4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o model/src: |
8 |
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fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b). |
9 |
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update output of exp. global_ocean.cs32x15.viscA4 |
10 |
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o update output of exp. global_ocean.cs32x15.icedyn after removing |
11 |
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#define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h |
12 |
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o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) |
13 |
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o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output |
14 |
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for complex grids, for now only to "state", "adstate", "adexf", "adseaice" |
15 |
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o model: add Christopher Wolfe's implemetation of the single reduction cg2d |
16 |
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(d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and |
17 |
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runtime flag useSRCGSolver. Modify verification experiment global_with_exf |
18 |
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to test this code |
19 |
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o pkg/cd_code: |
20 |
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Change defaut D-grid time-stepping to get the same for D-grid momentum as for |
21 |
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C-grid momentum. D-grid velocity used to be stepped forward in time with |
22 |
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Adams-Bashforth only on surface pressure term. Tests show that using AB on |
23 |
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D-grid coriolis term improves stability (as expected from CD-scheme paper). |
24 |
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To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h). |
25 |
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Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2), |
26 |
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lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD), |
27 |
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tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens. |
28 |
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Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2, |
29 |
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lobal_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD. |
30 |
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o pkg/obcs: |
31 |
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- fix bug in initialisation (broken since Oct 1rst modification) |
32 |
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for useOBCSprescribe without useEXF. |
33 |
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|
34 |
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checkpoint61y |
35 |
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o pkg/seaice |
36 |
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- change (once again) the discretization for the evp solver: rather than |
37 |
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squaring the averages of strain rates, average the squares to give |
38 |
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a better approximation to VP behavior (in simple test); this breaks |
39 |
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verification experiments that use EVP (lab_sea and lab_sea.hb87) |
40 |
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--> update outputs |
41 |
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o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit) |
42 |
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to improve vectorization of adjoint code on TARGET_NEC_SX |
43 |
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o verification/vermix: |
44 |
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- change vermix to a more "classical" 1d column with high vertical |
45 |
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resolution, seasonal heat flux forcing and constant wind forcing |
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--> update outputs |
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o pkg/seaice |
48 |
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- fix diagnostics of principal stress components for EVP |
49 |
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- add optional diagnostics of non-linear convergence for LSOR solver |
50 |
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- make maximum zeta a runtime parameter |
51 |
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o model/src (3-d solver): |
52 |
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Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49), |
53 |
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which consisted in removing the Surf. Non-Hydrostatic pressure from the |
54 |
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whole column and adding it to Eta (inspired from Casualli, 1999): |
55 |
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Only affects 3-D solver initial guess and only if using ExactConserv, |
56 |
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but tests did show a degradation of solver convergence. For this reason, |
57 |
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decide to disable this piece of code. |
58 |
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to recover previous version, just set zeroPsNH = exactConserv (line 78). |
59 |
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Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW |
60 |
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o pkg/ggl90: |
61 |
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- fix previous modif (unfortunatly has not been documented here). |
62 |
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o pkg/seaice/autodiff: |
63 |
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- add CPP flag to include clipping of zeta in EVP code; |
64 |
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although clipping of zeta is not necessary for EVP and not recommended |
65 |
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it was done by default, now clipping is disabled by default |
66 |
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- modify computation and store zetaC/Z in seaice_evp for TAF |
67 |
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- add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default) |
68 |
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- change seaice_calc_viscosities/strainrates for better |
69 |
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vectorization after AD by TAF |
70 |
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- rearrange common blocks in SEAICE.h once again for easier dumps of |
71 |
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adjoint output, adjust adcommon.h and g_common.h |
72 |
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- change flux form of default advection scheme for better vectorization |
73 |
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of adjoint code |
74 |
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- modify lab_sea/input.lsr to test the flux form of default advection |
75 |
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scheme |
76 |
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o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level |
77 |
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transition in checkpoint61r) |
78 |
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|
79 |
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checkpoint61x |
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o adjoint: adding two new verification experiments |
81 |
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* tutorial_global_biogeo: an online dic sensitivity experiment |
82 |
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(work with G. Forget) |
83 |
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* tutorial_dic_adjoffline: an offline dic sensitivity experiment |
84 |
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(an update of the Dutkiewicz et al., 2006 paper) |
85 |
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Both use the same CO2FLUX cost function, but different controls |
86 |
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Gradient checks look good, but some recomp. could still be traightened out |
87 |
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Should add xx_dic control variable to test at some point |
88 |
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o model/src: |
89 |
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add run-time parameters to check and/or mask initial Temp & Salt |
90 |
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o pkg/ptracers: |
91 |
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apply zonal filter (if used) to all passive tracers |
92 |
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|
93 |
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checkpoint61w |
94 |
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o adjoint: |
95 |
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* update and finish work on adjoint of dic package (G. Forget) |
96 |
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* start adjoint of offline package |
97 |
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* bug fix for cube-sphere TLM code (active_file_g.F) |
98 |
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o tutorial_global_oce_optim: |
99 |
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now tested with 4 tiles (change data.grdchk and update output_adm.txt) |
100 |
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and add SIZE.h_mpi for MPI testing |
101 |
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o pkg autodiff |
102 |
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- fix bug in autodiff_restore |
103 |
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- make genmake2 remove comments and empty lines from ad_input_code.f in |
104 |
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order to reduce file size (new script file remove_comments_sed) |
105 |
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o allows to specify vertical profile of vertical viscosity (viscArNr) |
106 |
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o pkg autodiff |
107 |
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autodiff_ini_model_io: comment out writing of grid information to netcdf |
108 |
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files, because at this time the grid fields are a bunch of zeros |
109 |
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(this is analogous to ini_mnc_vars.F) |
110 |
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o pkg seaice/autodiff: |
111 |
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left-over from removing the 3-time-level fields: |
112 |
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- small rearrangement of common blocks (SEAICE.h) |
113 |
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- fix field declaration in order to get meaningful output in |
114 |
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adseaice.*.nc (adcommon.h) |
115 |
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o pkg obcs: |
116 |
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- go through NH code only if nonHydrostatic=T |
117 |
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- fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart) |
118 |
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- move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields |
119 |
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=> Update output of experiment seaice_obcs |
120 |
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- useOBCSbalance: code is wrong with multi-tile / proc: add a stop. |
121 |
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- fix NH+Orlanski restart (add wvel OBC value in pickup file) |
122 |
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- fix restart for useOBCSprescribe + useEXF |
123 |
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o pkg ctrl |
124 |
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- make obcs as control parameter work also with useSingleCPUio |
125 |
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- replace a few sny and snx by Ny and Nx to be consistent with |
126 |
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ctrl_set_globfld_x/yz.F |
127 |
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o pkg seaice |
128 |
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- re-introduce global field frWtrAtm for the case of |
129 |
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ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F) |
130 |
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- catch the case of an empty filename in seaice_cost_init_fixed.F |
131 |
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o pkg ecco: |
132 |
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- small bug fixes in the_main_loop |
133 |
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. fix order of monitor arguments |
134 |
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. change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY |
135 |
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. move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so |
136 |
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that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF |
137 |
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- replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the |
138 |
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imbalance diagnostics for wmean_h/sflux = 0 |
139 |
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- add actual values to f_obcsn/s/w/e in ecco_cost_final.F |
140 |
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- catch the case of empty filenames in ecco_cost_init_fixed.F |
141 |
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and ecco_readparms.F |
142 |
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- fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta) |
143 |
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to make this statement meaningfull in ecco_cost_weights.F |
144 |
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o pkg zonal_filt: |
145 |
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- change ZONAL_FILTER S/R interface (allows to filter 2-D fields) |
146 |
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- when using rStar, filter uVel*hFacW instead of uVel |
147 |
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(tested without topography: fix a Pb of growing instability with NLFS) |
148 |
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o pkg/aim/thsice: |
149 |
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-Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F |
150 |
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(works as SST restoring) |
151 |
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o pkg/thsice: |
152 |
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-add specific parameter for salt restoring in slab mixed-layer |
153 |
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(by default equal to the temperature restoring) |
154 |
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|
155 |
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checkpoint61v |
156 |
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o pkg/kpp: |
157 |
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-add double diffusive contributions as a hack, turned off by default |
158 |
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for now, and the code can be excluded with a CPP-flag |
159 |
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EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX |
160 |
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-add a verification experiments to "vermix" to test this code |
161 |
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o pkg/mom_common: |
162 |
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Move computation of length scales to mom_init_fixed.F (avoid recomputation |
163 |
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at each time-steps*levels). |
164 |
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o pkg/layers: |
165 |
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Created a new package for computing volume fluxes in temperature or |
166 |
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[not yet implemented] density layers, e.g. for calculating residual |
167 |
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overturning circulations. |
168 |
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o pkg/diagnostics: |
169 |
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implement a RS type version for the set of DIAGNOSTICS-FILL subroutines |
170 |
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o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option) |
171 |
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o pkg/mdsio (& pkg/rw): rework high level S/R interface: |
172 |
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To avoid mixing type (RS/RL) of input/output array argument, |
173 |
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replace single mixed-type array with a pair from each type (RS/RL). |
174 |
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o setting pickupSuff force to start from a pickup (even if nIter0=0): this |
175 |
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is now implemented for all pkgs (previously only done for the main pickup) |
176 |
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|
177 |
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checkpoint61u |
178 |
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o pkg/obcs: |
179 |
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- change OB?eta from _RS to _RL and put them into a separate commen block |
180 |
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- add code to read OB?eta from a file via obcs_prescribe_read: the code |
181 |
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compiles and does not destroy any other experiments, the data is read |
182 |
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properly, but the code is not tested in actual applications |
183 |
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o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to |
184 |
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create a meaningful unit attribute for the time coordinate variable |
185 |
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o pkg/ebm: add plenty of missing "_d 0" ; |
186 |
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update results of experiment global_ocean_ebm (fwd + adjoint tests) |
187 |
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Notes: several pieces of code only works for (very) specific set up |
188 |
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(domain size, lat range, etc ...); should be documented & stop if one |
189 |
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of those assumptions is not meet. |
190 |
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o pkg/seaice: add missing "_d 0" in HSNOW initialisation |
191 |
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update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests) |
192 |
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and offline_exf_seaice (seaicetd + adjoint). |
193 |
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o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC): |
194 |
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update results of experiments: lab_sea (4 fwd tests + 3 adjoint), |
195 |
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seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2). |
196 |
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o few changes to pass when compiling with strick checking of arguments |
197 |
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across S/R (allow to find few bugs in S/R calls). |
198 |
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o pkg/seaice: |
199 |
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- seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new |
200 |
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2d-fields, for slightly better performance |
201 |
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|
202 |
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checkpoint61t |
203 |
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o pkg/seaice: |
204 |
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- remove unused variables in seaice_evp |
205 |
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- reduce number of SQRT in seaice_evp and seaice_calc_viscosities |
206 |
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o eeset_parms.F, open_copy_data_file.F & ini_parms.F: |
207 |
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named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT): |
208 |
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each processor opens a different file (a fix from Matt). |
209 |
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o cg2d: |
210 |
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use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F : |
211 |
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this reduces number of EXCH calls by 2 when using exch2. |
212 |
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For now, keep previous size array for gc2d_nsa.F to avoid Pb with store |
213 |
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directives and missing simple EXCH (exch_s3d_rx) adjoint code. |
214 |
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o pkg/thsice: |
215 |
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add code for Near Infra-Red albedo (from Jeff) |
216 |
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(turned on with run-time flag: thSIce_calc_albNIR, in data.ice). |
217 |
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o ini_model_io: |
218 |
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move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F |
219 |
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MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F |
220 |
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to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice. |
221 |
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|
222 |
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checkpoint61s |
223 |
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o pkg/exch2 (exch2_rxN_cube*): |
224 |
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remove last BARRIER (no need to synchronise after getting data from shared |
225 |
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buffer (get) as long as any change to buffer (put,recv) is between BARRIER) |
226 |
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o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH |
227 |
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and generate new output (for the 2 tests) using default rotationPeriod. |
228 |
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o pkg/exch2: |
229 |
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- always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F |
230 |
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(was already the case with AUTODIFF_EXCH2 defined) |
231 |
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- add bj in exch2 arrays and S/R. |
232 |
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- can now use pkg/exch2 for regular (non CS) set-up; switch test experiment |
233 |
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MLAdjust to exch2 (identical results except with MPI -> truncation diff); |
234 |
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o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep |
235 |
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- adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY |
236 |
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GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT |
237 |
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- verification experiment natl_box.longstep |
238 |
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o build_options: ifort+mpi_aces optfile (following Constantinos advise): |
239 |
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allow different versions of ifort (8 or 9) and different versions |
240 |
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of mpi (mpich or mpich2) to be used with the same optfile. |
241 |
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requires to load a netcdf module and set MPI_INC_DIR (see comments inside |
242 |
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optfile). Change testing scripts (example_scripts/ACESgrid) accordingly. |
243 |
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o pkg/seaice: |
244 |
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fix previous modif (3-level field removed) for old-pickup reading |
245 |
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|
246 |
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checkpoint61r |
247 |
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o pkg/seaice: |
248 |
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- clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps: |
249 |
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1. introduce fields for time step (N-1) |
250 |
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2. do not use levels 2 and 3 anymore (but keep them) |
251 |
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3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This |
252 |
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includes changes to pkg/thsice/thsice_get_velocity.F, |
253 |
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model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and |
254 |
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pkg/obcs/obcs_apply_uvice.F. |
255 |
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- completely remove code for leap-frog time stepping for second order |
256 |
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advection |
257 |
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- adjusted adjoint accordingly; |
258 |
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gradient checks have improved by an order of magnitude! |
259 |
|
|
260 |
|
checkpoint61q |
261 |
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o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver |
262 |
|
- the boundary conditions along open boundaries are unclear, because the |
263 |
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associated masks are set to zero and are thus treated as closed when |
264 |
|
applying the slip-boundary conditions. |
265 |
|
- move initialisation of grid variables from seaice_init_varia to _fixed |
266 |
|
o adding doc/diags_changes.txt |
267 |
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o model/src: |
268 |
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do_the_model_io: rename few pkg S/R which are called from do_the_model_io, |
269 |
|
to avoid "_diags" naming if no relation to pkg/diagnostics. |
270 |
|
ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF |
271 |
|
file and only call PLOT_FIELD_XYZ if debugMode=T. |
272 |
|
remove few PLOT_FIELD_XY calls outside initialisation. |
273 |
|
remove few unnecessary BARRIER. |
274 |
|
o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling |
275 |
|
of salt_plume package in Southern Ocean |
276 |
|
o pkg/thsice: |
277 |
|
- fix hOceMxL in overlap (needed for sea-ice advection); |
278 |
|
update output of experiment global_ocean.cs32x15.icedyn. |
279 |
|
o pkg/seaice: |
280 |
|
- make the (placeholder-)tracer IceAge a little more meaningful |
281 |
|
by avoiding ridging of age due to convergent ice flow |
282 |
|
- add diagnostics for surface temperature, atmospheric and oceanic |
283 |
|
heat flux, and atmospheric and oceanic ice growth |
284 |
|
|
285 |
|
checkpoint61p |
286 |
|
o eesupp (global_max & global_sum): |
287 |
|
- add one more element to buffer (start at index 0) for GL_MAX/SUM output; |
288 |
|
- remove starting & endding barrier (no longer needed) |
289 |
|
o pkg/mdsio, writelocal: |
290 |
|
works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined |
291 |
|
(remove the STOP): uses shared buffer IO to store data from all threads |
292 |
|
and then let master-thread write nThreads tiles. |
293 |
|
o pkg/mdsio (read/write field): |
294 |
|
- tiled IO done in 1 piece (all levels at a time); |
295 |
|
- new header file "MDSIO_BUFF_3D.h" with 3-D buffers. |
296 |
|
- multi-threaded: allow to read/write local (non-shared) array |
297 |
|
(was already working with singleCpuIO ; now works also without); |
298 |
|
=> no longer needs barrier call after reading a file (added inside |
299 |
|
mds_read/write field). |
300 |
|
- move barrier calls outside gather/scatter_2d to mds_read/write_field |
301 |
|
o pkg/obcs/exf |
302 |
|
- exf_getffieldrec.F: add a few ". _d 0" and |
303 |
|
add code to catch the case fldperiod = 0. |
304 |
|
- obcs_precribe_read.F: change if statements so that they match |
305 |
|
the variable type (_RL) |
306 |
|
- add a separate exf_iprec_obcs to exf_set_obcs (by default equal to |
307 |
|
exf_iprec) as part of namelist EXF_NML_01 |
308 |
|
o pkg/mdsio: |
309 |
|
- read/write tiled (local) files: read/write 1-level tile chunk at a time |
310 |
|
(instead of segment of length sNx); expected to speed up tiled IO. |
311 |
|
o pkg/exch2: |
312 |
|
- take buffer copy from/to array out of S/R exch2_send/recv into new |
313 |
|
S/R exch2_put/get ; Exch of local variable now works with MPI+MTH |
314 |
|
(tested by removing commom block statement in SOLVE_FOR_PRESSURE.h). |
315 |
|
- ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get) |
316 |
|
- simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds |
317 |
|
(which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by |
318 |
|
including Topology header file (and common blocks). |
319 |
|
- implement EXCH_IGNORE_CORNERS in scalar exchange (rx1); |
320 |
|
remove 2nd exch call in exch2_s3d_rx (no longer needed). |
321 |
|
- document S/R arg. list (+ update some comments) |
322 |
|
o pkg/seaice: |
323 |
|
- added SEAICE_CLIM_AIR code, which permits modulation of surface air |
324 |
|
temperature and humidity over sea ice based on climatological values. |
325 |
|
- clean up computation of Hibler+Bryan (1987) stress coupling for the case |
326 |
|
of LSR (this change is expected to change the results slightly because now |
327 |
|
it uses slightly difference moduli from the second last LSR solution, but |
328 |
|
that is more consistent with the stress computations; this part of the code |
329 |
|
is not tested in the verification experiments) |
330 |
|
- fix diagnostics for flux of ice in case of B-grid |
331 |
|
- turn strain rates eij and press into global fields within global |
332 |
|
common block in SEAICE.h for more straighforward diagnostics |
333 |
|
- fix diagnostics for principal stress components, press, zeta, eta |
334 |
|
to give something meaning full |
335 |
|
o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate |
336 |
|
new output (all 4 tests) using default rotationPeriod. |
337 |
|
o pkg KPP: |
338 |
|
- add flag (LimitHblStable) to avoid limiting BL depth under stable conditions |
339 |
|
- fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1 |
340 |
|
and normal grid from 1 to Nr) |
341 |
|
o Fix computations of L4rdt in mom_calc_visc.F |
342 |
|
o eesupp: |
343 |
|
new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg): |
344 |
|
should be called before a "stop" if we know that all process are going |
345 |
|
to stop; if one Proc does call this S/R, will hang in MPI_FINALISE. |
346 |
|
|
347 |
|
checkpoint61o |
348 |
|
o pkg/exch2: change check_depths to issue just a warning (instead of error+stop) |
349 |
|
o model/src/ini_curvilinear_grid.F: |
350 |
|
compute angleSin/CosC when they are not read from a file |
351 |
|
o pkg/seaice: |
352 |
|
add pseudo time stepping for LSOR |
353 |
|
o pkg/exch2: |
354 |
|
temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW |
355 |
|
o pkg/seaice: |
356 |
|
Adding separate sea ice albedo, drag coefficients, and HO in Southern |
357 |
|
Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h |
358 |
|
o SingleCpuIO: |
359 |
|
fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used. |
360 |
|
o pkg/seaice: |
361 |
|
put exchanged variable in (local) common block for MPI+Multi-Threads |
362 |
|
to work (necessary with exch1, and for now with exch2 too). |
363 |
|
o verification: to get more experiments tested with mpi, mth and mpi+mth, |
364 |
|
change tiling of: |
365 |
|
aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15, |
366 |
|
hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope |
367 |
|
update output of exp: |
368 |
|
exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5), |
369 |
|
tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod) |
370 |
|
+ ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU |
371 |
|
(note: output.txt generated on faulks using only 1 tile) |
372 |
|
o eesupp & mdsio (SingleCpuIO): |
373 |
|
- remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time |
374 |
|
parameter "W2_useE2ioLayOut" (read from file "data.exch2"). |
375 |
|
Note: was not effective for globalFile & useSingleCpuIO=F; now fixed. |
376 |
|
- move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc). |
377 |
|
- fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same |
378 |
|
gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array). |
379 |
|
o pkg/exch2: |
380 |
|
- new code to set-up W2-Exch2 topology (replace matlab-topology-generator): |
381 |
|
read parameter file "data.exch2" if it exists; otherwise try default regular |
382 |
|
cube without blank-tile; new header file "W2_EXCH2_SIZE.h"; |
383 |
|
- update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible |
384 |
|
with new code (not to be used, just as a backup solution). |
385 |
|
- add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2" |
386 |
|
in utils/exch2/input. |
387 |
|
|
388 |
|
checkpoint61n |
389 |
|
o eesupp & mdsio (SingleCpuIO): |
390 |
|
- move mapping to global io-buffer inside gather_2d/scater_2d: this save |
391 |
|
memory (1 less 2D global RL array); skip 1 buffer copy; and only send/ |
392 |
|
receive real*4 array (instead of real*8) to read/write 32.bit files. |
393 |
|
(new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S |
394 |
|
and remove new mapping S/R) |
395 |
|
o pkg/mdsio: in preparation for topology-generator within pkg/exch2: |
396 |
|
- Change declaration of SingleCpuIO buffer, reduced to only 1 dim.: |
397 |
|
xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h |
398 |
|
when using exch2. Add S/R to map global io-buffer to global model array. |
399 |
|
- uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt. |
400 |
|
|
401 |
|
checkpoint61m |
402 |
|
o write_utils : change WRITE_1D_R8 to WRITE_1D_RL |
403 |
|
and add 3 other S/R for other types (R4,R8,RS). |
404 |
|
Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument. |
405 |
|
o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros): |
406 |
|
- ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ; |
407 |
|
- reduce number of macro definitions (keep only those which are used); |
408 |
|
can always call directly the corrresponding S/R if needed. |
409 |
|
- everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix |
410 |
|
_R4/_R8 to _RS/_RL when applied to _RS/_RL variable. |
411 |
|
Fixed wrong type of arg in: |
412 |
|
atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F |
413 |
|
ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F |
414 |
|
To fix: global_sum of var in common block is wrong (multi-threaded) in: |
415 |
|
dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F |
416 |
|
To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops) |
417 |
|
o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd |
418 |
|
"nlfs" mpi test is going to stop when checking for unconnected tile egdes. |
419 |
|
o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error |
420 |
|
o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile |
421 |
|
edges are closed (zero depth); might happen with "blank tiles"; |
422 |
|
for now, disabled if using OBCS. |
423 |
|
o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi": |
424 |
|
link *_mpi files from "MODS" dir) to return to a strait-forward behavior. |
425 |
|
o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D) |
426 |
|
to reduce length of 1.D array print in STDOUT. |
427 |
|
o adjustment.cs-32x32x1: changed to oceanic test with 1 continent |
428 |
|
+ use 48 tiles (16x8): this will allow to test "blank tiles". |
429 |
|
o start to test MPI + multi-threaded (change testreport to skip tests |
430 |
|
where number of tiles do not match). |
431 |
|
o genmake2: add option "-omp" to turn on Open-MP ; |
432 |
|
passed to testreport (if using -mth) ; merge few (*+mth) optfiles. |
433 |
|
o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them) |
434 |
|
and keep the original tile numbering. Note: compatible with old |
435 |
|
W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files. |
436 |
|
|
437 |
|
checkpoint61l |
438 |
|
o Overlaps had been forgotten in calculating ijk keys : fixed |
439 |
|
o fix cyrus makedepend for gcc 4.4 |
440 |
|
o experiment fizhi-cs-aqualev20: |
441 |
|
switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE) |
442 |
|
and generate new output. Note: new output is much closer to the old |
443 |
|
one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from |
444 |
|
the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007. |
445 |
|
o pkg/fizhi: |
446 |
|
- change to avoid indices going deliberately over array-bounds |
447 |
|
- remove unnecessary MPI stuff |
448 |
|
- perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY" |
449 |
|
- new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE: |
450 |
|
does not go over array-bounds and therefore returns reliable output. |
451 |
|
- in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls: |
452 |
|
this S/R has 4 output arguments, which are used inside "get_alarm"; |
453 |
|
when it is called with the same variable "ndum" in place of several |
454 |
|
output arguments, this produces weird side effect inside "get_alarm" |
455 |
|
(e.g., datein=dates(n) is overwritten by timein=times(n) since both |
456 |
|
datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum" |
457 |
|
address) and produces error. |
458 |
|
o tools/gemake2: (March 27-29 2009) |
459 |
|
with option "-mpi": link *_mpi files from "MODS" dir (this is what |
460 |
|
testreport does). |
461 |
|
o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output |
462 |
|
o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F: |
463 |
|
update lab_sea.lsr & lab_sea.salt_plume results |
464 |
|
o pkg/seaice: |
465 |
|
Major overhaul of the LSOR solver: change discretization from original |
466 |
|
finite differences to finite volume. The old routine is still in the |
467 |
|
file seaice_lsr.F and can be turned on with the CPP-flag |
468 |
|
SEAICE_OLD_AND_BAD_DISCRETIZATION |
469 |
|
Along with this change, the discretization of the strain rates is changed. |
470 |
|
The same flag turns on the old discretization in seaice_calc_strainrates.F |
471 |
|
All verification experiments with seaice are affected (except for |
472 |
|
seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old |
473 |
|
results by setting the above flag. |
474 |
|
Further changes involve changes in defaults: |
475 |
|
- ALLOW_FLOODING is defined and turned on by default |
476 |
|
- SEAICEadvSnow = .true. is now the default |
477 |
|
- SEAICEadvSalt = .true. is now the default |
478 |
|
- SEAICEadvAge = .true. is now the default |
479 |
|
- SEAICE_clipVelocities = .false. is now the default |
480 |
|
(as per J. Zhang's recommendation) |
481 |
|
- B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE |
482 |
|
is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS |
483 |
|
- seaice_growth: replace computation of UG by a simple copy from wspeed |
484 |
|
|
485 |
|
checkpoint61k |
486 |
|
o pkg/seaice: a few bug fixes mostly concerning the metric terms: |
487 |
|
seaice_lsr: fixed a few metric terms, |
488 |
|
affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs |
489 |
|
add more debugging diagnostics |
490 |
|
seaice_evp: removed superfluous many metric terms of FV discretization |
491 |
|
of stress divergence |
492 |
|
affects lab_sea, lab_sea.hb87 |
493 |
|
seaice_ocean_stress: removed superfluous many metric terms of FV discretization |
494 |
|
of stress divergence for non-evp solver |
495 |
|
(this part is not tested anywhere) |
496 |
|
seaice_calc_strainrates: fixed a bug in no-slip boundary conditions, |
497 |
|
they were effectively only half slip |
498 |
|
affects lab_sea.hb87 |
499 |
|
updated all relevant verification experiments (except lab_sea//output_adm.txt |
500 |
|
which was left over, but fails at level 7 & 6) |
501 |
|
|
502 |
|
checkpoint61j |
503 |
|
o pkg/seaice: turn a few hard wired parameters into run time parameters |
504 |
|
o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model |
505 |
|
time in seconds as promised by the usints in seaice_monitor and exf_monitor |
506 |
|
o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids |
507 |
|
that are not cubed-sphere grids |
508 |
|
o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR |
509 |
|
o pkg/ctrl: |
510 |
|
fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low) |
511 |
|
o non-hydrostatic (calc_gw.F): |
512 |
|
fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec |
513 |
|
update output of exp. global_ocean.cs32x15.viscA4 |
514 |
|
o remove backward compatibility for thetaMin,phiMin |
515 |
|
(replaced by xgOrigin,ygOrigin on Jan 27, 2009) |
516 |
|
o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the |
517 |
|
interpolated wind field not only for curvilineargrid=.true., but also |
518 |
|
for a rotated grid (rotateGrid=.true.) |
519 |
|
o pkg/exf: add capability to bypass interpolation for runoff |
520 |
|
by setting yet another CPP-flag |
521 |
|
o eesupp/src, B-grid exchange: |
522 |
|
add simple (6 tiles, non MPI) CS exch + standard interface S/R. |
523 |
|
o autodiff |
524 |
|
new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV |
525 |
|
allows to switch to single-prec common blocks; |
526 |
|
corresponding switch occurs in tamc.h, integer isbyte |
527 |
|
TAF store directivs "byte" and "kind" seem equivalent; |
528 |
|
Most tamc.h have been updated correspondingly. |
529 |
|
|
530 |
|
checkpoint61i |
531 |
|
o autodiff: |
532 |
|
fix autodiff_sore/_restore indices for obcs |
533 |
|
(spotted by I. Hoteit, M. Mazloff) |
534 |
|
o pkg/autodiff, pkg/ctrl: |
535 |
|
Add flag to reduce all tapelev I/O to single-prec. |
536 |
|
In data.ctrl set |
537 |
|
doSinglePrecTapelev = .TRUE. |
538 |
|
o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2: |
539 |
|
check in hack for SX8 compiler (for dxV, dyU); remove it afterwards. |
540 |
|
o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for |
541 |
|
real fresh water flux (not yet) |
542 |
|
o pkg/mdsio & rw: |
543 |
|
- add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta) |
544 |
|
- add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX. |
545 |
|
o pkg/flt: |
546 |
|
- replace FLT_INIT by 3-steps standard initialization S/R: readparms, |
547 |
|
init_fixed & ini_varia. |
548 |
|
- clean-up & simplify linear interpolation S/R: |
549 |
|
move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid. |
550 |
|
- fix some indices (mainly vertical index) ; add IMPLICIT NONE. |
551 |
|
- more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R. |
552 |
|
- add vert. coordinate & horiz. indices to output files. |
553 |
|
- change vertical position in initial condition, from index to depth [m]. |
554 |
|
- store horizontal (decimal) indices i,j in common block (instead of coord. x,y) |
555 |
|
(easier to get to a curvilinear grid) ; delX,delY no longer used. |
556 |
|
o pkg/ggl90: a few modifications: |
557 |
|
- fix bottom boundary condition, and interpolation of KappaE |
558 |
|
near top and bottom |
559 |
|
- use same set of viscosity/diffusivity for TKE/momnetum/tracer |
560 |
|
- add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH) |
561 |
|
- add a few options for mixing-length upper limit (--> mxlMaxFlag) |
562 |
|
o rename thetaMin,phiMin -> xgOrigin,ygOrigin |
563 |
|
(maintain temporary backward compatibility, until next checkpoint) |
564 |
|
|
565 |
|
checkpoint61h |
566 |
|
o pkg/diagnostics with "periodic averaging diagnostics": |
567 |
|
fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. |
568 |
|
o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82 |
569 |
|
o pkg/obcs: fix loop ranges for balancing code |
570 |
|
o pkg/flt: |
571 |
|
- improve criteria for finding which tile owns a float. |
572 |
|
- fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case. |
573 |
|
o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg |
574 |
|
aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling |
575 |
|
with ocean biogeo) |
576 |
|
o pkg/flt: |
577 |
|
- do some cleaning and fix the restart ; |
578 |
|
- add output.txt in flt_example/results to get this pkg tested. |
579 |
|
o genmake2: add an EXTENDED_SRC option and flag. |
580 |
|
for now, cannot be turned on on command line (only through genmake_local) |
581 |
|
o pkg/mdsio: read/write vector: |
582 |
|
- singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS |
583 |
|
- singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR |
584 |
|
& MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. |
585 |
|
- affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) |
586 |
|
(drop to 4 digits matching for grad). But this test does not look very |
587 |
|
reliable (was already failling on eddy, fc5, at 6.digits). Update output. |
588 |
|
|
589 |
|
checkpoint61g |
590 |
|
o pkg/flt: |
591 |
|
- move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) |
592 |
|
+ make OPTIONS file more standard. |
593 |
|
- rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) |
594 |
|
- fix _BYTESWAPIO CPP-Flag |
595 |
|
- standard reading of file-parameter "data.flt" |
596 |
|
- fix argument list of S/R FLT_RESTART |
597 |
|
still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F |
598 |
|
o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell |
599 |
|
o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to |
600 |
|
a still unfixed compiler/optimization bug |
601 |
|
|
602 |
|
checkpoint61f |
603 |
|
o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; |
604 |
|
update results of global_ocean.cs32x15.icedyn test. |
605 |
|
o move getcon.F from model/src to pkg/fizhi. |
606 |
|
o pkg/exf: add parameter for extrapolation of temp up to the surface |
607 |
|
and option to prevent negative evap (in bulk_largeyeager04 only). |
608 |
|
o Prather Advection scheme: fix tracer conservation for divergent flow |
609 |
|
(e.g., when using NonLin Free-Surface). |
610 |
|
o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead |
611 |
|
o gmredi (Visbeck-variable-K): |
612 |
|
- add more parameters to Visbeck-variable-K. |
613 |
|
- use a 5 points average for dSigmaR in Visbeck-K calculation |
614 |
|
(more "homogenous": same stencil and same weights as in dSigmaH) |
615 |
|
- update output of ideal_2D_oce experiment. |
616 |
|
o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 |
617 |
|
(#undef REAL4_IS_SLOW) |
618 |
|
- pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 |
619 |
|
coordinate variable |
620 |
|
- pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables |
621 |
|
(surface forcing fields), removes some of the functionality |
622 |
|
- model/src/write_grid.F: write _RS variables as RS-netcdf variables |
623 |
|
- model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but |
624 |
|
probably not all: copy _RS surface flux fields to RL field before |
625 |
|
calling DIAGNOSTICS_FILL |
626 |
|
- model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into |
627 |
|
real*4 (CALL EXCH_*_RS) versions. |
628 |
|
- tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 |
629 |
|
(generate new output). |
630 |
|
|
631 |
|
checkpoint61e |
632 |
|
o gmredi (Visbeck-variable-K): |
633 |
|
- fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h |
634 |
|
- change computation of Visbeck-K where Slope > Smax : |
635 |
|
now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct) |
636 |
|
previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output. |
637 |
|
o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic |
638 |
|
to be the same as with Z-coord. (i.e., m/s & no-units respectively). |
639 |
|
o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc) |
640 |
|
o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz |
641 |
|
does not become too large (to avoid precision problems in implicit-diffusion |
642 |
|
solver); update ideal_2D_oce output. |
643 |
|
o pkg ggl90: |
644 |
|
- in ggl90_cal.F: compute only one set of visc/diff, used to |
645 |
|
step forward TKE/T/S/momentum |
646 |
|
- default value of GGL90viscMax/GGL90diffMax larger and equal (to |
647 |
|
have Prandlt =1) |
648 |
|
o gmredi (fm07): |
649 |
|
- add lower limit on Transition layer thickness + lower limit on 1/lambda |
650 |
|
- allow to set few more params from data.gmredi |
651 |
|
o pkg ggl90: |
652 |
|
- add missing sqrt(2) factor in computation of mixing length |
653 |
|
scale in ggl90_calc.F |
654 |
|
(see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) |
655 |
|
|
656 |
|
checkpoint61d |
657 |
|
o adjoint modifs |
658 |
|
- adapt to new field rhoInSitu |
659 |
|
- allow to revert from StoreDynVars2D, StoreDynVars3D |
660 |
|
to individual fields |
661 |
|
(switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) |
662 |
|
o store 3-D (in-situ) density in commom block (DYNVARS.h) |
663 |
|
- save 1 rho computation. |
664 |
|
- no longer modify T & S inland when using down_slope pkg. |
665 |
|
o gad_som : allow to switch to SOM advection for T & S without corresponding |
666 |
|
pickup files (using new S/R: MDS_CHECK4FILE). |
667 |
|
o keep removing _BEGIN/_END_MASTER between MDSIO S/R call |
668 |
|
(for useSingleCpuIO to work in multi-threaded) |
669 |
|
o pkg/shelfice: |
670 |
|
- disentangle parameters: retire shelfIceFile in data/PARM05 and substitute |
671 |
|
with SHELFICEtopoFile in data.shelfice |
672 |
|
- move code for reading ice shelf topography and modifying hFacC into separate |
673 |
|
subroutines of the shelfice package |
674 |
|
- separate initialisation of "fixed" and "variable" variables |
675 |
|
- kTopC is not (yet) replaced by kSurfC, although this is possible |
676 |
|
o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
677 |
|
o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
678 |
|
and rename: |
679 |
|
ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
680 |
|
ini_reference_state.F --> load_ref_files.F (- set anelastic factors) |
681 |
|
o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) |
682 |
|
|
683 |
|
checkpoint61c |
684 |
|
o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" |
685 |
|
to add mass source/sink of fluid in the interior (3-D generalisation |
686 |
|
of oceanic real-fresh water flux). |
687 |
|
o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) |
688 |
|
o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) |
689 |
|
o new pkg: down_slope |
690 |
|
density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). |
691 |
|
- presently, modify T & S inland (dwnslp_calc_rho.F). |
692 |
|
can be avoided if rho was stored in common bloc and used in calc_phi_hyd. |
693 |
|
- implementation for ocean in P-coords not tested. |
694 |
|
- add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. |
695 |
|
o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) |
696 |
|
(to facilitate conversion of oceanic pkg to p-coordinate). |
697 |
|
o change FIND_RHO to FIND_RHO_2D : |
698 |
|
pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. |
699 |
|
o new pkg: cheapaml |
700 |
|
|
701 |
|
checkpoint61b |
702 |
|
o exch2: |
703 |
|
change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) |
704 |
|
- no longer depend on the order sequence (N,S,E,W). |
705 |
|
- 3rd exchange no longer needed (tested with 24 tiles). |
706 |
|
- same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) |
707 |
|
- exch_UV_A-grid readily available (but not yet tested). |
708 |
|
comment out 3rd exch call and remove copy of V to U at SE & NE face-corners |
709 |
|
(both are no longer needed) in exch_uv: no effect in forward run; but |
710 |
|
get truncation error differences with adjoint exch. |
711 |
|
o exch2: |
712 |
|
- change index-bounds storage (moved from target to local tile, |
713 |
|
more intuitive this way) ; rename/remove some variables. |
714 |
|
- change utils/exch2/matlab-topology-generator & code_mods accordingly. |
715 |
|
|
716 |
|
checkpoint61a |
717 |
|
o exch2/matlab-topology-generator: |
718 |
|
fix bug in index bounds for N-S internal exchange (hard to tell if this |
719 |
|
had any effect on the solution). |
720 |
|
o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf |
721 |
|
is exceeded |
722 |
|
o testreport: modify syntax of awk, so that it works also with |
723 |
|
awk, and not only with nawk and gawk |
724 |
|
|
725 |
|
checkpoint61 |
726 |
|
o autodiff |
727 |
|
Change default for TAF usage by removing argument '-nonew_arg' |
728 |
|
This changes TAF subroutine argument list (ordering of active var.) |
729 |
|
Omission of this flag leads to incompatibility w.r.t. TAMC |
730 |
|
To restore TAMC-compatibility, need following modifs: |
731 |
|
* use adoptfile tools/adjoint_options/adjoint_tamc_compatibility |
732 |
|
* use CPP option #define AUTODIFF_TAMC_COMPATIBILITY |
733 |
|
Tested TAF version is 1.9.22 |
734 |
|
N.B.: exch2 hand-written adjoint code currently not TAMC compatible |
735 |
|
|
736 |
|
checkpoint60 |
737 |
|
--->>> This is the last checkpoint for which generating the adjoint |
738 |
|
--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" |
739 |
|
--->>> by default. |
740 |
|
--->>> Future checkpoints will ommit this flag by default. |
741 |
|
o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. |
742 |
|
o pkg/grdchk: Add gradient check to etan0 perturbations. |
743 |
|
o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). |
744 |
|
o pkg/autodiff: more flexibility in zeroadj. |
745 |
|
model/src: modifying do_oceanic_phys.F accordingly. |
746 |
|
o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. |
747 |
|
o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option |
748 |
|
special setup of gmredi for which the adjoint is stable |
749 |
|
enough for parameter optimization. |
750 |
|
o bridging the gap between eddy stress and GM. |
751 |
|
-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) |
752 |
|
along with a change in CPP option (now ALLOW_EDDYPSI). |
753 |
|
-> when using GM w/ GM_AdvForm: |
754 |
|
The total eddy streamfunction (Psi = eddyPsi + K x Slope) |
755 |
|
is applied either in the tracer Eq. or in momentum Eq. |
756 |
|
depending on data.gmredi (intro. GM_InMomAsStress). |
757 |
|
-> ALLOW_EDDYPSI_CONTROL for estimation purpose. |
758 |
|
The key modifications are in model/src/taueddy_external_forcing.F |
759 |
|
pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F |
760 |
|
|
761 |
|
checkpoint59r |
762 |
|
o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array |
763 |
|
from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); |
764 |
|
fix option to read coriolis(@ cell-corner) from files with CS-grid. |
765 |
|
o pkg/mnc: add some attributes to standard 1D-coordinate variables |
766 |
|
o pkg/diagnostics: enforce missing_value attribute for scalar variables at |
767 |
|
mass points, when using mnc for output |
768 |
|
- add runtime parameter (missing_value, missing_value_int) to override |
769 |
|
default (which is the value of getcon('UNDEF')) |
770 |
|
o pkg/mnc: prepare mnc for the actual use of missing values with the |
771 |
|
diagnostics package: small fix in mnc_cw_readwrite.template and more |
772 |
|
initialisation of never used fields |
773 |
|
- replace mnc_common.h and mnc_id_header.h with corresponding upper case |
774 |
|
versions |
775 |
|
o pkg/thsice/thsice_ini_vars.F added default initial values so that |
776 |
|
thermodynamics sea ice solver does not blow up when some initial fields |
777 |
|
are missing. |
778 |
o move from external_forcing_surf.F to ini_forcing.F |
o move from external_forcing_surf.F to ini_forcing.F |
779 |
the p-coord. hack consisting in using pLoad to set phi0surf ; |
the p-coord. hack consisting in using pLoad to set phi0surf ; |
780 |
update output of tutorial_global_oce_in_p (affected @ truncation level). |
update output of tutorial_global_oce_in_p (affected @ truncation level). |
781 |
o Freshen up a bit hs94.1x64x5, notably: |
o Freshen up a bit hs94.1x64x5, notably: |
782 |
remove rotationPeriod and tRef=5*0. (adjoint only), and add exactConserv=.TRUE. |
remove rotationPeriod and tRef=5*0. (adjoint only), and add |
783 |
|
exactConserv=.TRUE. |
784 |
o pkg/generic_advdiff: |
o pkg/generic_advdiff: |
785 |
change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
786 |
applies to files where Temperature & Salinity 2nd Order moments are used. |
applies to files where Temperature & Salinity 2nd Order moments are used. |
2882 |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
2883 |
- these scheme operate in a similar manner as KPP (without ghat, of |
- these scheme operate in a similar manner as KPP (without ghat, of |
2884 |
course), however there is only one diffusivity that is used for both |
course), however there is only one diffusivity that is used for both |
2885 |
temperature and salinity (and passive tracers)ç |
temperature and salinity (and passive tracers) |
2886 |
o add offline package |
o add offline package |
2887 |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
2888 |
provided by Stephanie Dutkiewicz |
provided by Stephanie Dutkiewicz |