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/diagnostcis: |
8 |
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- improve treatment of Open-Boundaries in Velocity-Potential calculation: |
9 |
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a) use non zero matrix element across OB and solve for Phi 1 grid point |
10 |
|
outside OB (i.e, where tracer OBCS are applied). |
11 |
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b) global imbalance of inFlow/outFlow across OB: instead of modifying |
12 |
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velocity across OB, spread it uniformly along the OB in the RHS. |
13 |
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|
14 |
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checkpoint65g (2014/11/19) |
15 |
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o pkg/diagnostcis: |
16 |
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- add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param |
17 |
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o pkg/my82,pp81,kl10: |
18 |
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- fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D |
19 |
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field diffKr as background diffusivity to set minimum diffusivity value. |
20 |
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o pkg/seaice: |
21 |
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- add new parameter SEAICEuseEVPrev (for revisited EVP by |
22 |
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Bouillon et al 2013) |
23 |
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- add SEAICE_evpAlpha/Beta to namelist |
24 |
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- modify seaice_evp code to able to use SEAICEuseEVPrev. These changes |
25 |
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involve trivial re-ordering of divisions/multiplications that should not |
26 |
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have any effects, but ... they do change the results of lab_sea.hb87 so |
27 |
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that only 2 digits of agreement remain, in line with the general |
28 |
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instability/fragility of the evp-code. For now, I do not care and just |
29 |
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update the verification experiment |
30 |
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o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc) |
31 |
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- remove xx_genarr2d_numsmooth etc |
32 |
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- use xx_genarr2d_preproc etc instead |
33 |
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- carry out smooth_correl2D at initialization stage rather than during |
34 |
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time stepping. |
35 |
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- get smoothOpNb from xx_gentim2d_preproc |
36 |
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o global_oce_cs32 : |
37 |
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- add test of generic ecco capabilities. |
38 |
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o pkg/exf/exf_getsurfacefluxes.F : |
39 |
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- add to tmpUE/tmpVN rather than re-initializing them (conventional behavior). |
40 |
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o pkg/ctrl,ecco : |
41 |
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- omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED |
42 |
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is defined. |
43 |
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o pkg/seaice: add diagnostics for Delta (deformation parameter) |
44 |
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o model/src: |
45 |
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- when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical |
46 |
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diffusivity (background) is specified but ignored. |
47 |
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o verification: |
48 |
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- in testreport, convert hostname to lower case for default output dir name |
49 |
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o model, pkg : add useCTRL, useECCO parameters (on/off run time switch). |
50 |
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o pkg/dic: add modifications from Hajoon: |
51 |
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- add iron sedimentation flux function of the flux of PO4 out of bottom layer |
52 |
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- light attenuation: add self-shading effect by climatological Chlorophyll |
53 |
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(read from file). |
54 |
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o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also |
55 |
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compiles when SEAICE_ALLOW_DYNAMICS is undefined |
56 |
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o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
57 |
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AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
58 |
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ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
59 |
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approach where CPP_OPTIONS.h includes an omnipotent |
60 |
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ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
61 |
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o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
62 |
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ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
63 |
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o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
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to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
65 |
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(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
66 |
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o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
67 |
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add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
68 |
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- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
69 |
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- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
70 |
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- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
71 |
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o pkg/ctrl,ecco,exf : |
72 |
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- remove variables associated with NON-generic costs, |
73 |
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unless ECCO_CTRL_DEPRECATED is defined. |
74 |
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- remove NON-generic NON-obcs controls, |
75 |
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unless ECCO_CTRL_DEPRECATED is defined. |
76 |
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o pkg/ctrl : added ctrl_local_params.h |
77 |
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o pkg/ecco : added ecco_local_params.h |
78 |
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o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
79 |
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experiments, which will progressively be removed once the |
80 |
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experiments are revised to use only generic controls/costs. |
81 |
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|
82 |
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checkpoint65f (2014/10/13) |
83 |
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o pkg/ctrl, ecco, seaice : minor changes in headers |
84 |
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o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
85 |
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cost function and control capabilities added since checkpoint65c. |
86 |
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o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
87 |
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o pkg/ecco: increase modularity and improve logic |
88 |
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- ecco_toolbox.F (new) : basic operations that are often used, |
89 |
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including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk, |
90 |
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ecco_addcost, ecco_add, ecco_div, ecco_readbar. |
91 |
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- cost_gencal.F (new) : determine filnames and records. |
92 |
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- cost_genread.F, cost_generic.F : condense code using ecco_toolbox. |
93 |
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- cost_generic.F : use spzeroloc rather than hard-coded -9999, |
94 |
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and exploit the above functions leading to more compact code. |
95 |
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- cost_genread.F : rm un-necessary arguments, re-arrange args order. |
96 |
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- ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj, |
97 |
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using_ers, using_gfo, using_mdt is now only defined within gencost) |
98 |
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o pkg/ecco: extend generic cost capabilities |
99 |
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- pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost |
100 |
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capabilities via gencost_preproc (+ _c,_i,_r related params), |
101 |
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gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod, |
102 |
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gencost_outputlevel arguments to cost_generic |
103 |
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- pkg/ecco/cost_genread.F (new) : interface between cost_generic |
104 |
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and active_read, making room for gencost_preproc to take effect. |
105 |
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Added preproc code ('climmon') to replace GENERIC_BAR_MONTH. |
106 |
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- pkg/ecco/cost_generic.F : |
107 |
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compute and store misfit maks*(model-data) in localdif that is |
108 |
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then used in cost and for output, output misfit if outlev.GT.0 |
109 |
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- pkg/ecco/cost_averagesfields.F : depend on gencost_barskip |
110 |
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rather gencost_barfile for deciding whether to write barfile |
111 |
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- pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd |
112 |
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- pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from |
113 |
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ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip |
114 |
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- pkg/ecco/ecco_summary.F : report gencost variables |
115 |
|
- pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs |
116 |
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o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA |
117 |
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o pkg/ecco: internal re-organization |
118 |
|
- resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl |
119 |
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(rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter, |
120 |
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mv relevant variables definition from ecco_cost.h to ecco.h, |
121 |
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make sure gencost routines only include ecco.h) |
122 |
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- throughout : add missing CCP switches, rm unused variables, |
123 |
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and rm un-necessary CPP switches |
124 |
|
- throughout gencost routines : replace modelstartdate with |
125 |
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gencost_startdate when needed |
126 |
|
- cost_bp_read.F : use arguments, instead of common blocs |
127 |
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so that it can be used also by (new) cost_gencost_bpv4.F |
128 |
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- ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0 |
129 |
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- ecco_phys.F : compute etanFull |
130 |
|
- ecco_readparms.F : rename using_topex as using_tpj, add |
131 |
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bpv4-grace to gencost list, initialize added parameters |
132 |
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- ecco_summary.F : include SIZE.h needed for augmented ecco.h |
133 |
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|
134 |
|
checkpoint65e (2014/09/28) |
135 |
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o pkg/obcs: |
136 |
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- replaced the just-added CPP options with run-time variables |
137 |
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(see pkg/obcs/OBCS_PARAMS.h for details) |
138 |
|
o pkg/obcs: |
139 |
|
- add additional CPP options for sponge boundary layers |
140 |
|
(see pkg/obcs/OBCS_OPTIONS.h for details) |
141 |
|
o pkg/atm_phys: |
142 |
|
- implement simple (obliquity only, assuming circular planet orbit) |
143 |
|
seasonal cycle for incoming insolation ; used when run-time parameter |
144 |
|
"select_incSW" is set to 1 ; by default (=0), uses old unchanged formula. |
145 |
|
o pkg/exf, pkg/ecco, pkg/ctrl: |
146 |
|
- add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets |
147 |
|
- activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip |
148 |
|
- implement gentim2d for xx_tauu, xx_tauv |
149 |
|
o pkg/ctrl, pkg/ecco : |
150 |
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- fix and complement the generic controls implementation |
151 |
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o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F, |
152 |
|
pkg/shelfice/shelfice_thermodynamics.F, |
153 |
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verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F, |
154 |
|
verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F : |
155 |
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- add weight in CTRL_GET_GEN calls |
156 |
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o pkg/ctrl : |
157 |
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- ctrl_get_gen.F : add weight as input parameter, and apply |
158 |
|
it directly rather than using smooth_correl2Dw (to be retired). |
159 |
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- ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call |
160 |
|
o pkg/ctrl : |
161 |
|
- introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, |
162 |
|
ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) |
163 |
|
- re-activate ctrl_summary (call in ctrl_init.F) |
164 |
|
o pkg/ctrl/ctrl_cost_gen.F : |
165 |
|
- fix CCP brackets, remove un-necessary myiter, mytime |
166 |
|
o pkg/ecco, pkg/ctrl : |
167 |
|
- remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) |
168 |
|
- remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) |
169 |
|
- add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) |
170 |
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- add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) |
171 |
|
|
172 |
|
checkpoint65d (2014/09/15) |
173 |
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o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : |
174 |
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- add xx_genarr2d_bounds,xx_genarr3d_bounds, |
175 |
|
xx_genarr2d_numsmooth, xx_genarr3d_numsmooth |
176 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : |
177 |
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- remove compilation failure |
178 |
|
- replace hard coded example |
179 |
|
- use ctrl_map_ini_gen2D, 3D |
180 |
|
o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : |
181 |
|
- on/off switch based upon xx_genarr2d_weight,3d |
182 |
|
o src/packages_init_variables.F : |
183 |
|
- regroup pkg/estimation calls |
184 |
|
- remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
185 |
|
(moved to ctrl_init_variables) |
186 |
|
o cost/cost_init_varia.F : |
187 |
|
- remove ecco_cost_init_varia |
188 |
|
(moved to ecco_init_varia) |
189 |
|
o ctrl/ctrl_init_variables.F : |
190 |
|
- add CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
191 |
|
- add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI |
192 |
|
o ctrl/ctrl_map_ini.F : |
193 |
|
- remove ctrl_map_ini_genarr, seaice_ctrl_map_ini |
194 |
|
(moved to ctrl_init_variables) |
195 |
|
o ctrl/ctrl_map_ini_ecco.F : |
196 |
|
- remove ECCO_PHYS (mv to ecco_init_varia) |
197 |
|
- remove seaice_ctrl_map_ini (mv to ctrl_init_variables) |
198 |
|
o ecco/ecco_ad_diff.list : |
199 |
|
- add ecco_init_varia.f |
200 |
|
o ecco/ecco_init_varia.F |
201 |
|
- new routine |
202 |
|
o pkg/streamice: |
203 |
|
- move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F |
204 |
|
to streamice_init_fixed.F ; fix setting of STREAMICEisOn. |
205 |
|
- from model/src, only call pkg/streamice routines if useStreamIce is TRUE. |
206 |
|
o pkg/generic_advdiff: |
207 |
|
- fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. |
208 |
|
o pkg/exf: |
209 |
|
- exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, |
210 |
|
xxg_precip capability |
211 |
|
- exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch |
212 |
|
o pkg/ctrl: |
213 |
|
- ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d |
214 |
|
o model/src/load_fields_driver.F : |
215 |
|
- move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING |
216 |
|
so xx_gentim2d can be applied to e.g. exf fields in a timely manner. |
217 |
|
o OpenAD verification experiments: |
218 |
|
- Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h |
219 |
|
in src files (to enable to skip the ECCO_CPPOPTIONS.h); |
220 |
|
for now, only in pkgs used in OpenAD verification experiments. |
221 |
|
- Change all except one (halfpipe_streamice) OpenAD experiments to use pkg |
222 |
|
specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) |
223 |
|
instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). |
224 |
|
This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. |
225 |
|
o OpenAD verification tests: |
226 |
|
- finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); |
227 |
|
- finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for |
228 |
|
tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. |
229 |
|
- leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) |
230 |
|
and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). |
231 |
|
o model/src & generic_advdiff: |
232 |
|
- change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S |
233 |
|
forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model |
234 |
|
dynamics requires valid tracer forcing only over tile interior but, for |
235 |
|
some diagnostics, may need to extend it over 1 point in tile halo region. |
236 |
|
- in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid |
237 |
|
tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max |
238 |
|
setting in temp/salt/ptracer_integrate.F |
239 |
|
o pkg/dic: |
240 |
|
- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
241 |
|
gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
242 |
|
in gchem_forcing_sep.F |
243 |
|
o pkg/autodiff & obcs: |
244 |
|
- add storage of current OB values for U & V (was already done for T & S). |
245 |
|
|
246 |
|
checkpoint65c (2014/08/30) |
247 |
|
o pkg/dic: |
248 |
|
- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
249 |
|
and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
250 |
|
AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
251 |
|
o verification: |
252 |
|
- new experiment testing OBCS and DIC pkgs, using params & output from |
253 |
|
tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
254 |
|
passage: take OBCS from the last year of a 2 yrs simulation and initial |
255 |
|
conditions from t=1.yr while keeping the same forcing. |
256 |
|
o model/src: |
257 |
|
- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
258 |
|
(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
259 |
|
o pkg/diagnostics (Stats-Diags): |
260 |
|
- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
261 |
|
a) refine region where stats are computed, excluding where arrhFac=0 ; |
262 |
|
b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
263 |
|
c) extend regional stats over the region edges (for U or V pt location). |
264 |
|
o pkg/gchem: |
265 |
|
- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
266 |
|
pkg/dic is currently changing/updating ptracers values beyond the OB). |
267 |
|
o verification (hs94): |
268 |
|
- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
269 |
|
bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
270 |
|
hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
271 |
|
apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
272 |
|
o pkg/ptracers: |
273 |
|
- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
274 |
|
switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
275 |
|
- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
276 |
|
with AB-2 code (so that it get tested). |
277 |
|
o model/src: |
278 |
|
- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
279 |
|
with AB-2 code (previously only available with AB-3 code). |
280 |
|
Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
281 |
|
to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
282 |
|
there, by calling CYCLE_AB_TRACER). |
283 |
|
o pkg/generic_advdiff: |
284 |
|
- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
285 |
|
GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
286 |
|
+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
287 |
|
S/R temp/salt/ptracers_integrate.F |
288 |
|
o model/src & pkg/ptracers: |
289 |
|
- remove common block variables gT,gS (in DYNVARS.h), except when |
290 |
|
USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
291 |
|
- remove common block variable gPtr. |
292 |
|
o model/src & pkgs: |
293 |
|
- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
294 |
|
ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
295 |
|
IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
296 |
|
GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
297 |
|
+ change accordingly all calling S/R. |
298 |
|
- use local temperature/salinity/ptracer tendency array (without bi,bj) |
299 |
|
in S/R temp/salt/ptracers_integrate.F |
300 |
|
o pkg/seaice: |
301 |
|
- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
302 |
|
to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
303 |
|
- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
304 |
|
in seaice_lsr |
305 |
|
- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
306 |
|
in s/r seaice_lsr_calc_coeffs |
307 |
|
o pkg/mdsio: |
308 |
|
- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
309 |
|
(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
310 |
|
too long (e.g., > MAX_LEN_FNAM/2 ) |
311 |
|
|
312 |
|
checkpoint65b (2014/08/12) |
313 |
|
o pkg/matrix: |
314 |
|
- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
315 |
|
o model/src: |
316 |
|
- fix initialisation of geothermalFile; compile geothermal-flux code in |
317 |
|
natl_box verification experiment. |
318 |
|
o model/src & pkg/down_slope: |
319 |
|
- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
320 |
|
- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
321 |
|
field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
322 |
|
results at machine truncation level: update output of experiments |
323 |
|
global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
324 |
|
o pkg/diagnostics (Stats-Diags): |
325 |
|
- do not cumulate the full volume when DIAGNOSTICS_FILL is |
326 |
|
called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
327 |
|
This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
328 |
|
times (but Min,Max and StD are still wrong). |
329 |
|
o model/src: |
330 |
|
- add geothermal flux forcing: read in ini_forcing.F as time-constant |
331 |
|
field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
332 |
|
o model/src: |
333 |
|
- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
334 |
|
_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
335 |
|
arrays are already updated while adjustments (filters, conv.adjustment) are |
336 |
|
still applied later, in S/R TRACERS_CORRECTION_STEP. |
337 |
|
o model/src: |
338 |
|
- store in common bloc array "rhoInSitu" the virtual potential temperature |
339 |
|
anomaly that is used to compute geopotential: this make the atmos code |
340 |
|
more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
341 |
|
o pkg/seaice/seaice_lsr.F |
342 |
|
- rename integer variable ilcall to ipass (that's what it is called |
343 |
|
in the residual diagnostics |
344 |
|
- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
345 |
|
default) for improved non-linear convergence of the first few steps |
346 |
|
- adjust a few comments and add new ones to explain some of the store |
347 |
|
directives |
348 |
|
o pkg/generic_advdiff (& ptracers): |
349 |
|
- re-work the code to check for valid advection scheme and for minimum |
350 |
|
size of overlap (now stored in local common bloc in gad_advscheme.F) |
351 |
|
o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
352 |
|
- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
353 |
|
- add an auxilliary variable "bet" and fix store directives and keys in |
354 |
|
seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
355 |
|
less exact gradients in my tests); but there are still |
356 |
|
recomputation warning (although gradients are sort of OK), when |
357 |
|
SEAICE_LSR_VECTORIZE is not defined, so this flag and |
358 |
|
SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
359 |
|
- update verification experiments lab_sea. |
360 |
|
- change some comments in S/R seaice_calc_viscosities |
361 |
|
o model/src: |
362 |
|
- if staggerTimeStep=T, always apply exchange to velocity field in |
363 |
|
do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
364 |
|
(independent of using multi-dim advection or not); no effect on FWD run |
365 |
|
but affects AD results (at machine truncation level): update output of |
366 |
|
experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
367 |
|
and isomip (oad: 12.d). |
368 |
|
o pkg/generic_advdiff: |
369 |
|
- stop if doAB_onGtGs is set to FALSE but ignored |
370 |
|
- refine warning related to stability of tracer time-stepping |
371 |
|
regarding internal wave dynamics. |
372 |
|
- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
373 |
|
on staggerTimeStep & implicitIntGravWave (will now get a warning |
374 |
|
if potentially unstable). |
375 |
|
o pkg/kl10: |
376 |
|
- add new pkg "kl10" for mixing due to internal wave breaking, from |
377 |
|
http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
378 |
|
(contribution from Jody Klymak), tested in verification experiment |
379 |
|
verification/internal_wave/input.kl10/ |
380 |
|
o isomip experiment: |
381 |
|
- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
382 |
|
(input.htd) and update the output. |
383 |
|
o cd_code experiments: |
384 |
|
- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
385 |
|
#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
386 |
|
global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
387 |
|
update the corresponding output. |
388 |
|
o pkg/seaice: |
389 |
|
- reduce the number of include files and store directives in |
390 |
|
S/R seaice_lsr_tridiagu/v |
391 |
|
- change the order of loops in one case in S/R seaice_lsr_tridiagv |
392 |
|
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
393 |
|
get rid off one store directive (a TAF bug?) |
394 |
|
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
395 |
|
S/R seaice_lsr_tridiagv to change the loop range for consistency |
396 |
|
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
397 |
|
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
398 |
|
S/R seaice_lsr_tridiagu/v (requires update of |
399 |
|
offline_exf_seaice/input.dyn_jfnk) |
400 |
|
|
401 |
|
checkpoint65a (2014/07/27) |
402 |
|
o model/src: |
403 |
|
- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
404 |
|
surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
405 |
|
(topo in p-coords, ice-shelf in z-coords); update output of experiments |
406 |
|
tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
407 |
|
o model/src: |
408 |
|
- collect momentum forcing tendency into local 2-D array (passed as argument |
409 |
|
to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
410 |
|
parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
411 |
|
affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
412 |
|
- collect T & S forcing tendency into local 2-D array (passed as argument to |
413 |
|
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
414 |
|
affects results at machine truncation level (e.g., ocean: if using |
415 |
|
SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
416 |
|
correction due to vertical advection). |
417 |
|
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
418 |
|
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
419 |
|
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
420 |
|
obcs_ctrl (ad & fwd grd @ 12 & 7). |
421 |
|
o pkg/ptracers & diagnostics: |
422 |
|
- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
423 |
|
title (to avoid some unexpected truncation); sort out ptracers diags units. |
424 |
|
- collect ptracer forcing tendency into local 2-D array (passed as argument |
425 |
|
to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
426 |
|
|
427 |
|
checkpoint65 (2014/07/18) |
428 |
|
o pkg/fizhi: |
429 |
|
- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
430 |
|
affects results at machine truncation level. Update output of experiments |
431 |
|
fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). |
432 |
|
o pkg/seaice: more clean up |
433 |
|
- rename TAF common block tapes to be more consistent and remove |
434 |
|
unnecessary duplicates |
435 |
|
- add store directives to remove more recomputations, but use smaller |
436 |
|
tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. |
437 |
|
The idea behind this flag is to reduce the memory footprint when the |
438 |
|
adjoint of the LSR is not required. As of now, defining the flag |
439 |
|
SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by |
440 |
|
a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). |
441 |
|
For experiment offline_exf_seaice, this means on a linux box with gfortran |
442 |
|
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
443 |
|
this experiment): |
444 |
|
> size mitgcmuv_ad |
445 |
|
text data bss dec hex |
446 |
|
5100659 1216 220458952 225560827 d71c8fb |
447 |
|
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
448 |
|
but only a moderate increase of 36% for global_ocean.cs32x15: |
449 |
|
text data bss dec hex |
450 |
|
6695027 1648 1014578664 1021275339 3cdf6ccb |
451 |
|
6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER) |
452 |
|
- note: there are still recomputations in global_ocean.cs32x15 and |
453 |
|
offline_exf_seaice and the gradient agreement changes (gets a |
454 |
|
little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) |
455 |
|
- in general, the AD gradients still are wrong |
456 |
o OpenAD |
o OpenAD |
457 |
- clean up code_oad/ directories somewhat by moving files |
- clean up code_oad/ directories somewhat by moving files |
458 |
dontCompile, dontTransform, keepOriginal to OAD_support/ |
dontCompile, dontTransform, keepOriginal to OAD_support/ |