4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
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o pkg/cal: |
8 |
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- start to clean-up cal_set.F ; fix for the case where baseTime is non-zero. |
9 |
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- remove 2 unsused and very short (1 line only) functions ; |
10 |
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- remove unsused subroutines from AD-Diff list. |
11 |
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o model/src: |
12 |
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- start to implement clean wait to stop in initialization S/R (config_check.F, |
13 |
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packages_check.F and pkg/obcs/obcs_check.F + pkg/mypackage) |
14 |
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o folowing PRINT_MESSAGE changes: |
15 |
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- remove reminder multiple print to the same file (STDOUT) when multi-threads. |
16 |
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o pkg/bbl: |
17 |
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- modification so it can work with z* |
18 |
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- replace deltaT with dTtracerLev(k) for asynchronous time stepping |
19 |
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- global_with_exf/input.yearly verification; changes output.yearly.txt |
20 |
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o eesupp/src: |
21 |
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- PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR); |
22 |
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writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1 |
23 |
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- CHECK_THREADS: specific code if using OpenMP threading: improve checking of |
24 |
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# of threads across processors (e.g., different env OMP_NUM_THREADS setting) |
25 |
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- improve special preliminary call to EESET_PARMS (if eedata is read 2 times). |
26 |
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- when using MPI, always set usingMPI=T ; set default accordingly and stop |
27 |
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if not consistent. |
28 |
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- ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread |
29 |
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argument is zero (in case called within single-thread section). |
30 |
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o pkg/fizhi: |
31 |
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clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored |
32 |
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in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO. |
33 |
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o pkg/exch2: |
34 |
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- add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to |
35 |
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activate EXCH_IGNORE_CORNERS in vector EXCH S/R). |
36 |
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- switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS) |
37 |
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but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data |
38 |
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with bad ones coming from a not-yet-updated halo. |
39 |
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This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx. |
40 |
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o pkg/frazil: |
41 |
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move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F |
42 |
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http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html |
43 |
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o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy |
44 |
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o verification/lab_sea |
45 |
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* #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING |
46 |
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* #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL |
47 |
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* nTimeSteps 3 -> 4 |
48 |
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* changed reference output accordingly |
49 |
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o pkg/ctrl: |
50 |
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* fix ctrl_get_gen for xx_sst, xx_sss |
51 |
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o pkg/fizhi: |
52 |
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- fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F |
53 |
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update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d) |
54 |
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- by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE); |
55 |
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fix few out-of-bounds indices in referencing vars (initialise igrd to 1); |
56 |
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clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array). |
57 |
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o pkg/gmredi: |
58 |
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- add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp |
59 |
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o pkg/fizhi: |
60 |
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- fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the |
61 |
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(old)aces open64 tuv test. |
62 |
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o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F |
63 |
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o pkg/mom_vecinv: |
64 |
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- fix 1 loop range in mom_vecinv.F to be like all the other loops which |
65 |
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set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv |
66 |
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with non-lin free-surf). |
67 |
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o model/src: move k-loop outside of i/j-loops when (re-)computing R_low |
68 |
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in ini/update_masks_etc.F in order to avoid -O3 optimization problems with |
69 |
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some compilers (gfortran 4.6.0 on MacOS) |
70 |
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o momentum: |
71 |
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- separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM |
72 |
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& MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised |
73 |
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fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control. |
74 |
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|
75 |
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checkpoint63k (2012/03/17) |
76 |
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o model/src: |
77 |
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- selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum |
78 |
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flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations. |
79 |
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- SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version |
80 |
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(#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp. |
81 |
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o model/src: solve_*diagonal.F |
82 |
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- replace division with multiplication by inverse (similar to original version) |
83 |
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update output of AD exp. global_ocean.90x40x15. |
84 |
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- fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F |
85 |
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to enable the use of the vectorized & differentiable solve_tridiagonal.F |
86 |
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- test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for |
87 |
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vertical advection (to get solve_tridiagonal tested in AD mode). |
88 |
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o pkg/seaice: ECCO-CLIVAR merge: |
89 |
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1. seaice AREA relaxation |
90 |
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* CPP option: SEAICE_ALLOW_AREA_RELAXATION |
91 |
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* runtime flag: SEAICE_tauAreaObsRelax |
92 |
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2. modified global mean cost imbalance code: CPP option |
93 |
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ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION |
94 |
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o another iteration on solve_*diagonal.F |
95 |
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Make choices independent of AUTODIFF |
96 |
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Default will be the adjoinable vectorized version. |
97 |
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Alternative choices are: |
98 |
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* non-adjoinable original version with low memory footprint: |
99 |
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#define SOLVE_DIAGONAL_LOWMEMORY |
100 |
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* still adjoinable but does not vectorize (k as inner-most loop): |
101 |
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#define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef) |
102 |
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o testreport |
103 |
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- add option to use a home made wrapper around "make" |
104 |
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- remove MITGCM_IEEE env. variable (no longer active) |
105 |
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o pkg/shelfice |
106 |
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- improve computation of friction velocity for velocity dependent |
107 |
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exchange coefficients: include velocities into SHELFICEBoundaryLayer |
108 |
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block to average velocities vertically |
109 |
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- add TAF store directives for SHI_ALLOW_GAMMAFRICT |
110 |
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o Modify diagonal solvers, now three versions (upon request): |
111 |
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#ifndef SOLVE_DIAGONAL_AUTODIFF |
112 |
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1. default version (dating back a while ago) |
113 |
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#else /* def SOLVE_DIAGONAL_AUTODIFF */ |
114 |
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# ifdef SOLVE_DIAGONAL_KINNER |
115 |
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2. adjoinable version with k-innermost loop (G. Forget) |
116 |
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# else |
117 |
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3. adjoinable vectorized version of 2. |
118 |
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# endif |
119 |
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#endif /* SOLVE_DIAGONAL_AUTODIFF */ |
120 |
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All flags are currently set within routines, but could/should be moved to CPP-options. |
121 |
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Array bounds for 1. are as before, for 2.,3. cover the entire domain |
122 |
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(could be changed for 1. too). |
123 |
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o verification/lab_sea (fwd): |
124 |
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- update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY, |
125 |
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use 7 categories (except hb87), new solve4temp params (except salt_plume), |
126 |
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constant salinity (=4) or variable salinity (salt_plume) done through |
127 |
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SItracer. |
128 |
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o pkg/seaice: |
129 |
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- rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0; |
130 |
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- remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t, |
131 |
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SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz) |
132 |
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from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when |
133 |
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SEAICE_freeze got retired) but already better than previously with |
134 |
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SEAICE_freeze=123456.7 deg.C; |
135 |
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- move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS |
136 |
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(safer multi-threaded setting); always set SEAICEuseEVP; |
137 |
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- setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to |
138 |
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SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report); |
139 |
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stop if multiple specifications for the same coeff; make sure default |
140 |
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SEAICE_mcPheePiston is compatible with drF(1) & deltaT. |
141 |
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o pkg/obcs: |
142 |
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- allow to switch to upwind 1rst order advection scheme for the advective |
143 |
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flux computation at the open-boundary; disabled for adjoint built. |
144 |
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o pkg/ptracers: |
145 |
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- rename PTRACERS_RESTART.h -> PTRACERS_START.h |
146 |
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- rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F |
147 |
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- add parameter to decide when to start a tracer; use internal flag to |
148 |
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know which tracer to step-forward; switch this internal flag at the top |
149 |
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of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled |
150 |
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for adjoint built. |
151 |
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o pkg/seaice: |
152 |
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- add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ; |
153 |
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- move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ; |
154 |
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- keep experiment offline_exf_seaice truly single category (set MULTDIM=1). |
155 |
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o pkg/ecco: |
156 |
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- fix writing of output file DiagnosCost_ClimSalt/Theta |
157 |
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and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc). |
158 |
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o pkg/seaice: |
159 |
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- add missing initialisation of COR_ICE array in dynsolver.F |
160 |
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- merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is |
161 |
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compiled either way, and is tested in all exps (multidim was only tested |
162 |
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in lab_sea ad before). |
163 |
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- cosmetic change to prepare for future addition of ITD. no change to results. |
164 |
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no defaults change. |
165 |
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- added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise). |
166 |
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- by lack of adequate verification experiments, I further used custom versions |
167 |
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of global_ocean.cs32x15 to test multicat or not, with pickup or not. All |
168 |
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should be correct. |
169 |
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- avoid recomputations in ad. |
170 |
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o array initialisation in adjoint mode: |
171 |
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1) pkg/mom_common/mom_calc_ke.F: |
172 |
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add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC): |
173 |
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The S/R which calls MOM_CALC_KE initialises KE but in some recomputation |
174 |
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part this initialisation is gone, resulting in Floating Point Exception |
175 |
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(caught by open64 compiler with debug option). |
176 |
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2) model/src/convective_weights.F |
177 |
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set output convectCount over the full array range (instead of doing |
178 |
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an update): this fix a similar issue when called within recomputation (adjoint) |
179 |
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which could by-pass the initialisation (normally done in the caller S/R). |
180 |
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o pkg/seaice: |
181 |
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- final version of turbulent flux params, as agreed at MIT ice meet: |
182 |
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SEAICE_mcPheePiston (default is ~ 0.000875) |
183 |
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SEAICE_mcPheeTaper (default is 0.) |
184 |
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SEAICE_frazilFrac (defualt is 1.) |
185 |
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SEAICE_mcPheeStepFunc (default is false) |
186 |
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- changes results at trunction error level |
187 |
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- ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo |
188 |
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o added pkg/frazil: |
189 |
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- see frazil_description.tex for details |
190 |
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- verification experiment is global_with_exf/input.yearly; changes output.yearly.txt |
191 |
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o pkg/shelfice/shelfice_thermodynamics.F |
192 |
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- fix exponents for velocity dependent exchange coefficients: change |
193 |
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from 2/3(=0) to 0.66666666666666667 |
194 |
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- move computation of velocity dependent exchange coefficients into |
195 |
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separate loop, so that it applies to both thermodynamics |
196 |
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- move some divisions by constants out of loops |
197 |
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|
198 |
|
checkpoint63j (2012/02/16) |
199 |
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o pkg/seaice: |
200 |
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- overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc. |
201 |
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- SItracer: added run time params, and allow coupling to ocn salinity. |
202 |
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o pkg/seaice: remove (almost) all divisions by constants within loops |
203 |
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in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d |
204 |
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results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only |
205 |
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those, caused by 1/QI -> recip_QI) -> update output.seaice.txt, |
206 |
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output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt |
207 |
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o pkg/seaice : |
208 |
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- simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula |
209 |
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= 1 or 2, using newly added run time parameter SEAICE_availHeatTaper. |
210 |
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- fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148. |
211 |
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- add permanent SItflux diag that corresponds to TFLUX but includes |
212 |
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ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget. |
213 |
|
- allow activation/testing of a fix for suspected missing term in |
214 |
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ocn-ice heat budget (to be confirmed). To test this, you want to |
215 |
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undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param |
216 |
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SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic. |
217 |
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- no change in results, fwd or ad. |
218 |
|
o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below: |
219 |
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- switch to variable freezing point. |
220 |
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Results change : cg2d -> 1 digits; ad -> 3-6-6 digits. |
221 |
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- bug fix : the sublimation term that was missing is now activated. |
222 |
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Results change : cg2d -> 2 digits; ad -> 8-6-6 digits. |
223 |
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- bug fix : flooding sign term for SIsal0.NE.0. |
224 |
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Result change : cg2d -> 8 digits; ad -> 11-12-9 digits. |
225 |
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o pkg/seaice: |
226 |
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- unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT |
227 |
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is now the default, and the old default constant freezing point is recovered |
228 |
|
with SEAICE_tempFrz0 = -1.96, |
229 |
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SEAICE_dTempFrz_dS = 0., |
230 |
|
- retire SEAICE_freeze (= the old way of specifycing the constant freezing point) |
231 |
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- remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there. |
232 |
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- bug fix (thanks to M. Losch) : the sublimation term that was missing is now |
233 |
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activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM. |
234 |
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- bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211) |
235 |
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was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail). |
236 |
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- bug fix (thanks to O. Jahn) : area loss for melting got messed up in |
237 |
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seaice_growth r149 for legacy branch (no results change). |
238 |
|
- introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code |
239 |
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from I. Fenty). |
240 |
|
- results did not change except for global_ocean.cs32x15, mostly due to the |
241 |
|
switch to variable freezing point (see above item for detail). |
242 |
|
o pkg/thsice: |
243 |
|
- fix and simplify interface to salt_plume pkg ; diagnose directly amount of |
244 |
|
seawater freezing in thsice_calc_thickn (not used). |
245 |
|
o pkg/seaice: turbulent flux term specification via run time params. |
246 |
|
- replace CPP switches with run time switches to facilitate testing |
247 |
|
- retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, |
248 |
|
GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR |
249 |
|
- added runtime parameter : SEAICEturbFluxFormula |
250 |
|
- move Mcphee constants to SEAICE_PARAMS.h |
251 |
|
- seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula; |
252 |
|
SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); |
253 |
|
remove seaice_summary call (moved to seaice_init_fixed) |
254 |
|
- seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on |
255 |
|
SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms) |
256 |
|
- seaice_summary.F : add missing report of read turbulent flux term set up |
257 |
|
and SITRACER. |
258 |
|
- seaice_check.F : check range; inform and stop if retired CPPs are used |
259 |
|
(incl. SEAICE_AGE). |
260 |
|
- seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without |
261 |
|
CPP switch, same computation as before for the different options. |
262 |
|
- change results at the truncation level. |
263 |
|
o pkg/seaice: |
264 |
|
- remove un-used parameters LAD & MAX_TICE ; add new run-time parameters: |
265 |
|
useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and |
266 |
|
SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY. |
267 |
|
- update verification/*/input*/data.seaice: |
268 |
|
to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY |
269 |
|
code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ; |
270 |
|
and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code, |
271 |
|
set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0. |
272 |
|
o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY): |
273 |
|
- remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same |
274 |
|
algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0); |
275 |
|
difference in results only due to machine truncation. |
276 |
|
- remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using |
277 |
|
MaykutPolySatVap; keep MIN_LWDOWN. |
278 |
|
- adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation. |
279 |
|
- update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87, |
280 |
|
+ 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits). |
281 |
|
o pkg/salt_plume: |
282 |
|
- isolate saltPlumeFlux array exch into a specific S/R called from |
283 |
|
do_oceanic_phys.F |
284 |
|
- add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice. |
285 |
|
o verification: |
286 |
|
- move untested set-up to MITgcm_contrib/verification_other. |
287 |
|
o pkg/seaice: |
288 |
|
- retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER. |
289 |
|
o pkg/seaice: |
290 |
|
- seaice_solve4temp.F (keeping results unchanged): |
291 |
|
* add 2 future run-time params to select which saturation vapor pressure |
292 |
|
formula is used and how post-iteration fluxes are set. |
293 |
|
Temporary set these 2 params according to option SOLVE4TEMP_LEGACY; |
294 |
|
* New piece of code (not used) to update surf. atmos. heat flux F_ia using |
295 |
|
the linearized expression to stay consistent with tsurf finding. |
296 |
|
- seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x |
297 |
|
can be < 0. |
298 |
|
o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef): |
299 |
|
- remove from F_ia (and from it's derivative dFiDTs1) the contribution of |
300 |
|
conductive heat flux F_c , and add it explicitly when updating tsurf as |
301 |
|
solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf |
302 |
|
so that now F_ia has a consistent meaning through the entire routine. |
303 |
|
This causes differences at truncation level: update output of fwd exp. |
304 |
|
global_ocean.cs32x15.seaice. |
305 |
|
o pkg/seaice: |
306 |
|
- lots of editing/cleaning in seaice_solve4temp.F + better documentation |
307 |
|
of arrays, sign/direction of fluxes; no effect on results. |
308 |
|
- replace hard coded 273.16 (=previous value of celsius2K) by celsius2K |
309 |
|
in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part); |
310 |
|
note: this should have been done before changing celsius2K default. |
311 |
|
- to keep results unchanged, add back old value of celsius2K in verification |
312 |
|
exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs |
313 |
|
- replace hard coded seawater freezing temp in seaice_solve4temp.F (part |
314 |
|
SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default |
315 |
|
value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater |
316 |
|
freezing temp is consistent with value in seaice_growth.F ; this causes |
317 |
|
differences at machine truncation level: update lab_sea AD output (3/4). |
318 |
|
o pkg/seaice: |
319 |
|
- mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask |
320 |
|
and climsst/sss even when using seaice (to prevent calculation that might |
321 |
|
use SST on land); does not affect any verification exp. |
322 |
|
- apply mask to taux,tauy (in seaice_get_dynforcing.F); update output |
323 |
|
of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix. |
324 |
|
o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness |
325 |
|
over land (non-legacy code) |
326 |
|
o vectorize salt_plume package: |
327 |
|
- add extra code to salt_plume_frac and salt_plume_tendency_apply_s |
328 |
|
- this code computes plumebk everywhere (also over land), thus requires |
329 |
|
code to avoid divisions by zero and catch the case of kLev=Nr. |
330 |
|
- efficiency of salt_plume_frac is still sub-optimal |
331 |
|
o tools (genmake2): |
332 |
|
- fix makefile NAME specification (option: -makefile NAME) by adding |
333 |
|
"-f $MAKEFILE" in few places where it was missing including makedepend |
334 |
|
command (contribution from Paul). |
335 |
|
|
336 |
|
checkpoint63i (2012/01/24) |
337 |
|
o model/src: |
338 |
|
- add factorized versions of some EOS code to find_rho.F, |
339 |
|
define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX) |
340 |
|
o model/src: |
341 |
|
- add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h; |
342 |
|
- change default celsius2K from 273.16 to 273.15 |
343 |
|
- to keep results unchanged, add back old value of celsius2K in verification |
344 |
|
exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd), |
345 |
|
global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm). |
346 |
|
o model/src: add a little initialisation trick to find_rho.F and find_alpha.F |
347 |
|
to make TAF generate vectorizable code |
348 |
|
o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows. |
349 |
|
Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers |
350 |
|
have flags that do this more efficiently. |
351 |
|
o pkg/diagnostics/diagstats_calc.F |
352 |
|
- for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact |
353 |
|
o pkg/obcs (with exch2): |
354 |
|
- derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F) |
355 |
|
and remove code (in obcs_readparms.F) which was based on EXCH of indices |
356 |
|
(through buffer) and did not account for exch2 (e.g., CS-grid) topology. |
357 |
|
o pkg/exf and seaice exp: |
358 |
|
- change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0) |
359 |
|
so that switching off area & heff advection flags does not affect results. |
360 |
|
- change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h |
361 |
|
- keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef |
362 |
|
EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update |
363 |
|
results of verification experiments: 1D_ocean_ice_column(fwd), |
364 |
|
global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8) |
365 |
|
and offline_exf_seaice (all 4). |
366 |
|
o pkg/seaice: |
367 |
|
- remove array YNEG, RIVER, TMIX (replaced by local var) from common block; |
368 |
|
remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef. |
369 |
|
- fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY) |
370 |
|
but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and |
371 |
|
not multi-dim advection; |
372 |
|
- fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and |
373 |
|
SHORTWAVE_HEATING #undef. |
374 |
|
o optim: make Makefile more robust (?) |
375 |
|
o pkg/obcs: |
376 |
|
* fix treatment of obcs_read_pickup for TAF |
377 |
|
o pkg/shelfice: |
378 |
|
* add missing initialisation of num_shifwflx |
379 |
|
* new adjoint verification exp. for isomip |
380 |
|
* change Prandtl and Schmidt numbers from generic formulations |
381 |
|
(in terms of model diffus. and visc.) to separate runtime |
382 |
|
parameters, with Holland and Jenkins (1999) default values. |
383 |
|
o pkg/exf (interpolation): |
384 |
|
- extended input field (2 rows) near the N & S poles: |
385 |
|
* fill in with the symetric value (when even Nb of data in longitude) |
386 |
|
* add average value at the poles only for scalar quantities ; for vector |
387 |
|
component interpolation, skip the averaging and keep duplicated values, |
388 |
|
unless the 2 components have same location (uvInterp=T) in which case |
389 |
|
interpolate the 2 components together using S/R EXF_INTERP_UV. |
390 |
|
- new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field |
391 |
|
together: this allows to account properly for local orientation when |
392 |
|
averaging at N & S pole. |
393 |
|
- add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding |
394 |
|
exf-interpolation near N & S poles. Undef by default. |
395 |
|
- add debug check/print on 1rst iter if debugLevel >=2. |
396 |
|
o pkg/exf: |
397 |
|
- change masking flags definition (no longer "parameter"), put them in |
398 |
|
common block and set them in S/R EXF_INIT_FIXED. |
399 |
|
- change recognized masking flag from s,u,v to c,w,s since the mask |
400 |
|
to use (maskC,W,S) depends on position on model grid and has little to |
401 |
|
do with scalar/vector difference; fix masking if using P-coordinates. |
402 |
|
- fix masking of wind-stress (was wrong if interpolated or read on A-grid) |
403 |
|
and update results of exp. global_with_exf (x2). |
404 |
|
- fix setting of zenith-angle table when SHORTWAVE_HEATING is undef. |
405 |
|
o pkg/obcs |
406 |
|
- S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate) |
407 |
|
o pkg/exf (interpolation): |
408 |
|
- assume periodicity in X only if input field cover full longitude range. |
409 |
|
- improve search for lat. index (supposed to be faster, in ~log2(ny) steps, |
410 |
|
and should vectorise). |
411 |
|
- fix input lat of the 2 added row (in case we provide N.pole data). |
412 |
|
|
413 |
|
checkpoint63h (2011/12/30) |
414 |
|
o pkg/seaice: |
415 |
|
- change declaration of UVM from _RL to _RS in order to get B-grid |
416 |
|
uIce,vIce monitor when _RS = real*4 |
417 |
|
o pkg/offline: |
418 |
|
- new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags); |
419 |
|
- compute vertical velocity if not read from file (switch on exactConserv |
420 |
|
& staggerTimeStep); |
421 |
|
- fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq. |
422 |
|
o verification: |
423 |
|
- update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input) |
424 |
|
with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m": |
425 |
|
fix Pb in yG definition @ 2 missing corners (previously yG was averaged); |
426 |
|
- update output of exp. global_ocean.cs32x15.viscA4 after changing |
427 |
|
grid-file angles (used here for coriolis-3d); |
428 |
|
- remove (or gzip) few files not needed to run fizhi-cs experiments. |
429 |
|
o pkg/exf (vector interpolation): |
430 |
|
- rotate vector component toward local grid-axis orientation using grid-angles |
431 |
|
(stored in GRID.h) instead of locally computed rotation angle; keep old code |
432 |
|
available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default). |
433 |
|
o pkg/seaice: |
434 |
|
- allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION |
435 |
|
undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined. |
436 |
|
o pkg/PKG_OPTIONS.h files: |
437 |
|
- move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h", |
438 |
|
outside of the #ifdef ALLOW_THISPKG / #endif block. |
439 |
|
- update verification/*/code/PKG_OPTIONS.h files. |
440 |
|
o add a verification experiment (offline_exf_seaice/input.seaice) that test |
441 |
|
the B-grid LSOR solver |
442 |
|
o pkg/seaice: sort out emissivity and long wave radiation step 2: |
443 |
|
- add emissivity for snow and ice as new run-time parameters |
444 |
|
(unfortunately) that default to the corresponding exf values; this |
445 |
|
changes results in most verification experiments so that for backward |
446 |
|
compatibility these parameter have to be set explicitly to inconsistent |
447 |
|
values (ugly); |
448 |
|
- the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired |
449 |
|
emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp |
450 |
|
until we agree how to handle this bug properly |
451 |
|
o pkg/exf (interpolation): |
452 |
|
- add a set of run-time param ({inputfield}_interpMethod), one for |
453 |
|
each interpolated input field, to select the interpolation method |
454 |
|
with a value of zero switching off the interpolation; |
455 |
|
- print interpolation parameters to standard output; |
456 |
|
- refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined |
457 |
|
(to use instead runoff_interpMethod=0 in data.exf). |
458 |
|
- simplify default setting of interpolation parameters (for all fields, |
459 |
|
set position to match model grid cell-center position, leading to trivial |
460 |
|
interpolation in case of regular Lat-Lon grid) and fix for the case of |
461 |
|
non-uniform delY. |
462 |
|
o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for |
463 |
|
within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1. |
464 |
|
this factor is absolutely required, because the lw exitance (= out-going |
465 |
|
long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown, |
466 |
|
where the reflectivity rho = 1-emissivity for conservation reasons. Once |
467 |
|
this is established, we can remove the CPP-Flag (if we want to). |
468 |
|
o pkg/seaice: |
469 |
|
- qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and |
470 |
|
ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined |
471 |
|
- sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity |
472 |
|
what the name implies (and not emissivity*BoltzmannConstant), this means |
473 |
|
the old default value of 5.5e-8 now means |
474 |
|
5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in |
475 |
|
S/R exf_readparms |
476 |
|
- FV-discretization of the B-grid LSOR solver, turn on with |
477 |
|
SEAICE_LSRBNEW. This new solver also involves a slight re-organization |
478 |
|
of the calling routine dynsolver, so that B and C-grid code look a |
479 |
|
little more alike. |
480 |
|
- fix index bugs in ostres.F (B-grid code) |
481 |
|
o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better |
482 |
|
o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the |
483 |
|
default for SEAICE_emissivity, if useEXF; requires setting a wrong |
484 |
|
parameter value in global_ocean.cs32x15/input.seaice/data.seaice for |
485 |
|
backward compatiblity |
486 |
|
o model/src: use sigmaR in calc_ivdc |
487 |
|
|
488 |
|
checkpoint63g (2011/12/16) |
489 |
|
o pkg/seaice/seaice_growth.F: |
490 |
|
fix heat conservation of the coupled ocean-seaice system. |
491 |
|
when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of |
492 |
|
solid vs liquid water treatment is resolved via QNET. |
493 |
|
o pkg/seaice/seaice_growth.F: |
494 |
|
add missing term for sublimation in saltFlux, which was breaking conservation. |
495 |
|
o pkg/seaice/seaice_model.F: |
496 |
|
Remove this patholigical case treatment in evolution branch, |
497 |
|
where it is un-necessary and breaks conservation. |
498 |
|
Update global_ocean.cs32x15/results accordingly for |
499 |
|
output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt |
500 |
|
o model/src: |
501 |
|
useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in |
502 |
|
external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE. |
503 |
|
o pkg/obcs: |
504 |
|
modify Stevens boundary conditions so that S/R obcs_calc_stevens computes |
505 |
|
tendency for temperature and salinity that is then applied to update |
506 |
|
theta and salt in S/R obcs_apply_ts; this requires proper masking of all |
507 |
|
horizontal advection and diffusion contributions on the boundary (in |
508 |
|
S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and |
509 |
|
removing the mask in S/R timestep_tracer. The advantage of this approach is |
510 |
|
that the updated tracer values include contributions from the surface |
511 |
|
forcing and vertical diffusion. |
512 |
|
This modification changes exp4.stevens because of vertical diffusion. |
513 |
|
o model/src: |
514 |
|
change non-curvilinear grid setting to also work with exch2 + blank tiles: |
515 |
|
- move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst |
516 |
|
face dimensions. |
517 |
|
- new S/R INI_LOCAL_GRID to define model tile-local grid (using same units |
518 |
|
as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID |
519 |
|
and INI_SPHERICAL_POLAR_GRID. |
520 |
|
change test-experiment global_ocean.90x40x15: |
521 |
|
- split the domain in many more tiles (9x4 tiles of 10x10 each); |
522 |
|
- switch to exch2 and remove 1 blank-tile (but only for MPI test). |
523 |
|
- update results of both test (std & dwnslp). |
524 |
|
o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in |
525 |
|
tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation |
526 |
|
o model/src: |
527 |
|
- take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS |
528 |
|
and fix initialisation when using sigma-coords. |
529 |
|
o model/src: |
530 |
|
- improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc. |
531 |
|
to their current value at the beginning of forward_step.F": add a new run-time |
532 |
|
switch "doResetHFactors" (default=false) and use it to do (or not) the resetting. |
533 |
|
- set doResetHFactors=T in the following test exp: |
534 |
|
global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS), |
535 |
|
global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS) |
536 |
|
and tutorial_global_oce_in_p (nonLinFS in p) |
537 |
|
o pkg/ecco |
538 |
|
- added IES cost term |
539 |
|
o verification/advect_xz |
540 |
|
- scale down the depth by 1/100 (from 200 km to just 2.km) |
541 |
|
- add secondary test using divergent flow, r-star and implicit vertical advection. |
542 |
|
- add note (check_conserve_TS.txt) and matlab script to check global |
543 |
|
conservation of T & S with NonLin-FreeSurf and Adams-Bashforth. |
544 |
|
o pkg/rbcs: |
545 |
|
- add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F). |
546 |
|
o pkg/obcs (Stevens BCs): |
547 |
|
- fix various problems in the phase speed computations of the Stevens |
548 |
|
boundary conditions: |
549 |
|
- sign error for western and southern boundaries, |
550 |
|
- time tendencies were underestimated by factor of dTracerLev and some just |
551 |
|
zero (for multidim advection schemes) -> now estimate time tendencies |
552 |
|
from difference between previous (n) time level and the one before (n-1); |
553 |
|
this requires storing a field per tracer per boundary, also in the pickup |
554 |
|
files. |
555 |
|
- replace deltaTmom in cflMer/Zon computation with dTracerLev |
556 |
|
- set default phase velocity to cflMer/Zon |
557 |
|
- update verification experiment exp4.stevens |
558 |
|
o pkg/generic_advdiff (implicit_r): |
559 |
|
- fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf |
560 |
|
(remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F); |
561 |
|
- fix implicit vertical diffusion or advection with NonLin FreeSurf |
562 |
|
(was using current recip_hFacC instead of future recip_hFacC): set future |
563 |
|
recip_hFac in thermodynamics.F and pass & use it in all vertical implicit |
564 |
|
solver S/R ; |
565 |
|
- fill diagnostics of vertical advective fluxes (computed from tendency) |
566 |
|
when using implicit vert. advection; |
567 |
|
- update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion: |
568 |
|
global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD), |
569 |
|
tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD) |
570 |
|
and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5. |
571 |
|
o pkg/diagnostics: |
572 |
|
- add diags for T & S tendency which goes through Adams-Bashforth. |
573 |
|
|
574 |
|
checkpoint63f (2011/11/30) |
575 |
|
o pkg/obcs/obcs_calc_stevens.F: |
576 |
|
- join some loops to reduce number of if-statements |
577 |
|
- fix a bug in code for northern and southern boundaries. |
578 |
|
o pkg/seaice/seaice_init_varia.F |
579 |
|
- undo resetting UVM=0 that has slipped in unnoticed in r1.49 and |
580 |
|
caused zero ice-velocities for the B-grid code |
581 |
|
o pkg/seaice/seaice_init_fixed.F |
582 |
|
- fix a bug in the initialisation of the second metric terms |
583 |
|
k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0. |
584 |
|
- this affects all seaice configurations with useCurviLinearGrid = .true. |
585 |
|
and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms |
586 |
|
= .true. (default) |
587 |
|
- the only verification experiment affected is global_ocean.cs32x15: |
588 |
|
icedyn, seaice, and seaice_dynmix (AD) |
589 |
|
o pkg/thsice/thsice_diagnostics_state.F |
590 |
|
- only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does |
591 |
|
not contain garbage that can lead to surprises in diagstats_calc.F |
592 |
|
o model/src: |
593 |
|
- move bi,bj loops inside INTEGR_CONTINUITY ; |
594 |
|
- call INTEGR_CONTINUITY directly from forward_step.F |
595 |
|
(previously called from momentum_correction_step.F) |
596 |
|
- call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F, |
597 |
|
forward_step.F and pkg/ecco/the_main_loop.F |
598 |
|
o model/src/do_oceanic_phys.F: |
599 |
|
- reset addMass to zero only if useICEFRONT ; |
600 |
|
- separated k-loop for rhoInSitu calculation ; |
601 |
|
- add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P) |
602 |
|
and at constant T,S (= WdRHOdP); |
603 |
|
NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport |
604 |
|
of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical |
605 |
|
transport of locally-referenced potential density); |
606 |
|
to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP) |
607 |
|
o gluemnc: |
608 |
|
- replace ncrcat with ncks when adding variables to *.glob.nc |
609 |
|
- change the way variables without record dimensions are handled so that |
610 |
|
files that have variables with and without record variables can be glued: |
611 |
|
add a record dimension with a new unique name to be able to differentiate |
612 |
|
between variable with and without a-prior record dimensions. Remove |
613 |
|
this record dimension before adding the variable to the *.glob.nc file. |
614 |
|
This procedure automatically works also for grid.*.nc files that do not |
615 |
|
have any record dimension. |
616 |
|
o verification/cpl_aim+ocn: |
617 |
|
- generate new reference output on baudelaire (gfortran, mpich2) (previously |
618 |
|
from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script. |
619 |
|
o pkg/obcs/obcs_calc_stevens.F: |
620 |
|
- add code for northern and southern boundaries. |
621 |
|
- reorder some loops to save some operations and so that drFBar can be scalar |
622 |
|
o model/src: |
623 |
|
- re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine |
624 |
|
truncation) and add diagnostics for Adams-Bashforth tendency increment. |
625 |
|
- update test-exp. AD output: |
626 |
|
1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl; |
627 |
|
and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20, |
628 |
|
front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5), |
629 |
|
global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4), |
630 |
|
matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre, |
631 |
|
tutorial_global_oce_in_p, tutorial_global_oce_latlon and |
632 |
|
tutorial_plume_on_slope. |
633 |
|
o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX |
634 |
|
that vectorises. This code uses 3 extra 2D fields, F90 array assignments |
635 |
|
and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX |
636 |
|
does not even come with an F77 compiler anymore, this should not be |
637 |
|
a limitation |
638 |
|
|
639 |
|
checkpoint63e (2011/11/06) |
640 |
|
o pkg/seaice adjoint of LSR: |
641 |
|
- substantially rework STORE dirs. |
642 |
|
- add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED |
643 |
|
this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields |
644 |
|
and only perform SOLV_MAX_FIXED adjoint iters. |
645 |
|
If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration |
646 |
|
always goes to same record, meaning that the last forward field will be |
647 |
|
the one used in the adjoint - an approximation. |
648 |
|
- now produces non-zero LSR-related gradients, and acceptable gradients for |
649 |
|
An's zonal (x-z) test case (to be checked in) |
650 |
|
- lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR |
651 |
|
(but these are screwed up by the thermodynamics in the first place); |
652 |
|
reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution; |
653 |
|
output_adm.txt also reflects changes to seaice_lsr |
654 |
|
- global_ocean.cs32x15: |
655 |
|
* the "default" input_ad.seaice has been re-defined to always exclude dynamics |
656 |
|
(output_adm.seaice.txt was updated) |
657 |
|
* new input_ad.seaice_dynmix tests a forward LSR / backward free-drift |
658 |
|
(output_adm.seaice_dynmix.txt) |
659 |
|
o test-exp. exp4+stevens: |
660 |
|
- switch off pTracers and nonHydrostatic (restart problems with NH); update output |
661 |
|
o pkg/seaice (lsr solver): |
662 |
|
- put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only); |
663 |
|
update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15 |
664 |
|
- fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD) |
665 |
|
- new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution |
666 |
|
into initial guess for linearised solver; use weight ~ (1/err)^2,4. |
667 |
|
- compute (with new S/R) and print initial (+ free-driff sol. if available) |
668 |
|
and final residual of linearised system. |
669 |
|
o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity |
670 |
|
(requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F) |
671 |
|
o pkg/obcs: Stevens BCs (still only for east and west) |
672 |
|
- fix Stevens BCs by using intermediate velocities of previous |
673 |
|
time step as "baroclinic" contribution rather velocity of one grid cell |
674 |
|
inside the boundaries; more consistent but makes the entire treatment |
675 |
|
more complicated, requires new pickup files and two new S/Rs: |
676 |
|
obcs_copy_uv_n and obcs_save_uv_n |
677 |
|
keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY |
678 |
|
(undefined by default) |
679 |
|
- silently move computation of some grid factors into separate loops to |
680 |
|
save some recomputations |
681 |
|
- add a hack for non-linear free surface |
682 |
|
- add a verification experiment to exp4 that tests this code |
683 |
|
o make gluemnc/xplodemnc work with (moron) non-GNU shell tools |
684 |
|
|
685 |
|
checkpoint63d (2011/10/25) |
686 |
|
o pkg/obcs + seaice-dynamics: |
687 |
|
- new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before |
688 |
|
solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB |
689 |
|
values (consistent with an implicit method). |
690 |
|
- add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to |
691 |
|
return to older implementation (same results as before); note that none of |
692 |
|
the "experimental" OBCS_SEAICE options are implemented in the new version. |
693 |
|
- switch test exp. seaice_obcs to use new version (update output). |
694 |
|
o pkg/seaice: |
695 |
|
- add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS) |
696 |
|
- add parenthesis in Water-Ice drag calculations (evp & lsr); |
697 |
|
- in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1; |
698 |
|
and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice) |
699 |
|
- update output of test exp lab_sea that uses evp or lsr (fwd+ad) |
700 |
|
and global_ocean.cs32x15 (icedyn & seaice fwd+ad). |
701 |
|
o pkg/layers: |
702 |
|
- Include potential density as new coordinate (Thanks to David Munday) |
703 |
|
o pkg/dic: |
704 |
|
- Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add |
705 |
|
carbonate computation/output to CALC_PCO2_APPROX |
706 |
|
o pkg/generic_advdiff |
707 |
|
- make TAF generate code that vectorizes: |
708 |
|
gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F |
709 |
|
o model/src: |
710 |
|
- improve vectorization also for adjoint code of |
711 |
|
solve_tridiagonal and solve_pentadiagonal. As this requires up to |
712 |
|
5 new 3D-fields, this code is only turned on for the combination of |
713 |
|
ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message |
714 |
|
for singular matrix check (only for TARGET_NEC_SX). |
715 |
|
- remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to |
716 |
|
ALLOW_AUTODIFF. This flag now needs to be set outside of |
717 |
|
solve_tri/pentadiagonal.F |
718 |
|
o pkg/exf: |
719 |
|
- fix previous modif in exf_readparms.F (revision 1.66: treatment of |
720 |
|
optional namelist EXF_NML_OBCS). |
721 |
|
- add many debug-print (to trace down where pkg/cal error msg comes from) |
722 |
|
o pkg/mom_vecinv/mom_vi_hdissip.F |
723 |
|
- rearrange loops so that vectorization is improved and in particular |
724 |
|
the adjoint routine vectorizes. The code is a little longer now, but I |
725 |
|
think easier to read. |
726 |
|
Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested. |
727 |
|
o pkg/seaice: |
728 |
|
- allow to specify initial seaice velocity from files (uIceFile,vIceFile) |
729 |
|
o pkg/exch2: |
730 |
|
- alternative code (without tile x tile matrix) for cumulated (global) sum; |
731 |
|
used as default; keep using matrix version in adjustment.cs-32x32x1. |
732 |
|
o tools/build_options: |
733 |
|
- after merging some MPI and/or multi-threads specific optfiles so that |
734 |
|
the modified default optfile support both built (using genmake2 -mpi |
735 |
|
for the MPI built, using genmake2 -omp for OpenMP built), |
736 |
|
move now obsolete optfiles to tools/build_options/unsupported/ |
737 |
|
(add copy of email sent to support list in doc/optfiles_changes.txt) |
738 |
|
|
739 |
|
checkpoint63c (2011/09/28) |
740 |
|
o pkg/ebm: |
741 |
|
- fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of |
742 |
|
test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d) |
743 |
|
o pkg/seaice (SItracer pickup) |
744 |
|
* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER) |
745 |
|
To be done: |
746 |
|
- thorough testing of missing fields in S/R seaice_read_pickup |
747 |
|
- thorough matching between generic tracers and specific fields used |
748 |
|
(e.g. volume-weighted age, area-weighted age, salinity, ...) |
749 |
|
o pkg/grdchk: |
750 |
|
- all procs calculate and print finite-difference gradient (for testreport) |
751 |
|
- change description output used by testreport; |
752 |
|
- AD testing: also compare and report Finite-difference gradient; |
753 |
|
=> update all output_adm*.txt |
754 |
|
o test exp. global_ocean_ebm: |
755 |
|
- switch back useRealFreshWaterFlux (no problem anymore with run-off); |
756 |
|
and turn on exactConserve; update (fwd) output. |
757 |
|
o pkg/seaice (LSR): |
758 |
|
- print to STDOUT number of solver iterations at SEAICE_monFreq interval. |
759 |
|
- modify solver to deal cleanly with u/v switch at face edges (CS-grid): |
760 |
|
* identical results with non-CS topology (but save up to half of EXCH calls) |
761 |
|
* no much changes in cs-32 verification tests since no ice at face edges |
762 |
|
(differences due to convergence criteria, since nb of iterations changed) |
763 |
|
* expect some differences on lat-lon-cap grid. |
764 |
|
update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice) |
765 |
|
o pkg/exch2: |
766 |
|
- add new CPP option to disable Cumul-Sum matrix (to save storage when using |
767 |
|
many tiles); until alternative coding is added, just add a stop. |
768 |
|
o pkg/kpp: |
769 |
|
- move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F |
770 |
|
to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list). |
771 |
|
o optfiles: |
772 |
|
- merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles |
773 |
|
into corresponding standard one, which now support different build: |
774 |
|
(when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built) |
775 |
|
- add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael) |
776 |
|
o pkg/obcs (seaice): |
777 |
|
- add missing EXCH for uIce,vIce after applying OBCS; |
778 |
|
- remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding |
779 |
|
argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R |
780 |
|
EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F; |
781 |
|
- fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared) |
782 |
|
- verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi |
783 |
|
and eedata.mth for MPI and mutlti-threaded testing. |
784 |
|
o pkg/flt: |
785 |
|
- make FLT EXCH working with multi-threads (and MPI + multi-threads); |
786 |
|
- use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h; |
787 |
|
- fix pickup and trajectories + profiles output with multi-threads; |
788 |
|
- add parameter to select group of fields to write along trajectory and |
789 |
|
profile (default unchanged); |
790 |
|
- only call PORT_RAND* function when flt_noise <> 0; |
791 |
|
- add multi-threaded test for verification exp. flt_example. |
792 |
|
o eesupp/src: |
793 |
|
- fix S/R ALL_PROC_DIE for MPI+multi-threads. |
794 |
|
- USE_OMP_THREADING: check that number of threads (from eedata) matches |
795 |
|
actual number (from env.var. setting). |
796 |
|
o pkg/ebm: |
797 |
|
- fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file. |
798 |
|
- add multi-threaded test for verification exp. global_ocean_ebm |
799 |
|
|
800 |
|
checkpoint63b (2011/08/29) |
801 |
|
o pkg/ebm: |
802 |
|
- fix sign of runoff; |
803 |
|
- update directly forcing fields (Qnet,EmPmR) to use standard |
804 |
|
external_forcing_surf.F (remove ebm_forcing_surf.F); |
805 |
|
- avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F); |
806 |
|
- set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm) |
807 |
|
and apply relaxation towards corresponding SST field (2-D map or ZonAver). |
808 |
|
- update global_ocean_ebm parameters file data and update output (fwd+ad). |
809 |
|
o verification/matrix_example: |
810 |
|
- split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for |
811 |
|
MPI and mutlti-threaded testing. |
812 |
|
o pkg/matrix: |
813 |
|
- change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ; |
814 |
|
- fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter); |
815 |
|
- fix for multi-threaded (remove DATA statement); |
816 |
|
- use standard DIFFERENT_MULTIPLE function; |
817 |
|
- add MATRIX_OPTIONS.h |
818 |
|
o verification/matrix_example: |
819 |
|
To allow to split the domain in several tiles, change the domain size |
820 |
|
from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on |
821 |
|
Western side) of land points. |
822 |
|
o (*_)write_pickup: |
823 |
|
- fix few bugs in mypackage_read/write_pickup.F |
824 |
|
- in MDS_WR_METAFILES calls, replace "myTime" by a local copy into |
825 |
|
array of length 1 (was caught by compiler syntax-check). |
826 |
|
o pkg/diagnostics (velocity potential solver): |
827 |
|
- fix initialisation of main diagonal matrix (for overlap values) |
828 |
|
o tools/build_options: |
829 |
|
- towards single optfile for MPI and non-MPI built: merge few +mpi optfile |
830 |
|
into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11) |
831 |
|
- linux_amd64_gfortran: merge +mpi_generic version into standard optfile: |
832 |
|
* move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ; |
833 |
|
* FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list; |
834 |
|
and use "-devel" testreport option for standard testing on baudelaire. |
835 |
|
o pkg/grdchk: |
836 |
|
- Assume that all gradient-check position are within the same tile |
837 |
|
corresponding to global indices (iGloTile,jGloTile) and that |
838 |
|
positions (i,j indices or nbeg) are local to this tile; |
839 |
|
- set tile local-indices and proc. number according to tile global-indices; |
840 |
|
- remove grdchkwhichproc from namelist (retired param); |
841 |
|
- send adjoint gradient to all procs so that all procs print it to STDOUT; |
842 |
|
- switch on MPI test for global_ocean.90x40x15 AD test experiment. |
843 |
|
o adding package bbl (Bottom Boundary Layer) |
844 |
|
description in MITgcm/pkg/bbl/bbl_description.tex |
845 |
|
example/test experiment in MITgcm_contrib/bbl |
846 |
|
o adjoint verifications |
847 |
|
- changed 5 experiments to multi-tiles |
848 |
|
* global_ocean.90x40x15 |
849 |
|
* obcs_ctrl |
850 |
|
* offline_exf_seaice |
851 |
|
* tutorial_dic_adjoffline |
852 |
|
* tutorial_tracer_adjsens |
853 |
|
changed reference output for those that crossed tile boundaries |
854 |
|
(changed choices of gradient check positions) |
855 |
|
- with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi) |
856 |
|
- temporary bug fix in grdchk_loc.F for obcs |
857 |
|
o genmake2 & testreport |
858 |
|
- add target "obj" (just for OBJFILES files) to Makefile; |
859 |
|
- add option to specify FEXTRAFLAGS on command line. |
860 |
|
o pkg/mypackage: |
861 |
|
- remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS |
862 |
|
|
863 |
|
checkpoint63a (2011/08/02) |
864 |
|
o pkg/diagnostics (velocity potential): |
865 |
|
- fix velocity-potential calculation when using OBCS: balance net inflow |
866 |
|
at each level (new S/R OBCS_DIAG_BALANCE). |
867 |
|
- fix some of the problems with OBCS in stream-function calculation. |
868 |
|
o pkg/exf/exf_readparms.F |
869 |
|
- make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF, |
870 |
|
EXF_NML_OBCS) more consistent, so that you need not have these lists |
871 |
|
in data.exf when they are not used. |
872 |
|
o optim/optim_readdata.F: |
873 |
|
- add some output about obcs variables that might help debugging |
874 |
|
- add a check about nvarlength |
875 |
|
o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec |
876 |
|
o pkg/diagnostics (velocity potential): |
877 |
|
- fix mask for OBCS (still problems in stream-function with OBCS); |
878 |
|
- add specific parameter (default = main code CG2D params) for solver; |
879 |
|
- in case of poor convergence, use solution corresponding to lowest residual. |
880 |
|
o pkg/seaice/seaice_growth.F: small changes that permit vectorizable |
881 |
|
adjoint code. In general statements like tmpscal=fld(i,j) are problematic |
882 |
|
and should be avoided where possible. |
883 |
|
o model/src (rStar): |
884 |
|
- include r* effect on reference-state (PhiRef) in totPhiHyd |
885 |
|
(so that it's really the potential anomaly at the cell center); |
886 |
|
affect solution only if z* with full pressure in EOS. |
887 |
|
- test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and |
888 |
|
update output (because of z* in totPhiHyd and viscA4 changes); |
889 |
|
- keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly |
890 |
|
@ constant r) until interpolation at constant r is implemented. |
891 |
|
o pkg/diagnostics |
892 |
|
- fix RCENTER diagnostics in case cell center is not at interface middle |
893 |
|
o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use |
894 |
|
this eos with eosType = 'TEOS10', in data (PARM01). This eos implies |
895 |
|
that THETA and SALT are "conservative temperature" and "absolute |
896 |
|
salinity" |
897 |
|
o pkg/ctrl |
898 |
|
- fix computation of endrec in s/r ctrl_init_rec |
899 |
|
- ctrl_pack/unpack_*: remove unused variables and some obsolete code |
900 |
|
o pkg/seaice/seaice_growth.F |
901 |
|
- fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code, |
902 |
|
remove then obsolete STORE directives |
903 |
|
- fix STORE directives for tice and tices, so that only the |
904 |
|
appropriate part of the fields are stored (and not the entire |
905 |
|
field); update global_ocean.cs32x15.seaice AD output. |
906 |
|
- cosmetic changes: adjust CPP flags and indentation for better |
907 |
|
legibilty |
908 |
|
o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by |
909 |
|
Chris Wilson) |
910 |
|
o pkg/gmredi: |
911 |
|
Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF), |
912 |
|
and test it in verification exp. "front_relax.bvp" (update output.bvp.txt) |
913 |
|
|
914 |
|
checkpoint63 (2011/07/11) |
915 |
|
o pkg/exch2: |
916 |
|
- rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h |
917 |
|
- exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the |
918 |
|
(2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y |
919 |
|
increments, calculates Cumul-Sum @ tile origin and sends results to each tile. |
920 |
|
o pkg/diagnostics: |
921 |
|
- deal with pairs of post-processed diags which are computed together; in |
922 |
|
particular, re-order list of diags within 1 file to save 2nd computation. |
923 |
|
- add S/R to compute velocity stream-function (called after velocity-potential |
924 |
|
calculation) from divergence free transport -> new diagnostics "PsiVEL". |
925 |
|
- add parameter to select grid-point location where PsiVEL == 0. |
926 |
|
o eesupp/src: |
927 |
|
new S/R to calculate cumulated sum on tiled array, corner grid-cell location |
928 |
|
(specific S/R needed with exch2 topology - for now, just print an error msg) |
929 |
|
o pkg/shelfice |
930 |
|
- Implement friction velocity-dependent transfer coefficients following |
931 |
|
Holland and Jenkins, JPO, 1999 |
932 |
|
Original code by M. Losch with small modifs. |
933 |
|
Enable with CPP option SHI_ALLOW_GAMMAFRICT |
934 |
|
and runtime flag SHELFICEuseGammaFrict |
935 |
|
o verification lab_sea & global_ocean.cs32x15: |
936 |
|
- use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local): |
937 |
|
does not miss some dependencies (but is slower) and also works with many files |
938 |
|
(default makedepend limitation for AD built). |
939 |
|
- use cyrus_makedepend in adjustment.128x64x1 (so that it still tested). |
940 |
|
o pkg/diagnostics: |
941 |
|
- add run-time parameter "useMissingValue" (def=False) to fill land-point |
942 |
|
(i.e., where mask=0) with MissingValue ; used only in MNC output file. |
943 |
|
This replaces CPP-option DIAGNOSTICS_MISSING_VALUE. |
944 |
|
- Extend the use of "missing_value" setting from data.diagnostics for the case |
945 |
|
of counter-diagnostics (where fraction-weight is zero). This applies both to |
946 |
|
MNC and MDS output files. |
947 |
|
o pkg/seaice/seaice_growth.F: |
948 |
|
- add 'a priori' cap of latent heat flux based on actual mass considerations |
949 |
|
when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the |
950 |
|
non-legacy seaice_solve4temp. |
951 |
|
- add diagnostic of the residual sublimation freshwater flux (the freshwater |
952 |
|
flux taken from the ocean if the total actual latent heat fluxes exceed |
953 |
|
the maximum) |
954 |
|
- remove the CPP switch around the *_FWbySublim unit change and move diagnostic |
955 |
|
fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F. |
956 |
|
- add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef |
957 |
|
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim). |
958 |
|
- bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET. |
959 |
|
- bug fix : missing part to Martin's r_FWbySublim pathological case fix. |
960 |
|
o verification 1D_ocean_ice_column: |
961 |
|
made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet |
962 |
|
update results |
963 |
|
o pkg/diagnostics: |
964 |
|
- Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P') |
965 |
|
which are not filled-up but computed from other diags ; In this case, the mate |
966 |
|
diag points to the primary (filled-up) diag to used for post processing. |
967 |
|
- Update Velocity-potential computation using post-processed diag framework. |
968 |
|
==> Change the ordering of fields and time-periods in MDS output file |
969 |
|
when using periodic averaging: now writes one time record with the full set |
970 |
|
of fields for this time period, then the next time reccord (it used to be |
971 |
|
one field with the full set of time records then the next field). |
972 |
|
Note: this is now similar to NetCDF (MNC) output file. <== |
973 |
|
|
974 |
|
checkpoint62z (2011/06/21) |
975 |
|
o adjoint monitor: |
976 |
|
- Add adjoint monitor output for packages exf, seaice |
977 |
|
and update relevant testreport output |
978 |
|
o pkg/seaice: |
979 |
|
- re-order diags inits so that they appear in order in available_diagnostics.log |
980 |
|
- added diags: hsnow thermo. rates of change, area preceeding ridiging process, |
981 |
|
area/heff/hsnow preceeding thermodynamic growth/melt. |
982 |
|
- modified diag: SIdA; output actual effect, as the description states. |
983 |
|
- modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. |
984 |
|
- retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. |
985 |
|
(SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; |
986 |
|
and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) |
987 |
|
- modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. |
988 |
|
- added diagnostics for seaice generic tracers (SItr*). |
989 |
|
- added SItrUnit and SItrNameLong run time param (for SItr* diags). |
990 |
|
- in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. |
991 |
|
I. Fenty: 18-Jun-2011: |
992 |
|
Minor changes to seaice package: |
993 |
|
1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and |
994 |
|
added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) |
995 |
|
- Differentiated "regularization variables" from "floor variables" |
996 |
|
* areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor |
997 |
|
* hiceMin became SEAICE_hice_reg (old hiceMin) |
998 |
|
(with _reg meaning regularization variable) |
999 |
|
- SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion |
1000 |
|
so as to ensure energy conservation when going between phases |
1001 |
|
- A22 was not used anywhere |
1002 |
|
2) Changed regularization procedure for heffActual and hsnowActual to ensure |
1003 |
|
well-boundedness and smooth adjoint in seaice_growth.F |
1004 |
|
3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells |
1005 |
|
because the old regularization always set heffActual >= 0.05 cm |
1006 |
|
4) Changed the model so that the default behavior is to put a small (10^-5) "floor" |
1007 |
|
on AREA when HEFF > 0. |
1008 |
|
- went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to |
1009 |
|
requiring that DISABLE_AREA_FLOOR *not* be defined |
1010 |
|
Affected verifications: |
1011 |
|
- 1D_ocean_ice_column (output.txt output_adm.txt) |
1012 |
|
- global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) |
1013 |
|
o pkg/diagnostics: |
1014 |
|
- move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). |
1015 |
|
- rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument |
1016 |
|
(was _RL, now integer) with option = 0 to retrieve all levels. |
1017 |
|
- add pieces of code to compute velocity potential at each level (new diagnostics |
1018 |
|
PhiVEL, works only when UVELMASS & VVELMASS are also turned on); |
1019 |
|
for now, using same params as CG2D (target-resisual, max Nb of iter ...). |
1020 |
|
- fix few issues with counter diagnostics in diagnostics_setdiag.F & |
1021 |
|
diagstats_setdiag.F (if diagnostic counter is itself a counter diag) |
1022 |
|
and in diagnostics_fract_fill.F (do not need a valid pointer for the |
1023 |
|
diagnostics counter-mate); check that definition of counter-diagnostic |
1024 |
|
includes a valid counter-mate (in diagnostics_set_levels.F). |
1025 |
|
o model/src (rStar): |
1026 |
|
- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
1027 |
|
affect solution only if z* with full pressure in EOS; |
1028 |
|
update output of test-exp global_ocean.90x40x15. |
1029 |
|
o pkg/seaice: |
1030 |
|
- introduce siEps=1e-5 parameter |
1031 |
|
- use areaMax in AREA update (part 4), consistent with ridging step (part 2.5). |
1032 |
|
- re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code. |
1033 |
|
- introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer. |
1034 |
|
For now it covers, and was tested for, ice salinity and age (attached to HEFF), |
1035 |
|
as well as ice cover age and ridging index (attached to AREA). |
1036 |
|
For now the run time parameters (in data.seaice/SEAICE_PARM03) are |
1037 |
|
SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA'). |
1038 |
|
Up to SItrMaxNum=3 tracers can be used simultaneously. |
1039 |
|
o pkg/salt_plume: |
1040 |
|
-introduce SPsalFRAC run time parameter that sets the fraction of the |
1041 |
|
salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically) |
1042 |
|
that gets vertically redistributed (fluxed down) by pkg/salt_plume. |
1043 |
|
o model debug options: |
1044 |
|
- Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored |
1045 |
|
in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h). |
1046 |
|
- Refine debug-msg printing selection (3 new levels): |
1047 |
|
debugMode : controls printing of debug messages (sequence of S/R calls). |
1048 |
|
debugLevel : controls printing of algorithm-relevant auxiliary/debug messages |
1049 |
|
debLevZero = 0 ; /* level of disabled aux. msg printing */ |
1050 |
|
debLevA = 1 ; /* level of minimum aux. msg printing */ |
1051 |
|
debLevB = 2 ; /* level of low aux. print (report read-file opening)*/ |
1052 |
|
debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */ |
1053 |
|
debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */ |
1054 |
|
debLevE = 5 ; /* level of extensive debug printing */ |
1055 |
|
New debugLevel default: with default debugMode value (=F), |
1056 |
|
= 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.; |
1057 |
|
and if debugMode=T, default debugLevel = 4 (debLevD). |
1058 |
|
Relation with previous settings: |
1059 |
|
debLevB (=2) corresponds to former debLevA (=1) |
1060 |
|
debLevD (=4) corresponds to former debLevB (=2) |
1061 |
|
Note: |
1062 |
|
a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before); |
1063 |
|
b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs); |
1064 |
|
to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5) |
1065 |
|
- Add new parameter (printResidualFreq, read from PARM02 namelist) to print |
1066 |
|
detailed CG solvers convergence; off (=0) by default, except if debugLevel=5. |
1067 |
|
o pkg/obcs: |
1068 |
|
- change OBCSfixTopo default from True to False (should not change the results); |
1069 |
|
keep OBCSfixTopo=T in verification-exp. seaice_obcs. |
1070 |
|
o pkg/thsice: |
1071 |
|
- fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in |
1072 |
|
2nd layer seaice sublimation (unlikely to happen) |
1073 |
|
- use Interior mask for OBCS in thsice_advection.F (similar to what is |
1074 |
|
done in gad_advection & seaice_advection). |
1075 |
|
o adjoint: |
1076 |
|
bug fix spotted by Gael Forget: |
1077 |
|
seaice_advection and thsice_advection still had |
1078 |
|
legacy CPP options to avoid CS corner updates for adjoint |
1079 |
|
o pkg/seaice: |
1080 |
|
=> Change some of the defaults (2011/05/29): |
1081 |
|
- change SEAICEuseFluxForm default (from False to True) |
1082 |
|
- change DIFF1 default (from 0.004 m/s to 0. m/s) |
1083 |
|
And print warnings if DIFF1 is not set in data.seaice and centered |
1084 |
|
avection scheme is used without any diffusion. |
1085 |
|
also: |
1086 |
|
- fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F; |
1087 |
|
- set SEAICEdiffKh[] default in the same way as SEAICEadvSch[] |
1088 |
|
- stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any |
1089 |
|
other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with |
1090 |
|
#undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE. |
1091 |
|
update results of test exp.: |
1092 |
|
lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20) |
1093 |
|
output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200) |
1094 |
|
output_adm.noseaicedyn (SEAICEuseFluxForm=T) |
1095 |
|
offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T) |
1096 |
|
seaice_obcs: output (SEAICEuseFluxForm=T) |
1097 |
|
and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004) |
1098 |
|
for standard fwd & AD lab_sea tests (to keep the same output). |
1099 |
|
o pkg/seaice/seaice_growth.F: |
1100 |
|
- use Ian Fenty's capping formulas for actual ice |
1101 |
|
thickness thoughout EVOLUTION branch. |
1102 |
|
- put treatment pathological case #2) in CPP brackets |
1103 |
|
(ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). |
1104 |
|
- update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. |
1105 |
|
o pkg/seaice: |
1106 |
|
- seaice_diffusion.F : remove the min(DX,DY) factor permanently; |
1107 |
|
pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter; |
1108 |
|
also pass fac as a param, which can be 1. (to update the tendency |
1109 |
|
field) or the time step (to update the field itself). |
1110 |
|
- seaice_advdiff.F: for multidim, call seaice_diffusion with |
1111 |
|
e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call |
1112 |
|
seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. |
1113 |
|
- SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : |
1114 |
|
hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
1115 |
|
o pkg/seaice: |
1116 |
|
diffusion with centered advection scheme (diffus.F & advect.F): |
1117 |
|
- simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) |
1118 |
|
to just compute the laplacian of input-field. |
1119 |
|
- unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call. |
1120 |
|
- fix flux-form version in diffus.F to conserve tracer. |
1121 |
|
update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects |
1122 |
|
machine truncation) and lab_sea.salt_plume (conservative flux-form modif) |
1123 |
|
|
1124 |
|
checkpoint62y (2011/05/26) |
1125 |
|
o pkg/seaice: |
1126 |
|
- seaice_growth.F : in EVOLUTION branch, always include |
1127 |
|
a_QSWbyATM_cover in qnet (as it should be). |
1128 |
|
- verification/global_ocean.cs32x15 : update results accordingly |
1129 |
|
(output.seaice.txt output_adm.seaice.txt). |
1130 |
|
o pkg/seaice + obcs: |
1131 |
|
- use maskInW & maskInS in multi-dim advection and biharmonic diffusion: |
1132 |
|
equivalent of assuming no tracer gradient outside the OB region. |
1133 |
|
update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion) |
1134 |
|
- remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed |
1135 |
|
after changes above); |
1136 |
|
- obcs+seaice cleaning: apply seaice-tracer OB values to tracer field |
1137 |
|
only at OB location (instead of over a band of OLx width). |
1138 |
|
o pkg/seaice: |
1139 |
|
- fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F |
1140 |
|
(dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid) |
1141 |
|
o pkg/obcs: |
1142 |
|
- split header file "OBCS.h" into 4 separated files: |
1143 |
|
OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h |
1144 |
|
Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h |
1145 |
|
(contain no conditional statement which depends on OBCS options). |
1146 |
|
- move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h) |
1147 |
|
to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h). |
1148 |
|
o ctrl, cost, grdchk & autodiff pkgs: |
1149 |
|
- make options file more standard (like other {PKG}_OPTIONS.h file but |
1150 |
|
with AD_CONFIG.h); clean-up some of the included header files. |
1151 |
|
o pkg/obcs: |
1152 |
|
- do not mask tracer when applying OB (tracer == 0 could generate problems) |
1153 |
|
- apply tracer OB values to tracer field only at OB location (instead of |
1154 |
|
over a band of OLx width) |
1155 |
|
- clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R) |
1156 |
|
- remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove |
1157 |
|
obcs_apply_tloc.F & obcs_apply_sloc.F |
1158 |
|
o obcs in model/src: |
1159 |
|
- call OBCS_APPLY_W only if NonHydrostatic. |
1160 |
|
- call OBCS_APPLY_ETA only if NonLinFreeSurf. |
1161 |
|
- reset dEtaHdt and wVel to zero outside OB interior region ; |
1162 |
|
- leave tracer unchanged outside OB interior region: This has no effect |
1163 |
|
on the solution but just to prevent unrealistic tracer value outside OB. |
1164 |
|
- zero out velocity outside OB interior region: This has no effect on |
1165 |
|
the solution but just to prevent unrealistic velocity outside OB. |
1166 |
|
o obcs and non-lin free-surf: |
1167 |
|
move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F |
1168 |
|
and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F |
1169 |
|
+ add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR: |
1170 |
|
this fixes missing EXCH + get consistent eta OB value (+ fix restart). |
1171 |
|
update results of test-exp. exp4(nlfs). |
1172 |
|
o exp4 (nlfs) test-exp: |
1173 |
|
use OBC for Eta at Western & Eastern OB (to test prescribing Eta |
1174 |
|
with NonLin-FreeSurf); update output.nlfs.txt |
1175 |
|
o obcs and 2d/3d solver norm: |
1176 |
|
use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB |
1177 |
|
and outside OB interior region (will allow to place OB further inside the |
1178 |
|
domain). Depending on the domain, can affects cg2d-Norm (previous |
1179 |
|
cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl, |
1180 |
|
and cg3d-Norm (previous Norm was computed before canceling OB terms), |
1181 |
|
e.g. in tutorial_plume_on_slope. |
1182 |
|
- update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope. |
1183 |
|
o pkg rbcs: |
1184 |
|
- split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h |
1185 |
|
- add capability to apply relaxation to horizontal velocity uVel & vVel. |
1186 |
|
o pkg/grdchk: add gradient check for control variable xx_shifwflx |
1187 |
|
o pkg/shelfice/shelfice_init_fixed.F |
1188 |
|
fix CPP-flag combinations |
1189 |
|
o pkg/seaice: Merge iceage code of Pierre Rampal |
1190 |
|
* update/change/correct ice age calculations |
1191 |
|
* add age updates for pathological cases |
1192 |
|
Probably needs more testing... |
1193 |
|
|
1194 |
|
checkpoint62x (2011/05/13) |
1195 |
|
o pkg/mom_vecinv: |
1196 |
|
high-order vorticity scheme: use interior masks (maskInW & S) |
1197 |
|
to zero-out (outside OB) gradient of vorticity. |
1198 |
|
o verification exp.: |
1199 |
|
turn on "useEnergyConservingCoriolis" (better discretisation) in exp. |
1200 |
|
hs94.128x64x5 and seaice_obcs ; update results. |
1201 |
|
o pkg/obcs: |
1202 |
|
fix bug in OBeta for YZ sections in obcs_exf_load.F |
1203 |
|
o pkg/ctrl, pkg/shelfice, and optim: |
1204 |
|
- add new control variable xx_shifwflx (fresh water flux underneath ice |
1205 |
|
shelves). This is almost as tedious as obcs-ctrl, because the |
1206 |
|
variables needs its own mask. |
1207 |
|
- add a cost function term that penalizes the deviation of xx_shifwflx |
1208 |
|
from the first guess (zero) in analogy to other control variables |
1209 |
|
o pkg/shelfice: |
1210 |
|
- start basic adjoint |
1211 |
|
o pkg/ctrl: |
1212 |
|
- remove extra 2D field "for good measure" when initializing in |
1213 |
|
ctrl_set_globfld_[xy/xz/yz].F |
1214 |
|
- replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec |
1215 |
|
- improve error messages in ctrl_set_unpack_* |
1216 |
|
o OBC implementation in momentum: |
1217 |
|
use interior masks (maskInC,W & S) in momentum S/R: |
1218 |
|
- multiply divergence, tension and some del^i.u or del^j.v by maskInC |
1219 |
|
- multiply del2u,del2v by maskInW/S (biharmonic viscosity) |
1220 |
|
- multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) |
1221 |
|
- multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) |
1222 |
|
Motivation: fix/clean implementation of OBC with biharmonic-viscosity |
1223 |
|
(and also with Leith/Smagorinsky harmonic-viscosity). |
1224 |
|
Update output of experiment dome and exp4 (+nlfs). |
1225 |
|
o exp4 test-exp: |
1226 |
|
- turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) |
1227 |
|
and prescribe time-varying OB (without pkg/exf) for zonal-velocity |
1228 |
|
at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
1229 |
|
time-varying OB at Western-side for wVel (NonHyd); update output. |
1230 |
|
- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
1231 |
|
and biharmonic-viscosity ; also use prescribed time varying OB. |
1232 |
|
o pkg/obcs: |
1233 |
|
fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
1234 |
|
o model/src: |
1235 |
|
- fix startTime setting when baseTime<>0 & nIter0=0 are specified ; |
1236 |
|
- initialise startTime & nIter0 with unlikely values: allows to set one |
1237 |
|
from the other without ambiguity. |
1238 |
|
o seaice_obcs test-exp.: |
1239 |
|
add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output. |
1240 |
|
o pkg/obcs: |
1241 |
|
- remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: |
1242 |
|
no longer needed with maskInC,W,S in pkg/generic_advdiff. |
1243 |
|
o pkg/seaice: |
1244 |
|
- retired SEAICE_SALINITY and SEAICE_salinity in favor of |
1245 |
|
SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively. |
1246 |
|
- fixed bug in the initialization of sea ice salinity variable HSALT |
1247 |
|
in seaice_init_varia.F (removed dependence on ICE2WATR) |
1248 |
|
o fizhi-cs test exp.: |
1249 |
|
switch reference output convention for these 2 non-standard test-exp, |
1250 |
|
from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5) |
1251 |
|
to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11) |
1252 |
|
reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran |
1253 |
|
o model/inc: |
1254 |
|
- change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4") |
1255 |
|
of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS) |
1256 |
|
o pkg/seaice: |
1257 |
|
- fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY |
1258 |
|
o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15 |
1259 |
|
- updated output*.txt files due to bug fixes in salt, saltPlumeFlux, |
1260 |
|
and initial HSALT |
1261 |
|
|
1262 |
|
checkpoint62w (2011/04/26) |
1263 |
|
o pkg/mom_fluxform: |
1264 |
|
- fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf. |
1265 |
|
- use parameter "sideDragFactor" in no-slip BC side-drag part. |
1266 |
|
- update output of exp. global_ocean.90x40x15 |
1267 |
|
o pkg/mom_vecinv: |
1268 |
|
mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform) |
1269 |
|
o update seaice exp.: |
1270 |
|
use more consistent parameter values (remove "backward compatability only": |
1271 |
|
ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh) |
1272 |
|
related to thermodynamics seaice. Update output (fwd+AD) of exp.: |
1273 |
|
1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs |
1274 |
|
o update test-exp global_ocean.90x40x15: |
1275 |
|
o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis). |
1276 |
|
o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.) |
1277 |
|
o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params) |
1278 |
|
o turn on zStar & viscA4 in standard set-up (dir input/) |
1279 |
|
and update output files: output.txt & output.dwnslp.txt |
1280 |
|
o new AD-test experiment: obcs_ctrl |
1281 |
|
(From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector. |
1282 |
|
o pkg/dic: |
1283 |
|
fix two bugs in handling water vapour pressure in carbonate chemistry |
1284 |
|
and air-sea fluxes. Found by Val Bennington and Galen McKinley |
1285 |
|
(add DIC Option = WATERVAP_BUG to recover old results) |
1286 |
|
update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline |
1287 |
|
o adding allowInteriorFreezing option to check for water below freezing point |
1288 |
|
at depth and bring the negative heat anomaly to the surface level |
1289 |
|
o pkgs _fields_load: |
1290 |
|
- extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs) |
1291 |
|
- use new S/R GET_PERIODIC_INTERVAL in pkgs: |
1292 |
|
bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and |
1293 |
|
rbcs to get interpolation weights and time reccord number. |
1294 |
|
- fix multi-threading in aim_fields_load.F |
1295 |
|
- apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F |
1296 |
|
o external_fields_load: |
1297 |
|
new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear |
1298 |
|
interpolation weights) to use in a periodic time-series ; do not divide by |
1299 |
|
time-step to convert to integer: |
1300 |
|
- this fixes case where externForcingPeriod is not multiple of time-step |
1301 |
|
(Thanks to Christopher L. Wolfe) |
1302 |
|
- this fixes case where externForcingPeriod is an odd multiple of time-step |
1303 |
|
(was wrong by half of time-step); update results of tutorial_global_oce_in_p. |
1304 |
|
store index of time-record which is currently loaded: |
1305 |
|
- works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ; |
1306 |
|
- needed for the adjoint but not yet used because of extensive recomputations; |
1307 |
|
(to be fixed soon) |
1308 |
|
|
1309 |
|
checkpoint62v (2011/04/02) |
1310 |
|
o verification/1D_ocean_ice_column added to test Ian Fenty's |
1311 |
|
pkg/seaice_growth.F modifications for improving sea ice code differentiability |
1312 |
|
o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope |
1313 |
|
(new velocity statistics after changing maskInW & maskInS definition) |
1314 |
o pkg/generic_advdiff with OBCS: |
o pkg/generic_advdiff with OBCS: |
1315 |
use maksInW & maskInS in advective flux and in biharmonic diffusion calculation: |
use maksInW & maskInS in advective flux and in biharmonic diffusion calculation: |
1316 |
equivalent to assumption of no tracer gradient outside the OB region. |
equivalent to assumption of no tracer gradient outside the OB region. |