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: |
8 |
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- mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask |
9 |
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and climsst/sss even when using seaice (to prevent calculation that might |
10 |
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use SST on land); does not affect any verification exp. |
11 |
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- apply mask to taux,tauy (in seaice_get_dynforcing.F); update output |
12 |
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of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix. |
13 |
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o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness |
14 |
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over land (non-legacy code) |
15 |
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o vectorize salt_plume package: |
16 |
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- add extra code to salt_plume_frac and salt_plume_tendency_apply_s |
17 |
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- this code computes plumebk everywhere (also over land), thus requires |
18 |
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code to avoid divisions by zero and catch the case of kLev=Nr. |
19 |
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- efficiency of salt_plume_frac is still sub-optimal |
20 |
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o tools (genmake2): |
21 |
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- fix makefile NAME specification (option: -makefile NAME) by adding |
22 |
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"-f $MAKEFILE" in few places where it was missing including makedepend |
23 |
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command (contribution from Paul). |
24 |
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|
25 |
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checkpoint63i (2012/01/24) |
26 |
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o model/src: |
27 |
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- add factorized versions of some EOS code to find_rho.F, |
28 |
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define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX) |
29 |
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o model/src: |
30 |
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- add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h; |
31 |
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- change default celsius2K from 273.16 to 273.15 |
32 |
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- to keep results unchanged, add back old value of celsius2K in verification |
33 |
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exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd), |
34 |
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global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm). |
35 |
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o model/src: add a little initialisation trick to find_rho.F and find_alpha.F |
36 |
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to make TAF generate vectorizable code |
37 |
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o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows. |
38 |
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Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers |
39 |
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have flags that do this more efficiently. |
40 |
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o pkg/diagnostics/diagstats_calc.F |
41 |
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- for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact |
42 |
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o pkg/obcs (with exch2): |
43 |
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- derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F) |
44 |
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and remove code (in obcs_readparms.F) which was based on EXCH of indices |
45 |
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(through buffer) and did not account for exch2 (e.g., CS-grid) topology. |
46 |
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o pkg/exf and seaice exp: |
47 |
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- change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0) |
48 |
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so that switching off area & heff advection flags does not affect results. |
49 |
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- change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h |
50 |
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- keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef |
51 |
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EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update |
52 |
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results of verification experiments: 1D_ocean_ice_column(fwd), |
53 |
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global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8) |
54 |
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and offline_exf_seaice (all 4). |
55 |
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o pkg/seaice: |
56 |
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- remove array YNEG, RIVER, TMIX (replaced by local var) from common block; |
57 |
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remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef. |
58 |
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- fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY) |
59 |
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but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and |
60 |
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not multi-dim advection; |
61 |
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- fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and |
62 |
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SHORTWAVE_HEATING #undef. |
63 |
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o optim: make Makefile more robust (?) |
64 |
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o pkg/obcs: |
65 |
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* fix treatment of obcs_read_pickup for TAF |
66 |
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o pkg/shelfice: |
67 |
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* add missing initialisation of num_shifwflx |
68 |
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* new adjoint verification exp. for isomip |
69 |
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* change Prandtl and Schmidt numbers from generic formulations |
70 |
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(in terms of model diffus. and visc.) to separate runtime |
71 |
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parameters, with Holland and Jenkins (1999) default values. |
72 |
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o pkg/exf (interpolation): |
73 |
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- extended input field (2 rows) near the N & S poles: |
74 |
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* fill in with the symetric value (when even Nb of data in longitude) |
75 |
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* add average value at the poles only for scalar quantities ; for vector |
76 |
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component interpolation, skip the averaging and keep duplicated values, |
77 |
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unless the 2 components have same location (uvInterp=T) in which case |
78 |
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interpolate the 2 components together using S/R EXF_INTERP_UV. |
79 |
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- new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field |
80 |
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together: this allows to account properly for local orientation when |
81 |
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averaging at N & S pole. |
82 |
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- add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding |
83 |
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exf-interpolation near N & S poles. Undef by default. |
84 |
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- add debug check/print on 1rst iter if debugLevel >=2. |
85 |
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o pkg/exf: |
86 |
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- change masking flags definition (no longer "parameter"), put them in |
87 |
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common block and set them in S/R EXF_INIT_FIXED. |
88 |
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- change recognized masking flag from s,u,v to c,w,s since the mask |
89 |
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to use (maskC,W,S) depends on position on model grid and has little to |
90 |
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do with scalar/vector difference; fix masking if using P-coordinates. |
91 |
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- fix masking of wind-stress (was wrong if interpolated or read on A-grid) |
92 |
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and update results of exp. global_with_exf (x2). |
93 |
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- fix setting of zenith-angle table when SHORTWAVE_HEATING is undef. |
94 |
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o pkg/obcs |
95 |
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- S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate) |
96 |
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o pkg/exf (interpolation): |
97 |
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- assume periodicity in X only if input field cover full longitude range. |
98 |
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- improve search for lat. index (supposed to be faster, in ~log2(ny) steps, |
99 |
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and should vectorise). |
100 |
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- fix input lat of the 2 added row (in case we provide N.pole data). |
101 |
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|
102 |
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checkpoint63h (2011/12/30) |
103 |
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o pkg/seaice: |
104 |
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- change declaration of UVM from _RL to _RS in order to get B-grid |
105 |
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uIce,vIce monitor when _RS = real*4 |
106 |
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o pkg/offline: |
107 |
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- new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags); |
108 |
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- compute vertical velocity if not read from file (switch on exactConserv |
109 |
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& staggerTimeStep); |
110 |
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- fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq. |
111 |
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o verification: |
112 |
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- update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input) |
113 |
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with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m": |
114 |
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fix Pb in yG definition @ 2 missing corners (previously yG was averaged); |
115 |
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- update output of exp. global_ocean.cs32x15.viscA4 after changing |
116 |
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grid-file angles (used here for coriolis-3d); |
117 |
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- remove (or gzip) few files not needed to run fizhi-cs experiments. |
118 |
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o pkg/exf (vector interpolation): |
119 |
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- rotate vector component toward local grid-axis orientation using grid-angles |
120 |
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(stored in GRID.h) instead of locally computed rotation angle; keep old code |
121 |
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available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default). |
122 |
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o pkg/seaice: |
123 |
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- allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION |
124 |
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undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined. |
125 |
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o pkg/PKG_OPTIONS.h files: |
126 |
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- move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h", |
127 |
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outside of the #ifdef ALLOW_THISPKG / #endif block. |
128 |
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- update verification/*/code/PKG_OPTIONS.h files. |
129 |
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o add a verification experiment (offline_exf_seaice/input.seaice) that test |
130 |
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the B-grid LSOR solver |
131 |
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o pkg/seaice: sort out emissivity and long wave radiation step 2: |
132 |
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- add emissivity for snow and ice as new run-time parameters |
133 |
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(unfortunately) that default to the corresponding exf values; this |
134 |
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changes results in most verification experiments so that for backward |
135 |
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compatibility these parameter have to be set explicitly to inconsistent |
136 |
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values (ugly); |
137 |
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- the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired |
138 |
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emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp |
139 |
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until we agree how to handle this bug properly |
140 |
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o pkg/exf (interpolation): |
141 |
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- add a set of run-time param ({inputfield}_interpMethod), one for |
142 |
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each interpolated input field, to select the interpolation method |
143 |
|
with a value of zero switching off the interpolation; |
144 |
|
- print interpolation parameters to standard output; |
145 |
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- refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined |
146 |
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(to use instead runoff_interpMethod=0 in data.exf). |
147 |
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- simplify default setting of interpolation parameters (for all fields, |
148 |
|
set position to match model grid cell-center position, leading to trivial |
149 |
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interpolation in case of regular Lat-Lon grid) and fix for the case of |
150 |
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non-uniform delY. |
151 |
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o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for |
152 |
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within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1. |
153 |
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this factor is absolutely required, because the lw exitance (= out-going |
154 |
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long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown, |
155 |
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where the reflectivity rho = 1-emissivity for conservation reasons. Once |
156 |
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this is established, we can remove the CPP-Flag (if we want to). |
157 |
|
o pkg/seaice: |
158 |
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- qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and |
159 |
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ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined |
160 |
|
- sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity |
161 |
|
what the name implies (and not emissivity*BoltzmannConstant), this means |
162 |
|
the old default value of 5.5e-8 now means |
163 |
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5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in |
164 |
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S/R exf_readparms |
165 |
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- FV-discretization of the B-grid LSOR solver, turn on with |
166 |
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SEAICE_LSRBNEW. This new solver also involves a slight re-organization |
167 |
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of the calling routine dynsolver, so that B and C-grid code look a |
168 |
|
little more alike. |
169 |
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- fix index bugs in ostres.F (B-grid code) |
170 |
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o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better |
171 |
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o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the |
172 |
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default for SEAICE_emissivity, if useEXF; requires setting a wrong |
173 |
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parameter value in global_ocean.cs32x15/input.seaice/data.seaice for |
174 |
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backward compatiblity |
175 |
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o model/src: use sigmaR in calc_ivdc |
176 |
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|
177 |
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checkpoint63g (2011/12/16) |
178 |
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o pkg/seaice/seaice_growth.F: |
179 |
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fix heat conservation of the coupled ocean-seaice system. |
180 |
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when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of |
181 |
|
solid vs liquid water treatment is resolved via QNET. |
182 |
|
o pkg/seaice/seaice_growth.F: |
183 |
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add missing term for sublimation in saltFlux, which was breaking conservation. |
184 |
|
o pkg/seaice/seaice_model.F: |
185 |
|
Remove this patholigical case treatment in evolution branch, |
186 |
|
where it is un-necessary and breaks conservation. |
187 |
|
Update global_ocean.cs32x15/results accordingly for |
188 |
|
output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt |
189 |
|
o model/src: |
190 |
|
useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in |
191 |
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external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE. |
192 |
|
o pkg/obcs: |
193 |
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modify Stevens boundary conditions so that S/R obcs_calc_stevens computes |
194 |
|
tendency for temperature and salinity that is then applied to update |
195 |
|
theta and salt in S/R obcs_apply_ts; this requires proper masking of all |
196 |
|
horizontal advection and diffusion contributions on the boundary (in |
197 |
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S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and |
198 |
|
removing the mask in S/R timestep_tracer. The advantage of this approach is |
199 |
|
that the updated tracer values include contributions from the surface |
200 |
|
forcing and vertical diffusion. |
201 |
|
This modification changes exp4.stevens because of vertical diffusion. |
202 |
|
o model/src: |
203 |
|
change non-curvilinear grid setting to also work with exch2 + blank tiles: |
204 |
|
- move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst |
205 |
|
face dimensions. |
206 |
|
- new S/R INI_LOCAL_GRID to define model tile-local grid (using same units |
207 |
|
as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID |
208 |
|
and INI_SPHERICAL_POLAR_GRID. |
209 |
|
change test-experiment global_ocean.90x40x15: |
210 |
|
- split the domain in many more tiles (9x4 tiles of 10x10 each); |
211 |
|
- switch to exch2 and remove 1 blank-tile (but only for MPI test). |
212 |
|
- update results of both test (std & dwnslp). |
213 |
|
o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in |
214 |
|
tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation |
215 |
|
o model/src: |
216 |
|
- take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS |
217 |
|
and fix initialisation when using sigma-coords. |
218 |
|
o model/src: |
219 |
|
- improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc. |
220 |
|
to their current value at the beginning of forward_step.F": add a new run-time |
221 |
|
switch "doResetHFactors" (default=false) and use it to do (or not) the resetting. |
222 |
|
- set doResetHFactors=T in the following test exp: |
223 |
|
global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS), |
224 |
|
global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS) |
225 |
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and tutorial_global_oce_in_p (nonLinFS in p) |
226 |
|
o pkg/ecco |
227 |
|
- added IES cost term |
228 |
|
o verification/advect_xz |
229 |
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- scale down the depth by 1/100 (from 200 km to just 2.km) |
230 |
|
- add secondary test using divergent flow, r-star and implicit vertical advection. |
231 |
|
- add note (check_conserve_TS.txt) and matlab script to check global |
232 |
|
conservation of T & S with NonLin-FreeSurf and Adams-Bashforth. |
233 |
|
o pkg/rbcs: |
234 |
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- add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F). |
235 |
|
o pkg/obcs (Stevens BCs): |
236 |
|
- fix various problems in the phase speed computations of the Stevens |
237 |
|
boundary conditions: |
238 |
|
- sign error for western and southern boundaries, |
239 |
|
- time tendencies were underestimated by factor of dTracerLev and some just |
240 |
|
zero (for multidim advection schemes) -> now estimate time tendencies |
241 |
|
from difference between previous (n) time level and the one before (n-1); |
242 |
|
this requires storing a field per tracer per boundary, also in the pickup |
243 |
|
files. |
244 |
|
- replace deltaTmom in cflMer/Zon computation with dTracerLev |
245 |
|
- set default phase velocity to cflMer/Zon |
246 |
|
- update verification experiment exp4.stevens |
247 |
|
o pkg/generic_advdiff (implicit_r): |
248 |
|
- fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf |
249 |
|
(remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F); |
250 |
|
- fix implicit vertical diffusion or advection with NonLin FreeSurf |
251 |
|
(was using current recip_hFacC instead of future recip_hFacC): set future |
252 |
|
recip_hFac in thermodynamics.F and pass & use it in all vertical implicit |
253 |
|
solver S/R ; |
254 |
|
- fill diagnostics of vertical advective fluxes (computed from tendency) |
255 |
|
when using implicit vert. advection; |
256 |
|
- update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion: |
257 |
|
global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD), |
258 |
|
tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD) |
259 |
|
and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5. |
260 |
|
o pkg/diagnostics: |
261 |
|
- add diags for T & S tendency which goes through Adams-Bashforth. |
262 |
|
|
263 |
|
checkpoint63f (2011/11/30) |
264 |
|
o pkg/obcs/obcs_calc_stevens.F: |
265 |
|
- join some loops to reduce number of if-statements |
266 |
|
- fix a bug in code for northern and southern boundaries. |
267 |
|
o pkg/seaice/seaice_init_varia.F |
268 |
|
- undo resetting UVM=0 that has slipped in unnoticed in r1.49 and |
269 |
|
caused zero ice-velocities for the B-grid code |
270 |
|
o pkg/seaice/seaice_init_fixed.F |
271 |
|
- fix a bug in the initialisation of the second metric terms |
272 |
|
k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0. |
273 |
|
- this affects all seaice configurations with useCurviLinearGrid = .true. |
274 |
|
and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms |
275 |
|
= .true. (default) |
276 |
|
- the only verification experiment affected is global_ocean.cs32x15: |
277 |
|
icedyn, seaice, and seaice_dynmix (AD) |
278 |
|
o pkg/thsice/thsice_diagnostics_state.F |
279 |
|
- only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does |
280 |
|
not contain garbage that can lead to surprises in diagstats_calc.F |
281 |
|
o model/src: |
282 |
|
- move bi,bj loops inside INTEGR_CONTINUITY ; |
283 |
|
- call INTEGR_CONTINUITY directly from forward_step.F |
284 |
|
(previously called from momentum_correction_step.F) |
285 |
|
- call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F, |
286 |
|
forward_step.F and pkg/ecco/the_main_loop.F |
287 |
|
o model/src/do_oceanic_phys.F: |
288 |
|
- reset addMass to zero only if useICEFRONT ; |
289 |
|
- separated k-loop for rhoInSitu calculation ; |
290 |
|
- add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P) |
291 |
|
and at constant T,S (= WdRHOdP); |
292 |
|
NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport |
293 |
|
of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical |
294 |
|
transport of locally-referenced potential density); |
295 |
|
to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP) |
296 |
|
o gluemnc: |
297 |
|
- replace ncrcat with ncks when adding variables to *.glob.nc |
298 |
|
- change the way variables without record dimensions are handled so that |
299 |
|
files that have variables with and without record variables can be glued: |
300 |
|
add a record dimension with a new unique name to be able to differentiate |
301 |
|
between variable with and without a-prior record dimensions. Remove |
302 |
|
this record dimension before adding the variable to the *.glob.nc file. |
303 |
|
This procedure automatically works also for grid.*.nc files that do not |
304 |
|
have any record dimension. |
305 |
|
o verification/cpl_aim+ocn: |
306 |
|
- generate new reference output on baudelaire (gfortran, mpich2) (previously |
307 |
|
from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script. |
308 |
|
o pkg/obcs/obcs_calc_stevens.F: |
309 |
|
- add code for northern and southern boundaries. |
310 |
|
- reorder some loops to save some operations and so that drFBar can be scalar |
311 |
|
o model/src: |
312 |
|
- re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine |
313 |
|
truncation) and add diagnostics for Adams-Bashforth tendency increment. |
314 |
|
- update test-exp. AD output: |
315 |
|
1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl; |
316 |
|
and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20, |
317 |
|
front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5), |
318 |
|
global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4), |
319 |
|
matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre, |
320 |
|
tutorial_global_oce_in_p, tutorial_global_oce_latlon and |
321 |
|
tutorial_plume_on_slope. |
322 |
|
o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX |
323 |
|
that vectorises. This code uses 3 extra 2D fields, F90 array assignments |
324 |
|
and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX |
325 |
|
does not even come with an F77 compiler anymore, this should not be |
326 |
|
a limitation |
327 |
|
|
328 |
|
checkpoint63e (2011/11/06) |
329 |
|
o pkg/seaice adjoint of LSR: |
330 |
|
- substantially rework STORE dirs. |
331 |
|
- add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED |
332 |
|
this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields |
333 |
|
and only perform SOLV_MAX_FIXED adjoint iters. |
334 |
|
If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration |
335 |
|
always goes to same record, meaning that the last forward field will be |
336 |
|
the one used in the adjoint - an approximation. |
337 |
|
- now produces non-zero LSR-related gradients, and acceptable gradients for |
338 |
|
An's zonal (x-z) test case (to be checked in) |
339 |
|
- lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR |
340 |
|
(but these are screwed up by the thermodynamics in the first place); |
341 |
|
reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution; |
342 |
|
output_adm.txt also reflects changes to seaice_lsr |
343 |
|
- global_ocean.cs32x15: |
344 |
|
* the "default" input_ad.seaice has been re-defined to always exclude dynamics |
345 |
|
(output_adm.seaice.txt was updated) |
346 |
|
* new input_ad.seaice_dynmix tests a forward LSR / backward free-drift |
347 |
|
(output_adm.seaice_dynmix.txt) |
348 |
|
o test-exp. exp4+stevens: |
349 |
|
- switch off pTracers and nonHydrostatic (restart problems with NH); update output |
350 |
|
o pkg/seaice (lsr solver): |
351 |
|
- put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only); |
352 |
|
update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15 |
353 |
|
- fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD) |
354 |
|
- new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution |
355 |
|
into initial guess for linearised solver; use weight ~ (1/err)^2,4. |
356 |
|
- compute (with new S/R) and print initial (+ free-driff sol. if available) |
357 |
|
and final residual of linearised system. |
358 |
|
o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity |
359 |
|
(requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F) |
360 |
|
o pkg/obcs: Stevens BCs (still only for east and west) |
361 |
|
- fix Stevens BCs by using intermediate velocities of previous |
362 |
|
time step as "baroclinic" contribution rather velocity of one grid cell |
363 |
|
inside the boundaries; more consistent but makes the entire treatment |
364 |
|
more complicated, requires new pickup files and two new S/Rs: |
365 |
|
obcs_copy_uv_n and obcs_save_uv_n |
366 |
|
keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY |
367 |
|
(undefined by default) |
368 |
|
- silently move computation of some grid factors into separate loops to |
369 |
|
save some recomputations |
370 |
|
- add a hack for non-linear free surface |
371 |
|
- add a verification experiment to exp4 that tests this code |
372 |
|
o make gluemnc/xplodemnc work with (moron) non-GNU shell tools |
373 |
|
|
374 |
|
checkpoint63d (2011/10/25) |
375 |
|
o pkg/obcs + seaice-dynamics: |
376 |
|
- new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before |
377 |
|
solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB |
378 |
|
values (consistent with an implicit method). |
379 |
|
- add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to |
380 |
|
return to older implementation (same results as before); note that none of |
381 |
|
the "experimental" OBCS_SEAICE options are implemented in the new version. |
382 |
|
- switch test exp. seaice_obcs to use new version (update output). |
383 |
|
o pkg/seaice: |
384 |
|
- add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS) |
385 |
|
- add parenthesis in Water-Ice drag calculations (evp & lsr); |
386 |
|
- in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1; |
387 |
|
and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice) |
388 |
|
- update output of test exp lab_sea that uses evp or lsr (fwd+ad) |
389 |
|
and global_ocean.cs32x15 (icedyn & seaice fwd+ad). |
390 |
|
o pkg/layers: |
391 |
|
- Include potential density as new coordinate (Thanks to David Munday) |
392 |
|
o pkg/dic: |
393 |
|
- Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add |
394 |
|
carbonate computation/output to CALC_PCO2_APPROX |
395 |
|
o pkg/generic_advdiff |
396 |
|
- make TAF generate code that vectorizes: |
397 |
|
gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F |
398 |
|
o model/src: |
399 |
|
- improve vectorization also for adjoint code of |
400 |
|
solve_tridiagonal and solve_pentadiagonal. As this requires up to |
401 |
|
5 new 3D-fields, this code is only turned on for the combination of |
402 |
|
ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message |
403 |
|
for singular matrix check (only for TARGET_NEC_SX). |
404 |
|
- remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to |
405 |
|
ALLOW_AUTODIFF. This flag now needs to be set outside of |
406 |
|
solve_tri/pentadiagonal.F |
407 |
|
o pkg/exf: |
408 |
|
- fix previous modif in exf_readparms.F (revision 1.66: treatment of |
409 |
|
optional namelist EXF_NML_OBCS). |
410 |
|
- add many debug-print (to trace down where pkg/cal error msg comes from) |
411 |
|
o pkg/mom_vecinv/mom_vi_hdissip.F |
412 |
|
- rearrange loops so that vectorization is improved and in particular |
413 |
|
the adjoint routine vectorizes. The code is a little longer now, but I |
414 |
|
think easier to read. |
415 |
|
Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested. |
416 |
|
o pkg/seaice: |
417 |
|
- allow to specify initial seaice velocity from files (uIceFile,vIceFile) |
418 |
|
o pkg/exch2: |
419 |
|
- alternative code (without tile x tile matrix) for cumulated (global) sum; |
420 |
|
used as default; keep using matrix version in adjustment.cs-32x32x1. |
421 |
|
o tools/build_options: |
422 |
|
- after merging some MPI and/or multi-threads specific optfiles so that |
423 |
|
the modified default optfile support both built (using genmake2 -mpi |
424 |
|
for the MPI built, using genmake2 -omp for OpenMP built), |
425 |
|
move now obsolete optfiles to tools/build_options/unsupported/ |
426 |
|
(add copy of email sent to support list in doc/optfiles_changes.txt) |
427 |
|
|
428 |
|
checkpoint63c (2011/09/28) |
429 |
|
o pkg/ebm: |
430 |
|
- fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of |
431 |
|
test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d) |
432 |
|
o pkg/seaice (SItracer pickup) |
433 |
|
* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER) |
434 |
|
To be done: |
435 |
|
- thorough testing of missing fields in S/R seaice_read_pickup |
436 |
|
- thorough matching between generic tracers and specific fields used |
437 |
|
(e.g. volume-weighted age, area-weighted age, salinity, ...) |
438 |
|
o pkg/grdchk: |
439 |
|
- all procs calculate and print finite-difference gradient (for testreport) |
440 |
|
- change description output used by testreport; |
441 |
|
- AD testing: also compare and report Finite-difference gradient; |
442 |
|
=> update all output_adm*.txt |
443 |
|
o test exp. global_ocean_ebm: |
444 |
|
- switch back useRealFreshWaterFlux (no problem anymore with run-off); |
445 |
|
and turn on exactConserve; update (fwd) output. |
446 |
|
o pkg/seaice (LSR): |
447 |
|
- print to STDOUT number of solver iterations at SEAICE_monFreq interval. |
448 |
|
- modify solver to deal cleanly with u/v switch at face edges (CS-grid): |
449 |
|
* identical results with non-CS topology (but save up to half of EXCH calls) |
450 |
|
* no much changes in cs-32 verification tests since no ice at face edges |
451 |
|
(differences due to convergence criteria, since nb of iterations changed) |
452 |
|
* expect some differences on lat-lon-cap grid. |
453 |
|
update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice) |
454 |
|
o pkg/exch2: |
455 |
|
- add new CPP option to disable Cumul-Sum matrix (to save storage when using |
456 |
|
many tiles); until alternative coding is added, just add a stop. |
457 |
|
o pkg/kpp: |
458 |
|
- move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F |
459 |
|
to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list). |
460 |
|
o optfiles: |
461 |
|
- merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles |
462 |
|
into corresponding standard one, which now support different build: |
463 |
|
(when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built) |
464 |
|
- add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael) |
465 |
|
o pkg/obcs (seaice): |
466 |
|
- add missing EXCH for uIce,vIce after applying OBCS; |
467 |
|
- remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding |
468 |
|
argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R |
469 |
|
EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F; |
470 |
|
- fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared) |
471 |
|
- verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi |
472 |
|
and eedata.mth for MPI and mutlti-threaded testing. |
473 |
|
o pkg/flt: |
474 |
|
- make FLT EXCH working with multi-threads (and MPI + multi-threads); |
475 |
|
- use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h; |
476 |
|
- fix pickup and trajectories + profiles output with multi-threads; |
477 |
|
- add parameter to select group of fields to write along trajectory and |
478 |
|
profile (default unchanged); |
479 |
|
- only call PORT_RAND* function when flt_noise <> 0; |
480 |
|
- add multi-threaded test for verification exp. flt_example. |
481 |
|
o eesupp/src: |
482 |
|
- fix S/R ALL_PROC_DIE for MPI+multi-threads. |
483 |
|
- USE_OMP_THREADING: check that number of threads (from eedata) matches |
484 |
|
actual number (from env.var. setting). |
485 |
|
o pkg/ebm: |
486 |
|
- fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file. |
487 |
|
- add multi-threaded test for verification exp. global_ocean_ebm |
488 |
|
|
489 |
|
checkpoint63b (2011/08/29) |
490 |
|
o pkg/ebm: |
491 |
|
- fix sign of runoff; |
492 |
|
- update directly forcing fields (Qnet,EmPmR) to use standard |
493 |
|
external_forcing_surf.F (remove ebm_forcing_surf.F); |
494 |
|
- avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F); |
495 |
|
- set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm) |
496 |
|
and apply relaxation towards corresponding SST field (2-D map or ZonAver). |
497 |
|
- update global_ocean_ebm parameters file data and update output (fwd+ad). |
498 |
|
o verification/matrix_example: |
499 |
|
- split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for |
500 |
|
MPI and mutlti-threaded testing. |
501 |
|
o pkg/matrix: |
502 |
|
- change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ; |
503 |
|
- fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter); |
504 |
|
- fix for multi-threaded (remove DATA statement); |
505 |
|
- use standard DIFFERENT_MULTIPLE function; |
506 |
|
- add MATRIX_OPTIONS.h |
507 |
|
o verification/matrix_example: |
508 |
|
To allow to split the domain in several tiles, change the domain size |
509 |
|
from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on |
510 |
|
Western side) of land points. |
511 |
|
o (*_)write_pickup: |
512 |
|
- fix few bugs in mypackage_read/write_pickup.F |
513 |
|
- in MDS_WR_METAFILES calls, replace "myTime" by a local copy into |
514 |
|
array of length 1 (was caught by compiler syntax-check). |
515 |
|
o pkg/diagnostics (velocity potential solver): |
516 |
|
- fix initialisation of main diagonal matrix (for overlap values) |
517 |
|
o tools/build_options: |
518 |
|
- towards single optfile for MPI and non-MPI built: merge few +mpi optfile |
519 |
|
into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11) |
520 |
|
- linux_amd64_gfortran: merge +mpi_generic version into standard optfile: |
521 |
|
* move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ; |
522 |
|
* FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list; |
523 |
|
and use "-devel" testreport option for standard testing on baudelaire. |
524 |
|
o pkg/grdchk: |
525 |
|
- Assume that all gradient-check position are within the same tile |
526 |
|
corresponding to global indices (iGloTile,jGloTile) and that |
527 |
|
positions (i,j indices or nbeg) are local to this tile; |
528 |
|
- set tile local-indices and proc. number according to tile global-indices; |
529 |
|
- remove grdchkwhichproc from namelist (retired param); |
530 |
|
- send adjoint gradient to all procs so that all procs print it to STDOUT; |
531 |
|
- switch on MPI test for global_ocean.90x40x15 AD test experiment. |
532 |
|
o adding package bbl (Bottom Boundary Layer) |
533 |
|
description in MITgcm/pkg/bbl/bbl_description.tex |
534 |
|
example/test experiment in MITgcm_contrib/bbl |
535 |
|
o adjoint verifications |
536 |
|
- changed 5 experiments to multi-tiles |
537 |
|
* global_ocean.90x40x15 |
538 |
|
* obcs_ctrl |
539 |
|
* offline_exf_seaice |
540 |
|
* tutorial_dic_adjoffline |
541 |
|
* tutorial_tracer_adjsens |
542 |
|
changed reference output for those that crossed tile boundaries |
543 |
|
(changed choices of gradient check positions) |
544 |
|
- with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi) |
545 |
|
- temporary bug fix in grdchk_loc.F for obcs |
546 |
|
o genmake2 & testreport |
547 |
|
- add target "obj" (just for OBJFILES files) to Makefile; |
548 |
|
- add option to specify FEXTRAFLAGS on command line. |
549 |
|
o pkg/mypackage: |
550 |
|
- remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS |
551 |
|
|
552 |
|
checkpoint63a (2011/08/02) |
553 |
|
o pkg/diagnostics (velocity potential): |
554 |
|
- fix velocity-potential calculation when using OBCS: balance net inflow |
555 |
|
at each level (new S/R OBCS_DIAG_BALANCE). |
556 |
|
- fix some of the problems with OBCS in stream-function calculation. |
557 |
|
o pkg/exf/exf_readparms.F |
558 |
|
- make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF, |
559 |
|
EXF_NML_OBCS) more consistent, so that you need not have these lists |
560 |
|
in data.exf when they are not used. |
561 |
|
o optim/optim_readdata.F: |
562 |
|
- add some output about obcs variables that might help debugging |
563 |
|
- add a check about nvarlength |
564 |
|
o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec |
565 |
|
o pkg/diagnostics (velocity potential): |
566 |
|
- fix mask for OBCS (still problems in stream-function with OBCS); |
567 |
|
- add specific parameter (default = main code CG2D params) for solver; |
568 |
|
- in case of poor convergence, use solution corresponding to lowest residual. |
569 |
|
o pkg/seaice/seaice_growth.F: small changes that permit vectorizable |
570 |
|
adjoint code. In general statements like tmpscal=fld(i,j) are problematic |
571 |
|
and should be avoided where possible. |
572 |
|
o model/src (rStar): |
573 |
|
- include r* effect on reference-state (PhiRef) in totPhiHyd |
574 |
|
(so that it's really the potential anomaly at the cell center); |
575 |
|
affect solution only if z* with full pressure in EOS. |
576 |
|
- test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and |
577 |
|
update output (because of z* in totPhiHyd and viscA4 changes); |
578 |
|
- keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly |
579 |
|
@ constant r) until interpolation at constant r is implemented. |
580 |
|
o pkg/diagnostics |
581 |
|
- fix RCENTER diagnostics in case cell center is not at interface middle |
582 |
|
o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use |
583 |
|
this eos with eosType = 'TEOS10', in data (PARM01). This eos implies |
584 |
|
that THETA and SALT are "conservative temperature" and "absolute |
585 |
|
salinity" |
586 |
|
o pkg/ctrl |
587 |
|
- fix computation of endrec in s/r ctrl_init_rec |
588 |
|
- ctrl_pack/unpack_*: remove unused variables and some obsolete code |
589 |
|
o pkg/seaice/seaice_growth.F |
590 |
|
- fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code, |
591 |
|
remove then obsolete STORE directives |
592 |
|
- fix STORE directives for tice and tices, so that only the |
593 |
|
appropriate part of the fields are stored (and not the entire |
594 |
|
field); update global_ocean.cs32x15.seaice AD output. |
595 |
|
- cosmetic changes: adjust CPP flags and indentation for better |
596 |
|
legibilty |
597 |
|
o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by |
598 |
|
Chris Wilson) |
599 |
|
o pkg/gmredi: |
600 |
|
Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF), |
601 |
|
and test it in verification exp. "front_relax.bvp" (update output.bvp.txt) |
602 |
|
|
603 |
|
checkpoint63 (2011/07/11) |
604 |
|
o pkg/exch2: |
605 |
|
- rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h |
606 |
|
- exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the |
607 |
|
(2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y |
608 |
|
increments, calculates Cumul-Sum @ tile origin and sends results to each tile. |
609 |
|
o pkg/diagnostics: |
610 |
|
- deal with pairs of post-processed diags which are computed together; in |
611 |
|
particular, re-order list of diags within 1 file to save 2nd computation. |
612 |
|
- add S/R to compute velocity stream-function (called after velocity-potential |
613 |
|
calculation) from divergence free transport -> new diagnostics "PsiVEL". |
614 |
|
- add parameter to select grid-point location where PsiVEL == 0. |
615 |
|
o eesupp/src: |
616 |
|
new S/R to calculate cumulated sum on tiled array, corner grid-cell location |
617 |
|
(specific S/R needed with exch2 topology - for now, just print an error msg) |
618 |
|
o pkg/shelfice |
619 |
|
- Implement friction velocity-dependent transfer coefficients following |
620 |
|
Holland and Jenkins, JPO, 1999 |
621 |
|
Original code by M. Losch with small modifs. |
622 |
|
Enable with CPP option SHI_ALLOW_GAMMAFRICT |
623 |
|
and runtime flag SHELFICEuseGammaFrict |
624 |
|
o verification lab_sea & global_ocean.cs32x15: |
625 |
|
- use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local): |
626 |
|
does not miss some dependencies (but is slower) and also works with many files |
627 |
|
(default makedepend limitation for AD built). |
628 |
|
- use cyrus_makedepend in adjustment.128x64x1 (so that it still tested). |
629 |
|
o pkg/diagnostics: |
630 |
|
- add run-time parameter "useMissingValue" (def=False) to fill land-point |
631 |
|
(i.e., where mask=0) with MissingValue ; used only in MNC output file. |
632 |
|
This replaces CPP-option DIAGNOSTICS_MISSING_VALUE. |
633 |
|
- Extend the use of "missing_value" setting from data.diagnostics for the case |
634 |
|
of counter-diagnostics (where fraction-weight is zero). This applies both to |
635 |
|
MNC and MDS output files. |
636 |
|
o pkg/seaice/seaice_growth.F: |
637 |
|
- add 'a priori' cap of latent heat flux based on actual mass considerations |
638 |
|
when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the |
639 |
|
non-legacy seaice_solve4temp. |
640 |
|
- add diagnostic of the residual sublimation freshwater flux (the freshwater |
641 |
|
flux taken from the ocean if the total actual latent heat fluxes exceed |
642 |
|
the maximum) |
643 |
|
- remove the CPP switch around the *_FWbySublim unit change and move diagnostic |
644 |
|
fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F. |
645 |
|
- add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef |
646 |
|
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim). |
647 |
|
- bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET. |
648 |
|
- bug fix : missing part to Martin's r_FWbySublim pathological case fix. |
649 |
|
o verification 1D_ocean_ice_column: |
650 |
|
made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet |
651 |
|
update results |
652 |
|
o pkg/diagnostics: |
653 |
|
- Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P') |
654 |
|
which are not filled-up but computed from other diags ; In this case, the mate |
655 |
|
diag points to the primary (filled-up) diag to used for post processing. |
656 |
|
- Update Velocity-potential computation using post-processed diag framework. |
657 |
|
==> Change the ordering of fields and time-periods in MDS output file |
658 |
|
when using periodic averaging: now writes one time record with the full set |
659 |
|
of fields for this time period, then the next time reccord (it used to be |
660 |
|
one field with the full set of time records then the next field). |
661 |
|
Note: this is now similar to NetCDF (MNC) output file. <== |
662 |
|
|
663 |
|
checkpoint62z (2011/06/21) |
664 |
|
o adjoint monitor: |
665 |
|
- Add adjoint monitor output for packages exf, seaice |
666 |
|
and update relevant testreport output |
667 |
|
o pkg/seaice: |
668 |
|
- re-order diags inits so that they appear in order in available_diagnostics.log |
669 |
|
- added diags: hsnow thermo. rates of change, area preceeding ridiging process, |
670 |
|
area/heff/hsnow preceeding thermodynamic growth/melt. |
671 |
|
- modified diag: SIdA; output actual effect, as the description states. |
672 |
|
- modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. |
673 |
|
- retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. |
674 |
|
(SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; |
675 |
|
and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) |
676 |
|
- modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. |
677 |
|
- added diagnostics for seaice generic tracers (SItr*). |
678 |
|
- added SItrUnit and SItrNameLong run time param (for SItr* diags). |
679 |
|
- in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. |
680 |
|
I. Fenty: 18-Jun-2011: |
681 |
|
Minor changes to seaice package: |
682 |
|
1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and |
683 |
|
added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) |
684 |
|
- Differentiated "regularization variables" from "floor variables" |
685 |
|
* areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor |
686 |
|
* hiceMin became SEAICE_hice_reg (old hiceMin) |
687 |
|
(with _reg meaning regularization variable) |
688 |
|
- SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion |
689 |
|
so as to ensure energy conservation when going between phases |
690 |
|
- A22 was not used anywhere |
691 |
|
2) Changed regularization procedure for heffActual and hsnowActual to ensure |
692 |
|
well-boundedness and smooth adjoint in seaice_growth.F |
693 |
|
3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells |
694 |
|
because the old regularization always set heffActual >= 0.05 cm |
695 |
|
4) Changed the model so that the default behavior is to put a small (10^-5) "floor" |
696 |
|
on AREA when HEFF > 0. |
697 |
|
- went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to |
698 |
|
requiring that DISABLE_AREA_FLOOR *not* be defined |
699 |
|
Affected verifications: |
700 |
|
- 1D_ocean_ice_column (output.txt output_adm.txt) |
701 |
|
- global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) |
702 |
|
o pkg/diagnostics: |
703 |
|
- move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). |
704 |
|
- rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument |
705 |
|
(was _RL, now integer) with option = 0 to retrieve all levels. |
706 |
|
- add pieces of code to compute velocity potential at each level (new diagnostics |
707 |
|
PhiVEL, works only when UVELMASS & VVELMASS are also turned on); |
708 |
|
for now, using same params as CG2D (target-resisual, max Nb of iter ...). |
709 |
|
- fix few issues with counter diagnostics in diagnostics_setdiag.F & |
710 |
|
diagstats_setdiag.F (if diagnostic counter is itself a counter diag) |
711 |
|
and in diagnostics_fract_fill.F (do not need a valid pointer for the |
712 |
|
diagnostics counter-mate); check that definition of counter-diagnostic |
713 |
|
includes a valid counter-mate (in diagnostics_set_levels.F). |
714 |
|
o model/src (rStar): |
715 |
|
- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
716 |
|
affect solution only if z* with full pressure in EOS; |
717 |
|
update output of test-exp global_ocean.90x40x15. |
718 |
|
o pkg/seaice: |
719 |
|
- introduce siEps=1e-5 parameter |
720 |
|
- use areaMax in AREA update (part 4), consistent with ridging step (part 2.5). |
721 |
|
- re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code. |
722 |
|
- introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer. |
723 |
|
For now it covers, and was tested for, ice salinity and age (attached to HEFF), |
724 |
|
as well as ice cover age and ridging index (attached to AREA). |
725 |
|
For now the run time parameters (in data.seaice/SEAICE_PARM03) are |
726 |
|
SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA'). |
727 |
|
Up to SItrMaxNum=3 tracers can be used simultaneously. |
728 |
|
o pkg/salt_plume: |
729 |
|
-introduce SPsalFRAC run time parameter that sets the fraction of the |
730 |
|
salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically) |
731 |
|
that gets vertically redistributed (fluxed down) by pkg/salt_plume. |
732 |
|
o model debug options: |
733 |
|
- Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored |
734 |
|
in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h). |
735 |
|
- Refine debug-msg printing selection (3 new levels): |
736 |
|
debugMode : controls printing of debug messages (sequence of S/R calls). |
737 |
|
debugLevel : controls printing of algorithm-relevant auxiliary/debug messages |
738 |
|
debLevZero = 0 ; /* level of disabled aux. msg printing */ |
739 |
|
debLevA = 1 ; /* level of minimum aux. msg printing */ |
740 |
|
debLevB = 2 ; /* level of low aux. print (report read-file opening)*/ |
741 |
|
debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */ |
742 |
|
debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */ |
743 |
|
debLevE = 5 ; /* level of extensive debug printing */ |
744 |
|
New debugLevel default: with default debugMode value (=F), |
745 |
|
= 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.; |
746 |
|
and if debugMode=T, default debugLevel = 4 (debLevD). |
747 |
|
Relation with previous settings: |
748 |
|
debLevB (=2) corresponds to former debLevA (=1) |
749 |
|
debLevD (=4) corresponds to former debLevB (=2) |
750 |
|
Note: |
751 |
|
a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before); |
752 |
|
b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs); |
753 |
|
to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5) |
754 |
|
- Add new parameter (printResidualFreq, read from PARM02 namelist) to print |
755 |
|
detailed CG solvers convergence; off (=0) by default, except if debugLevel=5. |
756 |
|
o pkg/obcs: |
757 |
|
- change OBCSfixTopo default from True to False (should not change the results); |
758 |
|
keep OBCSfixTopo=T in verification-exp. seaice_obcs. |
759 |
|
o pkg/thsice: |
760 |
|
- fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in |
761 |
|
2nd layer seaice sublimation (unlikely to happen) |
762 |
|
- use Interior mask for OBCS in thsice_advection.F (similar to what is |
763 |
|
done in gad_advection & seaice_advection). |
764 |
|
o adjoint: |
765 |
|
bug fix spotted by Gael Forget: |
766 |
|
seaice_advection and thsice_advection still had |
767 |
|
legacy CPP options to avoid CS corner updates for adjoint |
768 |
|
o pkg/seaice: |
769 |
|
=> Change some of the defaults (2011/05/29): |
770 |
|
- change SEAICEuseFluxForm default (from False to True) |
771 |
|
- change DIFF1 default (from 0.004 m/s to 0. m/s) |
772 |
|
And print warnings if DIFF1 is not set in data.seaice and centered |
773 |
|
avection scheme is used without any diffusion. |
774 |
|
also: |
775 |
|
- fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F; |
776 |
|
- set SEAICEdiffKh[] default in the same way as SEAICEadvSch[] |
777 |
|
- stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any |
778 |
|
other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with |
779 |
|
#undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE. |
780 |
|
update results of test exp.: |
781 |
|
lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20) |
782 |
|
output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200) |
783 |
|
output_adm.noseaicedyn (SEAICEuseFluxForm=T) |
784 |
|
offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T) |
785 |
|
seaice_obcs: output (SEAICEuseFluxForm=T) |
786 |
|
and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004) |
787 |
|
for standard fwd & AD lab_sea tests (to keep the same output). |
788 |
|
o pkg/seaice/seaice_growth.F: |
789 |
|
- use Ian Fenty's capping formulas for actual ice |
790 |
|
thickness thoughout EVOLUTION branch. |
791 |
|
- put treatment pathological case #2) in CPP brackets |
792 |
|
(ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). |
793 |
|
- update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. |
794 |
|
o pkg/seaice: |
795 |
|
- seaice_diffusion.F : remove the min(DX,DY) factor permanently; |
796 |
|
pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter; |
797 |
|
also pass fac as a param, which can be 1. (to update the tendency |
798 |
|
field) or the time step (to update the field itself). |
799 |
|
- seaice_advdiff.F: for multidim, call seaice_diffusion with |
800 |
|
e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call |
801 |
|
seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. |
802 |
|
- SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : |
803 |
|
hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
804 |
|
o pkg/seaice: |
805 |
|
diffusion with centered advection scheme (diffus.F & advect.F): |
806 |
|
- simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) |
807 |
|
to just compute the laplacian of input-field. |
808 |
|
- unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call. |
809 |
|
- fix flux-form version in diffus.F to conserve tracer. |
810 |
|
update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects |
811 |
|
machine truncation) and lab_sea.salt_plume (conservative flux-form modif) |
812 |
|
|
813 |
|
checkpoint62y (2011/05/26) |
814 |
|
o pkg/seaice: |
815 |
|
- seaice_growth.F : in EVOLUTION branch, always include |
816 |
|
a_QSWbyATM_cover in qnet (as it should be). |
817 |
|
- verification/global_ocean.cs32x15 : update results accordingly |
818 |
|
(output.seaice.txt output_adm.seaice.txt). |
819 |
|
o pkg/seaice + obcs: |
820 |
|
- use maskInW & maskInS in multi-dim advection and biharmonic diffusion: |
821 |
|
equivalent of assuming no tracer gradient outside the OB region. |
822 |
|
update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion) |
823 |
|
- remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed |
824 |
|
after changes above); |
825 |
|
- obcs+seaice cleaning: apply seaice-tracer OB values to tracer field |
826 |
|
only at OB location (instead of over a band of OLx width). |
827 |
|
o pkg/seaice: |
828 |
|
- fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F |
829 |
|
(dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid) |
830 |
|
o pkg/obcs: |
831 |
|
- split header file "OBCS.h" into 4 separated files: |
832 |
|
OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h |
833 |
|
Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h |
834 |
|
(contain no conditional statement which depends on OBCS options). |
835 |
|
- move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h) |
836 |
|
to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h). |
837 |
|
o ctrl, cost, grdchk & autodiff pkgs: |
838 |
|
- make options file more standard (like other {PKG}_OPTIONS.h file but |
839 |
|
with AD_CONFIG.h); clean-up some of the included header files. |
840 |
|
o pkg/obcs: |
841 |
|
- do not mask tracer when applying OB (tracer == 0 could generate problems) |
842 |
|
- apply tracer OB values to tracer field only at OB location (instead of |
843 |
|
over a band of OLx width) |
844 |
|
- clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R) |
845 |
|
- remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove |
846 |
|
obcs_apply_tloc.F & obcs_apply_sloc.F |
847 |
|
o obcs in model/src: |
848 |
|
- call OBCS_APPLY_W only if NonHydrostatic. |
849 |
|
- call OBCS_APPLY_ETA only if NonLinFreeSurf. |
850 |
|
- reset dEtaHdt and wVel to zero outside OB interior region ; |
851 |
|
- leave tracer unchanged outside OB interior region: This has no effect |
852 |
|
on the solution but just to prevent unrealistic tracer value outside OB. |
853 |
|
- zero out velocity outside OB interior region: This has no effect on |
854 |
|
the solution but just to prevent unrealistic velocity outside OB. |
855 |
|
o obcs and non-lin free-surf: |
856 |
|
move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F |
857 |
|
and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F |
858 |
|
+ add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR: |
859 |
|
this fixes missing EXCH + get consistent eta OB value (+ fix restart). |
860 |
|
update results of test-exp. exp4(nlfs). |
861 |
|
o exp4 (nlfs) test-exp: |
862 |
|
use OBC for Eta at Western & Eastern OB (to test prescribing Eta |
863 |
|
with NonLin-FreeSurf); update output.nlfs.txt |
864 |
|
o obcs and 2d/3d solver norm: |
865 |
|
use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB |
866 |
|
and outside OB interior region (will allow to place OB further inside the |
867 |
|
domain). Depending on the domain, can affects cg2d-Norm (previous |
868 |
|
cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl, |
869 |
|
and cg3d-Norm (previous Norm was computed before canceling OB terms), |
870 |
|
e.g. in tutorial_plume_on_slope. |
871 |
|
- update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope. |
872 |
|
o pkg rbcs: |
873 |
|
- split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h |
874 |
|
- add capability to apply relaxation to horizontal velocity uVel & vVel. |
875 |
|
o pkg/grdchk: add gradient check for control variable xx_shifwflx |
876 |
|
o pkg/shelfice/shelfice_init_fixed.F |
877 |
|
fix CPP-flag combinations |
878 |
|
o pkg/seaice: Merge iceage code of Pierre Rampal |
879 |
|
* update/change/correct ice age calculations |
880 |
|
* add age updates for pathological cases |
881 |
|
Probably needs more testing... |
882 |
|
|
883 |
|
checkpoint62x (2011/05/13) |
884 |
|
o pkg/mom_vecinv: |
885 |
|
high-order vorticity scheme: use interior masks (maskInW & S) |
886 |
|
to zero-out (outside OB) gradient of vorticity. |
887 |
|
o verification exp.: |
888 |
|
turn on "useEnergyConservingCoriolis" (better discretisation) in exp. |
889 |
|
hs94.128x64x5 and seaice_obcs ; update results. |
890 |
|
o pkg/obcs: |
891 |
|
fix bug in OBeta for YZ sections in obcs_exf_load.F |
892 |
|
o pkg/ctrl, pkg/shelfice, and optim: |
893 |
|
- add new control variable xx_shifwflx (fresh water flux underneath ice |
894 |
|
shelves). This is almost as tedious as obcs-ctrl, because the |
895 |
|
variables needs its own mask. |
896 |
|
- add a cost function term that penalizes the deviation of xx_shifwflx |
897 |
|
from the first guess (zero) in analogy to other control variables |
898 |
|
o pkg/shelfice: |
899 |
|
- start basic adjoint |
900 |
|
o pkg/ctrl: |
901 |
|
- remove extra 2D field "for good measure" when initializing in |
902 |
|
ctrl_set_globfld_[xy/xz/yz].F |
903 |
|
- replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec |
904 |
|
- improve error messages in ctrl_set_unpack_* |
905 |
|
o OBC implementation in momentum: |
906 |
|
use interior masks (maskInC,W & S) in momentum S/R: |
907 |
|
- multiply divergence, tension and some del^i.u or del^j.v by maskInC |
908 |
|
- multiply del2u,del2v by maskInW/S (biharmonic viscosity) |
909 |
|
- multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) |
910 |
|
- multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) |
911 |
|
Motivation: fix/clean implementation of OBC with biharmonic-viscosity |
912 |
|
(and also with Leith/Smagorinsky harmonic-viscosity). |
913 |
|
Update output of experiment dome and exp4 (+nlfs). |
914 |
|
o exp4 test-exp: |
915 |
|
- turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) |
916 |
|
and prescribe time-varying OB (without pkg/exf) for zonal-velocity |
917 |
|
at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
918 |
|
time-varying OB at Western-side for wVel (NonHyd); update output. |
919 |
|
- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
920 |
|
and biharmonic-viscosity ; also use prescribed time varying OB. |
921 |
|
o pkg/obcs: |
922 |
|
fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
923 |
|
o model/src: |
924 |
|
- fix startTime setting when baseTime<>0 & nIter0=0 are specified ; |
925 |
|
- initialise startTime & nIter0 with unlikely values: allows to set one |
926 |
|
from the other without ambiguity. |
927 |
|
o seaice_obcs test-exp.: |
928 |
|
add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output. |
929 |
|
o pkg/obcs: |
930 |
|
- remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: |
931 |
|
no longer needed with maskInC,W,S in pkg/generic_advdiff. |
932 |
|
o pkg/seaice: |
933 |
|
- retired SEAICE_SALINITY and SEAICE_salinity in favor of |
934 |
|
SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively. |
935 |
|
- fixed bug in the initialization of sea ice salinity variable HSALT |
936 |
|
in seaice_init_varia.F (removed dependence on ICE2WATR) |
937 |
|
o fizhi-cs test exp.: |
938 |
|
switch reference output convention for these 2 non-standard test-exp, |
939 |
|
from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5) |
940 |
|
to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11) |
941 |
|
reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran |
942 |
|
o model/inc: |
943 |
|
- change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4") |
944 |
|
of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS) |
945 |
|
o pkg/seaice: |
946 |
|
- fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY |
947 |
|
o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15 |
948 |
|
- updated output*.txt files due to bug fixes in salt, saltPlumeFlux, |
949 |
|
and initial HSALT |
950 |
|
|
951 |
|
checkpoint62w (2011/04/26) |
952 |
|
o pkg/mom_fluxform: |
953 |
|
- fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf. |
954 |
|
- use parameter "sideDragFactor" in no-slip BC side-drag part. |
955 |
|
- update output of exp. global_ocean.90x40x15 |
956 |
|
o pkg/mom_vecinv: |
957 |
|
mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform) |
958 |
|
o update seaice exp.: |
959 |
|
use more consistent parameter values (remove "backward compatability only": |
960 |
|
ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh) |
961 |
|
related to thermodynamics seaice. Update output (fwd+AD) of exp.: |
962 |
|
1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs |
963 |
|
o update test-exp global_ocean.90x40x15: |
964 |
|
o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis). |
965 |
|
o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.) |
966 |
|
o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params) |
967 |
|
o turn on zStar & viscA4 in standard set-up (dir input/) |
968 |
|
and update output files: output.txt & output.dwnslp.txt |
969 |
|
o new AD-test experiment: obcs_ctrl |
970 |
|
(From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector. |
971 |
|
o pkg/dic: |
972 |
|
fix two bugs in handling water vapour pressure in carbonate chemistry |
973 |
|
and air-sea fluxes. Found by Val Bennington and Galen McKinley |
974 |
|
(add DIC Option = WATERVAP_BUG to recover old results) |
975 |
|
update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline |
976 |
|
o adding allowInteriorFreezing option to check for water below freezing point |
977 |
|
at depth and bring the negative heat anomaly to the surface level |
978 |
|
o pkgs _fields_load: |
979 |
|
- extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs) |
980 |
|
- use new S/R GET_PERIODIC_INTERVAL in pkgs: |
981 |
|
bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and |
982 |
|
rbcs to get interpolation weights and time reccord number. |
983 |
|
- fix multi-threading in aim_fields_load.F |
984 |
|
- apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F |
985 |
|
o external_fields_load: |
986 |
|
new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear |
987 |
|
interpolation weights) to use in a periodic time-series ; do not divide by |
988 |
|
time-step to convert to integer: |
989 |
|
- this fixes case where externForcingPeriod is not multiple of time-step |
990 |
|
(Thanks to Christopher L. Wolfe) |
991 |
|
- this fixes case where externForcingPeriod is an odd multiple of time-step |
992 |
|
(was wrong by half of time-step); update results of tutorial_global_oce_in_p. |
993 |
|
store index of time-record which is currently loaded: |
994 |
|
- works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ; |
995 |
|
- needed for the adjoint but not yet used because of extensive recomputations; |
996 |
|
(to be fixed soon) |
997 |
|
|
998 |
|
checkpoint62v (2011/04/02) |
999 |
|
o verification/1D_ocean_ice_column added to test Ian Fenty's |
1000 |
|
pkg/seaice_growth.F modifications for improving sea ice code differentiability |
1001 |
|
o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope |
1002 |
|
(new velocity statistics after changing maskInW & maskInS definition) |
1003 |
|
o pkg/generic_advdiff with OBCS: |
1004 |
|
use maksInW & maskInS in advective flux and in biharmonic diffusion calculation: |
1005 |
|
equivalent to assumption of no tracer gradient outside the OB region. |
1006 |
|
This will affect the results if using obcs+biharmonic diffusion. |
1007 |
|
update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc) |
1008 |
|
o pkg/obcs: |
1009 |
|
change definition of maskInW & maskInS: leave OB edges inside (maskIn=1) |
1010 |
|
(e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still |
1011 |
|
in Interior region. No impact on solution but affects Velocity monitor stats. |
1012 |
|
o pkg/ptracers (adjoint) |
1013 |
|
New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate |
1014 |
|
tape file for each tracer |
1015 |
|
o model/inc/src and pkg/autodiff: add parameters that allow to turn |
1016 |
|
of parts of the adjoint code at run time. For now, there are only |
1017 |
|
useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These |
1018 |
|
parameters are set in data.pkg. |
1019 |
|
This is the lazy coward's version of doing this, but still useful for |
1020 |
|
debugging. In order to do it right, everything needs to be moved to |
1021 |
|
pkg/autodiff. |
1022 |
|
o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at |
1023 |
|
the end; this fixes the adjoint balancing code for open boundaries. |
1024 |
|
o pkg/ctrl: |
1025 |
|
- change behavior of xx_${varname}period to be analogous to exf-conventions: |
1026 |
|
xx_${varname}period = 0., means time-independent control part |
1027 |
|
xx_${varname}period = -12., means one-year-periodic monthly control part |
1028 |
|
- introduce helper routine ctrl_init_rec (part of ctrl_init.F) to |
1029 |
|
clean up ctrl_init a little, remove unused variables |
1030 |
|
- ctrl_init: fixed the handling of the start/endrec for obcs-variables |
1031 |
|
- move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec |
1032 |
|
|
1033 |
|
checkpoint62u (2011/03/15) |
1034 |
|
o model/src: |
1035 |
|
- for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in |
1036 |
|
h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ; |
1037 |
|
- in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to |
1038 |
|
INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF. |
1039 |
|
o pkg/ctrl/obcs/ecco: |
1040 |
|
- remove obsolete, unused, and partially broken code: |
1041 |
|
ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within |
1042 |
|
ALLOW_CTRL_OBCS_BALANCE |
1043 |
|
- put a stop statement into ecco/cost_obcsvol.F, but also add |
1044 |
|
cost_obcsvol to ecco_ad_diff.list |
1045 |
|
o pkg/ecco: fix counting cost function contributions for obcs (code |
1046 |
|
by Matt M.) and diffkr for diagnostics |
1047 |
|
o pkg/ecco, pkg/ctrl, pkg/grdchk: |
1048 |
|
add cost penalty terms for initial uvel, vvel, eta controls |
1049 |
|
and I/O for prior error files |
1050 |
|
o pkg/mdsio: |
1051 |
|
move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option |
1052 |
|
(new argument) to check for tiled file in mdsioLocalDir : this fix the |
1053 |
|
restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir. |
1054 |
|
o pkg/ctrl: |
1055 |
|
- ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by |
1056 |
|
ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove |
1057 |
|
unused and superfluous variables |
1058 |
|
- ctrl_get_gen_rec.F: catch the case of xx_genperiod=0. |
1059 |
|
o pkg/ecco |
1060 |
|
- enable adjoint of Stevens OB |
1061 |
|
o pkg/ctrl/ecco/grdchk: |
1062 |
|
- remove global declaration of tmpfldx/yz and tmpfldx/yz2. |
1063 |
|
Fortunately, we do not have any tests for the numerous cpp-flagged |
1064 |
|
option of "obcs as control parameters" so we will never know |
1065 |
|
if this is an improvement (but at least now things compile). |
1066 |
|
- remove an obsolete initialization from ecco_cost_init_barfiles.F |
1067 |
|
- fix some problems within never used ifdefs to make the code compile |
1068 |
|
o pkg/obcs: |
1069 |
|
- Refine Interior mask definition to work with more complex OB (e.g. |
1070 |
|
if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to |
1071 |
|
read in Interior mask from file. Check if Interior mask is consistent |
1072 |
|
with OB list of indices. |
1073 |
|
o pkg/seaice |
1074 |
|
- beginning code for a seaice tracer package, |
1075 |
|
but currently only used for seaice age: SEAICE_AGE |
1076 |
|
SEAICE_num = 4 |
1077 |
|
iTracer = 1: area-weighted ice age |
1078 |
|
= 2: volume-weighted ice age |
1079 |
|
= 3, 4: template for one-year vs. multi-year ice |
1080 |
|
data.seaice has new namelist SEAICE_PARM03 for arrays related to |
1081 |
|
SEAICE_num |
1082 |
|
|
1083 |
|
checkpoint62t (2011/03/05) |
1084 |
o pkg/obcs: |
o pkg/obcs: |
1085 |
- obcs_apply_uv.F: change to a 2 steps method, first tangential component; |
- obcs_apply_uv.F: change to a 2 steps method, first tangential component; |
1086 |
then normal component. This ensures that the normal component is set |
then normal component. This ensures that the normal component is set |
1105 |
- add new param to scale curvilinear grid distance and area when using |
- add new param to scale curvilinear grid distance and area when using |
1106 |
a different sphere radius from the grid-files. |
a different sphere radius from the grid-files. |
1107 |
- test/check multi-threads EXCH applied to local variable (cg2d_x) |
- test/check multi-threads EXCH applied to local variable (cg2d_x) |
1108 |
|
o adjoint: |
1109 |
|
- enable adjoint of Stevens OB |
1110 |
|
- add dummy_in_dynamics to enable extraction of ADJrhoinsitu |
1111 |
|
(a bit delicate because of potentially modified adj. common block structure; |
1112 |
|
current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later) |
1113 |
|
|
1114 |
checkpoint62s (2011/02/15) |
checkpoint62s (2011/02/15) |
1115 |
o pkg/seaice (seaice_growth v 1.112): |
o pkg/seaice (seaice_growth v 1.112): |