4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
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o pkg/flt: |
8 |
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- do some cleaning and fix the restart ; |
9 |
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- add output.txt in flt_example/results to get this pkg tested. |
10 |
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o genmake2: add an EXTENDED_SRC option and flag. |
11 |
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for now, cannot be turned on on command line (only through genmake_local) |
12 |
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o pkg/mdsio: read/write vector: |
13 |
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- singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS |
14 |
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- singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR |
15 |
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& MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. |
16 |
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- affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) |
17 |
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(drop to 4 digits matching for grad). But this test does not look very |
18 |
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reliable (was already failling on eddy, fc5, at 6.digits). Update output. |
19 |
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|
20 |
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checkpoint61g |
21 |
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o pkg/flt: |
22 |
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- move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) |
23 |
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+ make OPTIONS file more standard. |
24 |
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- rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) |
25 |
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- fix _BYTESWAPIO CPP-Flag |
26 |
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- standard reading of file-parameter "data.flt" |
27 |
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- fix argument list of S/R FLT_RESTART |
28 |
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still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F |
29 |
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o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell |
30 |
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o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to |
31 |
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a still unfixed compiler/optimization bug |
32 |
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|
33 |
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checkpoint61f |
34 |
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o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; |
35 |
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update results of global_ocean.cs32x15.icedyn test. |
36 |
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o move getcon.F from model/src to pkg/fizhi. |
37 |
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o pkg/exf: add parameter for extrapolation of temp up to the surface |
38 |
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and option to prevent negative evap (in bulk_largeyeager04 only). |
39 |
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o Prather Advection scheme: fix tracer conservation for divergent flow |
40 |
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(e.g., when using NonLin Free-Surface). |
41 |
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o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead |
42 |
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o gmredi (Visbeck-variable-K): |
43 |
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- add more parameters to Visbeck-variable-K. |
44 |
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- use a 5 points average for dSigmaR in Visbeck-K calculation |
45 |
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(more "homogenous": same stencil and same weights as in dSigmaH) |
46 |
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- update output of ideal_2D_oce experiment. |
47 |
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o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 |
48 |
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(#undef REAL4_IS_SLOW) |
49 |
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- pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 |
50 |
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coordinate variable |
51 |
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- pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables |
52 |
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(surface forcing fields), removes some of the functionality |
53 |
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- model/src/write_grid.F: write _RS variables as RS-netcdf variables |
54 |
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- model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but |
55 |
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probably not all: copy _RS surface flux fields to RL field before |
56 |
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calling DIAGNOSTICS_FILL |
57 |
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- model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into |
58 |
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real*4 (CALL EXCH_*_RS) versions. |
59 |
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- tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 |
60 |
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(generate new output). |
61 |
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|
62 |
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checkpoint61e |
63 |
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o gmredi (Visbeck-variable-K): |
64 |
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- fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h |
65 |
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- change computation of Visbeck-K where Slope > Smax : |
66 |
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now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct) |
67 |
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previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output. |
68 |
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o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic |
69 |
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to be the same as with Z-coord. (i.e., m/s & no-units respectively). |
70 |
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o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc) |
71 |
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o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz |
72 |
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does not become too large (to avoid precision problems in implicit-diffusion |
73 |
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solver); update ideal_2D_oce output. |
74 |
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o pkg ggl90: |
75 |
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- in ggl90_cal.F: compute only one set of visc/diff, used to |
76 |
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step forward TKE/T/S/momentum |
77 |
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- default value of GGL90viscMax/GGL90diffMax larger and equal (to |
78 |
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have Prandlt =1) |
79 |
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o gmredi (fm07): |
80 |
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- add lower limit on Transition layer thickness + lower limit on 1/lambda |
81 |
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- allow to set few more params from data.gmredi |
82 |
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o pkg ggl90: |
83 |
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- add missing sqrt(2) factor in computation of mixing length |
84 |
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scale in ggl90_calc.F |
85 |
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(see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) |
86 |
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|
87 |
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checkpoint61d |
88 |
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o adjoint modifs |
89 |
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- adapt to new field rhoInSitu |
90 |
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- allow to revert from StoreDynVars2D, StoreDynVars3D |
91 |
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to individual fields |
92 |
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(switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) |
93 |
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o store 3-D (in-situ) density in commom block (DYNVARS.h) |
94 |
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- save 1 rho computation. |
95 |
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- no longer modify T & S inland when using down_slope pkg. |
96 |
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o gad_som : allow to switch to SOM advection for T & S without corresponding |
97 |
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pickup files (using new S/R: MDS_CHECK4FILE). |
98 |
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o keep removing _BEGIN/_END_MASTER between MDSIO S/R call |
99 |
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(for useSingleCpuIO to work in multi-threaded) |
100 |
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o pkg/shelfice: |
101 |
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- disentangle parameters: retire shelfIceFile in data/PARM05 and substitute |
102 |
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with SHELFICEtopoFile in data.shelfice |
103 |
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- move code for reading ice shelf topography and modifying hFacC into separate |
104 |
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subroutines of the shelfice package |
105 |
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- separate initialisation of "fixed" and "variable" variables |
106 |
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- kTopC is not (yet) replaced by kSurfC, although this is possible |
107 |
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o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
108 |
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o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
109 |
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and rename: |
110 |
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ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
111 |
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ini_reference_state.F --> load_ref_files.F (- set anelastic factors) |
112 |
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o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) |
113 |
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|
114 |
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checkpoint61c |
115 |
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o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" |
116 |
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to add mass source/sink of fluid in the interior (3-D generalisation |
117 |
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of oceanic real-fresh water flux). |
118 |
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o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) |
119 |
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o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) |
120 |
|
o new pkg: down_slope |
121 |
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density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). |
122 |
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- presently, modify T & S inland (dwnslp_calc_rho.F). |
123 |
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can be avoided if rho was stored in common bloc and used in calc_phi_hyd. |
124 |
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- implementation for ocean in P-coords not tested. |
125 |
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- add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. |
126 |
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o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) |
127 |
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(to facilitate conversion of oceanic pkg to p-coordinate). |
128 |
|
o change FIND_RHO to FIND_RHO_2D : |
129 |
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pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. |
130 |
|
o new pkg: cheapaml |
131 |
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|
132 |
|
checkpoint61b |
133 |
|
o exch2: |
134 |
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change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) |
135 |
|
- no longer depend on the order sequence (N,S,E,W). |
136 |
|
- 3rd exchange no longer needed (tested with 24 tiles). |
137 |
|
- same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) |
138 |
|
- exch_UV_A-grid readily available (but not yet tested). |
139 |
|
comment out 3rd exch call and remove copy of V to U at SE & NE face-corners |
140 |
|
(both are no longer needed) in exch_uv: no effect in forward run; but |
141 |
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get truncation error differences with adjoint exch. |
142 |
|
o exch2: |
143 |
|
- change index-bounds storage (moved from target to local tile, |
144 |
|
more intuitive this way) ; rename/remove some variables. |
145 |
|
- change utils/exch2/matlab-topology-generator & code_mods accordingly. |
146 |
|
|
147 |
|
checkpoint61a |
148 |
|
o exch2/matlab-topology-generator: |
149 |
|
fix bug in index bounds for N-S internal exchange (hard to tell if this |
150 |
|
had any effect on the solution). |
151 |
|
o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf |
152 |
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is exceeded |
153 |
|
o testreport: modify syntax of awk, so that it works also with |
154 |
|
awk, and not only with nawk and gawk |
155 |
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|
156 |
|
checkpoint61 |
157 |
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o autodiff |
158 |
|
Change default for TAF usage by removing argument '-nonew_arg' |
159 |
|
This changes TAF subroutine argument list (ordering of active var.) |
160 |
|
Omission of this flag leads to incompatibility w.r.t. TAMC |
161 |
|
To restore TAMC-compatibility, need following modifs: |
162 |
|
* use adoptfile tools/adjoint_options/adjoint_tamc_compatibility |
163 |
|
* use CPP option #define AUTODIFF_TAMC_COMPATIBILITY |
164 |
|
Tested TAF version is 1.9.22 |
165 |
|
N.B.: exch2 hand-written adjoint code currently not TAMC compatible |
166 |
|
|
167 |
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checkpoint60 |
168 |
|
--->>> This is the last checkpoint for which generating the adjoint |
169 |
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--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" |
170 |
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--->>> by default. |
171 |
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--->>> Future checkpoints will ommit this flag by default. |
172 |
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o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. |
173 |
|
o pkg/grdchk: Add gradient check to etan0 perturbations. |
174 |
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o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). |
175 |
|
o pkg/autodiff: more flexibility in zeroadj. |
176 |
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model/src: modifying do_oceanic_phys.F accordingly. |
177 |
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o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. |
178 |
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o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option |
179 |
|
special setup of gmredi for which the adjoint is stable |
180 |
|
enough for parameter optimization. |
181 |
|
o bridging the gap between eddy stress and GM. |
182 |
|
-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) |
183 |
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along with a change in CPP option (now ALLOW_EDDYPSI). |
184 |
|
-> when using GM w/ GM_AdvForm: |
185 |
|
The total eddy streamfunction (Psi = eddyPsi + K x Slope) |
186 |
|
is applied either in the tracer Eq. or in momentum Eq. |
187 |
|
depending on data.gmredi (intro. GM_InMomAsStress). |
188 |
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-> ALLOW_EDDYPSI_CONTROL for estimation purpose. |
189 |
|
The key modifications are in model/src/taueddy_external_forcing.F |
190 |
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pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F |
191 |
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|
192 |
|
checkpoint59r |
193 |
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o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array |
194 |
|
from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); |
195 |
|
fix option to read coriolis(@ cell-corner) from files with CS-grid. |
196 |
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o pkg/mnc: add some attributes to standard 1D-coordinate variables |
197 |
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o pkg/diagnostics: enforce missing_value attribute for scalar variables at |
198 |
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mass points, when using mnc for output |
199 |
|
- add runtime parameter (missing_value, missing_value_int) to override |
200 |
|
default (which is the value of getcon('UNDEF')) |
201 |
|
o pkg/mnc: prepare mnc for the actual use of missing values with the |
202 |
|
diagnostics package: small fix in mnc_cw_readwrite.template and more |
203 |
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initialisation of never used fields |
204 |
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- replace mnc_common.h and mnc_id_header.h with corresponding upper case |
205 |
|
versions |
206 |
|
o pkg/thsice/thsice_ini_vars.F added default initial values so that |
207 |
|
thermodynamics sea ice solver does not blow up when some initial fields |
208 |
|
are missing. |
209 |
|
o move from external_forcing_surf.F to ini_forcing.F |
210 |
|
the p-coord. hack consisting in using pLoad to set phi0surf ; |
211 |
|
update output of tutorial_global_oce_in_p (affected @ truncation level). |
212 |
|
o Freshen up a bit hs94.1x64x5, notably: |
213 |
|
remove rotationPeriod and tRef=5*0. (adjoint only), and add |
214 |
|
exactConserv=.TRUE. |
215 |
|
o pkg/generic_advdiff: |
216 |
|
change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
217 |
|
applies to files where Temperature & Salinity 2nd Order moments are used. |
218 |
|
o pkg/ptracers: add second-order moment advection schemes (80 and 81); |
219 |
|
this uses a dynamically allocated internal state data structure |
220 |
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(#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) |
221 |
|
and requires a fortran 90 compiler |
222 |
|
|
223 |
|
checkpoint59q |
224 |
|
o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) |
225 |
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(from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) |
226 |
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o Refresh tutorial_global_oce_biogeo, notably: |
227 |
|
- change bathymetry (put back seamounts in ACC, use hFacs) |
228 |
|
- change EOS (POLY3 --> JMD95Z) |
229 |
|
- use Bryan-Lewis vertical diffusivity |
230 |
|
- use multidimensional advection |
231 |
|
- remove old virtual virtual in dic pkg, now done through ptracer pkg |
232 |
|
- change a couple of parameters in dic pkg |
233 |
|
o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F |
234 |
|
o pkg/obcs: change default to OBCSfixTopo = .true., |
235 |
|
- set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result |
236 |
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- replace "debugMode" with "debugLevel .GE. debLevB" |
237 |
|
o implementation of TAF directives for gchem,cfc,dic |
238 |
|
o remove "exp5" (replaced by tutorial_deep_convection). |
239 |
|
o pkg/obcs: add code to fix topography gradients normal to open boundaries; |
240 |
|
this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; |
241 |
|
the code can be turned on by setting OBCSfixTopo = .true. in data.obcs |
242 |
|
--> changes results in exp4, seaice_obcs |
243 |
|
o tutorial_deep_convection : |
244 |
|
update the set-up and increase resolution and domain size ; start |
245 |
|
from pseudo initial conditions = output at t=120mn in order to see |
246 |
|
something happening when running testreport. |
247 |
|
o pkg/seaice: add os7mp as an advection scheme |
248 |
|
add check for advection schemes |
249 |
|
add a flag for restoring T and S underneath sea ice |
250 |
|
o pkg/my82: add netcdf-support and diagnostics |
251 |
|
o thsice pkg: |
252 |
|
- Now hsMax limits snow height by turning it into ice following |
253 |
|
flooding scheme (and now conserving energy) |
254 |
|
- Slight rewriting of the formula in thsice_calc_thick.F |
255 |
|
- Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos |
256 |
|
--> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice |
257 |
|
|
258 |
|
checkpoint59p |
259 |
|
o gchem / dic / cfc : |
260 |
|
- add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); |
261 |
|
- add new parameter files: "data.dic" & "data.cfc" ; |
262 |
|
- various re-arrangement in initialisation & header file ; |
263 |
|
- fix tutorial_global_oce_biogeo for multi-threaded test. |
264 |
|
o pkg/dic: test for "pickup_dic" file when restarting ; |
265 |
|
if no pickup-file, can restart with a re-initialised pH (same as it did |
266 |
|
before) providing pickupStrictlyMatch is set to False. |
267 |
|
o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP |
268 |
|
+ fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP |
269 |
|
o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2 |
270 |
|
and staggerTimeStep is off (needed for stability of Internal-wave dynamics). |
271 |
|
o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax, |
272 |
|
& lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers |
273 |
|
(note: not clear to me what lambdaTr1ClimRelax is still used for ...) |
274 |
|
o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which |
275 |
|
scheme to use for vorticty-term ; |
276 |
|
- compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F |
277 |
|
(with default selectVortScheme, return to original discretisation) |
278 |
|
- remove weird combination (e.g.: upwindVorticity & highOrderVorticity) |
279 |
|
o pkg/seaice: add a line to the summary to indicate grid type (B/C) |
280 |
|
o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the |
281 |
|
bottom ; only used with variable horizontal viscosity and non-hydrostatic. |
282 |
|
also fix diagnostics VISCAHW & VISCA4W. |
283 |
|
|
284 |
|
checkpoint59o |
285 |
|
o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). |
286 |
|
o change the loop ordering in most gad_*_adv_x.F to improve vectorization: |
287 |
|
move a few statemens out the main loop into separate loops |
288 |
|
o pkg/shelfice: |
289 |
|
- sort out freshwater flux; convert freshwater fluxes to mass fluxes |
290 |
|
(kg/m^2/s), does not break tests, because in verification/isomip, |
291 |
|
rhoConstFresh=rhoConst (by accident) |
292 |
|
- rearrange computation of tLoc, sLoc, pLoc to make code more efficient |
293 |
|
- move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into |
294 |
|
new file model/src/seawater.F, so that they are available for all pkgs. |
295 |
|
- convert potential temperature into in-situ temperature. This changes the |
296 |
|
isomip tests => update tests |
297 |
|
o add a flag writePickupAtEnd (default=true) to be able to suppress |
298 |
|
writing a pickup at the last timestep |
299 |
|
o tools/mpack-1.6 : |
300 |
|
- disable automake (not working) and autoconf (not needed). |
301 |
|
- update to version 1.6.4 which fix MD5 code on some 64 bits platforms |
302 |
|
also cleaner with much less compilation warnings. |
303 |
|
o pkg/profiles: |
304 |
|
rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg |
305 |
|
(for "less than 32 characters name" compiler requirement) |
306 |
|
o pkg/obcs and pkg/exf: added capability to specify seaice open boundary |
307 |
|
conditions that have a different sampling frequency than S/T/U/V obcs |
308 |
|
o pkg/diagnostics (stats-diags): |
309 |
|
- fix global Min/Max in case 1 processor get only empty tiles |
310 |
|
o genmake2: replace (4 times) |
311 |
|
make genmake_tc_1.o >> genmake_warnings 2>&1 |
312 |
|
with |
313 |
|
COMM="$CC $CFLAGS -c genmake_tc_1.c" |
314 |
|
echo $COMM >> genmake_warnings |
315 |
|
$COMM >> genmake_warnings 2>&1 |
316 |
|
to make genmake2 always see the value of CC as specified in the optfile. |
317 |
|
o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid. |
318 |
|
- add diagnostics for 1srt & 2nd Order moments and sub-grid variance. |
319 |
|
- modify verification advect_cs test to test SOM-advection on CS-grid. |
320 |
|
o pkg/ctrl: |
321 |
|
- Rewrite of ctrl_map_ini_ecco.F, |
322 |
|
introducing a generic routine (ctrl_map_ini_gen.F). |
323 |
|
- Modification of ctrl_bound/adctrl_bound handling control vector bounds. |
324 |
|
|
325 |
|
checkpoint59n |
326 |
|
o pkg/diagnostics: for large number of diagnostics, store diagnostic mate |
327 |
|
number in dedicate array "hdiag": |
328 |
|
- new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST |
329 |
|
with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST. |
330 |
|
- many small changes (integer format) for large number of diagnostics |
331 |
|
- start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with |
332 |
|
a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23. |
333 |
|
o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For |
334 |
|
usingSphericalGrid, this allows to define the rotated grid coordinates |
335 |
|
via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the |
336 |
|
geographical coordinates according to the inverse of the rotation defined |
337 |
|
by the Euler angles, so that Coriolis parameter and online-interpolation by |
338 |
|
exf works with the geographical coordinates on XC/YC/XG/YG. |
339 |
|
Naturally, this feature does not work with all packages, so some |
340 |
|
combinations are prohibited in config_summary (flt, flt_zonal, ecco, |
341 |
|
profiles), because there the coordinates are assumed to be regular |
342 |
|
spherical grid coordinates. |
343 |
|
o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc: |
344 |
|
- introduce isopycnal diffusion coefficient control. |
345 |
|
o tools/adjoint_options: |
346 |
|
- additional control vector components. |
347 |
|
o pkg/mnc: have mnc create marginally meaning full coordinate variables |
348 |
|
(that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 |
349 |
|
o pkg/mypackage: |
350 |
|
- add example of read/write pickup for state-var ; |
351 |
|
- add entry points to the main code for state-vars diags & write-pickup. |
352 |
|
o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year |
353 |
|
transitions for useExfYearlyFields |
354 |
|
- add new subroutine that determines the file to read from for |
355 |
|
use*YearlyFields = .TRUE. and .FALSE. |
356 |
|
- add a verification experiment to global_with_exf that tests |
357 |
|
useExfYearlyFields with USE_EXF_INTERPOLATION defined |
358 |
|
o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in |
359 |
|
analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new |
360 |
|
subroutines (which could be generated from a template, because they are |
361 |
|
almost identical), for now they are included in obcs_prescribe_read.F for |
362 |
|
simplicity |
363 |
|
o pkg/exf: |
364 |
|
- add a little more diagnostic to exf_interp_read (in analogy to |
365 |
|
mds_read_field, can be turned off with debugLevel < debugLevA=1) |
366 |
|
- improve vectorizability of exf_interp for TARGET_NEC_SX, makes code |
367 |
|
ugly but fast by unrolling short inner loops, inserting a unroll=8 |
368 |
|
directive in routine lagran, and splitting a loop and making do while the |
369 |
|
outermost loop (the latter requires the intoduction of index arrays) |
370 |
|
o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice |
371 |
|
o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver |
372 |
|
http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html |
373 |
|
o verification/seaice_obcs: updated for restart test and latest options |
374 |
|
o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different |
375 |
|
ice rheology (so-called truncated ellipse, that gets rid of tensile stress); |
376 |
|
for now this is only available for the C-grid code and also within |
377 |
|
#ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code |
378 |
|
|
379 |
|
checkpoint59m |
380 |
|
o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) |
381 |
|
and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature |
382 |
|
o gad_som : fix flux output (& diagnostics) to have same units as other |
383 |
|
advection scheme fluxes (was previously multiplied by deltaT). |
384 |
|
o added verification/seaice_obcs both to test seaice open boundaries |
385 |
|
and to provide an example matlab scrpt for generating them |
386 |
|
o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume |
387 |
|
o pkg/salt_plume: clean up salt_plume_frac.F to |
388 |
|
remove redundancy in PlumeMethod 1 and 4 |
389 |
|
o pkg/kpp: added saltplume diagnostics |
390 |
|
o pkg/obcs and pkg/seaice: |
391 |
|
- do not set uice and vice to zero when OB*icefile are unspecified |
392 |
|
- OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default |
393 |
|
- moved seaice tracer obcs after call to seaice_growth |
394 |
|
o pkg/salt_plume: added various options for salt plume depth |
395 |
|
criterion and for vertical distribution of the salt |
396 |
|
|
397 |
|
checkpoint59l |
398 |
|
o pkg/ptracers: new version of ptracers pickup: |
399 |
|
read meta file and write only fields which are needed to restart. |
400 |
|
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
401 |
|
o pkg/seaice: |
402 |
|
- add timescale for melting due to warm mixed layer as a means of |
403 |
|
setting SEAICE_availHeatFrac more conveniently |
404 |
|
- add a CPP-flag/runtime parameter check for flooding algorithm |
405 |
|
- reformulated availHeat in seaice_growth.F to be independent of AREA |
406 |
|
o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent |
407 |
|
unit changes |
408 |
|
o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint |
409 |
|
o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC |
410 |
|
SX vector computer. |
411 |
|
o pkg/seaice: |
412 |
|
- removed SEAICE_FFIELDS.h and seaice_get_forcing.F |
413 |
|
seaice forcing fields can now be read only through pkg/exf |
414 |
|
- removed some unused halos |
415 |
|
o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP |
416 |
|
o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL |
417 |
|
or U/VICE from U/VWIND before computing U/VSTRESS |
418 |
|
|
419 |
|
checkpoint59k |
420 |
|
o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between |
421 |
|
dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. |
422 |
|
o fix un-initialised variable problem (in mom_vecinv & shap_filt): |
423 |
|
all experiments pass when compile with un-initialised var. checking option. |
424 |
|
o added pkg/salt_plume |
425 |
|
o script to test restart (for now, in MITgcm_contrib/jmc_script) |
426 |
|
o pkg/seaice: new read/write pickup version. |
427 |
|
read meta file and write only fields which are needed to restart. |
428 |
|
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
429 |
|
o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) |
430 |
|
o lab_sea.hb87: modify the domain & update output.hb87.txt : |
431 |
|
lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 |
432 |
|
at j=1 & j=Ny+1 : this case is not treated correctly in the restart |
433 |
|
process. Fixed here by closing the domain at the Northern boundary. |
434 |
|
o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. |
435 |
|
o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing |
436 |
|
a set of consecutive levels in/from a 3-D array. |
437 |
|
o pkg/ptracers: |
438 |
|
use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). |
439 |
|
to-do: fix pkg/diagnostics when large number of diagnostics are defined. |
440 |
|
|
441 |
|
checkpoint59j |
442 |
|
o in pkgs: dic, obcs, offline, rbcs: |
443 |
|
standard way to compute coeff. for time interpolation between 2 time reccords |
444 |
|
which retains full precision (& make results less dependent on compiler). |
445 |
|
update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. |
446 |
|
o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those |
447 |
|
packages instead of reading ice cover and wind speed separately |
448 |
|
o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h |
449 |
|
(keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad |
450 |
|
to allow to compile customized code before the update) |
451 |
|
o cleaning-up: |
452 |
|
- fix CPP instruction syntax in pkg/obcs |
453 |
|
- replace (some) call to MDSIO S/R with call to RW interface S/R ; and |
454 |
|
add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio) |
455 |
|
- fix some threads issue in IO parts. |
456 |
|
o pkg/dic: |
457 |
|
- add tons of "_d 0" (--> much better testreports !) |
458 |
|
and then update outputs of tutorial_global_oce_biogeo |
459 |
|
o pkg/mom_fluxform: |
460 |
|
add a special version of momentum advection intended to conserve momentum |
461 |
|
next to a bathymetry step or a coastline edge. (default = off = #undef) |
462 |
|
o new read/write pickup version: |
463 |
|
- for now, only implemented for main (mdsio) pickup file. |
464 |
|
- write out only what is needed to restart; merge pickup_nh , pickup_ph |
465 |
|
and main pickup together. |
466 |
|
- read meta file; read only what is needed to restart; stop if a field |
467 |
|
is missing (if pickupStrictlyMatch=T, = the default) or try to restart |
468 |
|
if it make sense (even if the restart is not perfect). |
469 |
|
- if no meta file, assume that pickup to read corresponds exactly to |
470 |
|
a pickup that would currently be written. |
471 |
|
- read pickup written in the old format (until checkpoint59i) if it |
472 |
|
recognizes an old meta file (no field-list). |
473 |
|
- add a meta file in exp. which starts from a pickup: 2 cases: |
474 |
|
a) minimal meta file (with just file precision) + pickupStrictlyMatch=F |
475 |
|
e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta |
476 |
|
b) a meta file describing the content of the associated pickup file |
477 |
|
e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta |
478 |
|
o pkg/mdsio & pkg/rw: |
479 |
|
- new routine to read a meta file ; new set of routine to read |
480 |
|
Multiple-fields file (with meta file). |
481 |
|
o added open boundary conditions capability for seaice |
482 |
|
HSNOW, HSALT, UICE, and VICE |
483 |
|
|
484 |
|
checkpoint59i |
485 |
|
o adjoint: |
486 |
|
* fix multiDimAdvection adjoint |
487 |
|
(partial recomputation problem by TAF for fVerT(:,:,kDown) |
488 |
|
and comlev1 size definition (maxpass vs. max. number of tracers) |
489 |
|
* verification/global_ocean.90x45x15 adjoint now tests |
490 |
|
NLFS and multiDimAdvection using DST3 (=30) |
491 |
|
* verification/lab_sea now tests multiDimAdvection using DST3 (=30) |
492 |
|
o pkg/kpp: add "_d 0" to real constant (if missing); |
493 |
|
update output of exp: natl_box (10.digits); vermix (std, 7.digits) |
494 |
|
and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). |
495 |
|
o prepare for "clever pickup" implementation: add new header file "RESTART.h" |
496 |
|
for internal parameters related to restart process (formerly from PARAMS.h) |
497 |
|
and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. |
498 |
|
o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed |
499 |
|
as argument. (only atm2d & obcs write_pickup have not yet been updated) |
500 |
|
o pkg/monitor: |
501 |
|
- use GLOBAL_SUM_TILE instead of _GLOBAL_SUM |
502 |
|
- fix mon_stats_rs (statistics over the full domain, even where field is zero) |
503 |
|
- account for deep Atmosphere factor and density factor (anelastic) |
504 |
|
o added open boundary conditions capability for seaice HEFF and AREA |
505 |
|
o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) |
506 |
|
thermodynamics |
507 |
|
- requires a little reorganization, which affects the testreport results |
508 |
|
of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, |
509 |
|
so that now the conservative form is tested |
510 |
|
- add a few comments |
511 |
|
o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* |
512 |
|
o add a little bit of code to gad_os7mp_adv_?.F to help vectorization |
513 |
|
o add new diagnostics to seaice: advective, diffusive fluxes (only for |
514 |
|
multidim-advection, for scheme 2 they are not filled) and transports, |
515 |
|
thermodynamic growth rates |
516 |
|
o change units of EmPmR (inside the code, + within coupling interface) |
517 |
|
from m/s to kg/m2/s (mass flux) but leave input file unchanged. |
518 |
|
Affects results @ truncation level (cg2d match) and update output of |
519 |
|
experiments: lab_sea(6), global_ocean.90x40x15(10), |
520 |
|
global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) |
521 |
|
+ adjoint results: global_ocean_ebm(11) and lab_sea (12). |
522 |
|
Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). |
523 |
|
Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). |
524 |
|
|
525 |
|
checkpoint59h |
526 |
|
o pkg/exf: |
527 |
|
- improve vectorization by moving if-statement out of loops in |
528 |
|
exf_mapfields, exf_radiation |
529 |
|
- exf_bulkformulae.F: introduce 2D fields and vectorize code |
530 |
|
o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package |
531 |
|
o testreport: |
532 |
|
- allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE |
533 |
|
monitor & update offline_exf_seaice exp. output. |
534 |
|
- AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) |
535 |
|
o pkg/seaice: |
536 |
|
- bug fix in the evp solver: boundary conditions were affected be |
537 |
|
masking of zMax/zMin (changes results) |
538 |
|
- minor bug fix in boundary conditions in seaice_calc_strainrates |
539 |
|
(changes results for no_slip) |
540 |
|
- seaice_lsr.F: make interpolation of eta dependent on boundaries |
541 |
|
- replace hardcoded lower limit for zeta (zMin) by runtime parameter |
542 |
|
- add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean |
543 |
|
stress formulation and no-slip boundary conditions |
544 |
|
o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP |
545 |
|
in gad_calc_rhs.F ; add few safety stops in initialisation phase. |
546 |
|
o pkg/seaice: a first HSALT time stepping equation has been checked in |
547 |
|
o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV |
548 |
|
in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem |
549 |
|
without requiring DO-IF statements |
550 |
|
o pkg/thsice: |
551 |
|
use continuous power-law function for partition of energy between lateral |
552 |
|
melting/freezing and thinning/thickening ; old code using step function |
553 |
|
still available with #undef THSICE_FRACEN_POWERLAW |
554 |
|
update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice |
555 |
|
o testreport: change AD testing : check against results/output_adm.txt |
556 |
|
using same scripts as for forward test. |
557 |
|
|
558 |
|
checkpoint59g |
559 |
|
o adjoint testing: in preparation for changing testreport: |
560 |
|
- output format: cost and grad written on separated lines |
561 |
|
- ad output results in directory "results" (instead of "results_ad") |
562 |
|
o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
563 |
|
o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
564 |
|
o pkg/ecco: allow user defined cost function contributions |
565 |
|
o testreport: |
566 |
|
Allow to choose (per experiment) the list of tested output variables |
567 |
|
and the main variable (used to issue a pass/FAIL ) ; |
568 |
|
- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
569 |
|
- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
570 |
|
Also modify printing of summary: |
571 |
|
a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
572 |
|
b) echo the list of tested variables in the individual summary.txt of |
573 |
|
each experiment. |
574 |
|
o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
575 |
|
threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
576 |
|
(but still depend on the tile decompostion of the domain). |
577 |
|
o pkg/seaice: change a discretization detail to make the B-grid code |
578 |
|
"more symmetric". This change is likely to remove all "ridges/leads" that |
579 |
|
where quasi-aligned with the grid in B-grid solutions. It may also be |
580 |
|
the solution to the stress coupling issues with the B-grid. |
581 |
|
o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
582 |
|
remove .cvsignore from input dir. (since testreport no longer run here). |
583 |
|
o pkg/thsice: |
584 |
|
- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
585 |
|
- fix reshaping of sea-ice just after advection: |
586 |
|
melt all the ice only if ice-volume is too small. |
587 |
|
- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
588 |
|
prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
589 |
|
and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
590 |
|
o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
591 |
|
tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
592 |
|
o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
593 |
|
forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
594 |
|
(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
595 |
|
and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
596 |
|
of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
597 |
|
-> update output.txt |
598 |
|
o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
599 |
|
this affects truncation error: -> update output.txt of exp: |
600 |
|
global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
601 |
|
ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
602 |
|
|
603 |
|
checkpoint59f |
604 |
|
o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
605 |
|
o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
606 |
|
a bounded range (in forward mode) |
607 |
|
o pkg/ecco, ctrl, autodiff and mom_common: |
608 |
|
internal parameter controls, completements of implementations |
609 |
|
o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
610 |
|
o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
611 |
|
(not seem any difference in testing results). |
612 |
|
o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
613 |
|
at face corners. |
614 |
|
o pkg/generic_advdiff: |
615 |
|
- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
616 |
|
loop range indices for computing vertical advection tendency |
617 |
|
and do the calculation in the interior only (no overlap) ; |
618 |
|
for now, only implemented for SOM advection (to save CPU time). |
619 |
|
- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
620 |
o exch2 adjoint |
o exch2 adjoint |
621 |
First set of changes: |
First set of changes: |
622 |
- add exch2 hand-written adjoint templates |
- add exch2 hand-written adjoint templates |
626 |
- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
627 |
that used to hide exch2 or cubed-sphere specific code |
that used to hide exch2 or cubed-sphere specific code |
628 |
(commented via 'cph-exch2') |
(commented via 'cph-exch2') |
629 |
|
o pkg/seaice |
630 |
|
- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
631 |
|
o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
632 |
|
output of global_ocean.cs32x15.thsice . |
633 |
|
|
634 |
checkpoint59e |
checkpoint59e |
635 |
o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
829 |
ATMOSPHERIC_LOADING is #define). |
ATMOSPHERIC_LOADING is #define). |
830 |
o pkg/kpp: replaced _KPP_RL with _RL |
o pkg/kpp: replaced _KPP_RL with _RL |
831 |
o bug fixes for vertical diffusivity computations when both KPP and |
o bug fixes for vertical diffusivity computations when both KPP and |
832 |
3D diffusivity arrays are used. |
3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F |
833 |
|
are no longer updating the vertical diffusivity array |
834 |
|
(passed as argument) but are (re-) setting those arrays. |
835 |
o pkg/seaice: fix bug in evp solver, while doing that |
o pkg/seaice: fix bug in evp solver, while doing that |
836 |
- change (improve?) discretization of stress computations for both |
- change (improve?) discretization of stress computations for both |
837 |
cgrid-lsr and evp solver |
cgrid-lsr and evp solver |