| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
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|
| 7 |
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o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness |
| 8 |
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over land (non-legacy code) |
| 9 |
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o vectorize salt_plume package: |
| 10 |
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- add extra code to salt_plume_frac and salt_plume_tendency_apply_s |
| 11 |
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- this code computes plumebk everywhere (also over land), thus requires |
| 12 |
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code to avoid divisions by zero and catch the case of kLev=Nr. |
| 13 |
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- efficiency of salt_plume_frac is still sub-optimal |
| 14 |
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o tools (genmake2): |
| 15 |
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- fix makefile NAME specification (option: -makefile NAME) by adding |
| 16 |
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"-f $MAKEFILE" in few places where it was missing including makedepend |
| 17 |
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command (contribution from Paul). |
| 18 |
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|
| 19 |
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checkpoint63i (2012/01/24) |
| 20 |
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o model/src: |
| 21 |
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- add factorized versions of some EOS code to find_rho.F, |
| 22 |
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define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX) |
| 23 |
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o model/src: |
| 24 |
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- add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h; |
| 25 |
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- change default celsius2K from 273.16 to 273.15 |
| 26 |
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- to keep results unchanged, add back old value of celsius2K in verification |
| 27 |
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exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd), |
| 28 |
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global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm). |
| 29 |
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o model/src: add a little initialisation trick to find_rho.F and find_alpha.F |
| 30 |
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to make TAF generate vectorizable code |
| 31 |
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o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows. |
| 32 |
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Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers |
| 33 |
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have flags that do this more efficiently. |
| 34 |
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o pkg/diagnostics/diagstats_calc.F |
| 35 |
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- for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact |
| 36 |
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o pkg/obcs (with exch2): |
| 37 |
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- derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F) |
| 38 |
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and remove code (in obcs_readparms.F) which was based on EXCH of indices |
| 39 |
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(through buffer) and did not account for exch2 (e.g., CS-grid) topology. |
| 40 |
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o pkg/exf and seaice exp: |
| 41 |
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- change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0) |
| 42 |
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so that switching off area & heff advection flags does not affect results. |
| 43 |
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- change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h |
| 44 |
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- keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef |
| 45 |
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EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update |
| 46 |
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results of verification experiments: 1D_ocean_ice_column(fwd), |
| 47 |
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global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8) |
| 48 |
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and offline_exf_seaice (all 4). |
| 49 |
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o pkg/seaice: |
| 50 |
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- remove array YNEG, RIVER, TMIX (replaced by local var) from common block; |
| 51 |
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remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef. |
| 52 |
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- fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY) |
| 53 |
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but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and |
| 54 |
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not multi-dim advection; |
| 55 |
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- fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and |
| 56 |
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SHORTWAVE_HEATING #undef. |
| 57 |
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o optim: make Makefile more robust (?) |
| 58 |
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o pkg/obcs: |
| 59 |
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* fix treatment of obcs_read_pickup for TAF |
| 60 |
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o pkg/shelfice: |
| 61 |
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* add missing initialisation of num_shifwflx |
| 62 |
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* new adjoint verification exp. for isomip |
| 63 |
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* change Prandtl and Schmidt numbers from generic formulations |
| 64 |
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(in terms of model diffus. and visc.) to separate runtime |
| 65 |
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parameters, with Holland and Jenkins (1999) default values. |
| 66 |
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o pkg/exf (interpolation): |
| 67 |
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- extended input field (2 rows) near the N & S poles: |
| 68 |
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* fill in with the symetric value (when even Nb of data in longitude) |
| 69 |
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* add average value at the poles only for scalar quantities ; for vector |
| 70 |
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component interpolation, skip the averaging and keep duplicated values, |
| 71 |
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unless the 2 components have same location (uvInterp=T) in which case |
| 72 |
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interpolate the 2 components together using S/R EXF_INTERP_UV. |
| 73 |
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- new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field |
| 74 |
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together: this allows to account properly for local orientation when |
| 75 |
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averaging at N & S pole. |
| 76 |
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- add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding |
| 77 |
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exf-interpolation near N & S poles. Undef by default. |
| 78 |
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- add debug check/print on 1rst iter if debugLevel >=2. |
| 79 |
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o pkg/exf: |
| 80 |
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- change masking flags definition (no longer "parameter"), put them in |
| 81 |
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common block and set them in S/R EXF_INIT_FIXED. |
| 82 |
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- change recognized masking flag from s,u,v to c,w,s since the mask |
| 83 |
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to use (maskC,W,S) depends on position on model grid and has little to |
| 84 |
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do with scalar/vector difference; fix masking if using P-coordinates. |
| 85 |
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- fix masking of wind-stress (was wrong if interpolated or read on A-grid) |
| 86 |
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and update results of exp. global_with_exf (x2). |
| 87 |
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- fix setting of zenith-angle table when SHORTWAVE_HEATING is undef. |
| 88 |
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o pkg/obcs |
| 89 |
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- S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate) |
| 90 |
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o pkg/exf (interpolation): |
| 91 |
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- assume periodicity in X only if input field cover full longitude range. |
| 92 |
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- improve search for lat. index (supposed to be faster, in ~log2(ny) steps, |
| 93 |
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and should vectorise). |
| 94 |
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- fix input lat of the 2 added row (in case we provide N.pole data). |
| 95 |
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|
| 96 |
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checkpoint63h (2011/12/30) |
| 97 |
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o pkg/seaice: |
| 98 |
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- change declaration of UVM from _RL to _RS in order to get B-grid |
| 99 |
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uIce,vIce monitor when _RS = real*4 |
| 100 |
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o pkg/offline: |
| 101 |
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- new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags); |
| 102 |
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- compute vertical velocity if not read from file (switch on exactConserv |
| 103 |
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& staggerTimeStep); |
| 104 |
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- fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq. |
| 105 |
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o verification: |
| 106 |
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- update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input) |
| 107 |
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with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m": |
| 108 |
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fix Pb in yG definition @ 2 missing corners (previously yG was averaged); |
| 109 |
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- update output of exp. global_ocean.cs32x15.viscA4 after changing |
| 110 |
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grid-file angles (used here for coriolis-3d); |
| 111 |
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- remove (or gzip) few files not needed to run fizhi-cs experiments. |
| 112 |
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o pkg/exf (vector interpolation): |
| 113 |
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- rotate vector component toward local grid-axis orientation using grid-angles |
| 114 |
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(stored in GRID.h) instead of locally computed rotation angle; keep old code |
| 115 |
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available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default). |
| 116 |
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o pkg/seaice: |
| 117 |
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- allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION |
| 118 |
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undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined. |
| 119 |
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o pkg/PKG_OPTIONS.h files: |
| 120 |
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- move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h", |
| 121 |
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outside of the #ifdef ALLOW_THISPKG / #endif block. |
| 122 |
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- update verification/*/code/PKG_OPTIONS.h files. |
| 123 |
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o add a verification experiment (offline_exf_seaice/input.seaice) that test |
| 124 |
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the B-grid LSOR solver |
| 125 |
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o pkg/seaice: sort out emissivity and long wave radiation step 2: |
| 126 |
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- add emissivity for snow and ice as new run-time parameters |
| 127 |
|
(unfortunately) that default to the corresponding exf values; this |
| 128 |
|
changes results in most verification experiments so that for backward |
| 129 |
|
compatibility these parameter have to be set explicitly to inconsistent |
| 130 |
|
values (ugly); |
| 131 |
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- the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired |
| 132 |
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emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp |
| 133 |
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until we agree how to handle this bug properly |
| 134 |
|
o pkg/exf (interpolation): |
| 135 |
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- add a set of run-time param ({inputfield}_interpMethod), one for |
| 136 |
|
each interpolated input field, to select the interpolation method |
| 137 |
|
with a value of zero switching off the interpolation; |
| 138 |
|
- print interpolation parameters to standard output; |
| 139 |
|
- refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined |
| 140 |
|
(to use instead runoff_interpMethod=0 in data.exf). |
| 141 |
|
- simplify default setting of interpolation parameters (for all fields, |
| 142 |
|
set position to match model grid cell-center position, leading to trivial |
| 143 |
|
interpolation in case of regular Lat-Lon grid) and fix for the case of |
| 144 |
|
non-uniform delY. |
| 145 |
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o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for |
| 146 |
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within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1. |
| 147 |
|
this factor is absolutely required, because the lw exitance (= out-going |
| 148 |
|
long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown, |
| 149 |
|
where the reflectivity rho = 1-emissivity for conservation reasons. Once |
| 150 |
|
this is established, we can remove the CPP-Flag (if we want to). |
| 151 |
|
o pkg/seaice: |
| 152 |
|
- qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and |
| 153 |
|
ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined |
| 154 |
|
- sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity |
| 155 |
|
what the name implies (and not emissivity*BoltzmannConstant), this means |
| 156 |
|
the old default value of 5.5e-8 now means |
| 157 |
|
5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in |
| 158 |
|
S/R exf_readparms |
| 159 |
|
- FV-discretization of the B-grid LSOR solver, turn on with |
| 160 |
|
SEAICE_LSRBNEW. This new solver also involves a slight re-organization |
| 161 |
|
of the calling routine dynsolver, so that B and C-grid code look a |
| 162 |
|
little more alike. |
| 163 |
|
- fix index bugs in ostres.F (B-grid code) |
| 164 |
|
o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better |
| 165 |
|
o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the |
| 166 |
|
default for SEAICE_emissivity, if useEXF; requires setting a wrong |
| 167 |
|
parameter value in global_ocean.cs32x15/input.seaice/data.seaice for |
| 168 |
|
backward compatiblity |
| 169 |
|
o model/src: use sigmaR in calc_ivdc |
| 170 |
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|
| 171 |
|
checkpoint63g (2011/12/16) |
| 172 |
|
o pkg/seaice/seaice_growth.F: |
| 173 |
|
fix heat conservation of the coupled ocean-seaice system. |
| 174 |
|
when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of |
| 175 |
|
solid vs liquid water treatment is resolved via QNET. |
| 176 |
|
o pkg/seaice/seaice_growth.F: |
| 177 |
|
add missing term for sublimation in saltFlux, which was breaking conservation. |
| 178 |
|
o pkg/seaice/seaice_model.F: |
| 179 |
|
Remove this patholigical case treatment in evolution branch, |
| 180 |
|
where it is un-necessary and breaks conservation. |
| 181 |
|
Update global_ocean.cs32x15/results accordingly for |
| 182 |
|
output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt |
| 183 |
|
o model/src: |
| 184 |
|
useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in |
| 185 |
|
external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE. |
| 186 |
|
o pkg/obcs: |
| 187 |
|
modify Stevens boundary conditions so that S/R obcs_calc_stevens computes |
| 188 |
|
tendency for temperature and salinity that is then applied to update |
| 189 |
|
theta and salt in S/R obcs_apply_ts; this requires proper masking of all |
| 190 |
|
horizontal advection and diffusion contributions on the boundary (in |
| 191 |
|
S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and |
| 192 |
|
removing the mask in S/R timestep_tracer. The advantage of this approach is |
| 193 |
|
that the updated tracer values include contributions from the surface |
| 194 |
|
forcing and vertical diffusion. |
| 195 |
|
This modification changes exp4.stevens because of vertical diffusion. |
| 196 |
|
o model/src: |
| 197 |
|
change non-curvilinear grid setting to also work with exch2 + blank tiles: |
| 198 |
|
- move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst |
| 199 |
|
face dimensions. |
| 200 |
|
- new S/R INI_LOCAL_GRID to define model tile-local grid (using same units |
| 201 |
|
as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID |
| 202 |
|
and INI_SPHERICAL_POLAR_GRID. |
| 203 |
|
change test-experiment global_ocean.90x40x15: |
| 204 |
|
- split the domain in many more tiles (9x4 tiles of 10x10 each); |
| 205 |
|
- switch to exch2 and remove 1 blank-tile (but only for MPI test). |
| 206 |
|
- update results of both test (std & dwnslp). |
| 207 |
|
o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in |
| 208 |
|
tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation |
| 209 |
|
o model/src: |
| 210 |
|
- take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS |
| 211 |
|
and fix initialisation when using sigma-coords. |
| 212 |
|
o model/src: |
| 213 |
|
- improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc. |
| 214 |
|
to their current value at the beginning of forward_step.F": add a new run-time |
| 215 |
|
switch "doResetHFactors" (default=false) and use it to do (or not) the resetting. |
| 216 |
|
- set doResetHFactors=T in the following test exp: |
| 217 |
|
global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS), |
| 218 |
|
global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS) |
| 219 |
|
and tutorial_global_oce_in_p (nonLinFS in p) |
| 220 |
|
o pkg/ecco |
| 221 |
|
- added IES cost term |
| 222 |
|
o verification/advect_xz |
| 223 |
|
- scale down the depth by 1/100 (from 200 km to just 2.km) |
| 224 |
|
- add secondary test using divergent flow, r-star and implicit vertical advection. |
| 225 |
|
- add note (check_conserve_TS.txt) and matlab script to check global |
| 226 |
|
conservation of T & S with NonLin-FreeSurf and Adams-Bashforth. |
| 227 |
|
o pkg/rbcs: |
| 228 |
|
- add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F). |
| 229 |
|
o pkg/obcs (Stevens BCs): |
| 230 |
|
- fix various problems in the phase speed computations of the Stevens |
| 231 |
|
boundary conditions: |
| 232 |
|
- sign error for western and southern boundaries, |
| 233 |
|
- time tendencies were underestimated by factor of dTracerLev and some just |
| 234 |
|
zero (for multidim advection schemes) -> now estimate time tendencies |
| 235 |
|
from difference between previous (n) time level and the one before (n-1); |
| 236 |
|
this requires storing a field per tracer per boundary, also in the pickup |
| 237 |
|
files. |
| 238 |
|
- replace deltaTmom in cflMer/Zon computation with dTracerLev |
| 239 |
|
- set default phase velocity to cflMer/Zon |
| 240 |
|
- update verification experiment exp4.stevens |
| 241 |
|
o pkg/generic_advdiff (implicit_r): |
| 242 |
|
- fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf |
| 243 |
|
(remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F); |
| 244 |
|
- fix implicit vertical diffusion or advection with NonLin FreeSurf |
| 245 |
|
(was using current recip_hFacC instead of future recip_hFacC): set future |
| 246 |
|
recip_hFac in thermodynamics.F and pass & use it in all vertical implicit |
| 247 |
|
solver S/R ; |
| 248 |
|
- fill diagnostics of vertical advective fluxes (computed from tendency) |
| 249 |
|
when using implicit vert. advection; |
| 250 |
|
- update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion: |
| 251 |
|
global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD), |
| 252 |
|
tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD) |
| 253 |
|
and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5. |
| 254 |
|
o pkg/diagnostics: |
| 255 |
|
- add diags for T & S tendency which goes through Adams-Bashforth. |
| 256 |
|
|
| 257 |
|
checkpoint63f (2011/11/30) |
| 258 |
|
o pkg/obcs/obcs_calc_stevens.F: |
| 259 |
|
- join some loops to reduce number of if-statements |
| 260 |
|
- fix a bug in code for northern and southern boundaries. |
| 261 |
|
o pkg/seaice/seaice_init_varia.F |
| 262 |
|
- undo resetting UVM=0 that has slipped in unnoticed in r1.49 and |
| 263 |
|
caused zero ice-velocities for the B-grid code |
| 264 |
|
o pkg/seaice/seaice_init_fixed.F |
| 265 |
|
- fix a bug in the initialisation of the second metric terms |
| 266 |
|
k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0. |
| 267 |
|
- this affects all seaice configurations with useCurviLinearGrid = .true. |
| 268 |
|
and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms |
| 269 |
|
= .true. (default) |
| 270 |
|
- the only verification experiment affected is global_ocean.cs32x15: |
| 271 |
|
icedyn, seaice, and seaice_dynmix (AD) |
| 272 |
|
o pkg/thsice/thsice_diagnostics_state.F |
| 273 |
|
- only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does |
| 274 |
|
not contain garbage that can lead to surprises in diagstats_calc.F |
| 275 |
|
o model/src: |
| 276 |
|
- move bi,bj loops inside INTEGR_CONTINUITY ; |
| 277 |
|
- call INTEGR_CONTINUITY directly from forward_step.F |
| 278 |
|
(previously called from momentum_correction_step.F) |
| 279 |
|
- call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F, |
| 280 |
|
forward_step.F and pkg/ecco/the_main_loop.F |
| 281 |
|
o model/src/do_oceanic_phys.F: |
| 282 |
|
- reset addMass to zero only if useICEFRONT ; |
| 283 |
|
- separated k-loop for rhoInSitu calculation ; |
| 284 |
|
- add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P) |
| 285 |
|
and at constant T,S (= WdRHOdP); |
| 286 |
|
NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport |
| 287 |
|
of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical |
| 288 |
|
transport of locally-referenced potential density); |
| 289 |
|
to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP) |
| 290 |
|
o gluemnc: |
| 291 |
|
- replace ncrcat with ncks when adding variables to *.glob.nc |
| 292 |
|
- change the way variables without record dimensions are handled so that |
| 293 |
|
files that have variables with and without record variables can be glued: |
| 294 |
|
add a record dimension with a new unique name to be able to differentiate |
| 295 |
|
between variable with and without a-prior record dimensions. Remove |
| 296 |
|
this record dimension before adding the variable to the *.glob.nc file. |
| 297 |
|
This procedure automatically works also for grid.*.nc files that do not |
| 298 |
|
have any record dimension. |
| 299 |
|
o verification/cpl_aim+ocn: |
| 300 |
|
- generate new reference output on baudelaire (gfortran, mpich2) (previously |
| 301 |
|
from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script. |
| 302 |
|
o pkg/obcs/obcs_calc_stevens.F: |
| 303 |
|
- add code for northern and southern boundaries. |
| 304 |
|
- reorder some loops to save some operations and so that drFBar can be scalar |
| 305 |
|
o model/src: |
| 306 |
|
- re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine |
| 307 |
|
truncation) and add diagnostics for Adams-Bashforth tendency increment. |
| 308 |
|
- update test-exp. AD output: |
| 309 |
|
1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl; |
| 310 |
|
and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20, |
| 311 |
|
front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5), |
| 312 |
|
global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4), |
| 313 |
|
matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre, |
| 314 |
|
tutorial_global_oce_in_p, tutorial_global_oce_latlon and |
| 315 |
|
tutorial_plume_on_slope. |
| 316 |
o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX |
o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX |
| 317 |
that vectorises. This code uses 3 extra 2D fields, F90 array assignments |
that vectorises. This code uses 3 extra 2D fields, F90 array assignments |
| 318 |
and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX |
and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX |
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