4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
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|
7 |
o pkg/seaice/seaice_do_ridging.F: clean up the insectarium |
o pkg/seaice |
8 |
|
- add overlap for restrictive additive Schwartz method also to LSR, but |
9 |
|
turn it off by default (because it only seems to work for non-cubed |
10 |
|
sphere/llc topologies) |
11 |
|
o pkg/autodiff |
12 |
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- add extra exchanges in addummy_in_steppging also for mnc output |
13 |
|
o pkg/seaice: |
14 |
|
- add extra exchanges before dumping adjoint fields in seaice_ad_dump.F |
15 |
|
to avoid stripes in the adjoint output (similar to addummy_in_stepping.F) |
16 |
|
o pkg/obcs: |
17 |
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- add option to specify domain-connected piece Id along OB though files |
18 |
|
(for now, only used to diagnose PhiVel; default =1 -> global correction) |
19 |
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- modify obcs_diag_balance.F to process each connected-part separately; |
20 |
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exclude OB where Id = 0 but keep the full divergence there (-> constant |
21 |
|
Psi along this portion of OB and all inflow derived from grad(Phi)) |
22 |
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- add example of OB-conect files in verification/so_box_biogeo/input. |
23 |
|
o pkg/diagnostics: |
24 |
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- improve treatment of Open-Boundaries in Velocity-Potential calculation: |
25 |
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a) use non zero matrix element across OB and solve for Phi 1 grid point |
26 |
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outside OB (i.e, where tracer OBCS are applied). |
27 |
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b) global imbalance of inFlow/outFlow across OB: instead of modifying |
28 |
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velocity across OB, spread it uniformly along the OB in the RHS. |
29 |
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|
30 |
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checkpoint65g (2014/11/19) |
31 |
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o pkg/diagnostcis: |
32 |
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- add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param |
33 |
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o pkg/my82,pp81,kl10: |
34 |
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- fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D |
35 |
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field diffKr as background diffusivity to set minimum diffusivity value. |
36 |
|
o pkg/seaice: |
37 |
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- add new parameter SEAICEuseEVPrev (for revisited EVP by |
38 |
|
Bouillon et al 2013) |
39 |
|
- add SEAICE_evpAlpha/Beta to namelist |
40 |
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- modify seaice_evp code to able to use SEAICEuseEVPrev. These changes |
41 |
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involve trivial re-ordering of divisions/multiplications that should not |
42 |
|
have any effects, but ... they do change the results of lab_sea.hb87 so |
43 |
|
that only 2 digits of agreement remain, in line with the general |
44 |
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instability/fragility of the evp-code. For now, I do not care and just |
45 |
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update the verification experiment |
46 |
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o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc) |
47 |
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- remove xx_genarr2d_numsmooth etc |
48 |
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- use xx_genarr2d_preproc etc instead |
49 |
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- carry out smooth_correl2D at initialization stage rather than during |
50 |
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time stepping. |
51 |
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- get smoothOpNb from xx_gentim2d_preproc |
52 |
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o global_oce_cs32 : |
53 |
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- add test of generic ecco capabilities. |
54 |
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o pkg/exf/exf_getsurfacefluxes.F : |
55 |
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- add to tmpUE/tmpVN rather than re-initializing them (conventional behavior). |
56 |
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o pkg/ctrl,ecco : |
57 |
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- omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED |
58 |
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is defined. |
59 |
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o pkg/seaice: add diagnostics for Delta (deformation parameter) |
60 |
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o model/src: |
61 |
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- when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical |
62 |
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diffusivity (background) is specified but ignored. |
63 |
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o verification: |
64 |
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- in testreport, convert hostname to lower case for default output dir name |
65 |
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o model, pkg : add useCTRL, useECCO parameters (on/off run time switch). |
66 |
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o pkg/dic: add modifications from Hajoon: |
67 |
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- add iron sedimentation flux function of the flux of PO4 out of bottom layer |
68 |
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- light attenuation: add self-shading effect by climatological Chlorophyll |
69 |
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(read from file). |
70 |
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o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also |
71 |
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compiles when SEAICE_ALLOW_DYNAMICS is undefined |
72 |
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o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
73 |
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AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
74 |
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ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
75 |
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approach where CPP_OPTIONS.h includes an omnipotent |
76 |
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ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
77 |
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o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
78 |
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ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
79 |
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o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
80 |
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to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
81 |
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(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
82 |
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o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
83 |
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add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
84 |
|
- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
85 |
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- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
86 |
|
- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
87 |
|
o pkg/ctrl,ecco,exf : |
88 |
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- remove variables associated with NON-generic costs, |
89 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
90 |
|
- remove NON-generic NON-obcs controls, |
91 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
92 |
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o pkg/ctrl : added ctrl_local_params.h |
93 |
|
o pkg/ecco : added ecco_local_params.h |
94 |
|
o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
95 |
|
experiments, which will progressively be removed once the |
96 |
|
experiments are revised to use only generic controls/costs. |
97 |
|
|
98 |
|
checkpoint65f (2014/10/13) |
99 |
|
o pkg/ctrl, ecco, seaice : minor changes in headers |
100 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
101 |
|
cost function and control capabilities added since checkpoint65c. |
102 |
|
o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
103 |
|
o pkg/ecco: increase modularity and improve logic |
104 |
|
- ecco_toolbox.F (new) : basic operations that are often used, |
105 |
|
including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk, |
106 |
|
ecco_addcost, ecco_add, ecco_div, ecco_readbar. |
107 |
|
- cost_gencal.F (new) : determine filnames and records. |
108 |
|
- cost_genread.F, cost_generic.F : condense code using ecco_toolbox. |
109 |
|
- cost_generic.F : use spzeroloc rather than hard-coded -9999, |
110 |
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and exploit the above functions leading to more compact code. |
111 |
|
- cost_genread.F : rm un-necessary arguments, re-arrange args order. |
112 |
|
- ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj, |
113 |
|
using_ers, using_gfo, using_mdt is now only defined within gencost) |
114 |
|
o pkg/ecco: extend generic cost capabilities |
115 |
|
- pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost |
116 |
|
capabilities via gencost_preproc (+ _c,_i,_r related params), |
117 |
|
gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod, |
118 |
|
gencost_outputlevel arguments to cost_generic |
119 |
|
- pkg/ecco/cost_genread.F (new) : interface between cost_generic |
120 |
|
and active_read, making room for gencost_preproc to take effect. |
121 |
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Added preproc code ('climmon') to replace GENERIC_BAR_MONTH. |
122 |
|
- pkg/ecco/cost_generic.F : |
123 |
|
compute and store misfit maks*(model-data) in localdif that is |
124 |
|
then used in cost and for output, output misfit if outlev.GT.0 |
125 |
|
- pkg/ecco/cost_averagesfields.F : depend on gencost_barskip |
126 |
|
rather gencost_barfile for deciding whether to write barfile |
127 |
|
- pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd |
128 |
|
- pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from |
129 |
|
ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip |
130 |
|
- pkg/ecco/ecco_summary.F : report gencost variables |
131 |
|
- pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs |
132 |
|
o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA |
133 |
|
o pkg/ecco: internal re-organization |
134 |
|
- resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl |
135 |
|
(rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter, |
136 |
|
mv relevant variables definition from ecco_cost.h to ecco.h, |
137 |
|
make sure gencost routines only include ecco.h) |
138 |
|
- throughout : add missing CCP switches, rm unused variables, |
139 |
|
and rm un-necessary CPP switches |
140 |
|
- throughout gencost routines : replace modelstartdate with |
141 |
|
gencost_startdate when needed |
142 |
|
- cost_bp_read.F : use arguments, instead of common blocs |
143 |
|
so that it can be used also by (new) cost_gencost_bpv4.F |
144 |
|
- ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0 |
145 |
|
- ecco_phys.F : compute etanFull |
146 |
|
- ecco_readparms.F : rename using_topex as using_tpj, add |
147 |
|
bpv4-grace to gencost list, initialize added parameters |
148 |
|
- ecco_summary.F : include SIZE.h needed for augmented ecco.h |
149 |
|
|
150 |
|
checkpoint65e (2014/09/28) |
151 |
|
o pkg/obcs: |
152 |
|
- replaced the just-added CPP options with run-time variables |
153 |
|
(see pkg/obcs/OBCS_PARAMS.h for details) |
154 |
|
o pkg/obcs: |
155 |
|
- add additional CPP options for sponge boundary layers |
156 |
|
(see pkg/obcs/OBCS_OPTIONS.h for details) |
157 |
|
o pkg/atm_phys: |
158 |
|
- implement simple (obliquity only, assuming circular planet orbit) |
159 |
|
seasonal cycle for incoming insolation ; used when run-time parameter |
160 |
|
"select_incSW" is set to 1 ; by default (=0), uses old unchanged formula. |
161 |
|
o pkg/exf, pkg/ecco, pkg/ctrl: |
162 |
|
- add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets |
163 |
|
- activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip |
164 |
|
- implement gentim2d for xx_tauu, xx_tauv |
165 |
|
o pkg/ctrl, pkg/ecco : |
166 |
|
- fix and complement the generic controls implementation |
167 |
|
o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F, |
168 |
|
pkg/shelfice/shelfice_thermodynamics.F, |
169 |
|
verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F, |
170 |
|
verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F : |
171 |
|
- add weight in CTRL_GET_GEN calls |
172 |
|
o pkg/ctrl : |
173 |
|
- ctrl_get_gen.F : add weight as input parameter, and apply |
174 |
|
it directly rather than using smooth_correl2Dw (to be retired). |
175 |
|
- ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call |
176 |
|
o pkg/ctrl : |
177 |
|
- introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, |
178 |
|
ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) |
179 |
|
- re-activate ctrl_summary (call in ctrl_init.F) |
180 |
|
o pkg/ctrl/ctrl_cost_gen.F : |
181 |
|
- fix CCP brackets, remove un-necessary myiter, mytime |
182 |
|
o pkg/ecco, pkg/ctrl : |
183 |
|
- remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) |
184 |
|
- remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) |
185 |
|
- add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) |
186 |
|
- add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) |
187 |
|
|
188 |
|
checkpoint65d (2014/09/15) |
189 |
|
o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : |
190 |
|
- add xx_genarr2d_bounds,xx_genarr3d_bounds, |
191 |
|
xx_genarr2d_numsmooth, xx_genarr3d_numsmooth |
192 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : |
193 |
|
- remove compilation failure |
194 |
|
- replace hard coded example |
195 |
|
- use ctrl_map_ini_gen2D, 3D |
196 |
|
o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : |
197 |
|
- on/off switch based upon xx_genarr2d_weight,3d |
198 |
|
o src/packages_init_variables.F : |
199 |
|
- regroup pkg/estimation calls |
200 |
|
- remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
201 |
|
(moved to ctrl_init_variables) |
202 |
|
o cost/cost_init_varia.F : |
203 |
|
- remove ecco_cost_init_varia |
204 |
|
(moved to ecco_init_varia) |
205 |
|
o ctrl/ctrl_init_variables.F : |
206 |
|
- add CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
207 |
|
- add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI |
208 |
|
o ctrl/ctrl_map_ini.F : |
209 |
|
- remove ctrl_map_ini_genarr, seaice_ctrl_map_ini |
210 |
|
(moved to ctrl_init_variables) |
211 |
|
o ctrl/ctrl_map_ini_ecco.F : |
212 |
|
- remove ECCO_PHYS (mv to ecco_init_varia) |
213 |
|
- remove seaice_ctrl_map_ini (mv to ctrl_init_variables) |
214 |
|
o ecco/ecco_ad_diff.list : |
215 |
|
- add ecco_init_varia.f |
216 |
|
o ecco/ecco_init_varia.F |
217 |
|
- new routine |
218 |
|
o pkg/streamice: |
219 |
|
- move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F |
220 |
|
to streamice_init_fixed.F ; fix setting of STREAMICEisOn. |
221 |
|
- from model/src, only call pkg/streamice routines if useStreamIce is TRUE. |
222 |
|
o pkg/generic_advdiff: |
223 |
|
- fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. |
224 |
|
o pkg/exf: |
225 |
|
- exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, |
226 |
|
xxg_precip capability |
227 |
|
- exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch |
228 |
|
o pkg/ctrl: |
229 |
|
- ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d |
230 |
|
o model/src/load_fields_driver.F : |
231 |
|
- move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING |
232 |
|
so xx_gentim2d can be applied to e.g. exf fields in a timely manner. |
233 |
|
o OpenAD verification experiments: |
234 |
|
- Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h |
235 |
|
in src files (to enable to skip the ECCO_CPPOPTIONS.h); |
236 |
|
for now, only in pkgs used in OpenAD verification experiments. |
237 |
|
- Change all except one (halfpipe_streamice) OpenAD experiments to use pkg |
238 |
|
specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) |
239 |
|
instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). |
240 |
|
This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. |
241 |
|
o OpenAD verification tests: |
242 |
|
- finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); |
243 |
|
- finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for |
244 |
|
tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. |
245 |
|
- leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) |
246 |
|
and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). |
247 |
|
o model/src & generic_advdiff: |
248 |
|
- change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S |
249 |
|
forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model |
250 |
|
dynamics requires valid tracer forcing only over tile interior but, for |
251 |
|
some diagnostics, may need to extend it over 1 point in tile halo region. |
252 |
|
- in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid |
253 |
|
tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max |
254 |
|
setting in temp/salt/ptracer_integrate.F |
255 |
|
o pkg/dic: |
256 |
|
- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
257 |
|
gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
258 |
|
in gchem_forcing_sep.F |
259 |
|
o pkg/autodiff & obcs: |
260 |
|
- add storage of current OB values for U & V (was already done for T & S). |
261 |
|
|
262 |
|
checkpoint65c (2014/08/30) |
263 |
|
o pkg/dic: |
264 |
|
- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
265 |
|
and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
266 |
|
AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
267 |
|
o verification: |
268 |
|
- new experiment testing OBCS and DIC pkgs, using params & output from |
269 |
|
tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
270 |
|
passage: take OBCS from the last year of a 2 yrs simulation and initial |
271 |
|
conditions from t=1.yr while keeping the same forcing. |
272 |
|
o model/src: |
273 |
|
- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
274 |
|
(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
275 |
|
o pkg/diagnostics (Stats-Diags): |
276 |
|
- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
277 |
|
a) refine region where stats are computed, excluding where arrhFac=0 ; |
278 |
|
b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
279 |
|
c) extend regional stats over the region edges (for U or V pt location). |
280 |
|
o pkg/gchem: |
281 |
|
- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
282 |
|
pkg/dic is currently changing/updating ptracers values beyond the OB). |
283 |
|
o verification (hs94): |
284 |
|
- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
285 |
|
bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
286 |
|
hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
287 |
|
apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
288 |
|
o pkg/ptracers: |
289 |
|
- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
290 |
|
switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
291 |
|
- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
292 |
|
with AB-2 code (so that it get tested). |
293 |
|
o model/src: |
294 |
|
- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
295 |
|
with AB-2 code (previously only available with AB-3 code). |
296 |
|
Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
297 |
|
to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
298 |
|
there, by calling CYCLE_AB_TRACER). |
299 |
|
o pkg/generic_advdiff: |
300 |
|
- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
301 |
|
GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
302 |
|
+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
303 |
|
S/R temp/salt/ptracers_integrate.F |
304 |
|
o model/src & pkg/ptracers: |
305 |
|
- remove common block variables gT,gS (in DYNVARS.h), except when |
306 |
|
USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
307 |
|
- remove common block variable gPtr. |
308 |
|
o model/src & pkgs: |
309 |
|
- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
310 |
|
ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
311 |
|
IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
312 |
|
GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
313 |
|
+ change accordingly all calling S/R. |
314 |
|
- use local temperature/salinity/ptracer tendency array (without bi,bj) |
315 |
|
in S/R temp/salt/ptracers_integrate.F |
316 |
|
o pkg/seaice: |
317 |
|
- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
318 |
|
to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
319 |
|
- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
320 |
|
in seaice_lsr |
321 |
|
- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
322 |
|
in s/r seaice_lsr_calc_coeffs |
323 |
|
o pkg/mdsio: |
324 |
|
- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
325 |
|
(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
326 |
|
too long (e.g., > MAX_LEN_FNAM/2 ) |
327 |
|
|
328 |
|
checkpoint65b (2014/08/12) |
329 |
|
o pkg/matrix: |
330 |
|
- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
331 |
|
o model/src: |
332 |
|
- fix initialisation of geothermalFile; compile geothermal-flux code in |
333 |
|
natl_box verification experiment. |
334 |
|
o model/src & pkg/down_slope: |
335 |
|
- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
336 |
|
- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
337 |
|
field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
338 |
|
results at machine truncation level: update output of experiments |
339 |
|
global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
340 |
|
o pkg/diagnostics (Stats-Diags): |
341 |
|
- do not cumulate the full volume when DIAGNOSTICS_FILL is |
342 |
|
called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
343 |
|
This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
344 |
|
times (but Min,Max and StD are still wrong). |
345 |
|
o model/src: |
346 |
|
- add geothermal flux forcing: read in ini_forcing.F as time-constant |
347 |
|
field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
348 |
|
o model/src: |
349 |
|
- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
350 |
|
_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
351 |
|
arrays are already updated while adjustments (filters, conv.adjustment) are |
352 |
|
still applied later, in S/R TRACERS_CORRECTION_STEP. |
353 |
|
o model/src: |
354 |
|
- store in common bloc array "rhoInSitu" the virtual potential temperature |
355 |
|
anomaly that is used to compute geopotential: this make the atmos code |
356 |
|
more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
357 |
|
o pkg/seaice/seaice_lsr.F |
358 |
|
- rename integer variable ilcall to ipass (that's what it is called |
359 |
|
in the residual diagnostics |
360 |
|
- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
361 |
|
default) for improved non-linear convergence of the first few steps |
362 |
|
- adjust a few comments and add new ones to explain some of the store |
363 |
|
directives |
364 |
|
o pkg/generic_advdiff (& ptracers): |
365 |
|
- re-work the code to check for valid advection scheme and for minimum |
366 |
|
size of overlap (now stored in local common bloc in gad_advscheme.F) |
367 |
|
o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
368 |
|
- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
369 |
|
- add an auxilliary variable "bet" and fix store directives and keys in |
370 |
|
seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
371 |
|
less exact gradients in my tests); but there are still |
372 |
|
recomputation warning (although gradients are sort of OK), when |
373 |
|
SEAICE_LSR_VECTORIZE is not defined, so this flag and |
374 |
|
SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
375 |
|
- update verification experiments lab_sea. |
376 |
|
- change some comments in S/R seaice_calc_viscosities |
377 |
|
o model/src: |
378 |
|
- if staggerTimeStep=T, always apply exchange to velocity field in |
379 |
|
do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
380 |
|
(independent of using multi-dim advection or not); no effect on FWD run |
381 |
|
but affects AD results (at machine truncation level): update output of |
382 |
|
experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
383 |
|
and isomip (oad: 12.d). |
384 |
|
o pkg/generic_advdiff: |
385 |
|
- stop if doAB_onGtGs is set to FALSE but ignored |
386 |
|
- refine warning related to stability of tracer time-stepping |
387 |
|
regarding internal wave dynamics. |
388 |
|
- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
389 |
|
on staggerTimeStep & implicitIntGravWave (will now get a warning |
390 |
|
if potentially unstable). |
391 |
|
o pkg/kl10: |
392 |
|
- add new pkg "kl10" for mixing due to internal wave breaking, from |
393 |
|
http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
394 |
|
(contribution from Jody Klymak), tested in verification experiment |
395 |
|
verification/internal_wave/input.kl10/ |
396 |
|
o isomip experiment: |
397 |
|
- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
398 |
|
(input.htd) and update the output. |
399 |
|
o cd_code experiments: |
400 |
|
- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
401 |
|
#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
402 |
|
global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
403 |
|
update the corresponding output. |
404 |
|
o pkg/seaice: |
405 |
|
- reduce the number of include files and store directives in |
406 |
|
S/R seaice_lsr_tridiagu/v |
407 |
|
- change the order of loops in one case in S/R seaice_lsr_tridiagv |
408 |
|
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
409 |
|
get rid off one store directive (a TAF bug?) |
410 |
|
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
411 |
|
S/R seaice_lsr_tridiagv to change the loop range for consistency |
412 |
|
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
413 |
|
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
414 |
|
S/R seaice_lsr_tridiagu/v (requires update of |
415 |
|
offline_exf_seaice/input.dyn_jfnk) |
416 |
|
|
417 |
|
checkpoint65a (2014/07/27) |
418 |
|
o model/src: |
419 |
|
- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
420 |
|
surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
421 |
|
(topo in p-coords, ice-shelf in z-coords); update output of experiments |
422 |
|
tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
423 |
|
o model/src: |
424 |
|
- collect momentum forcing tendency into local 2-D array (passed as argument |
425 |
|
to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
426 |
|
parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
427 |
|
affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
428 |
|
- collect T & S forcing tendency into local 2-D array (passed as argument to |
429 |
|
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
430 |
|
affects results at machine truncation level (e.g., ocean: if using |
431 |
|
SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
432 |
|
correction due to vertical advection). |
433 |
|
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
434 |
|
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
435 |
|
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
436 |
|
obcs_ctrl (ad & fwd grd @ 12 & 7). |
437 |
|
o pkg/ptracers & diagnostics: |
438 |
|
- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
439 |
|
title (to avoid some unexpected truncation); sort out ptracers diags units. |
440 |
|
- collect ptracer forcing tendency into local 2-D array (passed as argument |
441 |
|
to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
442 |
|
|
443 |
|
checkpoint65 (2014/07/18) |
444 |
|
o pkg/fizhi: |
445 |
|
- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
446 |
|
affects results at machine truncation level. Update output of experiments |
447 |
|
fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). |
448 |
|
o pkg/seaice: more clean up |
449 |
|
- rename TAF common block tapes to be more consistent and remove |
450 |
|
unnecessary duplicates |
451 |
|
- add store directives to remove more recomputations, but use smaller |
452 |
|
tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. |
453 |
|
The idea behind this flag is to reduce the memory footprint when the |
454 |
|
adjoint of the LSR is not required. As of now, defining the flag |
455 |
|
SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by |
456 |
|
a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). |
457 |
|
For experiment offline_exf_seaice, this means on a linux box with gfortran |
458 |
|
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
459 |
|
this experiment): |
460 |
|
> size mitgcmuv_ad |
461 |
|
text data bss dec hex |
462 |
|
5100659 1216 220458952 225560827 d71c8fb |
463 |
|
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
464 |
|
but only a moderate increase of 36% for global_ocean.cs32x15: |
465 |
|
text data bss dec hex |
466 |
|
6695027 1648 1014578664 1021275339 3cdf6ccb |
467 |
|
6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER) |
468 |
|
- note: there are still recomputations in global_ocean.cs32x15 and |
469 |
|
offline_exf_seaice and the gradient agreement changes (gets a |
470 |
|
little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) |
471 |
|
- in general, the AD gradients still are wrong |
472 |
|
o OpenAD |
473 |
|
- clean up code_oad/ directories somewhat by moving files |
474 |
|
dontCompile, dontTransform, keepOriginal to OAD_support/ |
475 |
|
o model/src: |
476 |
|
- using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F |
477 |
|
(not currently tested): add dissipation terms before NLFS rescaling of |
478 |
|
tendencies (previously done after). |
479 |
|
o pkg/diagnostics: |
480 |
|
- write stats-diags in ascii file with more digits (same as in monitor). |
481 |
|
o pkg/down_slope: |
482 |
|
- drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with |
483 |
|
NLFS (not tested), use new recip_hFac value in order to conserve tracer. |
484 |
|
o model/src: |
485 |
|
- new file "apply_forcing.F" containing all the code previously in |
486 |
|
external_forcing.F, but with new argument list: pass, as new argument, |
487 |
|
the current level tendency array to update (instead of a direct update |
488 |
|
of the common bloc array). Change the corresponding calls. |
489 |
|
- add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use |
490 |
|
EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility). |
491 |
|
o pkg/seaice/seaice_lsr, a little bit of clean up |
492 |
|
- rearrange some code blocks, so that now all calculations for |
493 |
|
setting up the right-hand-sides done within one single block |
494 |
|
(I find that easier to read and understand) |
495 |
|
- rearrange freedrift-code to reduce the number of ifdefs |
496 |
|
- adjust some indentations and comments |
497 |
|
|
498 |
|
checkpoint64z (2014/07/10) |
499 |
|
o model/src and several pkgs: |
500 |
|
- change argument list of all S/R called from external_forcing.F and |
501 |
|
called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F) |
502 |
|
to pass, as argument, the current level tendency array to update |
503 |
|
(instead of a direct update of the common bloc array). |
504 |
|
- change also (in the same way) argument list of PTRACERS_APPLY_FORCING; |
505 |
|
- rename taueddy_external_forcing.f to taueddy_tendency_apply.F |
506 |
|
o pkg/seaice/seaice_lsr.F |
507 |
|
- always initialize local arrays in seaice_lsr_tridiagu/v |
508 |
|
- add more local tapes to seaice_lsr_tridiagu/v |
509 |
|
- move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but |
510 |
|
keep it in bi/bj loop; this seems to be essential |
511 |
|
- gradients are still wrong but only by 4-7 orders of magnitude |
512 |
|
instead of 15 orders of magnitude, lab_sea improves a little |
513 |
|
o pkg/seaice |
514 |
|
- (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that |
515 |
|
generates unnecessary code in seaice_lsr_ad |
516 |
|
- add more store directives in seaice_lsr to avoid unnecessary code |
517 |
|
in seaice_lsr_ad |
518 |
|
- exclude some residual computations in seaice_lsr when |
519 |
|
ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code |
520 |
|
in seaice_lsr_ad |
521 |
|
- add more storing, a new tape (model/src/the_main_loop.F) and |
522 |
|
another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey |
523 |
|
and klockey should be checked by a specialist) |
524 |
|
- modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER ) |
525 |
|
and update lab_sea after previous changes in pkg/seaice below |
526 |
|
o pkg/autodiff: |
527 |
|
- introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and |
528 |
|
viscFacInAd : run time parameters allowing for adjoint switches |
529 |
|
note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F |
530 |
|
o pkg/ecco: |
531 |
|
- introduce cost_gencost_boxmean.F that computes a box mean |
532 |
|
temperature (for use in adjoint sensitivity studies). |
533 |
|
o model/src/set_defaults.F : initialize viscFacAdj to 1. |
534 |
|
o pkg/mom_common/mom_calc_visc.F: |
535 |
|
- ifdef ALLOW_AUTODIFF then include viscFacAdj factor. |
536 |
|
o pkg/seaice/seaice_summary.F: |
537 |
|
- statement for SEAICEadjMODE now in autodiff_readparms.F |
538 |
|
o pkg/seaice: |
539 |
|
- remove some store directives and add new ones in an effort to get |
540 |
|
finally rid off the recomputation warnings. This is successful |
541 |
|
when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are |
542 |
|
defined (i.e. no extensive recomputation warnings left), but there |
543 |
|
are still too many recomputations on the solver iteration level |
544 |
|
- define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h |
545 |
|
- move definition of MPSEUDOTIMESTEPS into TAMC-block in |
546 |
|
SEAICE_SIZE.h |
547 |
|
- add a store directive in S/R seaice_calc_viscosities |
548 |
|
o pkg/seaice (ITD code): |
549 |
|
- fix definition of Hlimit for multi-threaded case |
550 |
|
- use double precision arithmetic to compute Hlimit: this affects results; |
551 |
|
update output of experiment seaice_itd. |
552 |
|
o replace content of verification/seaice_itd |
553 |
|
- instead of a 1D column use the configuration of offline_exf_seaice |
554 |
|
to test the ice thickness distribution code with ridging |
555 |
|
- this is a first shot at this experiment |
556 |
|
- change of some defaults of ridging parameters SEAICEhStar (from |
557 |
|
100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F |
558 |
|
and lot of new comments. |
559 |
|
|
560 |
|
checkpoint64y (2014/06/20) |
561 |
|
o pkg/seaice/seaice_reg_ridge.F: |
562 |
|
- modify the regularization of very small volumes of ice; only check |
563 |
|
total volume HEFF, and do not apply correction to individual ice |
564 |
|
classes because that leads to funny patterns in the heat and fw-fluxes |
565 |
|
into the ocean. Adjust seaice_itd/results/output.txt |
566 |
|
- replace nITD by SEAICE_multDim in loop-ranges |
567 |
|
o pkg/exf: |
568 |
|
- add code to process the case field period = -12. with UV interpolation. |
569 |
|
- move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec |
570 |
|
into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F) |
571 |
|
o verification/global_with_exf: |
572 |
|
- switch all fields period to -12. (was previously untested) in input/data.exf |
573 |
|
(but keep secondary test ".yearly" unchanged); update the reference output. |
574 |
|
o pkg/cal: |
575 |
|
- new calendar type "noLeapYear" for 365 days calendar without any leap year. |
576 |
|
o pkg/exf: |
577 |
|
- new integer parameter "exf_debugLev" (default set to main model debugLevel) |
578 |
|
to replace logical switch "exf_verbose" |
579 |
|
- report in STDOUT when loading a new record (if exf_debugLev >= 3) |
580 |
|
o pkg/sbo: |
581 |
|
- update from Katherine Quinn: evaluate mass directly from density and SSH |
582 |
|
(budget using Finite Volume method) instead of from bottom pressure. |
583 |
|
- allow testreport to collect few selected SBO output ; tested in exp. |
584 |
|
global_ocean.90x40x15 (after updating the results, to include SBO output). |
585 |
|
- fix some multi-threading issues (in output part). |
586 |
|
o model/src & most packages: |
587 |
|
- always call {PKG}_READPARMS even if corresponding use{PKG}=F; |
588 |
|
- in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R |
589 |
|
PACKAGES_UNUSED_MSG to print a weak warning when parameter file |
590 |
|
"data.{pkg}" exist ; and leave the S/R (return) just after. |
591 |
|
- more standard LAND pkg interface (land_init_fixed.F, land_check.F). |
592 |
|
+ call LAND_READPARMS from packages_readparms.F |
593 |
|
o pkg/seaice: |
594 |
|
- remove code that resets useThSice in S/R seaice_readparms and |
595 |
|
replace it by a warning in S/R seaice_check |
596 |
|
- remove parameter MULTDIM, replace with nITD and runtime |
597 |
|
parameter SEAICE_multDim (still hard-wired to nITD if |
598 |
|
SEAICE_ITD is defined) |
599 |
|
|
600 |
|
checkpoint64x (2014/05/24) |
601 |
|
o verification/lab_sea: |
602 |
|
- update adjoint and TLM output following changes to pkg/salt_plume |
603 |
|
- un-do the update after putting back local recip_Cp in few places. |
604 |
|
o pkg/salt_plume: modifications by An Nguyen: |
605 |
|
- add capability to do brine rejection (salt-plume) as function of |
606 |
|
volume+tracers (instead of only salinity tracer). |
607 |
|
- conserve volume by exchanging volume from each kLev to above to |
608 |
|
accommodate in-coming brine volume |
609 |
|
- store surface and klev exchanged fraction + volume in 4 new 3-d arrays |
610 |
|
- switch KPP surf buoyancy due to brine forcing to 3-d |
611 |
|
(3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume) |
612 |
|
- add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t |
613 |
|
- unrelatedly, also add ad-hoc capability to vary salt_plume scheme |
614 |
|
in East/West Arctic. |
615 |
|
o pkg/sbo: |
616 |
|
- incorporate modifications from Katherine Quinn to enable the use of sbo |
617 |
|
pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like |
618 |
|
output for future testreport verification (unfinished). |
619 |
|
o pkg/atm_phys: |
620 |
|
- change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R: |
621 |
|
skip the reseting of t_ref & q_ref to initial t & q ; this preserve the |
622 |
|
output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics. |
623 |
|
o pkg/seaice |
624 |
|
seaice_calc_ice_strength.F: modify expression to avoid divisions |
625 |
|
(affects truncation) |
626 |
|
seaice_do_ridging.F: clean up the insectarium |
627 |
- fix a bug that was compensated by areaScaling (-> remove areaScaling code) |
- fix a bug that was compensated by areaScaling (-> remove areaScaling code) |
628 |
- added SEAICEsnowFracRidge to redistributed snow (2nd bug) |
- added SEAICEsnowFracRidge to redistributed snow (2nd bug) |
629 |
- set closing/openingRate to zero where no extra iteration is need (3rd bug) |
- set closing/openingRate to zero where no extra iteration is need (3rd bug) |
630 |
- add some debugging information and error messages (warnings) |
- add some debugging information and error messages (warnings) |
631 |
o model/src: modifications relatd to atmosphere p*: |
o model/src: modifications relatd to atmosphere p*: |
632 |
- Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F) |
- Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F) |
633 |
- With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead |
- With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead |