 |
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- add objf_genarr3d, num_genarr3d, mult_genarr3d |
49 |
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- add wgenarr2d, wgenarr3d |
50 |
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o pkg/ctrl/ctrl_readparms.F : |
51 |
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- add mult_genarr2d,mult_genarr3d in namelist |
52 |
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o pkg/ctrl_map_ini_genarr.F : |
53 |
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- bug fixes |
54 |
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o pkg/ctrl/ctrl_cost_driver.F : |
55 |
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- remove un-necessary cal.h, fix CCP brackets, remove un-necessary |
56 |
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myiter, mytime, add return |
57 |
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o pkg/ctrl/ctrl_cost_gen.F : |
58 |
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- fix CCP brackets, remove un-necessary myiter, mytime |
59 |
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o pkg/ecco : |
60 |
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- remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) |
61 |
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- remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) |
62 |
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- update cost_forcing_gen calls in cost_forcing.F |
63 |
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- update cost_genctrl call in ecco_cost_driver.F |
64 |
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- update ecco_ad_diff.list accordingly |
65 |
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o pkg/ctrl : |
66 |
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- add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) |
67 |
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- add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) |
68 |
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- update ctrl_ad_diff.list accordingly |
69 |
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|
70 |
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checkpoint65d (2014/09/15) |
71 |
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o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : |
72 |
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- add xx_genarr2d_bounds,xx_genarr3d_bounds, |
73 |
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xx_genarr2d_numsmooth, xx_genarr3d_numsmooth |
74 |
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o pkg/ctrl/ctrl_map_ini_genarr.F : |
75 |
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- remove compilation failure |
76 |
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- replace hard coded example |
77 |
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- use ctrl_map_ini_gen2D, 3D |
78 |
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o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : |
79 |
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- on/off switch based upon xx_genarr2d_weight,3d |
80 |
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o src/packages_init_variables.F : |
81 |
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- regroup pkg/estimation calls |
82 |
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- remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
83 |
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(moved to ctrl_init_variables) |
84 |
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o cost/cost_init_varia.F : |
85 |
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- remove ecco_cost_init_varia |
86 |
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(moved to ecco_init_varia) |
87 |
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o ctrl/ctrl_init_variables.F : |
88 |
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- add CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
89 |
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- add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI |
90 |
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o ctrl/ctrl_map_ini.F : |
91 |
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- remove ctrl_map_ini_genarr, seaice_ctrl_map_ini |
92 |
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(moved to ctrl_init_variables) |
93 |
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o ctrl/ctrl_map_ini_ecco.F : |
94 |
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- remove ECCO_PHYS (mv to ecco_init_varia) |
95 |
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- remove seaice_ctrl_map_ini (mv to ctrl_init_variables) |
96 |
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o ecco/ecco_ad_diff.list : |
97 |
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- add ecco_init_varia.f |
98 |
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o ecco/ecco_init_varia.F |
99 |
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- new routine |
100 |
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o pkg/streamice: |
101 |
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- move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F |
102 |
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to streamice_init_fixed.F ; fix setting of STREAMICEisOn. |
103 |
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- from model/src, only call pkg/streamice routines if useStreamIce is TRUE. |
104 |
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o pkg/generic_advdiff: |
105 |
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- fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. |
106 |
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o pkg/exf: |
107 |
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- exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, |
108 |
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xxg_precip capability |
109 |
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- exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch |
110 |
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o pkg/ctrl: |
111 |
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- ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d |
112 |
|
o model/src/load_fields_driver.F : |
113 |
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- move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING |
114 |
|
so xx_gentim2d can be applied to e.g. exf fields in a timely manner. |
115 |
|
o OpenAD verification experiments: |
116 |
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- Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h |
117 |
|
in src files (to enable to skip the ECCO_CPPOPTIONS.h); |
118 |
|
for now, only in pkgs used in OpenAD verification experiments. |
119 |
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- Change all except one (halfpipe_streamice) OpenAD experiments to use pkg |
120 |
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specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) |
121 |
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instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). |
122 |
|
This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. |
123 |
|
o OpenAD verification tests: |
124 |
|
- finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); |
125 |
|
- finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for |
126 |
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tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. |
127 |
|
- leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) |
128 |
|
and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). |
129 |
|
o model/src & generic_advdiff: |
130 |
|
- change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S |
131 |
|
forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model |
132 |
|
dynamics requires valid tracer forcing only over tile interior but, for |
133 |
|
some diagnostics, may need to extend it over 1 point in tile halo region. |
134 |
|
- in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid |
135 |
|
tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max |
136 |
|
setting in temp/salt/ptracer_integrate.F |
137 |
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o pkg/dic: |
138 |
|
- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
139 |
|
gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
140 |
|
in gchem_forcing_sep.F |
141 |
|
o pkg/autodiff & obcs: |
142 |
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- add storage of current OB values for U & V (was already done for T & S). |
143 |
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|
144 |
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checkpoint65c (2014/08/30) |
145 |
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o pkg/dic: |
146 |
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- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
147 |
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and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
148 |
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AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
149 |
|
o verification: |
150 |
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- new experiment testing OBCS and DIC pkgs, using params & output from |
151 |
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tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
152 |
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passage: take OBCS from the last year of a 2 yrs simulation and initial |
153 |
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conditions from t=1.yr while keeping the same forcing. |
154 |
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o model/src: |
155 |
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- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
156 |
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(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
157 |
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o pkg/diagnostics (Stats-Diags): |
158 |
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- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
159 |
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a) refine region where stats are computed, excluding where arrhFac=0 ; |
160 |
|
b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
161 |
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c) extend regional stats over the region edges (for U or V pt location). |
162 |
|
o pkg/gchem: |
163 |
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- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
164 |
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pkg/dic is currently changing/updating ptracers values beyond the OB). |
165 |
|
o verification (hs94): |
166 |
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- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
167 |
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bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
168 |
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hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
169 |
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apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
170 |
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o pkg/ptracers: |
171 |
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- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
172 |
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switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
173 |
|
- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
174 |
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with AB-2 code (so that it get tested). |
175 |
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o model/src: |
176 |
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- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
177 |
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with AB-2 code (previously only available with AB-3 code). |
178 |
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Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
179 |
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to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
180 |
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there, by calling CYCLE_AB_TRACER). |
181 |
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o pkg/generic_advdiff: |
182 |
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- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
183 |
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GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
184 |
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+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
185 |
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S/R temp/salt/ptracers_integrate.F |
186 |
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o model/src & pkg/ptracers: |
187 |
|
- remove common block variables gT,gS (in DYNVARS.h), except when |
188 |
|
USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
189 |
|
- remove common block variable gPtr. |
190 |
|
o model/src & pkgs: |
191 |
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- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
192 |
|
ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
193 |
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IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
194 |
|
GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
195 |
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+ change accordingly all calling S/R. |
196 |
|
- use local temperature/salinity/ptracer tendency array (without bi,bj) |
197 |
|
in S/R temp/salt/ptracers_integrate.F |
198 |
|
o pkg/seaice: |
199 |
|
- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
200 |
|
to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
201 |
|
- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
202 |
|
in seaice_lsr |
203 |
|
- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
204 |
|
in s/r seaice_lsr_calc_coeffs |
205 |
|
o pkg/mdsio: |
206 |
|
- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
207 |
|
(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
208 |
|
too long (e.g., > MAX_LEN_FNAM/2 ) |
209 |
|
|
210 |
|
checkpoint65b (2014/08/12) |
211 |
|
o pkg/matrix: |
212 |
|
- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
213 |
|
o model/src: |
214 |
|
- fix initialisation of geothermalFile; compile geothermal-flux code in |
215 |
|
natl_box verification experiment. |
216 |
|
o model/src & pkg/down_slope: |
217 |
|
- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
218 |
|
- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
219 |
|
field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
220 |
|
results at machine truncation level: update output of experiments |
221 |
|
global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
222 |
|
o pkg/diagnostics (Stats-Diags): |
223 |
|
- do not cumulate the full volume when DIAGNOSTICS_FILL is |
224 |
|
called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
225 |
|
This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
226 |
|
times (but Min,Max and StD are still wrong). |
227 |
|
o model/src: |
228 |
|
- add geothermal flux forcing: read in ini_forcing.F as time-constant |
229 |
|
field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
230 |
|
o model/src: |
231 |
|
- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
232 |
|
_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
233 |
|
arrays are already updated while adjustments (filters, conv.adjustment) are |
234 |
|
still applied later, in S/R TRACERS_CORRECTION_STEP. |
235 |
|
o model/src: |
236 |
|
- store in common bloc array "rhoInSitu" the virtual potential temperature |
237 |
|
anomaly that is used to compute geopotential: this make the atmos code |
238 |
|
more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
239 |
|
o pkg/seaice/seaice_lsr.F |
240 |
|
- rename integer variable ilcall to ipass (that's what it is called |
241 |
|
in the residual diagnostics |
242 |
|
- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
243 |
|
default) for improved non-linear convergence of the first few steps |
244 |
|
- adjust a few comments and add new ones to explain some of the store |
245 |
|
directives |
246 |
|
o pkg/generic_advdiff (& ptracers): |
247 |
|
- re-work the code to check for valid advection scheme and for minimum |
248 |
|
size of overlap (now stored in local common bloc in gad_advscheme.F) |
249 |
|
o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
250 |
|
- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
251 |
|
- add an auxilliary variable "bet" and fix store directives and keys in |
252 |
|
seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
253 |
|
less exact gradients in my tests); but there are still |
254 |
|
recomputation warning (although gradients are sort of OK), when |
255 |
|
SEAICE_LSR_VECTORIZE is not defined, so this flag and |
256 |
|
SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
257 |
|
- update verification experiments lab_sea. |
258 |
|
- change some comments in S/R seaice_calc_viscosities |
259 |
|
o model/src: |
260 |
|
- if staggerTimeStep=T, always apply exchange to velocity field in |
261 |
|
do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
262 |
|
(independent of using multi-dim advection or not); no effect on FWD run |
263 |
|
but affects AD results (at machine truncation level): update output of |
264 |
|
experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
265 |
|
and isomip (oad: 12.d). |
266 |
|
o pkg/generic_advdiff: |
267 |
|
- stop if doAB_onGtGs is set to FALSE but ignored |
268 |
|
- refine warning related to stability of tracer time-stepping |
269 |
|
regarding internal wave dynamics. |
270 |
|
- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
271 |
|
on staggerTimeStep & implicitIntGravWave (will now get a warning |
272 |
|
if potentially unstable). |
273 |
|
o pkg/kl10: |
274 |
|
- add new pkg "kl10" for mixing due to internal wave breaking, from |
275 |
|
http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
276 |
|
(contribution from Jody Klymak), tested in verification experiment |
277 |
|
verification/internal_wave/input.kl10/ |
278 |
|
o isomip experiment: |
279 |
|
- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
280 |
|
(input.htd) and update the output. |
281 |
|
o cd_code experiments: |
282 |
|
- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
283 |
|
#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
284 |
|
global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
285 |
|
update the corresponding output. |
286 |
|
o pkg/seaice: |
287 |
|
- reduce the number of include files and store directives in |
288 |
|
S/R seaice_lsr_tridiagu/v |
289 |
|
- change the order of loops in one case in S/R seaice_lsr_tridiagv |
290 |
|
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
291 |
|
get rid off one store directive (a TAF bug?) |
292 |
|
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
293 |
|
S/R seaice_lsr_tridiagv to change the loop range for consistency |
294 |
|
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
295 |
|
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
296 |
|
S/R seaice_lsr_tridiagu/v (requires update of |
297 |
|
offline_exf_seaice/input.dyn_jfnk) |
298 |
|
|
299 |
|
checkpoint65a (2014/07/27) |
300 |
|
o model/src: |
301 |
|
- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
302 |
|
surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
303 |
|
(topo in p-coords, ice-shelf in z-coords); update output of experiments |
304 |
|
tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
305 |
|
o model/src: |
306 |
|
- collect momentum forcing tendency into local 2-D array (passed as argument |
307 |
|
to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
308 |
|
parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
309 |
|
affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
310 |
|
- collect T & S forcing tendency into local 2-D array (passed as argument to |
311 |
|
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
312 |
|
affects results at machine truncation level (e.g., ocean: if using |
313 |
|
SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
314 |
|
correction due to vertical advection). |
315 |
|
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
316 |
|
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
317 |
|
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
318 |
|
obcs_ctrl (ad & fwd grd @ 12 & 7). |
319 |
|
o pkg/ptracers & diagnostics: |
320 |
|
- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
321 |
|
title (to avoid some unexpected truncation); sort out ptracers diags units. |
322 |
|
- collect ptracer forcing tendency into local 2-D array (passed as argument |
323 |
|
to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
324 |
|
|
325 |
|
checkpoint65 (2014/07/18) |
326 |
|
o pkg/fizhi: |
327 |
|
- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
328 |
|
affects results at machine truncation level. Update output of experiments |
329 |
|
fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). |
330 |
|
o pkg/seaice: more clean up |
331 |
|
- rename TAF common block tapes to be more consistent and remove |
332 |
|
unnecessary duplicates |
333 |
|
- add store directives to remove more recomputations, but use smaller |
334 |
|
tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. |
335 |
|
The idea behind this flag is to reduce the memory footprint when the |
336 |
|
adjoint of the LSR is not required. As of now, defining the flag |
337 |
|
SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by |
338 |
|
a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). |
339 |
|
For experiment offline_exf_seaice, this means on a linux box with gfortran |
340 |
|
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
341 |
|
this experiment): |
342 |
|
> size mitgcmuv_ad |
343 |
|
text data bss dec hex |
344 |
|
5100659 1216 220458952 225560827 d71c8fb |
345 |
|
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
346 |
|
but only a moderate increase of 36% for global_ocean.cs32x15: |
347 |
|
text data bss dec hex |
348 |
|
6695027 1648 1014578664 1021275339 3cdf6ccb |
349 |
|
6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER) |
350 |
|
- note: there are still recomputations in global_ocean.cs32x15 and |
351 |
|
offline_exf_seaice and the gradient agreement changes (gets a |
352 |
|
little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) |
353 |
|
- in general, the AD gradients still are wrong |
354 |
|
o OpenAD |
355 |
|
- clean up code_oad/ directories somewhat by moving files |
356 |
|
dontCompile, dontTransform, keepOriginal to OAD_support/ |
357 |
|
o model/src: |
358 |
|
- using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F |
359 |
|
(not currently tested): add dissipation terms before NLFS rescaling of |
360 |
|
tendencies (previously done after). |
361 |
|
o pkg/diagnostics: |
362 |
|
- write stats-diags in ascii file with more digits (same as in monitor). |
363 |
|
o pkg/down_slope: |
364 |
|
- drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with |
365 |
|
NLFS (not tested), use new recip_hFac value in order to conserve tracer. |
366 |
|
o model/src: |
367 |
|
- new file "apply_forcing.F" containing all the code previously in |
368 |
|
external_forcing.F, but with new argument list: pass, as new argument, |
369 |
|
the current level tendency array to update (instead of a direct update |
370 |
|
of the common bloc array). Change the corresponding calls. |
371 |
|
- add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use |
372 |
|
EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility). |
373 |
|
o pkg/seaice/seaice_lsr, a little bit of clean up |
374 |
|
- rearrange some code blocks, so that now all calculations for |
375 |
|
setting up the right-hand-sides done within one single block |
376 |
|
(I find that easier to read and understand) |
377 |
|
- rearrange freedrift-code to reduce the number of ifdefs |
378 |
|
- adjust some indentations and comments |
379 |
|
|
380 |
|
checkpoint64z (2014/07/10) |
381 |
|
o model/src and several pkgs: |
382 |
|
- change argument list of all S/R called from external_forcing.F and |
383 |
|
called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F) |
384 |
|
to pass, as argument, the current level tendency array to update |
385 |
|
(instead of a direct update of the common bloc array). |
386 |
|
- change also (in the same way) argument list of PTRACERS_APPLY_FORCING; |
387 |
|
- rename taueddy_external_forcing.f to taueddy_tendency_apply.F |
388 |
|
o pkg/seaice/seaice_lsr.F |
389 |
|
- always initialize local arrays in seaice_lsr_tridiagu/v |
390 |
|
- add more local tapes to seaice_lsr_tridiagu/v |
391 |
|
- move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but |
392 |
|
keep it in bi/bj loop; this seems to be essential |
393 |
|
- gradients are still wrong but only by 4-7 orders of magnitude |
394 |
|
instead of 15 orders of magnitude, lab_sea improves a little |
395 |
|
o pkg/seaice |
396 |
|
- (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that |
397 |
|
generates unnecessary code in seaice_lsr_ad |
398 |
|
- add more store directives in seaice_lsr to avoid unnecessary code |
399 |
|
in seaice_lsr_ad |
400 |
|
- exclude some residual computations in seaice_lsr when |
401 |
|
ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code |
402 |
|
in seaice_lsr_ad |
403 |
|
- add more storing, a new tape (model/src/the_main_loop.F) and |
404 |
|
another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey |
405 |
|
and klockey should be checked by a specialist) |
406 |
|
- modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER ) |
407 |
|
and update lab_sea after previous changes in pkg/seaice below |
408 |
|
o pkg/autodiff: |
409 |
|
- introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and |
410 |
|
viscFacInAd : run time parameters allowing for adjoint switches |
411 |
|
note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F |
412 |
|
o pkg/ecco: |
413 |
|
- introduce cost_gencost_boxmean.F that computes a box mean |
414 |
|
temperature (for use in adjoint sensitivity studies). |
415 |
|
o model/src/set_defaults.F : initialize viscFacAdj to 1. |
416 |
|
o pkg/mom_common/mom_calc_visc.F: |
417 |
|
- ifdef ALLOW_AUTODIFF then include viscFacAdj factor. |
418 |
|
o pkg/seaice/seaice_summary.F: |
419 |
|
- statement for SEAICEadjMODE now in autodiff_readparms.F |
420 |
|
o pkg/seaice: |
421 |
|
- remove some store directives and add new ones in an effort to get |
422 |
|
finally rid off the recomputation warnings. This is successful |
423 |
|
when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are |
424 |
|
defined (i.e. no extensive recomputation warnings left), but there |
425 |
|
are still too many recomputations on the solver iteration level |
426 |
|
- define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h |
427 |
|
- move definition of MPSEUDOTIMESTEPS into TAMC-block in |
428 |
|
SEAICE_SIZE.h |
429 |
|
- add a store directive in S/R seaice_calc_viscosities |
430 |
|
o pkg/seaice (ITD code): |
431 |
|
- fix definition of Hlimit for multi-threaded case |
432 |
|
- use double precision arithmetic to compute Hlimit: this affects results; |
433 |
|
update output of experiment seaice_itd. |
434 |
|
o replace content of verification/seaice_itd |
435 |
|
- instead of a 1D column use the configuration of offline_exf_seaice |
436 |
|
to test the ice thickness distribution code with ridging |
437 |
|
- this is a first shot at this experiment |
438 |
|
- change of some defaults of ridging parameters SEAICEhStar (from |
439 |
|
100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F |
440 |
|
and lot of new comments. |
441 |
|
|
442 |
|
checkpoint64y (2014/06/20) |
443 |
|
o pkg/seaice/seaice_reg_ridge.F: |
444 |
|
- modify the regularization of very small volumes of ice; only check |
445 |
|
total volume HEFF, and do not apply correction to individual ice |
446 |
|
classes because that leads to funny patterns in the heat and fw-fluxes |
447 |
|
into the ocean. Adjust seaice_itd/results/output.txt |
448 |
|
- replace nITD by SEAICE_multDim in loop-ranges |
449 |
|
o pkg/exf: |
450 |
|
- add code to process the case field period = -12. with UV interpolation. |
451 |
|
- move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec |
452 |
|
into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F) |
453 |
|
o verification/global_with_exf: |
454 |
|
- switch all fields period to -12. (was previously untested) in input/data.exf |
455 |
|
(but keep secondary test ".yearly" unchanged); update the reference output. |
456 |
|
o pkg/cal: |
457 |
|
- new calendar type "noLeapYear" for 365 days calendar without any leap year. |
458 |
|
o pkg/exf: |
459 |
|
- new integer parameter "exf_debugLev" (default set to main model debugLevel) |
460 |
|
to replace logical switch "exf_verbose" |
461 |
|
- report in STDOUT when loading a new record (if exf_debugLev >= 3) |
462 |
|
o pkg/sbo: |
463 |
|
- update from Katherine Quinn: evaluate mass directly from density and SSH |
464 |
|
(budget using Finite Volume method) instead of from bottom pressure. |
465 |
|
- allow testreport to collect few selected SBO output ; tested in exp. |
466 |
|
global_ocean.90x40x15 (after updating the results, to include SBO output). |
467 |
|
- fix some multi-threading issues (in output part). |
468 |
|
o model/src & most packages: |
469 |
|
- always call {PKG}_READPARMS even if corresponding use{PKG}=F; |
470 |
|
- in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R |
471 |
|
PACKAGES_UNUSED_MSG to print a weak warning when parameter file |
472 |
|
"data.{pkg}" exist ; and leave the S/R (return) just after. |
473 |
|
- more standard LAND pkg interface (land_init_fixed.F, land_check.F). |
474 |
|
+ call LAND_READPARMS from packages_readparms.F |
475 |
|
o pkg/seaice: |
476 |
|
- remove code that resets useThSice in S/R seaice_readparms and |
477 |
|
replace it by a warning in S/R seaice_check |
478 |
|
- remove parameter MULTDIM, replace with nITD and runtime |
479 |
|
parameter SEAICE_multDim (still hard-wired to nITD if |
480 |
|
SEAICE_ITD is defined) |
481 |
|
|
482 |
|
checkpoint64x (2014/05/24) |
483 |
|
o verification/lab_sea: |
484 |
|
- update adjoint and TLM output following changes to pkg/salt_plume |
485 |
|
- un-do the update after putting back local recip_Cp in few places. |
486 |
|
o pkg/salt_plume: modifications by An Nguyen: |
487 |
|
- add capability to do brine rejection (salt-plume) as function of |
488 |
|
volume+tracers (instead of only salinity tracer). |
489 |
|
- conserve volume by exchanging volume from each kLev to above to |
490 |
|
accommodate in-coming brine volume |
491 |
|
- store surface and klev exchanged fraction + volume in 4 new 3-d arrays |
492 |
|
- switch KPP surf buoyancy due to brine forcing to 3-d |
493 |
|
(3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume) |
494 |
|
- add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t |
495 |
|
- unrelatedly, also add ad-hoc capability to vary salt_plume scheme |
496 |
|
in East/West Arctic. |
497 |
|
o pkg/sbo: |
498 |
|
- incorporate modifications from Katherine Quinn to enable the use of sbo |
499 |
|
pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like |
500 |
|
output for future testreport verification (unfinished). |
501 |
|
o pkg/atm_phys: |
502 |
|
- change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R: |
503 |
|
skip the reseting of t_ref & q_ref to initial t & q ; this preserve the |
504 |
|
output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics. |
505 |
|
o pkg/seaice |
506 |
|
seaice_calc_ice_strength.F: modify expression to avoid divisions |
507 |
|
(affects truncation) |
508 |
|
seaice_do_ridging.F: clean up the insectarium |
509 |
|
- fix a bug that was compensated by areaScaling (-> remove areaScaling code) |
510 |
|
- added SEAICEsnowFracRidge to redistributed snow (2nd bug) |
511 |
|
- set closing/openingRate to zero where no extra iteration is need (3rd bug) |
512 |
|
- add some debugging information and error messages (warnings) |
513 |
|
o model/src: modifications relatd to atmosphere p*: |
514 |
|
- Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F) |
515 |
|
- With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead |
516 |
|
of vertical profile tRef in geopotential background and anomaly. |
517 |
|
- Acount for true p* correction in theta <-> T conversion in pkg/aim_v23 |
518 |
|
and pkg/atm_phys. |
519 |
|
- Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40, |
520 |
|
fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn. |
521 |
|
o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt |
522 |
|
o pkg/ptracers: compute ptracer source/sink due to linear free surface. |
523 |
|
not used right now, but can be used in BGC packages to fix conservation. |
524 |
|
o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by |
525 |
|
other packages too. |
526 |
|
o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by |
527 |
|
SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix) |
528 |
|
o model/src: |
529 |
|
- since we have several heat capacity (even in model/src), define "recip_Cp" |
530 |
|
as local variable (no longer in common block) to avoid any confusion. |
531 |
|
- add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords). |
532 |
|
o pkg/exf: |
533 |
|
- from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local |
534 |
|
air density as function of air Temp, Humidity and atm pressure. |
535 |
|
|
536 |
|
checkpoint64w (2014/05/02) |
537 |
|
o verification: |
538 |
|
- update output_adm.txt files for experiment global_ocean.cs32x15 (seaice & |
539 |
|
seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing |
540 |
|
code from seaice_growth.F & seaice_advdiff.F to new ridging routines |
541 |
|
seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient |
542 |
|
(down to 8-7 matching digits for global_ocean and 5-6 for lab_sea). |
543 |
|
o model/src: for atmosphere in p* coords: |
544 |
|
- store factor rStarFacC**atm_kappa (= pStarFacK) in common block |
545 |
|
- implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F), |
546 |
|
but not yet activated. |
547 |
|
o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation: |
548 |
|
- move computation of opnWtrFrac = 1-AREA to before computing ice strength |
549 |
|
- this changes the results (but not for any verification experiment, because |
550 |
|
none tests this), but avoids having an extra field in the restart files |
551 |
|
o pkg/seaice: remove global variable TICE (not needed) |
552 |
|
- replace by TICES or local variable where necessary (cost_seaice_test, |
553 |
|
seaice_diagnostics_state) |
554 |
|
- move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup |
555 |
|
- use specific read/write routines for reading and writing individual leves |
556 |
|
of a multilevel field |
557 |
|
o pkg/ctrl & model/inc: |
558 |
|
- move additional anomaly fields of control vars (related to options: |
559 |
|
ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL) |
560 |
|
from DYNVARS.h into new header file: CTRL_FIELDS.h |
561 |
|
o pkg/seaice: some small modifications to the ridging code |
562 |
|
- make fw2ObyRidge a global variable and add the freshwater flux to |
563 |
|
seaice_growth |
564 |
|
- pass actual thickness from seaice_prepare_ridging, so that it is |
565 |
|
computed only in one place and compute it in the same way as in |
566 |
|
seaice_growth |
567 |
|
- initialise more fields in seaice_do_ridging that where cause floating |
568 |
|
point exceptions over land |
569 |
|
o pkg/seaice: preparations for ridging code and first real ridging code |
570 |
|
- move most of "PART 1" of S/R seaice_growth into a new and separate |
571 |
|
S/R seaice_reg_ridge that will both regularize the state variable after |
572 |
|
advection call the actual ridging routine; |
573 |
|
- requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG, |
574 |
|
d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust; |
575 |
|
- remove ridging code from seaice_advdiff |
576 |
|
- clean up remaining part 1 of seaice_growth in an attempt to make it |
577 |
|
more readable (this is probably subjective) |
578 |
|
- call seaice_itd_redist once in the initialisation phase to have the initial |
579 |
|
conditions in the correct category |
580 |
|
- finally: add new ridging routine for ITD code |
581 |
|
|
582 |
|
checkpoint64v (2014/04/11) |
583 |
|
o pkg/ecco: |
584 |
|
- add runtime parameters mdt[start,end]date[1,2] |
585 |
|
- rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile" |
586 |
|
o pkg/seaice: |
587 |
|
- make deltaC a global variable, so that it can be used in ridging code |
588 |
|
- first step towards ridging: introduce new routines that compute |
589 |
|
ice strength based on ridging parameters |
590 |
|
- add diagnostic for HSNOWITD |
591 |
|
- add opnWtrFrac as a global variable (required for ridging scheme) |
592 |
|
o pkg/salt_plume + pkg/seaice/seaice_growth.F |
593 |
|
- add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice |
594 |
|
AREA exceeds a threshold (code contributed by I.Fenty in 2011) |
595 |
|
o verification/hs94.1x64x5: |
596 |
|
- leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h |
597 |
|
- do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests. |
598 |
|
o autodiff: |
599 |
|
- Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, |
600 |
|
and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h) |
601 |
|
For now, only in pkgs used in verification/hs94.1x64x5. |
602 |
|
- Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage |
603 |
|
which are specific to TAF/TAMC). |
604 |
|
- Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD: |
605 |
|
since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad |
606 |
|
is compiled), this simplifies/reduces which *_OPTIONS.h file to include. |
607 |
|
- OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when |
608 |
|
building mitgcmuv_ad (make adAll). |
609 |
|
o pkg/ecco: |
610 |
|
- cost_gencost_seaicev4.F: |
611 |
|
reformulate proxy cost as function of sst and local param SEAICE_freeze |
612 |
|
change cost names from siv4-[sst,vol] to siv4-[deconc,exconc] |
613 |
|
- add stop statement if old names siv4-[sst,vol] are used |
614 |
|
- add snapshots + cost reports for atmospheric longwave |
615 |
|
- remove factor 0.1 in front of wtau[u,v] |
616 |
|
- replace never used flag ALLOW_TMI_COST_CONTRIBUTION with |
617 |
|
ALLOW_TMI_SST_COST_CONTRIBUTION |
618 |
|
o pkg/atm_phys: |
619 |
|
- add some diagnostics for Short-wave and for convection S/R. |
620 |
|
o pkg/seaice/seaice_growth: |
621 |
|
- fix a bug in the lateral melt parameterization for SEAICE_ITD |
622 |
|
in seaice_growth; tempFrz needs to be computed inside the i/j-loop |
623 |
|
- rearrange loop order for better vector code in the same code block |
624 |
|
- rewrite the floeDiameter formula to have fewer divisions |
625 |
|
- (miraculously) none of this changes the results of seaice_itd |
626 |
|
o pkg/smooth: |
627 |
|
- move param smooth2Ddiffnbt to pkg/ecco |
628 |
|
o pkg/salt_plume: |
629 |
|
- salt_plume_frac.F: |
630 |
|
clean up local param names |
631 |
|
reformulate (1-frac) to frac; original 1-frac was based on swfrac code |
632 |
|
o pkg/rw: |
633 |
|
- add RS version of S/R READ_MFLDS_LEV. |
634 |
|
o pkg/streamice: |
635 |
|
- fix the restart test by writing/reading pickup_streamice files. |
636 |
|
o pkg/seaice: |
637 |
|
- refine checks for jfnk-related parameters |
638 |
|
- comment out if statement with SEAICEuseIMEX parameter as long as there |
639 |
|
is no IMEX code to avoid confusion and surprises |
640 |
|
|
641 |
|
checkpoint64u (2014/03/07) |
642 |
|
o verification/MLAdjust: |
643 |
|
- rename secondary test suffix: |
644 |
|
1.leith -> A4FlxF + switch to flux-form & add side-drag |
645 |
|
0.leithD -> AhFlxF + switch to flux-form |
646 |
|
0.smag -> AhVrDv (use Vorticity-Div. visc form) + add side-drag |
647 |
|
0.leith -> AhStTn (use Strain-Tension visc form) + add side-drag |
648 |
|
o pkg/mom_vecinv: |
649 |
|
- remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used |
650 |
|
to be before mom_calc_visc.F) |
651 |
|
- skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed. |
652 |
|
- add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip): |
653 |
|
this is simpler for the adjoint and for diagnostics. |
654 |
|
o model/src + pkg/momentum: |
655 |
|
- add input files for 2-D additional Western and Southern cell-edge wall |
656 |
|
(e.g., to add "thin-wall" where it is =1). |
657 |
|
- fix sideDrag option for thin-walls with Non-Lin Free-Surf |
658 |
|
using 2nd hFacZ that is computed from initial (fix domain) hFac |
659 |
|
- known limitations of thin wall implementation: not yet coded for sigma |
660 |
|
coords; not working with CD-scheme neither. |
661 |
|
o pkg/seaice: |
662 |
|
- rename recently introduced parameters from (wrong name) AB to |
663 |
|
BDF (backward difference time discretisation) |
664 |
|
- retire runtime parameters SEAICEuseAB2, SEAICE_abEps |
665 |
|
o tools/adjoint_options: |
666 |
|
- remove setting of "OPENAD=true" (now set by command line "genmake2 -oad") |
667 |
|
|
668 |
|
checkpoint64t (2014/02/01) |
669 |
|
o pkg/ecco |
670 |
|
- add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and |
671 |
|
runtime logical flag gencost_timevaryweight to read daily sea-ice sigma |
672 |
|
- replace hard-coded record number and period which only work for monthly |
673 |
|
with read-in runtime param that works for other periods (month,day,year) |
674 |
|
o pkg/thsice |
675 |
|
- corrected store directive fixes thsice adjoint gradient checks |
676 |
|
o genmake2 & testreport: |
677 |
|
- add genmake2 option "-oad" to generate a Makefile for OpenAD built and |
678 |
|
in this case, use tools/adjoint_options/adjoint_oad as default AD optfile. |
679 |
|
Update testreport accordingly. No need to set "export OPENAD=true" |
680 |
|
in adjoint_options/adjoint_oad anymore (will be removed later). |
681 |
|
o pkg/shelfice: |
682 |
|
- put T & S shelfice forcing into model surfaceForcing_T,_S (for now, |
683 |
|
only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F |
684 |
|
so that surface forcing applies to k=kSurf if using pkg/shelfice. |
685 |
|
o pkg/ctrl, pkg/grdchk, pkg/ecco: |
686 |
|
- Changes to make GENARR more modular (i.e. invisible if not used) |
687 |
|
o model/src/temp_integrate.F and salt_integrate.F |
688 |
|
- re-include store directives that were removed on Dec 27th. |
689 |
|
o model/src/external_forcing_surf.F |
690 |
|
- add storage directives for EmPmR and PmEpR to avoid recomputation of |
691 |
|
seaice_model in the adjoint that is problematic when seaice_model is |
692 |
|
turned off in the adjoint. The resolved issue dated back to July when |
693 |
|
EXTERNAL_FORCING_SURF call was moved. |
694 |
|
Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly. |
695 |
|
o pkg/exf/exf_check.F |
696 |
|
- fix a small bug again (originally found by Wentao Liu, now found again) |
697 |
|
- streamline error output |
698 |
|
o pkg/streamice and aim_v23: |
699 |
|
- replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that |
700 |
|
Apple's /usr/bin/cpp knows what to do: |
701 |
|
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) |
702 |
|
Target: x86_64-apple-darwin13.0.0 |
703 |
|
|
704 |
|
checkpoint64s (2014/01/05) |
705 |
|
o tools/adjoint_options: |
706 |
|
- switch to fastopt.net TAF server (instead of default fastopt.de) for |
707 |
|
AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default). |
708 |
|
o model/src: |
709 |
|
- remove some unnecessary TAF storage directives in forward_step.F and |
710 |
|
in dynamics.F (note: not always removed by TAF, e.g., double storage |
711 |
|
of kappaRU,kappaRV in former version of dynamics.F). |
712 |
|
o model/src & pkg/ptracers: |
713 |
|
- call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F |
714 |
|
salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F) |
715 |
|
and remove ptracers_dwnslp_apply.F & ptracers_implicit.F |
716 |
|
- call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F) |
717 |
|
- add fZon & fMer as output argument of S/R GAD_CALC_RHS. |
718 |
|
- update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad). |
719 |
|
o useSingleCpuInput separates single-CPU input from single-CPU output; |
720 |
|
for now only implemented for in exf_interp_read.F |
721 |
|
o verification/advect_xy: |
722 |
|
- fix missing EXCH call in local version of ini_salt.F and update output. |
723 |
|
o momentum diagnostics: |
724 |
|
- fix which deltaT is used in Total-Tendency diagnostics. |
725 |
|
- fix typo in diagnostics for momentum tendency from AB. |
726 |
|
o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the |
727 |
|
SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8 |
728 |
|
|
729 |
|
checkpoint64r (2013/12/08) |
730 |
|
o verification/*/results: |
731 |
|
- Update reference output of experiments that were passing with just 13 digits |
732 |
|
(make it easier to detect future changes in results) |
733 |
|
o model/src & pkg/ptracers: |
734 |
|
- move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to |
735 |
|
inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F |
736 |
|
to inside ptracers_integrate.F ; remove ptracers_advection.F |
737 |
|
o coupling interface pkgs: |
738 |
|
[atm_compon_interf, ocn_compon_interf & atm_ocn_coupler] |
739 |
|
- change the config check to test the agreement of Ocean Depth |
740 |
|
with ATM land/sea mask (instead of ATM orography); |
741 |
|
- send to coupler the number of coupler time-steps to do for this run: |
742 |
|
this allows to check for consistency and don't need anymore to be |
743 |
|
specified in parameter file "data"; |
744 |
|
in coupler: |
745 |
|
- check consistency of RunOff map versus Ocean Depth and ATM land/sea mask. |
746 |
|
- improve report to log-file of config setting (pass log-file unit to few S/R) |
747 |
|
o pkg/compon_communic: |
748 |
|
- add coupling send/receive for non-tiled integer vector; |
749 |
|
- add S/R to check and stop if any proc has an error (similar to |
750 |
|
eesupp/src/stop_if_error.F but single thread and across Comm_World). |
751 |
|
o pkg/exch2: |
752 |
|
- in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search |
753 |
|
through list of all tiles my proc owns. |
754 |
|
o model/src: |
755 |
|
- AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying |
756 |
|
from rTrans) to simplify dependencies (no need to store rTrans anymore in |
757 |
|
calling S/R); this affects AD results at machine truncation level: |
758 |
|
update AD-output (TAF) of experiments: 1D_ocean_ice_column, |
759 |
|
bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad). |
760 |
|
o tools/build_options: |
761 |
|
- simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran |
762 |
|
o coupling interface pkgs: |
763 |
|
[compon_communic, atm_compon_interf & ocn_compon_interf] |
764 |
|
- move declaration of local array "ibuf" out of header file "CPLR_SIG.h" |
765 |
|
to each S/R that needs it; remove un-used variables. |
766 |
|
- change component tile registration (cpl_register.F in both compon_interf |
767 |
|
and mitcomponent_tile_register.F) to pass the full list of tiles |
768 |
|
information (including bi,bj) in 1 vector (instead of in a bi,bj matrix). |
769 |
|
- with pkg/exch2: adopt the same convention used for I/O to define mapping |
770 |
|
towards coupler global array (unless W2_useE2ioLayOut=F): |
771 |
|
a) can now use different tiling between atm & ocn comp. |
772 |
|
b) no needs to modify the run-Off map when changing tiling (was needed |
773 |
|
even if using the same tiling between atm & ocn). |
774 |
|
c) will allow to run with blank-tiles in 1 component (e.g., for ocean |
775 |
|
full land tiles); not yet tested. |
776 |
|
- check for valid mapping from comp. tile to coupler global array |
777 |
|
- improve report of tile registration results to log file. |
778 |
|
o pkg/exch2: |
779 |
|
- in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler |
780 |
|
tile-registration (CPL_REGISTER); |
781 |
|
- activate (un-comment) definition and setting of "W2_tileIndex" list to |
782 |
|
store the local bi,bj indices of each tile; |
783 |
|
- also print bi,bj in local report to log file; |
784 |
|
- fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from |
785 |
|
Jun 2009 modif of pkg/exch2). |
786 |
|
o testing on baudelaire: |
787 |
|
- run 2 tests at a time: no significant slow down (since enough cpu) and |
788 |
|
get the full set of test done earlier |
789 |
|
- switch the ifort test to "-devel" ; run the OpenAD test everyday. |
790 |
|
o model/src/thermodynamics.F and routines called from it: |
791 |
|
- pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F & |
792 |
|
gmredi_calc_wflow.F) to update eulerian velocity (input) into residual |
793 |
|
velocity (outp) by adding bolus velocity. |
794 |
|
- model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute |
795 |
|
mass transport from velocity + lateral grid cell area |
796 |
|
- rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER) |
797 |
|
- rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER) |
798 |
|
in thermodynamics.F |
799 |
|
- remove k from thermodynamics.F and move it to temp_integrate.F |
800 |
|
salt_integrate.F and ptracers_integrate.F (now done inside the tracer |
801 |
|
loop). |
802 |
|
- compute locally (in thermodynamics.F) 3-D velocity field that is used to |
803 |
|
advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT, |
804 |
|
PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE, |
805 |
|
GAD_IMPLICIT_R and PTRACERS_IMPLICIT |
806 |
|
- update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column, |
807 |
|
global_ocean.90x40x15, tutorial_global_oce_biogeo and |
808 |
|
tutorial_tracer_adjsens (+ TLM output). |
809 |
|
o tools/OAD_support and (verification/*/) code_oad: |
810 |
|
- OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to |
811 |
|
module conversion ; remove unneeded CPP_EEOPTIONS.h. |
812 |
|
- code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard |
813 |
|
version (closer to model/inc/CPP_OPTIONS.h). |
814 |
|
o model/src: |
815 |
|
- remove parameter "useOldFreezing" from PARAMS.h and push it to the |
816 |
|
retired list of parameters (routine FREEZE has been replace by surface |
817 |
|
freezing (10.yrs ago) and by pkg/frazil (interior freezing). |
818 |
|
o pkg/gmredi: |
819 |
|
- add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from |
820 |
|
velocity (same scheme but affects machine truncation) for GM_AdvForm. |
821 |
|
- update output of FWD experiments: front_relax.bvp, |
822 |
|
global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce. |
823 |
|
|
824 |
|
checkpoint64q (2013/11/17) |
825 |
|
o verification: |
826 |
|
- generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments |
827 |
|
tutorial_global_oce_biogeo and global_ocean.90x40x15. |
828 |
|
- generate new output (growth & melt) for seaice_itd experiment after |
829 |
|
updating the input pickup_seaice files (previously wrong). |
830 |
|
o pkg/cost: |
831 |
|
- define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL |
832 |
|
(instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads: |
833 |
|
o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL |
834 |
|
cannot be applied to var in common block). |
835 |
|
o allows to get results independent of tile-per-proc setting (if using |
836 |
|
slower GLOBAL_SUM_SEND_RECV option). |
837 |
|
- update accordingly: seaice_cost_final.F, shelfice_cost_final.F, |
838 |
|
thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea |
839 |
|
forward gradients: update output). |
840 |
|
- update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL |
841 |
|
S/R and, for most exp., also comment out GLOBAL_SUM_R8. |
842 |
|
o pkg/mom_common: |
843 |
|
- move to pkg/mom_common and model/src (previously in tutorial_deep_convection |
844 |
|
code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and |
845 |
|
viscosity are locally declared in dynmics.F and pass as argument to CALC_GW; |
846 |
|
ensure that all field value that are used are set. |
847 |
|
o tutorial_deep_convection (smag3d): |
848 |
|
- add missing scaling in mom_calc_smag_3d.F; |
849 |
|
- set smag3D_coeff in input.smag3d such that results do not change. |
850 |
|
o pkg/dic: |
851 |
|
- change dic_cost.F to compute cost on each tile first and then apply |
852 |
|
GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments |
853 |
|
tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output. |
854 |
|
- remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea. |
855 |
|
o eesupp/src & pkg/mdsio: |
856 |
|
- remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F |
857 |
|
(from pkg/mdsio) since they are no longer used for tape IO. |
858 |
|
- move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src |
859 |
|
(+ keep a copy in pkg/atm_ocn_coupler). |
860 |
|
o verification/isomip: |
861 |
|
- split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests. |
862 |
|
o tools/build_options: |
863 |
|
- optfile linux_amd64_ifort11, fast (no ieee) case: |
864 |
|
to get a working restart for all experiments, add "-fp-model source" |
865 |
|
to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default). |
866 |
|
|
867 |
|
checkpoint64p (2013/10/20) |
868 |
|
o pkg/autodiff: |
869 |
|
- adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO |
870 |
|
criteria, return to simple (default) tape IO format. |
871 |
|
o pkg/mdsio (+ eesupp/src): |
872 |
|
- rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace |
873 |
|
previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8); |
874 |
|
- fix globalFile and singleCpuIO options using simpler global mapping. |
875 |
|
- new pairs of scatter/gather vector S/R (one for each type, generated from |
876 |
|
template) corresponding to simpler global mapping. |
877 |
|
- adread_write.F: switch to new S/R (but leave old calls commented) and write |
878 |
|
to globalFile when parameter globalFiles is set to True. |
879 |
|
- switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip. |
880 |
|
o pkg/autodiff: |
881 |
|
- adread_adwrite.F: add a hack for RS arrays (when RS=real*4); |
882 |
|
with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is |
883 |
|
missing, just add a STOP if array type do not match. |
884 |
|
o pkg/exf: |
885 |
|
- to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice: |
886 |
|
rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION |
887 |
|
and rename array obsSIce to exf_iceFraction. |
888 |
|
o tutorial_deep_convection: |
889 |
|
- add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe), |
890 |
|
for now all in this exp. code dir. |
891 |
|
- add secondary test using Smag-3D viscosity (keep very low backgroud visc for |
892 |
|
testing) and flux-limter advection scheme for Temp. (no explicit diffusion). |
893 |
|
o eesupp/src: |
894 |
|
- added SINGLE_DISK_IO option because reading of parameter files on |
895 |
|
very large number of processors did not work with existing set-up |
896 |
|
|
897 |
|
checkpoint64o (2013/09/25) |
898 |
|
o pkg/atm_phys & atm_compon_interf: |
899 |
|
- allows for coupling of gray-atmosphere (atm_phys) with ocean. |
900 |
|
o tools/build_options: |
901 |
|
- switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran |
902 |
|
& linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also |
903 |
|
remove CPP setting (was identical to genmake2 default). |
904 |
|
o pkg/gmredi & model/src: Some updating and work done on the residual model. |
905 |
|
- created new file model/src/calc_eddy_stress.F to calculate the eddy stress. |
906 |
|
- fixed up the calculation of the eddy stress and how it is added to the |
907 |
|
external forcing via taueddy_external_forcing.F |
908 |
|
- at the moment, it is very experimental and only works with the variable eddy |
909 |
|
diffusivity calculated in gmredi_k3d.F |
910 |
|
o pkg/seaice/seaice_check.F: add a check to catch the case of specifying |
911 |
|
lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice |
912 |
|
o testreport (& tools/do_tst_2+2): |
913 |
|
- for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}' |
914 |
|
o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11: |
915 |
|
- remove CPP='cpp -traditional -P' (this is genmake2 default) |
916 |
|
- add switch (for big setups) to use 'medium' memory-model (but leave it |
917 |
|
commented out for now). Note: needed with FC 19 to compile big setups. |
918 |
|
o pkg/atm_compon_interf: |
919 |
|
- regroup per field origin (model & pkgs) the coupling storage routines |
920 |
|
(which accumalate in time each coupling field) |
921 |
|
- move bi,bj loops inside atm_store_my_data.F and store also wind-stress; |
922 |
|
update accordingly + simplify aim_do_physics.F |
923 |
|
|
924 |
|
checkpoint64n (2013/08/26) |
925 |
|
o pkg/bbl: |
926 |
|
- update formulation to reduce dispersion of tracer properties in bbl |
927 |
|
- replaced horizontal and vertical transport parameters with velocities |
928 |
|
- changes results for verification/global_with_exf.yearly |
929 |
|
o verification/halfpipe_streamice: |
930 |
|
- change to matrix construction; update both Fwd & AD output. |
931 |
|
o verification/tutorial_tracer_adjsens: |
932 |
|
- OpenAD test: switch to vector-invariant momentum since fluxform with |
933 |
|
rStar causes problems with OpenAD; update output. |
934 |
|
o tools: |
935 |
|
- genmake2: define a common prefix for all temp-file names ; move them |
936 |
|
to local /tmp disk (but would be easy to move them back); |
937 |
|
- xmakedepend: apply the same switch for temp-files. |
938 |
|
o pkg/offline: |
939 |
|
- changes for use with rStar (NLFS): assume that we continue to provide |
940 |
|
UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid |
941 |
|
output files) and apply r* scaling at each time-step (function of the time |
942 |
|
varying Eta field); use normal pickup files (needed for restart with NLFS). |
943 |
|
o adjoint with OpenAD: |
944 |
|
- move OpenAD-specific files from verification/OpenAD/code_oad_all to a new |
945 |
|
package openad. This package has to be compiled for all runs with OpenAD |
946 |
|
instead of specifying code_oad_all as a modification directory. |
947 |
|
- link the fortran templates from tools/OAD_support to the build directory |
948 |
|
for preprocessing to avoid conflicts between different setups compiled |
949 |
|
simultaneously and simplify cleanup. |
950 |
|
o pkg/exf: |
951 |
|
- in exf_getforcing.F: comment out most of the EXCH calls (fields used by |
952 |
|
main model or other pkgs are exchanged in EXF_MAPFIELDS). |
953 |
|
o model/src: |
954 |
|
- do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline |
955 |
|
(similar to do_fields_blocking_exchanges.F). |
956 |
|
o tools/genmake2: |
957 |
|
- remove TAF output src code just before calling staf (when not doing a fresh |
958 |
|
built, will stop if things go wrong with staf). |
959 |
|
- fix target "adobj" (left from TAF version-2 transition) |
960 |
|
o pkg/diagnostics: |
961 |
|
- add a parameter to track the status of pkg/diagnostics activation; |
962 |
|
this replace/extend the use of logical param "settingDiags" (to check |
963 |
|
when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call. |
964 |
|
New S/R to print error message and stop when pkgStatus is not right. |
965 |
|
- to try: add a warning when "data.diagnostics" exist but useDiagnostics=F. |
966 |
|
|
967 |
|
checkpoint64m (2013/08/13) |
968 |
|
o model/inc: |
969 |
|
- move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from |
970 |
|
8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) |
971 |
|
o pkg/kpp & aim_v23: |
972 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
973 |
|
o pkg/seaice: |
974 |
|
- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
975 |
|
undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
976 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
977 |
|
o eesupp/src: |
978 |
|
- fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) |
979 |
|
in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). |
980 |
|
o switch to TAF version-2: |
981 |
|
- add flow directives to "freeze" naming convention for ad-routines that |
982 |
|
are used in I/O routines of adjoint state and associated common blocks |
983 |
|
that are used in adcommon.h (backward compatible with version-1) |
984 |
|
- update all ad-optfiles (in tools/adjoint_options + few local to some |
985 |
|
verification exp) to switch to latest TAF version (currently 2.5.5); |
986 |
|
merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented |
987 |
|
out except for diva). |
988 |
|
- the major change with TAF version-2 is that both the differentiated |
989 |
|
routines and the forward routines (new) are returned as part of the TAF |
990 |
|
output source code. Update genmake2 accordingly. |
991 |
|
- new output for AD experiment tutorial_global_oce_biogeo (better AD gradient |
992 |
|
with version-2 when compared to TLM or FWD gradient); other experiments |
993 |
|
output show minor changes (machine truncation level); update the few AD & |
994 |
|
TLM output with 12 matching digits only (some prior to version-2 switch). |
995 |
|
|
996 |
|
checkpoint64l (2013/08/05) |
997 |
|
o model/src: |
998 |
|
- in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F |
999 |
|
- main_do_loop.F: no longer includes additional (AUTODIFF) header files |
1000 |
|
when using TAF but only if using OpenAD. |
1001 |
|
o pkg/mom_common+fluxform+vecinv: |
1002 |
|
- always set horiz. viscosity arrays to background value before calling |
1003 |
|
MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC |
1004 |
|
only when using variable horiz. viscosity (useVariableVisc=T); |
1005 |
|
- simplify mom_vecinv.F (only 1 block for momViscosity). |
1006 |
|
o pkg/mom_common: variable horiz. viscosity in NH code |
1007 |
|
- move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F) |
1008 |
|
from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h |
1009 |
|
- store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, |
1010 |
|
useBiharmonicVisc & useVariableVisc. |
1011 |
|
- fix old bug (already in 1rst implementation of variable horizontal viscosity |
1012 |
|
in calc_gw.F, version 1.27, 2006/06/20): |
1013 |
|
horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 |
1014 |
|
even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. |
1015 |
|
- change background horiz viscosity in vertical momentum (gW) to always be |
1016 |
|
viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using |
1017 |
|
any type of variable viscosity, e.g., viscAh/4Grid) |
1018 |
|
- change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of |
1019 |
|
viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing |
1020 |
|
horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since |
1021 |
|
default viscAh,viscA4 is zero). |
1022 |
|
o model/src: |
1023 |
|
- extend length of drC & recip_drC from Nr to Nr+1. |
1024 |
|
o Divided Adjoint (DIVA) with MPI: |
1025 |
|
- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
1026 |
|
- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
1027 |
|
and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h. |
1028 |
|
|
1029 |
|
checkpoint64k (2013/07/23) |
1030 |
|
o tools/OAD_support: |
1031 |
|
- avoid the need for file "oadtempflile" in insertTemplateDir.bash |
1032 |
|
and remove it from genmake2. |
1033 |
|
o tools/build_options: |
1034 |
|
- remove MPI_HEADER_FILES_INC setting (no longer used) and comment out |
1035 |
|
MPI_HEADER_FILES list (let genmake2 find the missing headers) |
1036 |
|
o verification/halfpipe_streamice: |
1037 |
|
- change to driving stress formulation; update both Fwd & AD output. |
1038 |
|
o tools/genmake2 and Divided Adjoint with MPI: |
1039 |
|
- remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken); |
1040 |
|
- only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set; |
1041 |
|
- add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in |
1042 |
|
Makefile, which is set by genmake2, and check which mpi-headers are needed. |
1043 |
|
Note: need to update adjoint_options/adjoint_diva_mpi accordingly. |
1044 |
|
- update target "CLEAN" (to also remove ./mpi_headers/ dir). |
1045 |
|
o testreport: |
1046 |
|
- changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, |
1047 |
|
perform additional runs (number of additional runs is "add_DIVA_runs" taken |
1048 |
|
from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h"). |
1049 |
|
o verification/lab_sea (AD test): |
1050 |
|
- change to test Divided Adjoint Run in this set-up (both standard AD test |
1051 |
|
and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test. |
1052 |
|
o pkg atm_ & ocn_compon_interf: |
1053 |
|
- remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old |
1054 |
|
staggerTimeStep implementation) and disable (retired) corresponding |
1055 |
|
parameter. |
1056 |
|
o pkg/offline: |
1057 |
|
- comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01]; |
1058 |
|
- add S/R OFFLINE_CHECK to print offline parameter summary |
1059 |
|
and stop if loading a file that is not used; |
1060 |
|
- enable to calculate GMRedi tensor, KPP mixing and convective index |
1061 |
|
when the corresponding file(s) is/are not specified (but pkg is used). |
1062 |
|
- comment out resetting of monitorFreq (to endTime) since it still useful |
1063 |
|
for monitoring CFL numbers and checking offline fields. |
1064 |
|
o OpenAD: |
1065 |
|
- do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get |
1066 |
|
smaller standard output) and generate new (smaller) output (on baudelaire |
1067 |
|
using gfortran with -ieee) for exp. tutorial_tracer_adjsens |
1068 |
|
o model/src: |
1069 |
|
- call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F), |
1070 |
|
(where external_forcing_adjust was called) and change list of arguments; |
1071 |
|
- merge external_forcing_adjust.F into external_forcing_surf.F |
1072 |
|
- put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F) |
1073 |
|
which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX, |
1074 |
|
previously in file "balance_relax.F", now removed); remove corresponding |
1075 |
|
arrays in FFIELDS.h. |
1076 |
|
- EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement |
1077 |
|
a hack for getting back surfaceForcingS (loaded from file) when using |
1078 |
|
ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up. |
1079 |
|
- update output of AD test experiment global_ocean.cs32x15.seaice_dynmix |
1080 |
|
(was getting only 11 digits for AD-grad, due to different truncation |
1081 |
|
error in AD code). |
1082 |
|
|
1083 |
|
checkpoint64j (2013/07/04) |
1084 |
|
o pkg/offline: |
1085 |
|
- to enable the use of other features with pkg offline (e.g., obcs), |
1086 |
|
also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come. |
1087 |
|
- comment out "allowFreezing" (now active) in 2 offline testing exp. |
1088 |
|
o pkg/exf ALLOW_RUNOFTEMP |
1089 |
|
- fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL |
1090 |
|
- ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice |
1091 |
|
- changes verification/global_ocean.cs32x15/results/output.seaice.txt |
1092 |
|
o pkg/atm_phys: |
1093 |
|
- allows to add some damping on uVel,vVel (strength only function of k). |
1094 |
|
o verification, ad-tests: |
1095 |
|
- reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, |
1096 |
|
global_ocean_ebm and offline_exf_seaice.thsice. |
1097 |
|
o verification/halfpipe_streamice: |
1098 |
|
- found a bug in s/r pkg/streamice/streamice_advect_thickness which caused |
1099 |
|
flux input boundary conditions to be ignored; a fix for this bug changed |
1100 |
|
verification results for forward test. |
1101 |
|
- add adjoint test. |
1102 |
|
o pkg/ptracers: |
1103 |
|
- allow to restart without SOM pickup (resetting SOM to zero). |
1104 |
|
o pkg/gmredi: |
1105 |
|
- New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added. |
1106 |
|
- It uses mixing length theory and suppression by steering level effects to |
1107 |
|
calculate a diffusivity used in the Redi tensor (see Bates et al., submitted |
1108 |
|
to JPO, for more details). |
1109 |
|
- It also uses the diffusivity to calculate an eddy induced streamfunction |
1110 |
|
based on a PV closure (rather than a buoyancy closure as in GM). |
1111 |
|
- New files added to pkg/gmredi: |
1112 |
|
gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy |
1113 |
|
induced overturning streamfunction (called from gmredi_calc_tensor) |
1114 |
|
gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required |
1115 |
|
for use in gmredi_k3d |
1116 |
|
gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate |
1117 |
|
the eddy diffusivity |
1118 |
|
|
1119 |
|
checkpoint64i (2013/06/18) |
1120 |
|
o pkg/cheapaml: |
1121 |
|
- take src files from MITgcm_contrib/verification_other/offline_cheapaml/code |
1122 |
|
that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics) |
1123 |
|
with pkg/cheapaml. |
1124 |
|
o utils/python: add subpackage for cubed sphere function, first example is |
1125 |
|
simple cs.pcol to plot 2D fields on a map |
1126 |
|
o pkg/streamice: |
1127 |
|
- This is a new package in MITgcm, which solves dynamic equations for ice |
1128 |
|
sheets and ice streams |
1129 |
|
- At the moment it is independent of atmosphere/ocean dynamics, or any |
1130 |
|
other physical packages in MITgcm, even ShelfIce (although it is anticipat- |
1131 |
|
ed that this will change) |
1132 |
|
- There is a new verification exercise that tests it, halfpipe_streamice, |
1133 |
|
evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a |
1134 |
|
rectangular embayment |
1135 |
|
- halfpipe_streamice is forward-only for now, will have TAF test soon |
1136 |
|
- for questions, email dgoldber@mit.edu |
1137 |
|
o pkg/thsice: |
1138 |
|
- fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing |
1139 |
|
of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40); |
1140 |
|
- remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new |
1141 |
|
call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect ); |
1142 |
|
- allow precip from pkg/cheapaml to make snow over seaice. |
1143 |
|
o pkg/cfc: |
1144 |
|
- move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC |
1145 |
|
- remove atmos CFC 2-D arrays from common bloc (now local variables) |
1146 |
|
- change some hard-coded constant to run time parameter for reading and |
1147 |
|
and interpolating atmospheric CFC ; keep same default as previously. |
1148 |
|
- more flexible reading of Atmos CFC (number of records no longer hard-coded) |
1149 |
|
- put arguments in standard order: myTime, myIter, myThid |
1150 |
|
- use standard S/R GET_PERIODIC_INTERVAL for time interpolation of |
1151 |
|
atmospheric CFC ; fix for the case myIter < PTRACERS_iter0. |
1152 |
|
- fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf |
1153 |
|
- new routine to print summary of CFC params and check for consistency. |
1154 |
|
o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff, |
1155 |
|
similar to thsice_advdiff. |
1156 |
|
Note that for the B-grid case the routine parameters uc/vc are overwritten. |
1157 |
|
o pkg/cfc: |
1158 |
|
- change time interpolation for atmospheric CFC-11 (now same as for CFC-12); |
1159 |
|
update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline. |
1160 |
|
- fix interpolation of atmphspheric CFC between Sorthern and Northern |
1161 |
|
hemisphere value. |
1162 |
|
o pkg/seaice: |
1163 |
|
- allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml) |
1164 |
|
o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics; |
1165 |
|
so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE. |
1166 |
|
- requires an additional time level that is stored in the pickup |
1167 |
|
- you can start with AB2 from a pickup without this time level with |
1168 |
|
pickupStrictlyMatch = .false. |
1169 |
|
|
1170 |
|
checkpoint64h (2013/05/26) |
1171 |
|
o pkg/cheapaml: |
1172 |
|
- replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux); |
1173 |
|
affect machine truncation (but exp cheapAML_box still pass with 13 digits). |
1174 |
|
- consistent treatment of uWind,vWind location: assume everywhere in |
1175 |
|
pkg/cheapaml that they are on C-grid (@ uVel,vVel location) |
1176 |
|
(Note: was already the case for Tair,Qair advection); |
1177 |
|
add option (INCONSISTENT_WIND_LOCATION) to recover old results. |
1178 |
|
- compute diabatic forcing only in the interior (excluding overlap regions) |
1179 |
|
- fill in array "Qsw" (for short-wave heating); |
1180 |
|
- add diagnostic for precip ; fill-in diagnostics for cheapAML state vars |
1181 |
|
before any update (consistent with MITgcm state var diagnostics); |
1182 |
|
- cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if |
1183 |
|
non periodic ; + adjusted for uWind,vWind (C-grid). |
1184 |
|
o pkg/seaice: |
1185 |
|
- remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and |
1186 |
|
add explicitly pkg/exf in experiments that currently use pkg/seaice. |
1187 |
|
- allows to compile pkg/seaice without pkg/exf. |
1188 |
|
o tools/OAD_support: |
1189 |
|
- use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds |
1190 |
|
of array "ourStepOf" in function rvNextAction (revolve.F90). |
1191 |
|
o pkg/aim_compon_interf renamed to pkg/atm_compon_interf |
1192 |
|
- change pkg name (to be used with other atmospheric physics pkg) |
1193 |
|
but by-pass CVS when making the new pkg so that we keep the CVS history. |
1194 |
|
o pkg/offline: |
1195 |
|
- call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F |
1196 |
|
(previously called from pkg/dic_surfforcing_init.F) |
1197 |
|
o model/src: |
1198 |
|
- re-order sequence of calls within packages_init_variables.F, using |
1199 |
|
standard order, except for: |
1200 |
|
DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top), |
1201 |
|
CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom) |
1202 |
|
o new pkg: atm_phys |
1203 |
|
- add entry point and source code (previously in contrib |
1204 |
|
verification_other/atm_gray/code_gray/) for new pkg "atm_phys" |
1205 |
|
(atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008). |
1206 |
|
- re-order sequence of calls within packages_readparms.F, |
1207 |
|
packages_init_fixed.F and packages_write_pickup.F |
1208 |
|
(but skip packages_init_variables.F because of TAF issues). |
1209 |
|
- update contrib/*/atm_gray/ experiment. |
1210 |
|
o pkg/seaice (ITD code): |
1211 |
|
- simplify and fix the writing of pickup-files for ITD case |
1212 |
|
o pkg/seaice (ITD code): |
1213 |
|
- introduce floe size dependent lateral melt for ITD case; |
1214 |
|
- cleaning (avoid division by zero, change to f77 syntax, remove tabs) |
1215 |
|
- update seaice_itd experiment main output. |
1216 |
|
o pkg/thsice: |
1217 |
|
- remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and |
1218 |
|
declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F; |
1219 |
|
changed accordingly pkg/atm2d. |
1220 |
|
|
1221 |
|
checkpoint64g (2013/05/01) |
1222 |
|
o pkg/exf ALLOW_RUNOFTEMP |
1223 |
|
- if defined, river and glacier runoff temperature can be read-in from |
1224 |
|
runoftempfile; runoftempfile needs to have same format as runofffile |
1225 |
|
o pkg/thsice (& pkg/bulk_force): |
1226 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
1227 |
|
for energy content of Precip + RunOff & Evap (like with pkg/exf). |
1228 |
|
- change computation domain to always be the interior (without overlap). |
1229 |
|
- fix bug (wrong overlap) when using EXF and stressReduction > 0. |
1230 |
|
o verification/tutorial_global_oce_biogeo: |
1231 |
|
- add preliminary OpenAD setup (still has problems) |
1232 |
|
o pkg/seaice: |
1233 |
|
- turn some parameters for choosing the convergence criterion of |
1234 |
|
the inexact Newton method (JFNK) into runtime parameters for convenience |
1235 |
|
- clean up seaice_calc_viscosities.F: remove/retire two options for |
1236 |
|
SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes |
1237 |
|
the results of lab_sea/input because a division has been replaced by |
1238 |
|
a multiplication with the reciprocal (sumNorm) |
1239 |
|
- modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve |
1240 |
|
convergence of solver (changes results, of course), and to test some |
1241 |
|
new features |
1242 |
|
o model/src: |
1243 |
|
- remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call. |
1244 |
|
- remove unused forcing field "dQdT" and associated parameter "dQdTFile". |
1245 |
|
- move forcing adjustment (balancing surface forcing) in specific S/R |
1246 |
|
where might also be applied exchanges (if needed) to forcing arrays. |
1247 |
|
o pkg/shelfice: |
1248 |
|
- allow to specify the Ice-Shelf mass per unit area (instead of |
1249 |
|
shelficeLoadAnomaly) and do the conversion from one to the other |
1250 |
|
- move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA |
1251 |
|
to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and |
1252 |
|
(b) will be loaded in time (before calling INI_PRESSURE) in case it is |
1253 |
|
needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc |
1254 |
|
- update isomip experiment forward output (get machine truncation error |
1255 |
|
from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly) |
1256 |
|
o verification/offline_exf_seaice: |
1257 |
|
revise data.seaice in input.thermo and input_ad and update results accordingly |
1258 |
|
HO = 0.2, SEAICE_areaLossFormula = 2, |
1259 |
|
SEAICE_growMeltByConv = .TRUE., |
1260 |
|
SEAICE_doOpenWaterMelt = .TRUE., |
1261 |
|
Improve consistency with input.thsice and fix the spurious 500m ice corners |
1262 |
|
o verification/global_ocean.cs32x15: |
1263 |
|
- set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0., |
1264 |
|
in icedyn (thsice+seaice-dyn) test and update output. |
1265 |
|
o verification/offline_exf_seaice: |
1266 |
|
- adjust list of tested variables (with testreport) and update |
1267 |
|
standard test output with better slection of monitored fields. |
1268 |
|
o pkg/cd_code: |
1269 |
|
- swtich off Adams-Bashforth on the 1rst iteration. Update output of |
1270 |
|
experiment lab_sea.hb87 |
1271 |
|
o tools/genmake2: |
1272 |
|
- change default makedepend from the system default to tools/xmakedepend: |
1273 |
|
When no makedepend is specified, select tools/xmakedepend it the test pass, |
1274 |
|
otherwise select the system default (if exist and pass the test) or |
1275 |
|
try to build cyrus-makedepend ; stop if none of the 3 works. |
1276 |
|
o pkg/exf & pkg/thsice: |
1277 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
1278 |
|
for energy content of Precip + RunOff & Evap. Assumes: |
1279 |
|
1) Rain has same temp as Air. |
1280 |
|
2) Snow has no heat capacity (consistent with seaice & thsice pkgs) |
1281 |
|
3) Run-Off comes at the temp of surface water (with same Cp) |
1282 |
|
4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be |
1283 |
|
put directly into Latent Heat flux & should use water-vapor heat capacity. |
1284 |
|
5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent |
1285 |
|
with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL). |
1286 |
|
o pkg/seaice: simplify the use of CPP flags in JFNK-related files |
1287 |
|
(compile when SEAICE_ALLOW_JFNK is defined) |
1288 |
|
o pkg/thsice: |
1289 |
|
- fix oceanic flux diagnostics & timeave (left from new sequence of calls |
1290 |
|
implementation): move THSICE_AVE call after the advection (called directly |
1291 |
|
from thsice_do_advect.F). |
1292 |
|
o verification/global_ocean.90x40x15 and OpenAD: |
1293 |
|
New experiment for OpenAD is identical to the one in input_ad except that |
1294 |
|
multiDimAdvection=.FALSE., |
1295 |
|
There is still an issue with this. |
1296 |
|
o pkg/thsice: |
1297 |
|
- account for ice velocity (ocean relative velocity) in turbulent heat flux |
1298 |
|
at the base of the ice; update output of global_ocean.cs32x15 (icedyn) |
1299 |
|
and offline_exf_seaice (main test). |
1300 |
|
|
1301 |
|
checkpoint64f (2013/03/31) |
1302 |
|
o verification/OpenAD: |
1303 |
|
- new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran. |
1304 |
|
o verification/isomip, pkg/shelfice and OpenAD: |
1305 |
|
- add OpenAD setup to this exp and make shelfice package work with OpenAD |
1306 |
|
o verification/tutorial_global_oce_biogeo: |
1307 |
|
- update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h) |
1308 |
|
o verification/offline_exf_seaice: |
1309 |
|
- replace adjoint experiment (now similar to fwd input.thermo/ setup). |
1310 |
|
o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD: |
1311 |
|
- add OpenAD setup to this exp and make ptracers package work with OpenAD |
1312 |
|
o pkg/seaice/seaice_evp.F: |
1313 |
|
mask the asymmetric contribution of the ice-ocean stress (when |
1314 |
|
the turningAngle is non-zero) over open water to avoid stripes |
1315 |
|
in the EVP-solutions after many EVP-substeps. This does not change |
1316 |
|
the verification experiment (because turningAngle=0 in that experiment), |
1317 |
|
but will affect other EVP solutions with turningAngle.ne.0 |
1318 |
|
o verification, AD & TLM output: |
1319 |
|
- new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple |
1320 |
|
additions and multiplications which affect results at machine truncation |
1321 |
|
level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5, |
1322 |
|
lab_sea.noseaicedyn & offline_exf_seaice) and TLM output |
1323 |
|
(1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12 |
1324 |
|
digits of matching. |
1325 |
|
o pkg/seaice: |
1326 |
|
modify lsr-algorithm so that it vectorizes AND converges by using a |
1327 |
|
"zebra" method: split vector loop into two with step size 2; this |
1328 |
|
solves a general convergence problem for the JFNK solver on a vector |
1329 |
|
computer. It has the potential to even improve convergence for |
1330 |
|
non-vector machines, but it does change the results so it is turned |
1331 |
|
off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and |
1332 |
|
SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h |
1333 |
|
|
1334 |
|
checkpoint64e (2013/03/05) |
1335 |
|
o pkg/ecco and several verification experiments: |
1336 |
|
Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F |
1337 |
|
from ecco package, and revert to unified routine in model/src/ |
1338 |
|
Adjust verification experiments accordingly, especially gloal_oce_llc90 |
1339 |
|
Should conclude long-standing work by Gael to reconsile the_main_loop with |
1340 |
|
ECCO and will enable OpenAD's revolve loop in ECCO setup. |
1341 |
|
o pkg/generic_advdiff: |
1342 |
|
- implement compressible flow method for multi-dim advection (similar to |
1343 |
|
gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since |
1344 |
|
TAF generates many recomputations) to use it; no yet coded with implicit |
1345 |
|
vertical advection. |
1346 |
|
- change experiment advect_cs (new output) and advect_xy (same output) |
1347 |
|
to test compressible flow multi-dim advection. |
1348 |
|
o pkg/generic_advdiff: |
1349 |
|
- fix SOM advection for unusual cases (linear Free-Surf in r*, other |
1350 |
|
cases where linear Free-Surf is not @ k=1, e.g., useShelfIce) |
1351 |
|
o pkg/seaice: |
1352 |
|
- fix bug in the no-slip implementation in seaice_calc_strainrates.F, this |
1353 |
|
bug affects two verification experiments (lab_sea and lab_sea.hb87), |
1354 |
|
recover old (wrong) results by setting noSlipFac = 2. in |
1355 |
|
seaice_calc_strainrates.F; |
1356 |
|
- add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0 |
1357 |
|
- add runtime parameter SEAICE_JFNKepsilon for that finite difference |
1358 |
|
gradient in the Jacobian times vector operation (s/r seaice_jacvec) |
1359 |
|
- fix line search in seaice_jfnk.F (s/r seaice_jfnk_update) |
1360 |
|
o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code: |
1361 |
|
- new subroutines seaice_lsr_tridiagu/v |
1362 |
|
- introduce loop bounds i/jmin/max to be able to use a restricted |
1363 |
|
additive Schwarz method, but not used for now. |
1364 |
|
- rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS |
1365 |
|
- use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner |
1366 |
|
o OpenAD support |
1367 |
|
Reorganize S/R call for overall time-stepping loop to facilitate |
1368 |
|
OpenAD revolve loop replacement |
1369 |
|
(new S/R main_do_loop.F) |
1370 |
|
o model/src: |
1371 |
|
- add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3; |
1372 |
|
- pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R |
1373 |
|
ADAMS_BASHFORTH2. |
1374 |
|
o pkg/cheapaml: |
1375 |
|
- add new parameter (default=F, same as before) to disable full domain |
1376 |
|
(including land) periodicity in X & Y dir. |
1377 |
|
- new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of |
1378 |
|
prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer |
1379 |
|
into single S/R CHEAPAML_TIMESTEP. |
1380 |
|
|
1381 |
|
checkpoint64d (2013/02/17) |
1382 |
|
o pkg/monitor (angular momentum): |
1383 |
|
- do not add Eta contribution to the total AM if using rigid-lid; |
1384 |
|
- correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta). |
1385 |
|
- horizontal discretisation: compute Zonal wind contribution separately for |
1386 |
|
each component (instead of from cell centered averaged) and use the 4 |
1387 |
|
grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part. |
1388 |
|
- Check that AM is conserved with linear dynamics (momAdvection=F and linear |
1389 |
|
FreeSurf) if using vectorInvariant momentum. |
1390 |
|
o model/src (horizontal grid): |
1391 |
|
- move initialisation of all horizontal grid arrays to null value |
1392 |
|
from specific horizontal grid S/R to main S/R INI_GRID; |
1393 |
|
- add 2 new arrays to project model C-grid velocity on to zonal direction |
1394 |
|
(similar to AngleCosC & -AngleSinC but at U and V point location) and |
1395 |
|
compute them in S/R CALC_GRID_ANGLES. |
1396 |
|
o pkg/seaice: replace a hard coded parameter by a runtime parameter |
1397 |
|
SEAICE_JFNK_tolIter |
1398 |
|
o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in |
1399 |
|
preconditioner for JFNK (run LSR into the overlaps as far as possible, |
1400 |
|
i.e OLx/y-2, but overwrite the solution in the overlaps) |
1401 |
|
- extend loop range in seaice_calc_viscosity |
1402 |
|
- add new parameters SEAICE_OLx/y (default = OLx/y-2) |
1403 |
|
- add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs |
1404 |
|
- slightly modify loops in tridiagonal solver lsr-preconditioner |
1405 |
|
- by default remove the extra exchange in seaice_preconditioner with a |
1406 |
|
replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE |
1407 |
|
- modify offline_exf_seaice so that old results without RAS are reproduced |
1408 |
|
for output.dyn_jfnk.txt |
1409 |
|
in seaice_fgmres.F (unrelated to RAS) |
1410 |
|
- add a cpp-flag option for a re-ordered mapping (potentially more |
1411 |
|
efficient), but because this changes the results, turn it off by |
1412 |
|
default |
1413 |
|
- replace the save statement by local common blocks |
1414 |
|
o utils/matlab: |
1415 |
|
- fix tile-offset in rdmnc.m when output was produced using EXCH2. |
1416 |
|
- update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab) |
1417 |
|
instead of local script "load_cs.m". |
1418 |
|
o pkg/seaice: |
1419 |
|
- fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected |
1420 |
|
to the scalarProductMetric and the unrolling. By chance this does not |
1421 |
|
change the verification experiment, because of the particular domain |
1422 |
|
decomposition |
1423 |
|
o pkg/diagnostics: |
1424 |
|
- change default missing_value from UNSET_RL to -999. |
1425 |
|
o pkg/layers: improve vectorization of layers_fluxcalc.F |
1426 |
|
- step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu |
1427 |
|
time spent in this routine by more than a factor of 3 on an NEC-SX8 |
1428 |
|
- step 2: replace search algorithm by a bisection algorithm found in |
1429 |
|
Press et al. Numerical Recipes in Fortran. This algorithm can be |
1430 |
|
vectorized and finds the correct bin in approx. log2(Nlayers) steps. |
1431 |
|
For now, use this algorithm only for TARGET_NEC_SX defined. |
1432 |
|
- moved the search algorithm into a separate subroutine, that is kept |
1433 |
|
within the same file for automatic inlining. |
1434 |
|
- modified catching potential errors |
1435 |
|
o pkg/ecco: |
1436 |
|
- add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY. |
1437 |
|
o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk : |
1438 |
|
- modifications for ALLOW_GENTIM2D_CONTROL |
1439 |
|
-- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes. |
1440 |
|
-- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid ) |
1441 |
|
-- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc |
1442 |
|
-- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F |
1443 |
|
o model/src: |
1444 |
|
- account for moist thermodynamics in (dry) potential temperature equation; |
1445 |
|
update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev) |
1446 |
|
and cpl_aim+ocn. |
1447 |
|
- also switch to standard compiler (gfortran, was using ifort previously) |
1448 |
|
for fizhi-cs experiments reference output. |
1449 |
|
o pkg/ctrl: |
1450 |
|
- 1st step toward generic time-varying control variable (2D) via CPP option |
1451 |
|
ALLOW_GENTIM2D_CONTROL |
1452 |
|
- note new namelist ctrl_nml_genarr in data.ctrl |
1453 |
|
o verification/global_ocean.cs32x15: |
1454 |
|
- switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new |
1455 |
|
thsice calling sequence and update "output.icedyn.txt" output file. |
1456 |
|
o pkg/ptracers: |
1457 |
|
- from Ryan A.: code to allow to restart a tracer at regular time interval |
1458 |
|
specifying a reset frequency and a reset-phase (for each tracers). |
1459 |
|
o pkg/thsice: |
1460 |
|
- implement new sequence of calls for thsice+seaice: |
1461 |
|
previously: ice-Dyn,ice-Advect,ice-Thermo(thsice) |
1462 |
|
new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect |
1463 |
|
- allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE" |
1464 |
|
in CPP_OPTIONS.h) to recover old sequence; |
1465 |
|
- update diagnostics for Intermediate State thsice diagnostics: now filled |
1466 |
|
just before advection (instead of just after advection in old sequence); |
1467 |
|
- update output of experiment offline_exf_seaice (standard test); |
1468 |
|
- in global_ocean.cs32x15 exp., postpone output.icedyn.txt update |
1469 |
|
by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h |
1470 |
|
o pkg/aim_v23: |
1471 |
|
- use tiled array for aim_CO2 and surface wind speed for export to coupler; |
1472 |
|
- use standard pkg/mdsio routines to read & write CO2 pickup file; |
1473 |
|
- in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F; |
1474 |
|
- Implement new sequence of calls for seaice advection (with thsice and |
1475 |
|
seaice diffusion): do ice advection after ice-Thermodynamic (previously |
1476 |
|
was done before); change aim_do_physics.F (split the bi,bj loops block); |
1477 |
|
- use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence; |
1478 |
|
o pkg/thsice: |
1479 |
|
- add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case |
1480 |
|
where just seaice diffusion is used without seaice-dynamics. |
1481 |
|
|
1482 |
|
checkpoint64c (2013/01/18) |
1483 |
|
o pkg/seaice: |
1484 |
|
- add a parameter JFNKres_tFac that can replace JFNKres_t |
1485 |
|
(= JFNKres_tFac*JFNKresidual before JFNK solver) |
1486 |
|
- add a line search option to the JFNK solver |
1487 |
|
- move update of u/vIce and computation of initial residual into a separate |
1488 |
|
routine (same file); makes the code a little easier to read (?) |
1489 |
|
- the line search requires computation of the residual and for some reason |
1490 |
|
I cannot do the update of u/vIce at the beginning of the Newton loop |
1491 |
|
without changing the results, so we move computation of the new residual |
1492 |
|
also to the end of the Newton loop, even without the line search |
1493 |
|
o pkg/mdsio: |
1494 |
|
- write missing value (corresponding to undefined array value) to meta files; |
1495 |
|
skip this if missing value is one (UNSET_RL would be a better value for the |
1496 |
|
case of undefined missing value but it's current the default missing-value); |
1497 |
|
Also update mdsio_read_meta.F (reading timeInterval & missing-value). |
1498 |
|
o pkg/exf & thsice: |
1499 |
|
- for diagnostics purpose, fill-up and update Qsw array (+ fill the |
1500 |
|
diagnostics) even when SHORTWAVE_HEATING is #undef; |
1501 |
|
o verification/cfc_example: |
1502 |
|
- turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to |
1503 |
|
illustrate how to use it). |
1504 |
|
o verification/offline_exf_seaice: |
1505 |
|
in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing |
1506 |
|
files to only one time-record. |
1507 |
|
in input.thermo: narrow the 2 bands of low initial ice-concentration near |
1508 |
|
N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for |
1509 |
|
snapshot output; same mcPheePiston value as in thsice with |
1510 |
|
surf-current=0.2m/s. |
1511 |
|
in input.thsice: similar set-up as in input.thermo (channel with same seaice |
1512 |
|
initial conditions). |
1513 |
|
o verification/cfc_example: |
1514 |
|
- update file "data" with more standard choice (default rotationPeriod, |
1515 |
|
exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F, |
1516 |
|
set deltaTFreeSurf to deltaTtracer) and update the output. |
1517 |
|
o pkg/layers: |
1518 |
|
- fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC; |
1519 |
|
- ensure that "layers_bolus" is switched to False when useGMRedi=False. |
1520 |
|
o verification/offline_exf_seaice: |
1521 |
|
- set all {field}period to zero for constant-in-time forcing (not tested |
1522 |
|
anywhere else). |
1523 |
|
o verification/offline_exf_seaice: |
1524 |
|
- dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice; |
1525 |
|
- dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice. |
1526 |
|
o model/src: |
1527 |
|
- implement Finite-Volume method for (hydrostatic) presure gradient |
1528 |
|
from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate. |
1529 |
|
o pkg/seaice: implement EVP* by Lemieux et al. (2012). |
1530 |
|
- In order to be compatible with the default EVP code, this requires changing |
1531 |
|
the EVP code around a little; and because any small change immediately |
1532 |
|
breaks the lab_sea.hb87 verification experiment, the reference output is |
1533 |
|
updated two times (each time the remaining aggrement was only 2 digits): |
1534 |
|
- after replacing 1/dt by 1*recip_dt with a precomputed recip_dt |
1535 |
|
- after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt |
1536 |
|
The adjoint test lab_sea.evp also needed to be updated. |
1537 |
|
- Turn on EVP* by setting SEAICE_deltaTevp as before, and setting |
1538 |
|
SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be |
1539 |
|
a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps |
1540 |
|
explicitly with SEAICEnEVPstarSteps (thereby overriding the default of |
1541 |
|
INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately |
1542 |
|
kept obscure, because I need to test it a little more. |
1543 |
|
o pkg/cheapaml: |
1544 |
|
- fix few incorrect type (_RL/_RS) in subroutine calls. |
1545 |
|
o pkg/seaice: |
1546 |
|
- new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays |
1547 |
|
to _RL vector; this fixes JFNK code when compiling with "-use_r4" option. |
1548 |
|
o model/src: |
1549 |
|
- add a warning if using select_rStar=2 with nonlinFreeSurf <> 4; |
1550 |
|
change (in input_ad*/data) select_rStar from 2 to 1 for AD verification |
1551 |
|
experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output) |
1552 |
|
o pkg/cheapaml: |
1553 |
|
- replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and |
1554 |
|
update output of experiment cheapAML_box. |
1555 |
|
- store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity, |
1556 |
|
and set them only in one place (cheapaml_readparms.F). |
1557 |
|
- replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI" |
1558 |
|
- remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms) |
1559 |
|
and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia). |
1560 |
|
o model/src/the_main_loop.F: |
1561 |
|
- fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION. |
1562 |
|
o pkg/seaice: |
1563 |
|
- remove legacy branch code. |
1564 |
|
- retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly. |
1565 |
|
o verification/*/code*/SEAICE_OPTIONS.h: |
1566 |
|
- remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY, |
1567 |
|
SEAICE_CAP_HEFF). |
1568 |
|
o pkg/cheapaml: |
1569 |
|
- use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time |
1570 |
|
to load new forcing fields. |
1571 |
|
- add missing "_d 0" where it's needed; + some editing (improve indentation). |
1572 |
|
- remove switch to "-r8" compiler option (no longer needed) in verification |
1573 |
|
cheapAML_box, keep same output (small trucation error differences). |
1574 |
|
o verification/offline_exf_seaice: |
1575 |
|
- add thermodynamics only test. |
1576 |
|
o verification/cheapAML_box: |
1577 |
|
- split the domain in 8 (2x4) tiles; add MPI and multi-threaded test; |
1578 |
|
keep same output (same 14 digits for cg2d). |
1579 |
|
- switch on "-r8" compiler option (some numerical values are missing |
1580 |
|
the "_d 0") and update output (only 6 digits for cg2d were preserved). |
1581 |
|
|
1582 |
|
checkpoint64b (2012/12/24) |
1583 |
|
o pkg/cheapaml: |
1584 |
|
- remove un-used variables (Qnet,EmPmR) from pickup files. |
1585 |
|
- store tendency of advected variables into cheapaml pickup file |
1586 |
|
and fix the AB-2 restart. |
1587 |
|
o verification/offline_exf_seaice and lab_sea adjoint: |
1588 |
|
- switch to new code (#undef SEAICE_GROWTH_LEGACY). |
1589 |
|
- switch to 4 time steps in offline, consistent with lab_sea. |
1590 |
|
- match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice. |
1591 |
|
- update results after change of experiment seaice. |
1592 |
|
o pkg/seaice: |
1593 |
|
- remove option SEAICE_MULTICATEGORY; has been replaced with run-time |
1594 |
|
parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is |
1595 |
|
still defined since SEAICE_multDim needs to be set to MULTDIM value (from |
1596 |
|
SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default. |
1597 |
|
o model/src: |
1598 |
|
- add run-time parameter to select CG2D solver minimum-residual solution |
1599 |
|
(in case of a poor convergence). |
1600 |
|
o pkg/seaice/seaice_lsr.F |
1601 |
|
- move calculation of matrix coefficients into new |
1602 |
|
S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same |
1603 |
|
file; the main purpose of this change is to be able to reuse the code |
1604 |
|
in S/R SEAICE_PRECONDITIONER |
1605 |
|
- modify the computation of the residual so that the mass of sea-ice |
1606 |
|
is not used twice; this simplifies the calculations, but since |
1607 |
|
the residual is never used except when LSR_mixIniGuess.ge.4---and this is |
1608 |
|
not tested in testreport---this does not affect the testreport results. |
1609 |
|
o verification/seaice_obcs: |
1610 |
|
- disable SEAICE_GROWTH_LEGACY; reset input files to match those of |
1611 |
|
verification/lab_sea/input.salt_plume; changes results/output.txt* |
1612 |
|
o model/src: |
1613 |
|
- adapt quasi-hydrostatic formulation to work with p or p* coordinate. |
1614 |
|
o pkg/seaice: |
1615 |
|
- improve description of parameters in seaice_fgmres.F and start |
1616 |
|
cleaning up the code |
1617 |
|
- change name of SCALPROD to SEAICE_SCALPROD and modify meaning of |
1618 |
|
second argument |
1619 |
|
- add a metric based on grid cell area to SEAICE_SCALPROD; update |
1620 |
|
results of offline_exf_seaice.dyn_jfnk |
1621 |
|
- compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD |
1622 |
|
o pkg/aim_v23: |
1623 |
|
- fix an other bug in dissipation heating (grid-cell area was missing). |
1624 |
|
o model/src + pkg/seaice: |
1625 |
|
- add global (multi-tile) linear solver for pair of tri-diagonal system |
1626 |
|
along X and Y lines, respectively for U and V component. |
1627 |
|
Note: 1) MPI and cube-exchange not yet coded. |
1628 |
|
2) probably not accurate for poorly conditioned / large size problem. |
1629 |
|
- add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver; |
1630 |
|
default: not compiled and not used. |
1631 |
|
o pkg/seaice: |
1632 |
|
- first attempt at a multi-threaded fgmres solver for the JFNK solver: |
1633 |
|
introduce bi/bj loops and use global_sum_tile_rl instead of |
1634 |
|
mpi_allreduce in seaice_fgmres.F |
1635 |
|
- improve diagnostics output for fgmres solver (seaice_fgmres.F) |
1636 |
|
- replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F) |
1637 |
|
- add a verification experiment for JFNK in offline_exf_seaice |
1638 |
|
o verification: |
1639 |
|
- change (for now, only fwd test) offline_exf_seaice experiment: |
1640 |
|
use a re-entrant channel with idealized coastline (trapezoidal shape) |
1641 |
|
at southern boundary to explore seaice dynamics and thermodynamics |
1642 |
|
with simple forcing. Main set-up has dynamics+thermo and SST relaxation; |
1643 |
|
secondary test (input.thsice) use thermodynamics only with SST relaxation. |
1644 |
|
- add seaice-dynamics only secondary test using LSR and pkg/thsice advection. |
1645 |
|
o pkg/exf: |
1646 |
|
- disable "sstExtrapol" when Nr=1 |
1647 |
|
o verification: |
1648 |
|
- add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble) |
1649 |
|
to test pkg/cheapaml. |
1650 |
|
o pkg/aim_v23 & pkg/shap_filt: |
1651 |
|
- fix dissipation heating (erroneous gravity multiplication factor). |
1652 |
|
o pkg/seaice: |
1653 |
|
- remove unused field pressPre from jfnk solver |
1654 |
|
- rename two subroutines in seaice_preconditioner.F |
1655 |
|
o eesupp/src: |
1656 |
|
- S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...) |
1657 |
|
o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again |
1658 |
|
- remove wrong parts of the rhs and the lhs (were in there |
1659 |
|
because I did not understand the concept of this preconditioner) |
1660 |
|
- add an exchange between u- and v-sweep. This increases communication |
1661 |
|
by a factor of two but improves the convergence of jfnk. Ideally, |
1662 |
|
one would like the u- and v-sweep to be independent. So far within |
1663 |
|
undocumented ifdefs |
1664 |
|
- reorganize the extra computations for printing the residuals |
1665 |
|
o tools/genmake2: |
1666 |
|
- comment out the "mpif.h" include in NetCDF test programm (for MPI built) |
1667 |
|
since it's not necessary (and was preventing to use MNC in some cases). |
1668 |
|
|
1669 |
|
checkpoint64a (2012/11/16) |
1670 |
|
o pkg/autodiff: |
1671 |
|
- improve pkg-internal logical parameter switch (inAd/inFwd mode) so that |
1672 |
|
autodiff_readparms.F no longer depends on calling order (within |
1673 |
|
packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h): |
1674 |
|
rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd |
1675 |
|
and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd. |
1676 |
|
o pkg/obcs: |
1677 |
|
- adding tidal velocity forcing capability to obcs |
1678 |
|
for usage example, see verification/seaice_obcs/input.tides |
1679 |
|
o pkg/seaice: |
1680 |
|
- turn the LSR-relaxation parameters WFAU/V into runtime parameters |
1681 |
|
SEAICE_LSRrelaxU/V |
1682 |
|
- introduce runtime parameter SEAICEetaZmethod (=0 by default) |
1683 |
|
o pkg/aim_v23: |
1684 |
|
- implement heating from friction (bottom friction and stratospheric drag). |
1685 |
|
o pkg/shap_filt: |
1686 |
|
- fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from |
1687 |
|
dissipation but only for Shap_funct=2, active when addFrictionHeating=T. |
1688 |
|
o model/src: |
1689 |
|
- move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in |
1690 |
|
time-constant addMass field from file (addMassFile); |
1691 |
|
- support for heating due to friction (and Kinetic Energy dissipation): |
1692 |
|
add option, run-time switch and 3-D field array + support code ; each pkg |
1693 |
|
or S/R can add heating contribution (if there is a sink of KE); the sum is |
1694 |
|
accounted for as a Temperature tendency term (EXTERNAL_FORCING_T). |
1695 |
|
o pkg/seaice: |
1696 |
|
- complete merge of ITD code into seaice_growth.F |
1697 |
|
from MITgcm_contrib/torge/itd/code/ |
1698 |
|
no verification so far, but Torge Martin tested |
1699 |
|
"1-D test case and Beaufort set up; |
1700 |
|
deliver okay results after 1 model year." |
1701 |
|
- complete merge of SEAICE_SIZE.h into all relevant routines |
1702 |
|
- move computation of eta at Z-points into calc_viscosities |
1703 |
|
+ introduce global field etaZ |
1704 |
|
+ add different methods for computing etaZ, for now the old |
1705 |
|
method (simple averages of eta to Z-points) is hardwired |
1706 |
|
+ replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual, |
1707 |
|
seaice_preconditioner |
1708 |
|
- simplify computations for SEAICE_ZETA_SMOOTHREG |
1709 |
|
- seaice_preconditioner: |
1710 |
|
+ replace one remaining press by pressLoc (mistake) |
1711 |
|
+ adjust printing of residuals |
1712 |
|
- improve I/O of diagnostics of JFNK in seaice_jfnk.F: |
1713 |
|
+ add (SEAICE.h) and rename some counters (initiliased in |
1714 |
|
seaice_init_fixed.F) |
1715 |
|
+ add _BEGIN/END_MASTER (myThid) around print statements |
1716 |
|
+ print total number of iterations and failures over SEAICE_monFreq |
1717 |
|
interval to STDOUT |
1718 |
|
- move control over output-messages by fgmres to seaice_jfnk to save |
1719 |
|
some operations |
1720 |
|
- move resetting initial guess for fgmres outside of seaice_fgmres_driver |
1721 |
|
in order to make restarts with sol .ne. zero (fgmres with restarts) |
1722 |
|
(seaice_jfnk.F, seaice_fgmres.F) |
1723 |
|
- seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes |
1724 |
|
a serious convergence problem when open boundaries are involved |
1725 |
|
o pkg/ggl90: fix computation of control volumes for the case of |
1726 |
|
ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes |
1727 |
|
up half a grid cell from C-centered to W-centered (pointed out by C. Eden) |
1728 |
|
o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC |
1729 |
|
o pkg/autodiff |
1730 |
|
- Add inAdMode switch for SEAICEuseDYNAMICS: |
1731 |
|
SEAICEuseDYNAMICSinAdMode |
1732 |
|
(extend logic in ADAUTODIFF_INADMODE_SET) |
1733 |
|
o pkg/seaice |
1734 |
|
- Step 1 of merging ice-thickness distribution (ITD) code from |
1735 |
|
MITgcm_contrib/torge/itd/ (author: Torge Martin) |
1736 |
|
The code implements concept laid out in Thorndike et al. (1975); |
1737 |
|
code is enabled via CPP flag SEAICE_ITD |
1738 |
|
nITD (in SEAICE_SIZE.h) defines number of ice thickness categories; |
1739 |
|
code is not complete yet!! |
1740 |
|
- SEAICE_SIZE.h now included in almost all seaice routines |
1741 |
|
o verification (using seaice): |
1742 |
|
- switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp. |
1743 |
|
global_ocean.cs32x15.seaice ; update results. |
1744 |
|
- compile B-grid dynamics in FW test exp 1D_ocean_ice_column ; |
1745 |
|
- compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp |
1746 |
|
offline_exf_seaice (previously compiling B-grid). |
1747 |
|
o pkg/exf: |
1748 |
|
- fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow |
1749 |
|
to specify neither just 1 comp of wind or wind-stress, nor no surface momentum |
1750 |
|
forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind. |
1751 |
|
o pkg/layers (adjust changes from Sept 19): |
1752 |
|
- do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F) |
1753 |
|
this allows to remove "layers_maxNum" dimension from all layers arrays. |
1754 |
|
o pkg/layers (adjust changes from Sept 19): |
1755 |
|
- remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ; |
1756 |
|
- snap-shot extended to all type of layers (not just the 1rst type); |
1757 |
|
- remove layers variables when corresponding CPP option is undef. |
1758 |
|
o pkg/layers: |
1759 |
|
- rename pkg/layers variable and add new output (layer exist & un-weighted |
1760 |
|
velocity in layer) |
1761 |
|
o pkg/seaice: |
1762 |
|
- simplify (?) ocean-drag coefficent computations by using |
1763 |
|
the same routine in all three solvers (saves some code lines) |
1764 |
|
- remove global fields DRAGA and DRAGS from C-grid code and |
1765 |
|
declare them locally in lsr.F (the only place where they are |
1766 |
|
still used) |
1767 |
|
- update AD output of lab_sea.evp (very sensitive anyway). |
1768 |
|
o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics |
1769 |
|
(Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK |
1770 |
|
and SEAICEuseJFNK=.true. A few things to note: |
1771 |
|
- involves a FGMRES, that is parallel but very inefficient, |
1772 |
|
because of many scalar products (global sums) in the Gram-Schmidt |
1773 |
|
orthogonalization method. Needs to be replaced. Original code |
1774 |
|
from J.-F. Lemieux |
1775 |
|
- preconditioner for FGMRES is a stripped down version of LSOR |
1776 |
|
- SOLV_MAX_ITERS is now used for LSOR as a solver and as a |
1777 |
|
preconditioner. For the preconditioner, the default is set to 10. |
1778 |
|
- Jacobian times vector is computed with finite differences |
1779 |
|
- marginally related to JFNK-solver: add a smooth regularization for |
1780 |
|
zeta with tanh that will improve convergence (Lemieux and Tremblay, |
1781 |
|
2009) for any implicit solver (not implemented for EVP because EVP |
1782 |
|
does not need this regularization in the first place). Define |
1783 |
|
SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use. |
1784 |
|
o eesupp/src: |
1785 |
|
- check in genmake2 that intrinsic S/R flush is available. |
1786 |
|
- add S/R to flush IO unit (if intrinsic S/R flush is available) |
1787 |
|
- flush standard & error msg unit before MPI termination |
1788 |
|
- if debugMode, flush IO unit after printing msg |
1789 |
|
o pkg/ctrl: |
1790 |
|
- ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call |
1791 |
|
to ctrl_set_unpack_xyz. |
1792 |
|
|
1793 |
|
checkpoint64 (2012/10/09) |
1794 |
|
o pkg/shelfice |
1795 |
|
- in mom_fluxform.F, mom_vecinv.F: |
1796 |
|
CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid) |
1797 |
|
Bug fix KappaRU -> KappaRV |
1798 |
|
does not change verification/isomip but may change other setups |
1799 |
|
(presumably constant KappaRU=KappaRV) |
1800 |
|
- fix diagnostics SHIU/Vdrag (thanks to Tom Millgate) |
1801 |
|
o pkg/obcs: |
1802 |
|
- fixed some indexing bugs in obcs_seaice_sponge.F |
1803 |
|
- added obcs relaxation subroutines for HSALT and HSNOW |
1804 |
|
- changes verification/seaice_obcs/results/obcs_seaice_sponge.F |
1805 |
|
o pkg/seaice: |
1806 |
|
- add "multicategory" parameterization for snow in analogy to ice, |
1807 |
|
default is off for now. |
1808 |
|
o pkg/obcs: |
1809 |
|
- added obcs_seaice_sponge.F for obcs relaxation of seaice variables; |
1810 |
|
see verification/seaice_obcs/input.seaiceSponge for example application. |
1811 |
|
- remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB |
1812 |
|
index setting by master-thread. This fix multi-threads Pb in previous modifs. |
1813 |
|
o pkg/layers : |
1814 |
|
- add diagnostics to pkg/layers |
1815 |
|
- move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F |
1816 |
|
(from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly. |
1817 |
|
o pkg/generic_advdiff/gad_implicit_r.F : |
1818 |
|
- fix ADVr diagnostics in case of both implicit vertical advection and diffusion. |
1819 |
|
o pkg/seaice/seaice_growth.F: |
1820 |
|
- fix SItflux diagnostics in virtual salt flux + balanceEmpmr case. |
1821 |
|
o pkg/obcs: |
1822 |
|
- change default setting of OBCS_UVICE_OLD from defined to undef; |
1823 |
|
- use new parameter OB_indexNone for null index value (instead of hard-coded 0) |
1824 |
|
in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F; |
1825 |
|
- pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z; |
1826 |
|
- change OB null index value (OB_indexNone) to -99 ; this fix the problem |
1827 |
|
with Southern & Western OB at a tile edge (at least in a simple set-up). |
1828 |
|
o pkg/obcs: |
1829 |
|
- change settings of OB index in case OB coincides with tile edge (shared by |
1830 |
|
2 tiles), so that common OB location is registered by both tiles (instead of |
1831 |
|
only 1). However, for Southern and Western OB, index value = 0 is not |
1832 |
|
recognized as valid OB index (=default null value) and needs to be fixed. |
1833 |
|
- modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting) |
1834 |
|
- new parameter "OB_indexNone" for null index value (for now, still zero) |
1835 |
|
to replace hard-coded null index value of zero. |
1836 |
|
o pkg/exch2: |
1837 |
|
- improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON: |
1838 |
|
always check buffer-size (but outside the loop); move checking for valid |
1839 |
|
index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON, |
1840 |
|
print each tile and point connection only if |W2_printMsg|>= 2 and 3. |
1841 |
|
o pkg/ctrl (pack & unpack): |
1842 |
|
- in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable |
1843 |
|
(locally defined) for different variables (+ remove the variable-specific |
1844 |
|
file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL |
1845 |
|
(to be extended to other local file names in ctrl.h). |
1846 |
|
o pkg/flt: |
1847 |
|
- add a FLT_Iter0 option (similar to PTRACERS_Iter0). |
1848 |
|
o pkg/mdsio: |
1849 |
|
- fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing |
1850 |
|
o tools/genmake2: |
1851 |
|
- add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE |
1852 |
|
(added by Alistair in version 1.51 for building without make depend); |
1853 |
|
- remove Header files list (H_SRC_FILES) from the dependence of targets |
1854 |
|
ad_input_code.f & ftl_input_code.f (not clear why it was added in the first |
1855 |
|
place in version 1.23): this save going through staf when unrelated header |
1856 |
|
file has been modified. |
1857 |
|
Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without |
1858 |
|
"make depend" step, still need to do "make links" before "make adtaf". |
1859 |
|
o eesupp/src (+ few pkg src files) & genmake2: |
1860 |
|
- finish to remove ALWAYS_USE_MPI in source code that TAF does not see; |
1861 |
|
- no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2). |
1862 |
|
- improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish |
1863 |
|
upper/lower case ; account for space between "#" and undef/define) |
1864 |
|
o pkg/flt (with exch2): |
1865 |
|
- cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F; |
1866 |
|
- simplify threads synchronisation; fix (many issues) multi-threaded with MPI. |
1867 |
|
|
1868 |
|
checkpoint63s (2012/09/05) |
1869 |
|
o pkg/ecco: |
1870 |
|
- remove #ifdef ALLOW_SMOOTH_CORREL3D brackets. |
1871 |
|
- add more relevant #ifdef ALLOW_SMOOTH ones. |
1872 |
|
- sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D. |
1873 |
|
o pkg/ctrl: |
1874 |
|
- CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D, |
1875 |
|
ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D. |
1876 |
|
- ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag, |
1877 |
|
doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and |
1878 |
|
ctrlSmoothCorrel3D (new). |
1879 |
|
The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP. |
1880 |
|
- ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist. |
1881 |
|
- ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress |
1882 |
|
controls when useAtmWind, and vice versa. |
1883 |
|
- ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers. |
1884 |
|
- ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with |
1885 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH. |
1886 |
|
- ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with |
1887 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH. |
1888 |
|
- ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F: |
1889 |
|
replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D. |
1890 |
|
o pkg/smooth: |
1891 |
|
- remove un-necessary includes. |
1892 |
|
- remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets. |
1893 |
|
Those CPP options were never defined, and not necessary. |
1894 |
|
o model/src: |
1895 |
|
- fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi). |
1896 |
|
- standard treatment of useSMOOTH. |
1897 |
|
o pkg/autodiff: |
1898 |
|
- add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode, |
1899 |
|
useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint. |
1900 |
|
o pkg/exch2: |
1901 |
|
- add "if usingMPI" where it was missing (in exch2_rx?_cube*.template) |
1902 |
|
+ start to remove ALWAYS_USE_MPI in source code that TAF does not see. |
1903 |
|
- make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag |
1904 |
|
and tiles to process mapping. |
1905 |
|
- re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h) |
1906 |
|
moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h; |
1907 |
|
rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX |
1908 |
|
from w2_eeboot.F to w2_readparms.F. |
1909 |
|
o eesupp/src: |
1910 |
|
- set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of |
1911 |
|
ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F; |
1912 |
|
also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F |
1913 |
|
- in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI |
1914 |
|
is defined (remove condition on usingMPI) to match cases where MPI_INIT |
1915 |
|
has been called. |
1916 |
|
- fix bug I put in previous modif of exch_sm_3d_rx.template (not much used); |
1917 |
|
- change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings |
1918 |
|
(so that on 1 proc, get same myPid independently of usingMPI) |
1919 |
|
- add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and |
1920 |
|
useCubedSphereExchange with EXCH-1 (safer). |
1921 |
|
- add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI). |
1922 |
|
o pkg/ggl90: |
1923 |
|
- fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call) |
1924 |
|
used in ALLOW_GGL90_SMOOTH code. |
1925 |
|
o pkg/flt: |
1926 |
|
- fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping |
1927 |
|
floats at the Southern end of the domain). |
1928 |
|
o eesupp/inc: |
1929 |
|
- add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h); |
1930 |
|
but not used (and not to be used) anywhere, just for documentation. |
1931 |
|
o pkg/autodiff, exf, ptracers & seaice (AD & TL output): |
1932 |
|
- comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since: |
1933 |
|
a) can damage previously written records in any other multi-record files. |
1934 |
|
b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S. |
1935 |
|
o tools/genmake2: |
1936 |
|
- define variable MAKE within Makefile and use it in place of 'make'; |
1937 |
|
- update AD_CONFIG.h (if needed) before building any of the executable |
1938 |
|
(forward, adjoint or tangent-lin); this involves a 2nd invocation of make; |
1939 |
|
and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h; |
1940 |
|
- always print usual warning comment 'this file is automatically generated' |
1941 |
|
from script convert_cpp_cmd2defines (+ remove this warning from genmake2). |
1942 |
|
o pkg/cheapaml: |
1943 |
|
- updated to correspond to the code used in accepted paper (Nico Wienders). |
1944 |
|
o pkg/exf: |
1945 |
|
added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch. |
1946 |
|
ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F) |
1947 |
|
and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h). |
1948 |
|
o pkg/exf, autodiff, ctrl, ecco and seaice: |
1949 |
|
remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones. |
1950 |
|
o pkg/ctrl, ecco: |
1951 |
|
allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL. |
1952 |
|
Depending on useAtmWind, one is inactive, and the other is active (see |
1953 |
|
exf_getffields.F/exf_getsurfacefluxes.F). |
1954 |
|
o tools/genmake2: |
1955 |
|
- improve error msg when failing in 2nd test of check_for_broken_Ff |
1956 |
|
- fix option '-makefile' short-name (-mf according to genmake2 -help) |
1957 |
|
- source local config file "genmake_local" just after processing the genmake2 |
1958 |
|
command arguments (previously done before processing arg). |
1959 |
|
o pkg/grdchk: |
1960 |
|
- add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call |
1961 |
|
to this routine from cost_final has been dropped in g_cost_final) |
1962 |
|
- improve printed information (more explicit msg, no longer using "print *," |
1963 |
|
fix fcpertminus printed value). |
1964 |
|
o model/src: |
1965 |
|
- move call to COST_INIT_VARIA out of packages_init_variables.F directly |
1966 |
|
into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES): |
1967 |
|
this prevents getting cost-funct reset in adinitialise_varia recomputations. |
1968 |
|
o pkg/dic: |
1969 |
|
- move initialisation of "freefe" array from from dic_biotic_forcing.F to |
1970 |
|
fe_chem.F: this prevents TAF from dropping this initialisation in TLM code. |
1971 |
|
o pkg/grdchk: |
1972 |
|
- grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid ) |
1973 |
|
- grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0 |
1974 |
|
o pkg/autodiff/ctrl/grdchk : |
1975 |
|
- attempt to sort out what works and what does not, |
1976 |
|
with regard to I/O, and to warn/stop accordingly. |
1977 |
|
o pkg/grdchk: |
1978 |
|
- attempt to fix grdchk in the case of useSingleCpuIO. |
1979 |
|
- "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )" |
1980 |
|
statements were moved from grdchk_main.F and into |
1981 |
|
grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F. |
1982 |
|
- a global sum is applied to record numbers icvrec/layer |
1983 |
|
out of grdchk_loc so that they be passed to I/O routines. |
1984 |
|
o pkg/smooth: |
1985 |
|
- fix recomputation that appeared with nlfs : use smooth_recip_hFacC, |
1986 |
|
smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case. |
1987 |
|
o verification/testreport: |
1988 |
|
- add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive); |
1989 |
|
- can also use compressed (gzip) reference output file; |
1990 |
|
- change format (in pkg/grdchk) of TLM output (+ add forward gradient) |
1991 |
|
to be easier to collect by testreport. |
1992 |
|
- update existing TLM output (half out-of-date by more than 3 yrs). |
1993 |
|
- report NETCDF & LAPACK settings (from genmake2) in output dir. |
1994 |
|
- report run-time in each individual summary (previously only for AD test); |
1995 |
|
for TLM test, add also TAF version. |
1996 |
|
- add daily TLM test on (old) aces cluster + weekly test on baudelaire. |
1997 |
|
|
1998 |
|
checkpoint63r (2012/08/15) |
1999 |
|
o tools/genmake2: |
2000 |
|
- fix Makefile for target ftlall (+ update files to clean after make ftlall) |
2001 |
|
o pkg/ecco/ecco_cost_final.F : |
2002 |
|
- fix fc print statements (to stdout and costfunction0000) so |
2003 |
|
that the printed value is always after the global sum. |
2004 |
|
o pkg/seaice/seaice_dynsolver.F : |
2005 |
|
- fix ice strength assymptote at SEAICE_area_max<1 |
2006 |
|
(no change for the standard case of SEAICE_area_max=1) |
2007 |
|
o some cleaning: |
2008 |
|
- pkg source files: ensure that all *.F files from each pkg included the |
2009 |
|
corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which |
2010 |
|
only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment |
2011 |
|
code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding |
2012 |
|
includes; |
2013 |
|
- model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used. |
2014 |
|
- ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR |
2015 |
|
is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when |
2016 |
|
ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop. |
2017 |
|
- update option-file CPP_OPTIONS.h of all AD experiments: |
2018 |
|
* no longer include PACKAGES_CONFIG.h ; |
2019 |
|
* includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ; |
2020 |
|
* def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before |
2021 |
|
including ECCO_CPPOPTIONS.h). |
2022 |
|
o pkg/cost, pkg/ctrl, pkg/ecco option-file: |
2023 |
|
- clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into |
2024 |
|
separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h, |
2025 |
|
not necessary accurate). |
2026 |
|
- add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in |
2027 |
|
pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to |
2028 |
|
deliberately break compilation (a remainder that it needs to be customized) |
2029 |
|
- in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h |
2030 |
|
- rename COST_CPPOPTIONS.h to COST_OPTIONS.h |
2031 |
|
- rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h |
2032 |
|
o tools/genamke2: |
2033 |
|
- check for lapack. |
2034 |
|
o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies. |
2035 |
|
- pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions |
2036 |
|
jointly. The exclusive ifdefs were removed, to add costs terms (when defined) |
2037 |
|
from both packages. |
2038 |
|
- the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly. |
2039 |
|
- for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs. |
2040 |
|
- pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes |
2041 |
|
of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly. |
2042 |
|
o pkg/cost : add comments to explain special and/or untested setups. |
2043 |
|
o pkg/exf: |
2044 |
|
- use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h |
2045 |
|
(previously, ALLOW_AUTODIFF_TAMC was controling this switch). |
2046 |
|
o verification/*/code_ad: |
2047 |
|
mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file: |
2048 |
|
- reccord when this file is included (define ECCO_CPPOPTIONS_H) |
2049 |
|
- remove the most obvious obsolete features (e.g., #define ALLOW_COST not |
2050 |
|
allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h) |
2051 |
|
o pkg/seaice : |
2052 |
|
- added possibility to change ice strength/PRESS0 relationship to |
2053 |
|
HEFF, according to the following run time parameters |
2054 |
|
SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0) |
2055 |
|
SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0) |
2056 |
|
SEAICEpresH0 :: HEFF threshold for ice strength (m) |
2057 |
|
o pkg/ggl90 : |
2058 |
|
- added run time flag mxlSurfFlag to include the code that ensure |
2059 |
|
mixing between first and second level (previously included as a comment) |
2060 |
|
o verification/1D_ocean_ice_column/input_ad/data.autodiff : |
2061 |
|
- add test of newly added dumpAdByRec=T option where |
2062 |
|
we write all records to one file per variable. |
2063 |
|
o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h : |
2064 |
|
- switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES |
2065 |
|
to check that this code is ok with taf and compiles in adjoint. |
2066 |
|
o pkg/autodiff : |
2067 |
|
- added run time param dumpAdByRec : ad dump format switch. |
2068 |
|
If true then write all records to one file per variable. |
2069 |
|
Else write one file per record (remains the default). |
2070 |
|
- revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly. |
2071 |
|
o pkg/seaice: |
2072 |
|
- Added SEAICEuseTILT run time switch : if set to |
2073 |
|
false then omit the tilt term in seaice dynamics. |
2074 |
|
- Fix free drift calculation. |
2075 |
|
o pkg/shelfice: |
2076 |
|
When initializing SHELFICEDragQuadratic, set default to be |
2077 |
|
consistent with shiCdrag in case SHELFICEuseGammaFrict is used, |
2078 |
|
but retain option to set it independently |
2079 |
|
(inconsistenty spotted by Veronique Dansereau) |
2080 |
|
o eesupp/inc: |
2081 |
|
- in EEPARAMS.h, add real-type constant for some frequently used simple number |
2082 |
|
(0,1,2,1/2), with name explicitly referring to RS/RL type. |
2083 |
|
o model/src: |
2084 |
|
- move balancing of relaxation terms to new S/R balance_relax.F. |
2085 |
|
o pkg/autodiff: |
2086 |
|
re-write active I/O high-level (control) S/R: |
2087 |
|
- rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL |
2088 |
|
- add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R. |
2089 |
|
- use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and |
2090 |
|
MDS_READ/WRITE_FIELD); change loops to multi-threads. |
2091 |
|
- update and merge active_file_control_slice.flow into active_file_control.flow |
2092 |
|
- update the calls in lower level S/R (active_file.F, active_file_g.F and |
2093 |
|
active_file_ad.F) keeping the argument list and function unchanged. |
2094 |
|
- also update lower-level "_LOC" version (call same S/R with "useCurrentDir |
2095 |
|
=.TRUE.") and remove high-level (control) _loc version (not called anymore). |
2096 |
|
- new low-level active I/O routines, one for each type (RL/RS), for active var |
2097 |
|
of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr); |
2098 |
|
fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the |
2099 |
|
right type. |
2100 |
|
o autodiff and RS=real*4: |
2101 |
|
- call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf |
2102 |
|
ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ; |
2103 |
|
- change argument type of 3-D mask argument to _RS to match type in the call |
2104 |
|
(in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued. |
2105 |
|
o pkg/thsice: |
2106 |
|
- re-anable balanceEmPmR when useSEAICE=T with useThSIce=T. |
2107 |
|
- option to correct ocean fresh-water flux for imbalance of Atmos+Land |
2108 |
|
fresh-water flux: uniform correction or proportional to local precip. |
2109 |
|
o pkg/ctrl: |
2110 |
|
- new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D |
2111 |
|
- redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to |
2112 |
|
ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC |
2113 |
|
- verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL |
2114 |
|
|
2115 |
|
checkpoint63q (2012/07/30) |
2116 |
|
o pkg/autodiff: |
2117 |
|
note about monitor and snap-shot of ad-variables: |
2118 |
|
a) need to apply ADEXCH before monitor or output of ad-vars to include |
2119 |
|
overlap contributions (was done for adjDump but missing for monitor). |
2120 |
|
b) since ADEXCH implies adding overlap values to interior array, machine |
2121 |
|
truncation error is expected when adding an ADEXCH call in the middle of |
2122 |
|
the time-stepping (although mathematically identical). |
2123 |
|
modifs: |
2124 |
|
- fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars |
2125 |
|
declaration (adEddyPsiX,adEddyPsiY in adcommon.h). |
2126 |
|
- add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to |
2127 |
|
apply ADEXCH before monitor or snap-shot of ad-variables: |
2128 |
|
=0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy. |
2129 |
|
- implement new method (copy+adexch) for snap-shot and monitor of main model |
2130 |
|
ad-vars (initially not used by default -> output unchanged). |
2131 |
|
- change default (set to 2) to use new method and update few output_adm.txt |
2132 |
|
with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo |
2133 |
|
and both tutorial_tracer_adjsens tests). |
2134 |
|
- switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice) |
2135 |
|
and turn off momDissip_In_AB in the 2 other (needed for stable AB-3). |
2136 |
|
o pkg/ctrl: |
2137 |
|
enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of |
2138 |
|
generic control variables via |
2139 |
|
#define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL |
2140 |
|
Only required customization should be S/R ctrl_map_ini_genarr.F |
2141 |
|
(routine in repository contains example) |
2142 |
|
o pkg/exf: |
2143 |
|
- fix and refine checking of surface-relaxation setting when using EXF |
2144 |
|
o verification (adjoint exp): |
2145 |
|
- reduce length of simulation by half for experiment global_ocean.cs32x15 |
2146 |
|
(std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output. |
2147 |
|
o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag) |
2148 |
|
- replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers |
2149 |
|
of KE that can occur with aggressive optimization |
2150 |
|
+ put quadratic bottom drag calculation in separated loops (only done if |
2151 |
|
using bottomDragQuadratic) |
2152 |
|
o model/src: CG2D_NSA |
2153 |
|
- clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF |
2154 |
|
and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE. |
2155 |
|
- in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens), |
2156 |
|
change cg2d residual target to be expressed in Wunits (=> do not normalise |
2157 |
|
RHS ; this fix global_max Pb with TAF); update output. |
2158 |
|
o verification/tutorial_tracer_adjsens: |
2159 |
|
improve parameter consistency (and get rid of warnings): |
2160 |
|
- use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf); |
2161 |
|
- switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical) |
2162 |
|
- use staggerTimeStep (for stability) in som81; use default rotation period. |
2163 |
|
o pkg/exch2: |
2164 |
|
- with empty facet: fix compact-format (W2_mapIO=1) definition (was previously |
2165 |
|
reset to 0 = 1 long line in X) |
2166 |
|
o pkg/mdsio: |
2167 |
|
- fix reading of dimensions from meta file for large-size domain |
2168 |
|
o model/src: |
2169 |
|
- fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long); |
2170 |
|
- to refine CS-grid check, add logical flag "hasWetCSCorners": true if using |
2171 |
|
Cubed-Sphere Exch with CS-corners inside the domain; |
2172 |
|
make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate |
2173 |
|
globalArea and to set hasWetCSCorners. |
2174 |
|
- add warning if usingCurvilinearGrid and momAdvection in flux-form (missing |
2175 |
|
metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form. |
2176 |
|
- re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if |
2177 |
|
useCDscheme and useCubedSphereExchange). |
2178 |
|
o pkg/seaice/seaice_growth.F : |
2179 |
|
- compute the SEAICE_DISABLE_HEATCONSFIX term accordingly |
2180 |
|
for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0) |
2181 |
|
when the previous code was not correct. |
2182 |
|
- in all cases diagnoze the boundary condition mismatch to SIaaflux |
2183 |
|
- in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add |
2184 |
|
that term to QNET (essentially to set the melt/freeze water to 0degC). |
2185 |
|
when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed. |
2186 |
|
o verification/global_ocean.cs32x15/input.seaice : |
2187 |
|
- add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget. |
2188 |
|
- add diagnostics (commented out) for budget test using my matlab codes (gcmfaces). |
2189 |
|
- update results (output.seaice.txt) accordingly. |
2190 |
|
o verification/lab_sea/input/data.seaice : |
2191 |
|
- remove SEAICEheatConsFix, which is now be tested |
2192 |
|
in global_ocean.cs32x15. The presently coded fix |
2193 |
|
is only consistent with real fresh water + nlfs. |
2194 |
|
- update results (output.txt) accordingly. |
2195 |
|
o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd). |
2196 |
|
o AD_CONFIG.h file: |
2197 |
|
- in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h; |
2198 |
|
- remove #include "AD_CONFIG.h" from all included OPTIONS files and |
2199 |
|
add it explicitly in each fortran src file where it is needed. |
2200 |
|
motivation: header file AD_CONFIG.h is generated/modified after "make depend" |
2201 |
|
thus introducing potentially wrong dependency; therefore, better to include |
2202 |
|
it only where it's really needed, and after any other included OPTIONS file |
2203 |
|
(less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN |
2204 |
|
or ALLOW_TANGENTLINEAR_RUN). |
2205 |
|
|
2206 |
|
checkpoint63p (2012/07/06) |
2207 |
|
o pkg/autodiff: |
2208 |
|
- rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ; |
2209 |
|
- create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters |
2210 |
|
which are now read from new parameter file "data.autodiff" (inAdExact |
2211 |
|
previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg) |
2212 |
|
- add file "data.autodiff" in all verification/*/input_ad/ directories. |
2213 |
|
- add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward |
2214 |
|
mode (used in global_ocean.cs32x15.seaice_dynmix test exp.) |
2215 |
|
o verification/tutorial_tracer_adjsens/ |
2216 |
|
- add extra sub-verification which uses "SOM" advection scheme |
2217 |
|
(2nd Order-Moment Advection Scheme, Prather Limiter) with |
2218 |
|
#define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h |
2219 |
|
and in data: |
2220 |
|
multiDimAdvection=.TRUE., |
2221 |
|
tempAdvScheme=81, |
2222 |
|
saltAdvScheme=81, |
2223 |
|
o model/src: |
2224 |
|
- introduce ALLOW_BALANCE_RELAX which allow the removal |
2225 |
|
of the global mean of relaxation terms by setting |
2226 |
|
balanceThetaClimRelax and balanceSaltClimRelax |
2227 |
|
- disable balanceEmPmR and balanceQnet in the case when useSeaice. |
2228 |
|
This case is now treated appropriately in seaice_growth.F |
2229 |
|
o pkg/seaice: |
2230 |
|
- do balanceEmPmR and balanceQnet based on the net fluxes |
2231 |
|
(SItflux) that enter the ocean+ice system rather than QNET |
2232 |
|
and EMPMR. Works best in real fresh water. |
2233 |
|
- SIatmFW, SIatmQnet, and SItflux computations had to be moved |
2234 |
|
out of the diagnotics bloc, and stored in global arrays. |
2235 |
|
|
2236 |
|
checkpoint63o (2012/06/29) |
2237 |
|
o vertical mixing schemes: |
2238 |
|
- remove unused S/R CALC_BUOYANCY (left from branch-atmos merging) |
2239 |
|
- replace computation of density (in Function STATE1, opps_calc.F) by a call |
2240 |
|
to S/R FIND_RHO_SCALAR |
2241 |
|
- pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC |
2242 |
|
and use it for N^2 calculation in ggl90_calc.F (save 2 density computations); |
2243 |
|
affects output (vermix.ggl90) at truncation level. |
2244 |
|
o testreport: |
2245 |
|
- change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles |
2246 |
|
(nSx,nSy) for the number of threads (from eedata.mth) |
2247 |
|
o model/src: |
2248 |
|
- remove 2nd set of calls at the top of initialise_varia.F (Adjoint part) |
2249 |
|
related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary). |
2250 |
|
o verification/tutorial_tracer_adjsens/ |
2251 |
|
- compile with ALLOW_CG2D_NSA |
2252 |
|
- run with nonlinFreeSurf=3 |
2253 |
|
- update reference output_adm.txt |
2254 |
|
o tools/genmake2: |
2255 |
|
- add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ; |
2256 |
|
refine usePROFILES switching off (only when NetCDF is not available). |
2257 |
|
o verification (atmospheric set-up): |
2258 |
|
- change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration |
2259 |
|
o pkg/profiles : refine profiles and files handling. |
2260 |
|
o model/src and pkg/ecco : introduce run-time switch usePROFILES. |
2261 |
|
o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h : |
2262 |
|
- changes to use model/src/the_main_loop.F rather than the ecco version |
2263 |
|
in ecco type adjoint runs. |
2264 |
|
o model/src: |
2265 |
|
- move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID |
2266 |
|
- move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC |
2267 |
|
- update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL) |
2268 |
|
o model/src: |
2269 |
|
- fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before); |
2270 |
|
update output of test experiment bottom_ctrl_5x5. |
2271 |
|
o pkg/generic_advdiff: |
2272 |
|
- implement vertical bi-harmonic diffusion (for now, only for T & S and |
2273 |
|
only explicitly). |
2274 |
|
o verification/bottom_ctrl_5x5/ |
2275 |
|
update reference output (results changed quite some time ago, |
2276 |
|
not sure when; but new reference results look ok in terms of grdchk) |
2277 |
|
o verification/1D_ocean_ice_column/ |
2278 |
|
For verification purposes, the exact adjoint rather than an approx. |
2279 |
|
should be used (e.g., to comare against F.D. or TLM). |
2280 |
|
removed autodiff_inadmode*_ad.F routines in code_ad/ |
2281 |
|
Update results/ accordingly. |
2282 |
|
o pkg/cal: |
2283 |
|
- change cal_getdate.F so that output date is function of input time only |
2284 |
|
(less ambiguous, not mixed up with input iteration number). |
2285 |
|
- fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP). |
2286 |
|
o pkg/diagnostics: |
2287 |
|
- implement calendarDumps also for stats-diags |
2288 |
|
- implement calendarDumps also for snap-shot output (negative freq) |
2289 |
|
- for now, ignores calendarDumps if non-zero phase-lag. |
2290 |
|
|
2291 |
|
checkpoint63n (2012/06/04) |
2292 |
|
o model/src: |
2293 |
|
- recompute rSurfW & S to ensure consistent column thickness (needed for rStar) |
2294 |
|
between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice; |
2295 |
|
- use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more |
2296 |
|
similar to calc_r_star.F); update results of experiment internal_wave and |
2297 |
|
tutorial_global_oce_in_p (affected @ truncation level). |
2298 |
|
o pkg/shelfice: |
2299 |
|
- add parameterisation of advective-diffusive flux into the ice shelf |
2300 |
|
according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd |
2301 |
|
- simply eps3/3a computation |
2302 |
|
o eesupp: |
2303 |
|
- add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange |
2304 |
|
between tiles, just fill-in edges assuming locally periodic subdomain) and |
2305 |
|
add corresponding exchange subroutines (EXCH0); |
2306 |
|
- new CG-solver version (_EX0) for disconnected-tiles special case. |
2307 |
|
o model/src (CG-solvers): |
2308 |
|
- modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached |
2309 |
|
(similar final residual output and max-Iter number as with standard version); |
2310 |
|
- allows to store and use lowest-residual solution (standard & _SR versions); |
2311 |
|
- cleaning up (remove old, commented out code, LETS_MAKE_JAM ...). |
2312 |
|
- by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h) |
2313 |
|
o eesup/src: |
2314 |
|
- global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef |
2315 |
|
ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012) |
2316 |
|
o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn |
2317 |
|
|
2318 |
|
checkpoint63m (2012/04/27) |
2319 |
|
o pkg/shelfice: |
2320 |
|
- account for partical cells in surface level below ice-shelf for hydrostatic |
2321 |
|
pressure calculion (set uniformFreeSurfLev to F); update isomip experiments. |
2322 |
|
o ad test experiments: |
2323 |
|
- update and rename to "ad_optfile.local" local AD-optfile specific to a |
2324 |
|
particular adjoint verification experiment (in verification/*/code_ad/) |
2325 |
|
o pkg/seaice & pkg/exf: |
2326 |
|
- Part two of ECCO-CLIVAR code merges. |
2327 |
|
Completes merge of seaice area relax. code. |
2328 |
|
Requires unified CPP option EXF_ALLOW_SEAICE_RELAX |
2329 |
|
to be set in EXF_OPTIONS.h since this pkg controls its I/O |
2330 |
|
(and avoids second CPP option in SEAICE_OPTIONS.h) |
2331 |
|
- change default value of costIceStart & costIceEnd to a valid date. |
2332 |
|
- add snowPrecip to HSNOW in seaice_growth |
2333 |
|
o pkg/ptracers: |
2334 |
|
- move ptracers summary and setup check into separated S/R ; add a check for |
2335 |
|
valid PTRACERS_Iter0 value (error+stop or just warning). |
2336 |
|
o pkg/cal (+ pkg/ecco): |
2337 |
|
- avoid calling a S/R with 2 times the same arg (FWD: unless both are only used |
2338 |
|
as input; and for AD, unless both are not differentiable (e.g., k index)). |
2339 |
|
o model/src: |
2340 |
|
- define internal flag "uniformFreeSurfLev" (=T when free-surface level-index |
2341 |
|
is everywhere k=1) to speed-up some calculations (by pass kSurf reference); |
2342 |
|
temporary set to usingZCoords value (to be changed to F when using shelfice). |
2343 |
|
- hydrostatic pressure: implement partial cell near the surface also for |
2344 |
|
Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on |
2345 |
|
usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code). |
2346 |
|
o pkg/ctrl/ctrl_init.F: |
2347 |
|
- add a formal parameter to s/r ctrl_init_rec to print |
2348 |
|
xx_$(ctrl_valiable)_file for easier debugging |
2349 |
|
- move call of cal_* routines into the if-block where they are really |
2350 |
|
needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having |
2351 |
|
to specify a startdate |
2352 |
|
o pkg/seaice: |
2353 |
|
- update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and |
2354 |
|
global_ocean.cs32x15/code versions). |
2355 |
|
- turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for |
2356 |
|
verification experiment global_ocean.cs32x15.seaice and update results. |
2357 |
|
o pkg/exf: |
2358 |
|
- new S/R EXF_GETFIELD_START to return starting-time of a forcing field |
2359 |
|
(according to useExfYearlyFields). |
2360 |
|
o pkg/cal: |
2361 |
|
- move calendar setting & summary (previously in cal_readparams.F) into new |
2362 |
|
S/R CAL_INIT_FIXED to be called later in the initialisation process, once |
2363 |
|
length of the simulation is set (after SET_PARMS call); This is an attempt |
2364 |
|
to fix Pb when, e.g.: pkg/longstep, modifies the length of the run. |
2365 |
|
- For safety: keep a record of pkg/cal parameter settings status |
2366 |
|
to allow to STOP if one pkg/cal S/R is called too early. |
2367 |
|
- add a stop in all basic pkg/cal subroutines if called before setting is done. |
2368 |
|
- modify cal_getdate.F: stop when nothing was returned; |
2369 |
|
if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2); |
2370 |
|
this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F. |
2371 |
|
|
2372 |
|
checkpoint63l (2012/04/04) |
2373 |
|
o pkg/bbl: |
2374 |
|
- fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc); |
2375 |
|
update global_with_exf output.yearly.txt file. |
2376 |
|
o pkg/cal: |
2377 |
|
- start to clean-up cal_set.F ; fix for the case where baseTime is non-zero. |
2378 |
|
- remove 2 unsused and very short (1 line only) functions ; |
2379 |
|
- remove unsused subroutines from AD-Diff list. |
2380 |
|
o model/src: |
2381 |
|
- start to implement clean wait to stop in initialization S/R (config_check.F, |
2382 |
|
packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage) |
2383 |
|
o folowing PRINT_MESSAGE changes: |
2384 |
|
- remove reminder multiple print to the same file (STDOUT) when multi-threads. |
2385 |
|
o pkg/bbl: |
2386 |
|
- modification so it can work with z* |
2387 |
|
- replace deltaT with dTtracerLev(k) for asynchronous time stepping |
2388 |
|
- global_with_exf/input.yearly verification; changes output.yearly.txt |
2389 |
|
o eesupp/src: |
2390 |
|
- PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR); |
2391 |
|
writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1 |
2392 |
|
- CHECK_THREADS: specific code if using OpenMP threading: improve checking of |
2393 |
|
# of threads across processors (e.g., different env OMP_NUM_THREADS setting) |
2394 |
|
- improve special preliminary call to EESET_PARMS (if eedata is read 2 times). |
2395 |
|
- when using MPI, always set usingMPI=T ; set default accordingly and stop |
2396 |
|
if not consistent. |
2397 |
|
- ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread |
2398 |
|
argument is zero (in case called within single-thread section). |
2399 |
|
o pkg/fizhi: |
2400 |
|
clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored |
2401 |
|
in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO. |
2402 |
|
o pkg/exch2: |
2403 |
|
- add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to |
2404 |
|
activate EXCH_IGNORE_CORNERS in vector EXCH S/R). |
2405 |
|
- switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS) |
2406 |
|
but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data |
2407 |
|
with bad ones coming from a not-yet-updated halo. |
2408 |
|
This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx. |
2409 |
|
o pkg/frazil: |
2410 |
|
move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F |
2411 |
|
http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html |
2412 |
|
o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy |
2413 |
|
o verification/lab_sea |
2414 |
|
* #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING |
2415 |
|
* #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL |
2416 |
|
* nTimeSteps 3 -> 4 |
2417 |
|
* changed reference output accordingly |
2418 |
|
o pkg/ctrl: |
2419 |
|
* fix ctrl_get_gen for xx_sst, xx_sss |
2420 |
|
o pkg/fizhi: |
2421 |
|
- fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F |
2422 |
|
update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d) |
2423 |
|
- by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE); |
2424 |
|
fix few out-of-bounds indices in referencing vars (initialise igrd to 1); |
2425 |
|
clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array). |
2426 |
|
o pkg/gmredi: |
2427 |
|
- add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp |
2428 |
|
o pkg/fizhi: |
2429 |
|
- fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the |
2430 |
|
(old)aces open64 tuv test. |
2431 |
|
o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F |
2432 |
|
o pkg/mom_vecinv: |
2433 |
|
- fix 1 loop range in mom_vecinv.F to be like all the other loops which |
2434 |
|
set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv |
2435 |
|
with non-lin free-surf). |
2436 |
|
o model/src: move k-loop outside of i/j-loops when (re-)computing R_low |
2437 |
|
in ini/update_masks_etc.F in order to avoid -O3 optimization problems with |
2438 |
|
some compilers (gfortran 4.6.0 on MacOS) |
2439 |
|
o momentum: |
2440 |
|
- separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM |
2441 |
|
& MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised |
2442 |
|
fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control. |
2443 |
|
|
2444 |
|
checkpoint63k (2012/03/17) |
2445 |
|
o model/src: |
2446 |
|
- selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum |
2447 |
|
flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations. |
2448 |
|
- SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version |
2449 |
|
(#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp. |
2450 |
|
o model/src: solve_*diagonal.F |
2451 |
|
- replace division with multiplication by inverse (similar to original version) |
2452 |
|
update output of AD exp. global_ocean.90x40x15. |
2453 |
|
- fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F |
2454 |
|
to enable the use of the vectorized & differentiable solve_tridiagonal.F |
2455 |
|
- test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for |
2456 |
|
vertical advection (to get solve_tridiagonal tested in AD mode). |
2457 |
|
o pkg/seaice: ECCO-CLIVAR merge: |
2458 |
|
1. seaice AREA relaxation |
2459 |
|
* CPP option: SEAICE_ALLOW_AREA_RELAXATION |
2460 |
|
* runtime flag: SEAICE_tauAreaObsRelax |
2461 |
|
2. modified global mean cost imbalance code: CPP option |
2462 |
|
ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION |
2463 |
|
o another iteration on solve_*diagonal.F |
2464 |
|
Make choices independent of AUTODIFF |
2465 |
|
Default will be the adjoinable vectorized version. |
2466 |
|
Alternative choices are: |
2467 |
|
* non-adjoinable original version with low memory footprint: |
2468 |
|
#define SOLVE_DIAGONAL_LOWMEMORY |
2469 |
|
* still adjoinable but does not vectorize (k as inner-most loop): |
2470 |
|
#define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef) |
2471 |
|
o testreport |
2472 |
|
- add option to use a home made wrapper around "make" |
2473 |
|
- remove MITGCM_IEEE env. variable (no longer active) |
2474 |
|
o pkg/shelfice |
2475 |
|
- improve computation of friction velocity for velocity dependent |
2476 |
|
exchange coefficients: include velocities into SHELFICEBoundaryLayer |
2477 |
|
block to average velocities vertically |
2478 |
|
- add TAF store directives for SHI_ALLOW_GAMMAFRICT |
2479 |
|
o Modify diagonal solvers, now three versions (upon request): |
2480 |
|
#ifndef SOLVE_DIAGONAL_AUTODIFF |
2481 |
|
1. default version (dating back a while ago) |
2482 |
|
#else /* def SOLVE_DIAGONAL_AUTODIFF */ |
2483 |
|
# ifdef SOLVE_DIAGONAL_KINNER |
2484 |
|
2. adjoinable version with k-innermost loop (G. Forget) |
2485 |
|
# else |
2486 |
|
3. adjoinable vectorized version of 2. |
2487 |
|
# endif |
2488 |
|
#endif /* SOLVE_DIAGONAL_AUTODIFF */ |
2489 |
|
All flags are currently set within routines, but could/should be moved to CPP-options. |
2490 |
|
Array bounds for 1. are as before, for 2.,3. cover the entire domain |
2491 |
|
(could be changed for 1. too). |
2492 |
|
o verification/lab_sea (fwd): |
2493 |
|
- update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY, |
2494 |
|
use 7 categories (except hb87), new solve4temp params (except salt_plume), |
2495 |
|
constant salinity (=4) or variable salinity (salt_plume) done through |
2496 |
|
SItracer. |
2497 |
|
o pkg/seaice: |
2498 |
|
- rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0; |
2499 |
|
- remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t, |
2500 |
|
SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz) |
2501 |
|
from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when |
2502 |
|
SEAICE_freeze got retired) but already better than previously with |
2503 |
|
SEAICE_freeze=123456.7 deg.C; |
2504 |
|
- move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS |
2505 |
|
(safer multi-threaded setting); always set SEAICEuseEVP; |
2506 |
|
- setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to |
2507 |
|
SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report); |
2508 |
|
stop if multiple specifications for the same coeff; make sure default |
2509 |
|
SEAICE_mcPheePiston is compatible with drF(1) & deltaT. |
2510 |
|
o pkg/obcs: |
2511 |
|
- allow to switch to upwind 1rst order advection scheme for the advective |
2512 |
|
flux computation at the open-boundary; disabled for adjoint built. |
2513 |
|
o pkg/ptracers: |
2514 |
|
- rename PTRACERS_RESTART.h -> PTRACERS_START.h |
2515 |
|
- rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F |
2516 |
|
- add parameter to decide when to start a tracer; use internal flag to |
2517 |
|
know which tracer to step-forward; switch this internal flag at the top |
2518 |
|
of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled |
2519 |
|
for adjoint built. |
2520 |
|
o pkg/seaice: |
2521 |
|
- add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ; |
2522 |
|
- move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ; |
2523 |
|
- keep experiment offline_exf_seaice truly single category (set MULTDIM=1). |
2524 |
|
o pkg/ecco: |
2525 |
|
- fix writing of output file DiagnosCost_ClimSalt/Theta |
2526 |
|
and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc). |
2527 |
|
o pkg/seaice: |
2528 |
|
- add missing initialisation of COR_ICE array in dynsolver.F |
2529 |
|
- merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is |
2530 |
|
compiled either way, and is tested in all exps (multidim was only tested |
2531 |
|
in lab_sea ad before). |
2532 |
|
- cosmetic change to prepare for future addition of ITD. no change to results. |
2533 |
|
no defaults change. |
2534 |
|
- added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise). |
2535 |
|
- by lack of adequate verification experiments, I further used custom versions |
2536 |
|
of global_ocean.cs32x15 to test multicat or not, with pickup or not. All |
2537 |
|
should be correct. |
2538 |
|
- avoid recomputations in ad. |
2539 |
|
o array initialisation in adjoint mode: |
2540 |
|
1) pkg/mom_common/mom_calc_ke.F: |
2541 |
|
add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC): |
2542 |
|
The S/R which calls MOM_CALC_KE initialises KE but in some recomputation |
2543 |
|
part this initialisation is gone, resulting in Floating Point Exception |
2544 |
|
(caught by open64 compiler with debug option). |
2545 |
|
2) model/src/convective_weights.F |
2546 |
|
set output convectCount over the full array range (instead of doing |
2547 |
|
an update): this fix a similar issue when called within recomputation (adjoint) |
2548 |
|
which could by-pass the initialisation (normally done in the caller S/R). |
2549 |
|
o pkg/seaice: |
2550 |
|
- final version of turbulent flux params, as agreed at MIT ice meet: |
2551 |
|
SEAICE_mcPheePiston (default is ~ 0.000875) |
2552 |
|
SEAICE_mcPheeTaper (default is 0.) |
2553 |
|
SEAICE_frazilFrac (defualt is 1.) |
2554 |
|
SEAICE_mcPheeStepFunc (default is false) |
2555 |
|
- changes results at trunction error level |
2556 |
|
- ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo |
2557 |
|
o added pkg/frazil: |
2558 |
|
- see frazil_description.tex for details |
2559 |
|
- verification experiment is global_with_exf/input.yearly; changes output.yearly.txt |
2560 |
|
o pkg/shelfice/shelfice_thermodynamics.F |
2561 |
|
- fix exponents for velocity dependent exchange coefficients: change |
2562 |
|
from 2/3(=0) to 0.66666666666666667 |
2563 |
|
- move computation of velocity dependent exchange coefficients into |
2564 |
|
separate loop, so that it applies to both thermodynamics |
2565 |
|
- move some divisions by constants out of loops |
2566 |
|
|
2567 |
|
checkpoint63j (2012/02/16) |
2568 |
|
o pkg/seaice: |
2569 |
|
- overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc. |
2570 |
|
- SItracer: added run time params, and allow coupling to ocn salinity. |
2571 |
|
o pkg/seaice: remove (almost) all divisions by constants within loops |
2572 |
|
in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d |
2573 |
|
results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only |
2574 |
|
those, caused by 1/QI -> recip_QI) -> update output.seaice.txt, |
2575 |
|
output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt |
2576 |
|
o pkg/seaice : |
2577 |
|
- simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula |
2578 |
|
= 1 or 2, using newly added run time parameter SEAICE_availHeatTaper. |
2579 |
|
- fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148. |
2580 |
|
- add permanent SItflux diag that corresponds to TFLUX but includes |
2581 |
|
ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget. |
2582 |
|
- allow activation/testing of a fix for suspected missing term in |
2583 |
|
ocn-ice heat budget (to be confirmed). To test this, you want to |
2584 |
|
undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param |
2585 |
|
SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic. |
2586 |
|
- no change in results, fwd or ad. |
2587 |
|
o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below: |
2588 |
|
- switch to variable freezing point. |
2589 |
|
Results change : cg2d -> 1 digits; ad -> 3-6-6 digits. |
2590 |
|
- bug fix : the sublimation term that was missing is now activated. |
2591 |
|
Results change : cg2d -> 2 digits; ad -> 8-6-6 digits. |
2592 |
|
- bug fix : flooding sign term for SIsal0.NE.0. |
2593 |
|
Result change : cg2d -> 8 digits; ad -> 11-12-9 digits. |
2594 |
|
o pkg/seaice: |
2595 |
|
- unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT |
2596 |
|
is now the default, and the old default constant freezing point is recovered |
2597 |
|
with SEAICE_tempFrz0 = -1.96, |
2598 |
|
SEAICE_dTempFrz_dS = 0., |
2599 |
|
- retire SEAICE_freeze (= the old way of specifycing the constant freezing point) |
2600 |
|
- remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there. |
2601 |
|
- bug fix (thanks to M. Losch) : the sublimation term that was missing is now |
2602 |
|
activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM. |
2603 |
|
- bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211) |
2604 |
|
was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail). |
2605 |
|
- bug fix (thanks to O. Jahn) : area loss for melting got messed up in |
2606 |
|
seaice_growth r149 for legacy branch (no results change). |
2607 |
|
- introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code |
2608 |
|
from I. Fenty). |
2609 |
|
- results did not change except for global_ocean.cs32x15, mostly due to the |
2610 |
|
switch to variable freezing point (see above item for detail). |
2611 |
|
o pkg/thsice: |
2612 |
|
- fix and simplify interface to salt_plume pkg ; diagnose directly amount of |
2613 |
|
seawater freezing in thsice_calc_thickn (not used). |
2614 |
|
o pkg/seaice: turbulent flux term specification via run time params. |
2615 |
|
- replace CPP switches with run time switches to facilitate testing |
2616 |
|
- retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, |
2617 |
|
GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR |
2618 |
|
- added runtime parameter : SEAICEturbFluxFormula |
2619 |
|
- move Mcphee constants to SEAICE_PARAMS.h |
2620 |
|
- seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula; |
2621 |
|
SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); |
2622 |
|
remove seaice_summary call (moved to seaice_init_fixed) |
2623 |
|
- seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on |
2624 |
|
SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms) |
2625 |
|
- seaice_summary.F : add missing report of read turbulent flux term set up |
2626 |
|
and SITRACER. |
2627 |
|
- seaice_check.F : check range; inform and stop if retired CPPs are used |
2628 |
|
(incl. SEAICE_AGE). |
2629 |
|
- seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without |
2630 |
|
CPP switch, same computation as before for the different options. |
2631 |
|
- change results at the truncation level. |
2632 |
|
o pkg/seaice: |
2633 |
|
- remove un-used parameters LAD & MAX_TICE ; add new run-time parameters: |
2634 |
|
useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and |
2635 |
|
SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY. |
2636 |
|
- update verification/*/input*/data.seaice: |
2637 |
|
to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY |
2638 |
|
code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ; |
2639 |
|
and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code, |
2640 |
|
set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0. |
2641 |
|
o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY): |
2642 |
|
- remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same |
2643 |
|
algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0); |
2644 |
|
difference in results only due to machine truncation. |
2645 |
|
- remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using |
2646 |
|
MaykutPolySatVap; keep MIN_LWDOWN. |
2647 |
|
- adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation. |
2648 |
|
- update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87, |
2649 |
|
+ 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits). |
2650 |
|
o pkg/salt_plume: |
2651 |
|
- isolate saltPlumeFlux array exch into a specific S/R called from |
2652 |
|
do_oceanic_phys.F |
2653 |
|
- add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice. |
2654 |
|
o verification: |
2655 |
|
- move untested set-up to MITgcm_contrib/verification_other. |
2656 |
|
o pkg/seaice: |
2657 |
|
- retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER. |
2658 |
|
o pkg/seaice: |
2659 |
|
- seaice_solve4temp.F (keeping results unchanged): |
2660 |
|
* add 2 future run-time params to select which saturation vapor pressure |
2661 |
|
formula is used and how post-iteration fluxes are set. |
2662 |
|
Temporary set these 2 params according to option SOLVE4TEMP_LEGACY; |
2663 |
|
* New piece of code (not used) to update surf. atmos. heat flux F_ia using |
2664 |
|
the linearized expression to stay consistent with tsurf finding. |
2665 |
|
- seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x |
2666 |
|
can be < 0. |
2667 |
|
o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef): |
2668 |
|
- remove from F_ia (and from it's derivative dFiDTs1) the contribution of |
2669 |
|
conductive heat flux F_c , and add it explicitly when updating tsurf as |
2670 |
|
solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf |
2671 |
|
so that now F_ia has a consistent meaning through the entire routine. |
2672 |
|
This causes differences at truncation level: update output of fwd exp. |
2673 |
|
global_ocean.cs32x15.seaice. |
2674 |
|
o pkg/seaice: |
2675 |
|
- lots of editing/cleaning in seaice_solve4temp.F + better documentation |
2676 |
|
of arrays, sign/direction of fluxes; no effect on results. |
2677 |
|
- replace hard coded 273.16 (=previous value of celsius2K) by celsius2K |
2678 |
|
in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part); |
2679 |
|
note: this should have been done before changing celsius2K default. |
2680 |
|
- to keep results unchanged, add back old value of celsius2K in verification |
2681 |
|
exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs |
2682 |
|
- replace hard coded seawater freezing temp in seaice_solve4temp.F (part |
2683 |
|
SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default |
2684 |
|
value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater |
2685 |
|
freezing temp is consistent with value in seaice_growth.F ; this causes |
2686 |
|
differences at machine truncation level: update lab_sea AD output (3/4). |
2687 |
|
o pkg/seaice: |
2688 |
|
- mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask |
2689 |
|
and climsst/sss even when using seaice (to prevent calculation that might |
2690 |
|
use SST on land); does not affect any verification exp. |
2691 |
|
- apply mask to taux,tauy (in seaice_get_dynforcing.F); update output |
2692 |
|
of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix. |
2693 |
|
o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness |
2694 |
|
over land (non-legacy code) |
2695 |
|
o vectorize salt_plume package: |
2696 |
|
- add extra code to salt_plume_frac and salt_plume_tendency_apply_s |
2697 |
|
- this code computes plumebk everywhere (also over land), thus requires |
2698 |
|
code to avoid divisions by zero and catch the case of kLev=Nr. |
2699 |
|
- efficiency of salt_plume_frac is still sub-optimal |
2700 |
|
o tools (genmake2): |
2701 |
|
- fix makefile NAME specification (option: -makefile NAME) by adding |
2702 |
|
"-f $MAKEFILE" in few places where it was missing including makedepend |
2703 |
|
command (contribution from Paul). |
2704 |
|
|
2705 |
|
checkpoint63i (2012/01/24) |
2706 |
|
o model/src: |
2707 |
|
- add factorized versions of some EOS code to find_rho.F, |
2708 |
|
define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX) |
2709 |
|
o model/src: |
2710 |
|
- add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h; |
2711 |
|
- change default celsius2K from 273.16 to 273.15 |
2712 |
|
- to keep results unchanged, add back old value of celsius2K in verification |
2713 |
|
exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd), |
2714 |
|
global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm). |
2715 |
|
o model/src: add a little initialisation trick to find_rho.F and find_alpha.F |
2716 |
|
to make TAF generate vectorizable code |
2717 |
|
o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows. |
2718 |
|
Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers |
2719 |
|
have flags that do this more efficiently. |
2720 |
|
o pkg/diagnostics/diagstats_calc.F |
2721 |
|
- for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact |
2722 |
|
o pkg/obcs (with exch2): |
2723 |
|
- derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F) |
2724 |
|
and remove code (in obcs_readparms.F) which was based on EXCH of indices |
2725 |
|
(through buffer) and did not account for exch2 (e.g., CS-grid) topology. |
2726 |
|
o pkg/exf and seaice exp: |
2727 |
|
- change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0) |
2728 |
|
so that switching off area & heff advection flags does not affect results. |
2729 |
|
- change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h |
2730 |
|
- keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef |
2731 |
|
EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update |
2732 |
|
results of verification experiments: 1D_ocean_ice_column(fwd), |
2733 |
|
global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8) |
2734 |
|
and offline_exf_seaice (all 4). |
2735 |
|
o pkg/seaice: |
2736 |
|
- remove array YNEG, RIVER, TMIX (replaced by local var) from common block; |
2737 |
|
remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef. |
2738 |
|
- fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY) |
2739 |
|
but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and |
2740 |
|
not multi-dim advection; |
2741 |
|
- fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and |
2742 |
|
SHORTWAVE_HEATING #undef. |
2743 |
|
o optim: make Makefile more robust (?) |
2744 |
|
o pkg/obcs: |
2745 |
|
* fix treatment of obcs_read_pickup for TAF |
2746 |
|
o pkg/shelfice: |
2747 |
|
* add missing initialisation of num_shifwflx |
2748 |
|
* new adjoint verification exp. for isomip |
2749 |
|
* change Prandtl and Schmidt numbers from generic formulations |
2750 |
|
(in terms of model diffus. and visc.) to separate runtime |
2751 |
|
parameters, with Holland and Jenkins (1999) default values. |
2752 |
|
o pkg/exf (interpolation): |
2753 |
|
- extended input field (2 rows) near the N & S poles: |
2754 |
|
* fill in with the symetric value (when even Nb of data in longitude) |
2755 |
|
* add average value at the poles only for scalar quantities ; for vector |
2756 |
|
component interpolation, skip the averaging and keep duplicated values, |
2757 |
|
unless the 2 components have same location (uvInterp=T) in which case |
2758 |
|
interpolate the 2 components together using S/R EXF_INTERP_UV. |
2759 |
|
- new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field |
2760 |
|
together: this allows to account properly for local orientation when |
2761 |
|
averaging at N & S pole. |
2762 |
|
- add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding |
2763 |
|
exf-interpolation near N & S poles. Undef by default. |
2764 |
|
- add debug check/print on 1rst iter if debugLevel >=2. |
2765 |
|
o pkg/exf: |
2766 |
|
- change masking flags definition (no longer "parameter"), put them in |
2767 |
|
common block and set them in S/R EXF_INIT_FIXED. |
2768 |
|
- change recognized masking flag from s,u,v to c,w,s since the mask |
2769 |
|
to use (maskC,W,S) depends on position on model grid and has little to |
2770 |
|
do with scalar/vector difference; fix masking if using P-coordinates. |
2771 |
|
- fix masking of wind-stress (was wrong if interpolated or read on A-grid) |
2772 |
|
and update results of exp. global_with_exf (x2). |
2773 |
|
- fix setting of zenith-angle table when SHORTWAVE_HEATING is undef. |
2774 |
|
o pkg/obcs |
2775 |
|
- S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate) |
2776 |
o pkg/exf (interpolation): |
o pkg/exf (interpolation): |
2777 |
- assume periodicity in X only if input field cover full longitude range. |
- assume periodicity in X only if input field cover full longitude range. |
2778 |
- improve search for lat. index (supposed to be faster, in ~log2(ny) steps, |
- improve search for lat. index (supposed to be faster, in ~log2(ny) steps, |