4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
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|
7 |
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checkpoint63h (2011/12/30) |
8 |
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o pkg/offline: |
9 |
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- new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags); |
10 |
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- compute vertical velocity if not read from file (switch on exactConserv |
11 |
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& staggerTimeStep); |
12 |
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- fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq. |
13 |
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o verification: |
14 |
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- update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input) |
15 |
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with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m": |
16 |
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fix Pb in yG definition @ 2 missing corners (previously yG was averaged); |
17 |
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- update output of exp. global_ocean.cs32x15.viscA4 after changing |
18 |
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grid-file angles (used here for coriolis-3d); |
19 |
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- remove (or gzip) few files not needed to run fizhi-cs experiments. |
20 |
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o pkg/exf (vertor interpolation): |
21 |
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- rotate vector component toward local grid-axis orientation using grid-angles |
22 |
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(stored in GRID.h) instead of locally computed rotation angle; keep old code |
23 |
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available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default). |
24 |
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o pkg/seaice: |
25 |
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- allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION |
26 |
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undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined. |
27 |
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o pkg/PKG_OPTIONS.h files: |
28 |
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- move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h", |
29 |
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outside of the #ifdef ALLOW_THISPKG / #endif block. |
30 |
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- update verification/*/code/PKG_OPTIONS.h files. |
31 |
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o add a verification experiment (offline_exf_seaice/input.seaice) that test |
32 |
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the B-grid LSOR solver |
33 |
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o pkg/seaice: sort out emissivity and long wave radiation step 2: |
34 |
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- add emissivity for snow and ice as new run-time parameters |
35 |
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(unfortunately) that default to the corresponding exf values; this |
36 |
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changes results in most verification experiments so that for backward |
37 |
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compatibility these parameter have to be set explicitly to inconsistent |
38 |
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values (ugly); |
39 |
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- the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired |
40 |
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emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp |
41 |
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until we agree how to handle this bug properly |
42 |
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o pkg/exf (interpolation): |
43 |
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- add a set of run-time param ({inputfield}_interpMethod), one for |
44 |
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each interpolated input field, to select the interpolation method |
45 |
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with a value of zero switching off the interpolation; |
46 |
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- print interpolation parameters to standard output; |
47 |
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- refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined |
48 |
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(to use instead runoff_interpMethod=0 in data.exf). |
49 |
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- simplify default setting of interpolation parameters (for all fields, |
50 |
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set position to match model grid cell-center position, leading to trivial |
51 |
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interpolation in case of regular Lat-Lon grid) and fix for the case of |
52 |
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non-uniform delY. |
53 |
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o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for |
54 |
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within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1. |
55 |
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this factor is absolutely required, because the lw exitance (= out-going |
56 |
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long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown, |
57 |
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where the reflectivity rho = 1-emissivity for conservation reasons. Once |
58 |
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this is established, we can remove the CPP-Flag (if we want to). |
59 |
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o pkg/seaice: |
60 |
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- qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and |
61 |
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ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined |
62 |
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- sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity |
63 |
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what the name implies (and not emissivity*BoltzmannConstant), this means |
64 |
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the old default value of 5.5e-8 now means |
65 |
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5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in |
66 |
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S/R exf_readparms |
67 |
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- FV-discretization of the B-grid LSOR solver, turn on with |
68 |
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SEAICE_LSRBNEW. This new solver also involves a slight re-organization |
69 |
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of the calling routine dynsolver, so that B and C-grid code look a |
70 |
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little more alike. |
71 |
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- fix index bugs in ostres.F (B-grid code) |
72 |
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o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better |
73 |
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o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the |
74 |
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default for SEAICE_emissivity, if useEXF; requires setting a wrong |
75 |
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parameter value in global_ocean.cs32x15/input.seaice/data.seaice for |
76 |
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backward compatiblity |
77 |
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o model/src: use sigmaR in calc_ivdc |
78 |
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|
79 |
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checkpoint63g (2011/12/16) |
80 |
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o pkg/seaice/seaice_growth.F: |
81 |
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fix heat conservation of the coupled ocean-seaice system. |
82 |
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when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of |
83 |
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solid vs liquid water treatment is resolved via QNET. |
84 |
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o pkg/seaice/seaice_growth.F: |
85 |
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add missing term for sublimation in saltFlux, which was breaking conservation. |
86 |
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o pkg/seaice/seaice_model.F: |
87 |
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Remove this patholigical case treatment in evolution branch, |
88 |
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where it is un-necessary and breaks conservation. |
89 |
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Update global_ocean.cs32x15/results accordingly for |
90 |
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output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt |
91 |
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o model/src: |
92 |
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useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in |
93 |
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external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE. |
94 |
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o pkg/obcs: |
95 |
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modify Stevens boundary conditions so that S/R obcs_calc_stevens computes |
96 |
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tendency for temperature and salinity that is then applied to update |
97 |
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theta and salt in S/R obcs_apply_ts; this requires proper masking of all |
98 |
|
horizontal advection and diffusion contributions on the boundary (in |
99 |
|
S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and |
100 |
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removing the mask in S/R timestep_tracer. The advantage of this approach is |
101 |
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that the updated tracer values include contributions from the surface |
102 |
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forcing and vertical diffusion. |
103 |
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This modification changes exp4.stevens because of vertical diffusion. |
104 |
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o model/src: |
105 |
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change non-curvilinear grid setting to also work with exch2 + blank tiles: |
106 |
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- move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst |
107 |
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face dimensions. |
108 |
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- new S/R INI_LOCAL_GRID to define model tile-local grid (using same units |
109 |
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as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID |
110 |
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and INI_SPHERICAL_POLAR_GRID. |
111 |
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change test-experiment global_ocean.90x40x15: |
112 |
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- split the domain in many more tiles (9x4 tiles of 10x10 each); |
113 |
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- switch to exch2 and remove 1 blank-tile (but only for MPI test). |
114 |
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- update results of both test (std & dwnslp). |
115 |
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o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in |
116 |
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tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation |
117 |
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o model/src: |
118 |
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- take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS |
119 |
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and fix initialisation when using sigma-coords. |
120 |
|
o model/src: |
121 |
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- improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc. |
122 |
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to their current value at the beginning of forward_step.F": add a new run-time |
123 |
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switch "doResetHFactors" (default=false) and use it to do (or not) the resetting. |
124 |
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- set doResetHFactors=T in the following test exp: |
125 |
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global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS), |
126 |
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global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS) |
127 |
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and tutorial_global_oce_in_p (nonLinFS in p) |
128 |
|
o pkg/ecco |
129 |
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- added IES cost term |
130 |
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o verification/advect_xz |
131 |
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- scale down the depth by 1/100 (from 200 km to just 2.km) |
132 |
|
- add secondary test using divergent flow, r-star and implicit vertical advection. |
133 |
|
- add note (check_conserve_TS.txt) and matlab script to check global |
134 |
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conservation of T & S with NonLin-FreeSurf and Adams-Bashforth. |
135 |
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o pkg/rbcs: |
136 |
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- add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F). |
137 |
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o pkg/obcs (Stevens BCs): |
138 |
|
- fix various problems in the phase speed computations of the Stevens |
139 |
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boundary conditions: |
140 |
|
- sign error for western and southern boundaries, |
141 |
|
- time tendencies were underestimated by factor of dTracerLev and some just |
142 |
|
zero (for multidim advection schemes) -> now estimate time tendencies |
143 |
|
from difference between previous (n) time level and the one before (n-1); |
144 |
|
this requires storing a field per tracer per boundary, also in the pickup |
145 |
|
files. |
146 |
|
- replace deltaTmom in cflMer/Zon computation with dTracerLev |
147 |
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- set default phase velocity to cflMer/Zon |
148 |
|
- update verification experiment exp4.stevens |
149 |
|
o pkg/generic_advdiff (implicit_r): |
150 |
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- fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf |
151 |
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(remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F); |
152 |
|
- fix implicit vertical diffusion or advection with NonLin FreeSurf |
153 |
|
(was using current recip_hFacC instead of future recip_hFacC): set future |
154 |
|
recip_hFac in thermodynamics.F and pass & use it in all vertical implicit |
155 |
|
solver S/R ; |
156 |
|
- fill diagnostics of vertical advective fluxes (computed from tendency) |
157 |
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when using implicit vert. advection; |
158 |
|
- update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion: |
159 |
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global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD), |
160 |
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tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD) |
161 |
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and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5. |
162 |
|
o pkg/diagnostics: |
163 |
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- add diags for T & S tendency which goes through Adams-Bashforth. |
164 |
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|
165 |
|
checkpoint63f (2011/11/30) |
166 |
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o pkg/obcs/obcs_calc_stevens.F: |
167 |
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- join some loops to reduce number of if-statements |
168 |
|
- fix a bug in code for northern and southern boundaries. |
169 |
|
o pkg/seaice/seaice_init_varia.F |
170 |
|
- undo resetting UVM=0 that has slipped in unnoticed in r1.49 and |
171 |
|
caused zero ice-velocities for the B-grid code |
172 |
|
o pkg/seaice/seaice_init_fixed.F |
173 |
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- fix a bug in the initialisation of the second metric terms |
174 |
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k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0. |
175 |
|
- this affects all seaice configurations with useCurviLinearGrid = .true. |
176 |
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and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms |
177 |
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= .true. (default) |
178 |
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- the only verification experiment affected is global_ocean.cs32x15: |
179 |
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icedyn, seaice, and seaice_dynmix (AD) |
180 |
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o pkg/thsice/thsice_diagnostics_state.F |
181 |
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- only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does |
182 |
|
not contain garbage that can lead to surprises in diagstats_calc.F |
183 |
|
o model/src: |
184 |
|
- move bi,bj loops inside INTEGR_CONTINUITY ; |
185 |
|
- call INTEGR_CONTINUITY directly from forward_step.F |
186 |
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(previously called from momentum_correction_step.F) |
187 |
|
- call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F, |
188 |
|
forward_step.F and pkg/ecco/the_main_loop.F |
189 |
|
o model/src/do_oceanic_phys.F: |
190 |
|
- reset addMass to zero only if useICEFRONT ; |
191 |
|
- separated k-loop for rhoInSitu calculation ; |
192 |
|
- add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P) |
193 |
|
and at constant T,S (= WdRHOdP); |
194 |
|
NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport |
195 |
|
of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical |
196 |
|
transport of locally-referenced potential density); |
197 |
|
to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP) |
198 |
|
o gluemnc: |
199 |
|
- replace ncrcat with ncks when adding variables to *.glob.nc |
200 |
|
- change the way variables without record dimensions are handled so that |
201 |
|
files that have variables with and without record variables can be glued: |
202 |
|
add a record dimension with a new unique name to be able to differentiate |
203 |
|
between variable with and without a-prior record dimensions. Remove |
204 |
|
this record dimension before adding the variable to the *.glob.nc file. |
205 |
|
This procedure automatically works also for grid.*.nc files that do not |
206 |
|
have any record dimension. |
207 |
|
o verification/cpl_aim+ocn: |
208 |
|
- generate new reference output on baudelaire (gfortran, mpich2) (previously |
209 |
|
from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script. |
210 |
|
o pkg/obcs/obcs_calc_stevens.F: |
211 |
|
- add code for northern and southern boundaries. |
212 |
|
- reorder some loops to save some operations and so that drFBar can be scalar |
213 |
|
o model/src: |
214 |
|
- re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine |
215 |
|
truncation) and add diagnostics for Adams-Bashforth tendency increment. |
216 |
|
- update test-exp. AD output: |
217 |
|
1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl; |
218 |
|
and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20, |
219 |
|
front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5), |
220 |
|
global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4), |
221 |
|
matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre, |
222 |
|
tutorial_global_oce_in_p, tutorial_global_oce_latlon and |
223 |
|
tutorial_plume_on_slope. |
224 |
|
o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX |
225 |
|
that vectorises. This code uses 3 extra 2D fields, F90 array assignments |
226 |
|
and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX |
227 |
|
does not even come with an F77 compiler anymore, this should not be |
228 |
|
a limitation |
229 |
|
|
230 |
|
checkpoint63e (2011/11/06) |
231 |
|
o pkg/seaice adjoint of LSR: |
232 |
|
- substantially rework STORE dirs. |
233 |
|
- add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED |
234 |
|
this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields |
235 |
|
and only perform SOLV_MAX_FIXED adjoint iters. |
236 |
|
If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration |
237 |
|
always goes to same record, meaning that the last forward field will be |
238 |
|
the one used in the adjoint - an approximation. |
239 |
|
- now produces non-zero LSR-related gradients, and acceptable gradients for |
240 |
|
An's zonal (x-z) test case (to be checked in) |
241 |
|
- lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR |
242 |
|
(but these are screwed up by the thermodynamics in the first place); |
243 |
|
reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution; |
244 |
|
output_adm.txt also reflects changes to seaice_lsr |
245 |
|
- global_ocean.cs32x15: |
246 |
|
* the "default" input_ad.seaice has been re-defined to always exclude dynamics |
247 |
|
(output_adm.seaice.txt was updated) |
248 |
|
* new input_ad.seaice_dynmix tests a forward LSR / backward free-drift |
249 |
|
(output_adm.seaice_dynmix.txt) |
250 |
|
o test-exp. exp4+stevens: |
251 |
|
- switch off pTracers and nonHydrostatic (restart problems with NH); update output |
252 |
|
o pkg/seaice (lsr solver): |
253 |
|
- put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only); |
254 |
|
update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15 |
255 |
|
- fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD) |
256 |
|
- new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution |
257 |
|
into initial guess for linearised solver; use weight ~ (1/err)^2,4. |
258 |
|
- compute (with new S/R) and print initial (+ free-driff sol. if available) |
259 |
|
and final residual of linearised system. |
260 |
|
o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity |
261 |
|
(requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F) |
262 |
|
o pkg/obcs: Stevens BCs (still only for east and west) |
263 |
|
- fix Stevens BCs by using intermediate velocities of previous |
264 |
|
time step as "baroclinic" contribution rather velocity of one grid cell |
265 |
|
inside the boundaries; more consistent but makes the entire treatment |
266 |
|
more complicated, requires new pickup files and two new S/Rs: |
267 |
|
obcs_copy_uv_n and obcs_save_uv_n |
268 |
|
keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY |
269 |
|
(undefined by default) |
270 |
|
- silently move computation of some grid factors into separate loops to |
271 |
|
save some recomputations |
272 |
|
- add a hack for non-linear free surface |
273 |
|
- add a verification experiment to exp4 that tests this code |
274 |
|
o make gluemnc/xplodemnc work with (moron) non-GNU shell tools |
275 |
|
|
276 |
|
checkpoint63d (2011/10/25) |
277 |
|
o pkg/obcs + seaice-dynamics: |
278 |
|
- new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before |
279 |
|
solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB |
280 |
|
values (consistent with an implicit method). |
281 |
|
- add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to |
282 |
|
return to older implementation (same results as before); note that none of |
283 |
|
the "experimental" OBCS_SEAICE options are implemented in the new version. |
284 |
|
- switch test exp. seaice_obcs to use new version (update output). |
285 |
|
o pkg/seaice: |
286 |
|
- add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS) |
287 |
|
- add parenthesis in Water-Ice drag calculations (evp & lsr); |
288 |
|
- in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1; |
289 |
|
and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice) |
290 |
|
- update output of test exp lab_sea that uses evp or lsr (fwd+ad) |
291 |
|
and global_ocean.cs32x15 (icedyn & seaice fwd+ad). |
292 |
|
o pkg/layers: |
293 |
|
- Include potential density as new coordinate (Thanks to David Munday) |
294 |
|
o pkg/dic: |
295 |
|
- Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add |
296 |
|
carbonate computation/output to CALC_PCO2_APPROX |
297 |
|
o pkg/generic_advdiff |
298 |
|
- make TAF generate code that vectorizes: |
299 |
|
gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F |
300 |
|
o model/src: |
301 |
|
- improve vectorization also for adjoint code of |
302 |
|
solve_tridiagonal and solve_pentadiagonal. As this requires up to |
303 |
|
5 new 3D-fields, this code is only turned on for the combination of |
304 |
|
ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message |
305 |
|
for singular matrix check (only for TARGET_NEC_SX). |
306 |
|
- remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to |
307 |
|
ALLOW_AUTODIFF. This flag now needs to be set outside of |
308 |
|
solve_tri/pentadiagonal.F |
309 |
|
o pkg/exf: |
310 |
|
- fix previous modif in exf_readparms.F (revision 1.66: treatment of |
311 |
|
optional namelist EXF_NML_OBCS). |
312 |
|
- add many debug-print (to trace down where pkg/cal error msg comes from) |
313 |
|
o pkg/mom_vecinv/mom_vi_hdissip.F |
314 |
|
- rearrange loops so that vectorization is improved and in particular |
315 |
|
the adjoint routine vectorizes. The code is a little longer now, but I |
316 |
|
think easier to read. |
317 |
|
Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested. |
318 |
|
o pkg/seaice: |
319 |
|
- allow to specify initial seaice velocity from files (uIceFile,vIceFile) |
320 |
|
o pkg/exch2: |
321 |
|
- alternative code (without tile x tile matrix) for cumulated (global) sum; |
322 |
|
used as default; keep using matrix version in adjustment.cs-32x32x1. |
323 |
|
o tools/build_options: |
324 |
|
- after merging some MPI and/or multi-threads specific optfiles so that |
325 |
|
the modified default optfile support both built (using genmake2 -mpi |
326 |
|
for the MPI built, using genmake2 -omp for OpenMP built), |
327 |
|
move now obsolete optfiles to tools/build_options/unsupported/ |
328 |
|
(add copy of email sent to support list in doc/optfiles_changes.txt) |
329 |
|
|
330 |
|
checkpoint63c (2011/09/28) |
331 |
|
o pkg/ebm: |
332 |
|
- fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of |
333 |
|
test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d) |
334 |
o pkg/seaice (SItracer pickup) |
o pkg/seaice (SItracer pickup) |
335 |
* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER) |
* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER) |
336 |
To be done: |
To be done: |