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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o model/src: solve_*diagonal.F |
8 |
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- replace division with multiplication by inverse (similar to original version) |
9 |
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- fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F |
10 |
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to enable the use of the vectorized & differentiable solve_tridiagonal.F |
11 |
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o pkg/seaice: ECCO-CLIVAR merge: |
12 |
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1. seaice AREA relaxation |
13 |
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* CPP option: SEAICE_ALLOW_AREA_RELAXATION |
14 |
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* runtime flag: SEAICE_tauAreaObsRelax |
15 |
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2. modified global mean cost imbalance code: CPP option |
16 |
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ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION |
17 |
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o another iteration on solve_*diagonal.F |
18 |
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Make choices independent of AUTODIFF |
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Default will be the adjoinable vectorized version. |
20 |
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Alternative choices are: |
21 |
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* non-adjoinable original version with low memory footprint: |
22 |
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#define SOLVE_DIAGONAL_LOWMEMORY |
23 |
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* still adjoinable but does not vectorize (k as inner-most loop): |
24 |
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#define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef) |
25 |
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o testreport |
26 |
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- add option to use a home made wrapper around "make" |
27 |
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- remove MITGCM_IEEE env. variable (no longer active) |
28 |
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o pkg/shelfice |
29 |
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- improve computation of friction velocity for velocity dependent |
30 |
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exchange coefficients: include velocities into SHELFICEBoundaryLayer |
31 |
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block to average velocities vertically |
32 |
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- add TAF store directives for SHI_ALLOW_GAMMAFRICT |
33 |
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o Modify diagonal solvers, now three versions (upon request): |
34 |
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#ifndef SOLVE_DIAGONAL_AUTODIFF |
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1. default version (dating back a while ago) |
36 |
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#else /* def SOLVE_DIAGONAL_AUTODIFF */ |
37 |
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# ifdef SOLVE_DIAGONAL_KINNER |
38 |
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2. adjoinable version with k-innermost loop (G. Forget) |
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# else |
40 |
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3. adjoinable vectorized version of 2. |
41 |
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# endif |
42 |
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#endif /* SOLVE_DIAGONAL_AUTODIFF */ |
43 |
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All flags are currently set within routines, but could/should be moved to CPP-options. |
44 |
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Array bounds for 1. are as before, for 2.,3. cover the entire domain |
45 |
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(could be changed for 1. too). |
46 |
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o verification/lab_sea (fwd): |
47 |
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- update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY, |
48 |
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use 7 categories (except hb87), new solve4temp params (except salt_plume), |
49 |
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constant salinity (=4) or variable salinity (salt_plume) done through |
50 |
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SItracer. |
51 |
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o pkg/seaice: |
52 |
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- rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0; |
53 |
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- remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t, |
54 |
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SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz) |
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from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when |
56 |
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SEAICE_freeze got retired) but already better than previously with |
57 |
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SEAICE_freeze=123456.7 deg.C; |
58 |
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- move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS |
59 |
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(safer multi-threaded setting); always set SEAICEuseEVP; |
60 |
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- setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to |
61 |
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SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report); |
62 |
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stop if multiple specifications for the same coeff; make sure default |
63 |
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SEAICE_mcPheePiston is compatible with drF(1) & deltaT. |
64 |
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o pkg/obcs: |
65 |
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- allow to switch to upwind 1rst order advection scheme for the advective |
66 |
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flux computation at the open-boundary; disabled for adjoint built. |
67 |
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o pkg/ptracers: |
68 |
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- rename PTRACERS_RESTART.h -> PTRACERS_START.h |
69 |
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- rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F |
70 |
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- add parameter to decide when to start a tracer; use internal flag to |
71 |
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know which tracer to step-forward; switch this internal flag at the top |
72 |
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of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled |
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for adjoint built. |
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o pkg/seaice: |
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- add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ; |
76 |
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- move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ; |
77 |
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- keep experiment offline_exf_seaice truly single category (set MULTDIM=1). |
78 |
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o pkg/ecco: |
79 |
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- fix writing of output file DiagnosCost_ClimSalt/Theta |
80 |
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and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc). |
81 |
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o pkg/seaice: |
82 |
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- add missing initialisation of COR_ICE array in dynsolver.F |
83 |
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- merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is |
84 |
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compiled either way, and is tested in all exps (multidim was only tested |
85 |
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in lab_sea ad before). |
86 |
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- cosmetic change to prepare for future addition of ITD. no change to results. |
87 |
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no defaults change. |
88 |
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- added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise). |
89 |
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- by lack of adequate verification experiments, I further used custom versions |
90 |
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of global_ocean.cs32x15 to test multicat or not, with pickup or not. All |
91 |
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should be correct. |
92 |
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- avoid recomputations in ad. |
93 |
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o array initialisation in adjoint mode: |
94 |
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1) pkg/mom_common/mom_calc_ke.F: |
95 |
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add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC): |
96 |
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The S/R which calls MOM_CALC_KE initialises KE but in some recomputation |
97 |
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part this initialisation is gone, resulting in Floating Point Exception |
98 |
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(caught by open64 compiler with debug option). |
99 |
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2) model/src/convective_weights.F |
100 |
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set output convectCount over the full array range (instead of doing |
101 |
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an update): this fix a similar issue when called within recomputation (adjoint) |
102 |
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which could by-pass the initialisation (normally done in the caller S/R). |
103 |
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o pkg/seaice: |
104 |
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- final version of turbulent flux params, as agreed at MIT ice meet: |
105 |
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SEAICE_mcPheePiston (default is ~ 0.000875) |
106 |
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SEAICE_mcPheeTaper (default is 0.) |
107 |
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SEAICE_frazilFrac (defualt is 1.) |
108 |
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SEAICE_mcPheeStepFunc (default is false) |
109 |
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- changes results at trunction error level |
110 |
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- ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo |
111 |
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o added pkg/frazil: |
112 |
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- see frazil_description.tex for details |
113 |
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- verification experiment is global_with_exf/input.yearly; changes output.yearly.txt |
114 |
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o pkg/shelfice/shelfice_thermodynamics.F |
115 |
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- fix exponents for velocity dependent exchange coefficients: change |
116 |
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from 2/3(=0) to 0.66666666666666667 |
117 |
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- move computation of velocity dependent exchange coefficients into |
118 |
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separate loop, so that it applies to both thermodynamics |
119 |
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- move some divisions by constants out of loops |
120 |
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|
121 |
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checkpoint63j (2012/02/16) |
122 |
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o pkg/seaice: |
123 |
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- overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc. |
124 |
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- SItracer: added run time params, and allow coupling to ocn salinity. |
125 |
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o pkg/seaice: remove (almost) all divisions by constants within loops |
126 |
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in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d |
127 |
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results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only |
128 |
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those, caused by 1/QI -> recip_QI) -> update output.seaice.txt, |
129 |
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output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt |
130 |
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o pkg/seaice : |
131 |
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- simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula |
132 |
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= 1 or 2, using newly added run time parameter SEAICE_availHeatTaper. |
133 |
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- fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148. |
134 |
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- add permanent SItflux diag that corresponds to TFLUX but includes |
135 |
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ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget. |
136 |
|
- allow activation/testing of a fix for suspected missing term in |
137 |
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ocn-ice heat budget (to be confirmed). To test this, you want to |
138 |
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undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param |
139 |
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SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic. |
140 |
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- no change in results, fwd or ad. |
141 |
|
o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below: |
142 |
|
- switch to variable freezing point. |
143 |
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Results change : cg2d -> 1 digits; ad -> 3-6-6 digits. |
144 |
|
- bug fix : the sublimation term that was missing is now activated. |
145 |
|
Results change : cg2d -> 2 digits; ad -> 8-6-6 digits. |
146 |
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- bug fix : flooding sign term for SIsal0.NE.0. |
147 |
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Result change : cg2d -> 8 digits; ad -> 11-12-9 digits. |
148 |
|
o pkg/seaice: |
149 |
|
- unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT |
150 |
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is now the default, and the old default constant freezing point is recovered |
151 |
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with SEAICE_tempFrz0 = -1.96, |
152 |
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SEAICE_dTempFrz_dS = 0., |
153 |
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- retire SEAICE_freeze (= the old way of specifycing the constant freezing point) |
154 |
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- remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there. |
155 |
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- bug fix (thanks to M. Losch) : the sublimation term that was missing is now |
156 |
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activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM. |
157 |
|
- bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211) |
158 |
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was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail). |
159 |
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- bug fix (thanks to O. Jahn) : area loss for melting got messed up in |
160 |
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seaice_growth r149 for legacy branch (no results change). |
161 |
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- introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code |
162 |
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from I. Fenty). |
163 |
|
- results did not change except for global_ocean.cs32x15, mostly due to the |
164 |
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switch to variable freezing point (see above item for detail). |
165 |
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o pkg/thsice: |
166 |
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- fix and simplify interface to salt_plume pkg ; diagnose directly amount of |
167 |
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seawater freezing in thsice_calc_thickn (not used). |
168 |
|
o pkg/seaice: turbulent flux term specification via run time params. |
169 |
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- replace CPP switches with run time switches to facilitate testing |
170 |
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- retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, |
171 |
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GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR |
172 |
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- added runtime parameter : SEAICEturbFluxFormula |
173 |
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- move Mcphee constants to SEAICE_PARAMS.h |
174 |
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- seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula; |
175 |
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SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); |
176 |
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remove seaice_summary call (moved to seaice_init_fixed) |
177 |
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- seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on |
178 |
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SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms) |
179 |
|
- seaice_summary.F : add missing report of read turbulent flux term set up |
180 |
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and SITRACER. |
181 |
|
- seaice_check.F : check range; inform and stop if retired CPPs are used |
182 |
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(incl. SEAICE_AGE). |
183 |
|
- seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without |
184 |
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CPP switch, same computation as before for the different options. |
185 |
|
- change results at the truncation level. |
186 |
|
o pkg/seaice: |
187 |
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- remove un-used parameters LAD & MAX_TICE ; add new run-time parameters: |
188 |
|
useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and |
189 |
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SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY. |
190 |
|
- update verification/*/input*/data.seaice: |
191 |
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to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY |
192 |
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code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ; |
193 |
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and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code, |
194 |
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set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0. |
195 |
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o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY): |
196 |
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- remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same |
197 |
|
algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0); |
198 |
|
difference in results only due to machine truncation. |
199 |
|
- remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using |
200 |
|
MaykutPolySatVap; keep MIN_LWDOWN. |
201 |
|
- adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation. |
202 |
|
- update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87, |
203 |
|
+ 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits). |
204 |
|
o pkg/salt_plume: |
205 |
|
- isolate saltPlumeFlux array exch into a specific S/R called from |
206 |
|
do_oceanic_phys.F |
207 |
|
- add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice. |
208 |
|
o verification: |
209 |
|
- move untested set-up to MITgcm_contrib/verification_other. |
210 |
|
o pkg/seaice: |
211 |
|
- retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER. |
212 |
|
o pkg/seaice: |
213 |
|
- seaice_solve4temp.F (keeping results unchanged): |
214 |
|
* add 2 future run-time params to select which saturation vapor pressure |
215 |
|
formula is used and how post-iteration fluxes are set. |
216 |
|
Temporary set these 2 params according to option SOLVE4TEMP_LEGACY; |
217 |
|
* New piece of code (not used) to update surf. atmos. heat flux F_ia using |
218 |
|
the linearized expression to stay consistent with tsurf finding. |
219 |
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- seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x |
220 |
|
can be < 0. |
221 |
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o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef): |
222 |
|
- remove from F_ia (and from it's derivative dFiDTs1) the contribution of |
223 |
|
conductive heat flux F_c , and add it explicitly when updating tsurf as |
224 |
|
solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf |
225 |
|
so that now F_ia has a consistent meaning through the entire routine. |
226 |
|
This causes differences at truncation level: update output of fwd exp. |
227 |
|
global_ocean.cs32x15.seaice. |
228 |
|
o pkg/seaice: |
229 |
|
- lots of editing/cleaning in seaice_solve4temp.F + better documentation |
230 |
|
of arrays, sign/direction of fluxes; no effect on results. |
231 |
|
- replace hard coded 273.16 (=previous value of celsius2K) by celsius2K |
232 |
|
in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part); |
233 |
|
note: this should have been done before changing celsius2K default. |
234 |
|
- to keep results unchanged, add back old value of celsius2K in verification |
235 |
|
exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs |
236 |
|
- replace hard coded seawater freezing temp in seaice_solve4temp.F (part |
237 |
|
SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default |
238 |
|
value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater |
239 |
|
freezing temp is consistent with value in seaice_growth.F ; this causes |
240 |
|
differences at machine truncation level: update lab_sea AD output (3/4). |
241 |
|
o pkg/seaice: |
242 |
|
- mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask |
243 |
|
and climsst/sss even when using seaice (to prevent calculation that might |
244 |
|
use SST on land); does not affect any verification exp. |
245 |
|
- apply mask to taux,tauy (in seaice_get_dynforcing.F); update output |
246 |
|
of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix. |
247 |
|
o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness |
248 |
|
over land (non-legacy code) |
249 |
|
o vectorize salt_plume package: |
250 |
|
- add extra code to salt_plume_frac and salt_plume_tendency_apply_s |
251 |
|
- this code computes plumebk everywhere (also over land), thus requires |
252 |
|
code to avoid divisions by zero and catch the case of kLev=Nr. |
253 |
|
- efficiency of salt_plume_frac is still sub-optimal |
254 |
|
o tools (genmake2): |
255 |
|
- fix makefile NAME specification (option: -makefile NAME) by adding |
256 |
|
"-f $MAKEFILE" in few places where it was missing including makedepend |
257 |
|
command (contribution from Paul). |
258 |
|
|
259 |
|
checkpoint63i (2012/01/24) |
260 |
|
o model/src: |
261 |
|
- add factorized versions of some EOS code to find_rho.F, |
262 |
|
define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX) |
263 |
|
o model/src: |
264 |
|
- add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h; |
265 |
|
- change default celsius2K from 273.16 to 273.15 |
266 |
|
- to keep results unchanged, add back old value of celsius2K in verification |
267 |
|
exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd), |
268 |
|
global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm). |
269 |
|
o model/src: add a little initialisation trick to find_rho.F and find_alpha.F |
270 |
|
to make TAF generate vectorizable code |
271 |
|
o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows. |
272 |
|
Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers |
273 |
|
have flags that do this more efficiently. |
274 |
|
o pkg/diagnostics/diagstats_calc.F |
275 |
|
- for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact |
276 |
|
o pkg/obcs (with exch2): |
277 |
|
- derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F) |
278 |
|
and remove code (in obcs_readparms.F) which was based on EXCH of indices |
279 |
|
(through buffer) and did not account for exch2 (e.g., CS-grid) topology. |
280 |
|
o pkg/exf and seaice exp: |
281 |
|
- change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0) |
282 |
|
so that switching off area & heff advection flags does not affect results. |
283 |
|
- change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h |
284 |
|
- keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef |
285 |
|
EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update |
286 |
|
results of verification experiments: 1D_ocean_ice_column(fwd), |
287 |
|
global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8) |
288 |
|
and offline_exf_seaice (all 4). |
289 |
|
o pkg/seaice: |
290 |
|
- remove array YNEG, RIVER, TMIX (replaced by local var) from common block; |
291 |
|
remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef. |
292 |
|
- fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY) |
293 |
|
but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and |
294 |
|
not multi-dim advection; |
295 |
|
- fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and |
296 |
|
SHORTWAVE_HEATING #undef. |
297 |
|
o optim: make Makefile more robust (?) |
298 |
|
o pkg/obcs: |
299 |
|
* fix treatment of obcs_read_pickup for TAF |
300 |
|
o pkg/shelfice: |
301 |
|
* add missing initialisation of num_shifwflx |
302 |
|
* new adjoint verification exp. for isomip |
303 |
|
* change Prandtl and Schmidt numbers from generic formulations |
304 |
|
(in terms of model diffus. and visc.) to separate runtime |
305 |
|
parameters, with Holland and Jenkins (1999) default values. |
306 |
|
o pkg/exf (interpolation): |
307 |
|
- extended input field (2 rows) near the N & S poles: |
308 |
|
* fill in with the symetric value (when even Nb of data in longitude) |
309 |
|
* add average value at the poles only for scalar quantities ; for vector |
310 |
|
component interpolation, skip the averaging and keep duplicated values, |
311 |
|
unless the 2 components have same location (uvInterp=T) in which case |
312 |
|
interpolate the 2 components together using S/R EXF_INTERP_UV. |
313 |
|
- new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field |
314 |
|
together: this allows to account properly for local orientation when |
315 |
|
averaging at N & S pole. |
316 |
|
- add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding |
317 |
|
exf-interpolation near N & S poles. Undef by default. |
318 |
|
- add debug check/print on 1rst iter if debugLevel >=2. |
319 |
|
o pkg/exf: |
320 |
|
- change masking flags definition (no longer "parameter"), put them in |
321 |
|
common block and set them in S/R EXF_INIT_FIXED. |
322 |
|
- change recognized masking flag from s,u,v to c,w,s since the mask |
323 |
|
to use (maskC,W,S) depends on position on model grid and has little to |
324 |
|
do with scalar/vector difference; fix masking if using P-coordinates. |
325 |
|
- fix masking of wind-stress (was wrong if interpolated or read on A-grid) |
326 |
|
and update results of exp. global_with_exf (x2). |
327 |
|
- fix setting of zenith-angle table when SHORTWAVE_HEATING is undef. |
328 |
|
o pkg/obcs |
329 |
|
- S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate) |
330 |
|
o pkg/exf (interpolation): |
331 |
|
- assume periodicity in X only if input field cover full longitude range. |
332 |
|
- improve search for lat. index (supposed to be faster, in ~log2(ny) steps, |
333 |
|
and should vectorise). |
334 |
|
- fix input lat of the 2 added row (in case we provide N.pole data). |
335 |
|
|
336 |
|
checkpoint63h (2011/12/30) |
337 |
|
o pkg/seaice: |
338 |
|
- change declaration of UVM from _RL to _RS in order to get B-grid |
339 |
|
uIce,vIce monitor when _RS = real*4 |
340 |
|
o pkg/offline: |
341 |
|
- new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags); |
342 |
|
- compute vertical velocity if not read from file (switch on exactConserv |
343 |
|
& staggerTimeStep); |
344 |
|
- fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq. |
345 |
|
o verification: |
346 |
|
- update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input) |
347 |
|
with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m": |
348 |
|
fix Pb in yG definition @ 2 missing corners (previously yG was averaged); |
349 |
|
- update output of exp. global_ocean.cs32x15.viscA4 after changing |
350 |
|
grid-file angles (used here for coriolis-3d); |
351 |
|
- remove (or gzip) few files not needed to run fizhi-cs experiments. |
352 |
|
o pkg/exf (vector interpolation): |
353 |
|
- rotate vector component toward local grid-axis orientation using grid-angles |
354 |
|
(stored in GRID.h) instead of locally computed rotation angle; keep old code |
355 |
|
available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default). |
356 |
|
o pkg/seaice: |
357 |
|
- allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION |
358 |
|
undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined. |
359 |
|
o pkg/PKG_OPTIONS.h files: |
360 |
|
- move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h", |
361 |
|
outside of the #ifdef ALLOW_THISPKG / #endif block. |
362 |
|
- update verification/*/code/PKG_OPTIONS.h files. |
363 |
|
o add a verification experiment (offline_exf_seaice/input.seaice) that test |
364 |
|
the B-grid LSOR solver |
365 |
|
o pkg/seaice: sort out emissivity and long wave radiation step 2: |
366 |
|
- add emissivity for snow and ice as new run-time parameters |
367 |
|
(unfortunately) that default to the corresponding exf values; this |
368 |
|
changes results in most verification experiments so that for backward |
369 |
|
compatibility these parameter have to be set explicitly to inconsistent |
370 |
|
values (ugly); |
371 |
|
- the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired |
372 |
|
emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp |
373 |
|
until we agree how to handle this bug properly |
374 |
|
o pkg/exf (interpolation): |
375 |
|
- add a set of run-time param ({inputfield}_interpMethod), one for |
376 |
|
each interpolated input field, to select the interpolation method |
377 |
|
with a value of zero switching off the interpolation; |
378 |
|
- print interpolation parameters to standard output; |
379 |
|
- refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined |
380 |
|
(to use instead runoff_interpMethod=0 in data.exf). |
381 |
|
- simplify default setting of interpolation parameters (for all fields, |
382 |
|
set position to match model grid cell-center position, leading to trivial |
383 |
|
interpolation in case of regular Lat-Lon grid) and fix for the case of |
384 |
|
non-uniform delY. |
385 |
|
o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for |
386 |
|
within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1. |
387 |
|
this factor is absolutely required, because the lw exitance (= out-going |
388 |
|
long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown, |
389 |
|
where the reflectivity rho = 1-emissivity for conservation reasons. Once |
390 |
|
this is established, we can remove the CPP-Flag (if we want to). |
391 |
|
o pkg/seaice: |
392 |
|
- qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and |
393 |
|
ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined |
394 |
|
- sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity |
395 |
|
what the name implies (and not emissivity*BoltzmannConstant), this means |
396 |
|
the old default value of 5.5e-8 now means |
397 |
|
5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in |
398 |
|
S/R exf_readparms |
399 |
|
- FV-discretization of the B-grid LSOR solver, turn on with |
400 |
|
SEAICE_LSRBNEW. This new solver also involves a slight re-organization |
401 |
|
of the calling routine dynsolver, so that B and C-grid code look a |
402 |
|
little more alike. |
403 |
|
- fix index bugs in ostres.F (B-grid code) |
404 |
|
o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better |
405 |
|
o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the |
406 |
|
default for SEAICE_emissivity, if useEXF; requires setting a wrong |
407 |
|
parameter value in global_ocean.cs32x15/input.seaice/data.seaice for |
408 |
|
backward compatiblity |
409 |
|
o model/src: use sigmaR in calc_ivdc |
410 |
|
|
411 |
|
checkpoint63g (2011/12/16) |
412 |
|
o pkg/seaice/seaice_growth.F: |
413 |
|
fix heat conservation of the coupled ocean-seaice system. |
414 |
|
when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of |
415 |
|
solid vs liquid water treatment is resolved via QNET. |
416 |
|
o pkg/seaice/seaice_growth.F: |
417 |
|
add missing term for sublimation in saltFlux, which was breaking conservation. |
418 |
|
o pkg/seaice/seaice_model.F: |
419 |
|
Remove this patholigical case treatment in evolution branch, |
420 |
|
where it is un-necessary and breaks conservation. |
421 |
|
Update global_ocean.cs32x15/results accordingly for |
422 |
|
output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt |
423 |
|
o model/src: |
424 |
|
useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in |
425 |
|
external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE. |
426 |
|
o pkg/obcs: |
427 |
|
modify Stevens boundary conditions so that S/R obcs_calc_stevens computes |
428 |
|
tendency for temperature and salinity that is then applied to update |
429 |
|
theta and salt in S/R obcs_apply_ts; this requires proper masking of all |
430 |
|
horizontal advection and diffusion contributions on the boundary (in |
431 |
|
S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and |
432 |
|
removing the mask in S/R timestep_tracer. The advantage of this approach is |
433 |
|
that the updated tracer values include contributions from the surface |
434 |
|
forcing and vertical diffusion. |
435 |
|
This modification changes exp4.stevens because of vertical diffusion. |
436 |
|
o model/src: |
437 |
|
change non-curvilinear grid setting to also work with exch2 + blank tiles: |
438 |
|
- move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst |
439 |
|
face dimensions. |
440 |
|
- new S/R INI_LOCAL_GRID to define model tile-local grid (using same units |
441 |
|
as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID |
442 |
|
and INI_SPHERICAL_POLAR_GRID. |
443 |
|
change test-experiment global_ocean.90x40x15: |
444 |
|
- split the domain in many more tiles (9x4 tiles of 10x10 each); |
445 |
|
- switch to exch2 and remove 1 blank-tile (but only for MPI test). |
446 |
|
- update results of both test (std & dwnslp). |
447 |
|
o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in |
448 |
|
tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation |
449 |
|
o model/src: |
450 |
|
- take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS |
451 |
|
and fix initialisation when using sigma-coords. |
452 |
|
o model/src: |
453 |
|
- improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc. |
454 |
|
to their current value at the beginning of forward_step.F": add a new run-time |
455 |
|
switch "doResetHFactors" (default=false) and use it to do (or not) the resetting. |
456 |
|
- set doResetHFactors=T in the following test exp: |
457 |
|
global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS), |
458 |
|
global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS) |
459 |
|
and tutorial_global_oce_in_p (nonLinFS in p) |
460 |
|
o pkg/ecco |
461 |
|
- added IES cost term |
462 |
|
o verification/advect_xz |
463 |
|
- scale down the depth by 1/100 (from 200 km to just 2.km) |
464 |
|
- add secondary test using divergent flow, r-star and implicit vertical advection. |
465 |
|
- add note (check_conserve_TS.txt) and matlab script to check global |
466 |
|
conservation of T & S with NonLin-FreeSurf and Adams-Bashforth. |
467 |
|
o pkg/rbcs: |
468 |
|
- add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F). |
469 |
|
o pkg/obcs (Stevens BCs): |
470 |
|
- fix various problems in the phase speed computations of the Stevens |
471 |
|
boundary conditions: |
472 |
|
- sign error for western and southern boundaries, |
473 |
|
- time tendencies were underestimated by factor of dTracerLev and some just |
474 |
|
zero (for multidim advection schemes) -> now estimate time tendencies |
475 |
|
from difference between previous (n) time level and the one before (n-1); |
476 |
|
this requires storing a field per tracer per boundary, also in the pickup |
477 |
|
files. |
478 |
|
- replace deltaTmom in cflMer/Zon computation with dTracerLev |
479 |
|
- set default phase velocity to cflMer/Zon |
480 |
|
- update verification experiment exp4.stevens |
481 |
|
o pkg/generic_advdiff (implicit_r): |
482 |
|
- fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf |
483 |
|
(remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F); |
484 |
|
- fix implicit vertical diffusion or advection with NonLin FreeSurf |
485 |
|
(was using current recip_hFacC instead of future recip_hFacC): set future |
486 |
|
recip_hFac in thermodynamics.F and pass & use it in all vertical implicit |
487 |
|
solver S/R ; |
488 |
|
- fill diagnostics of vertical advective fluxes (computed from tendency) |
489 |
|
when using implicit vert. advection; |
490 |
|
- update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion: |
491 |
|
global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD), |
492 |
|
tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD) |
493 |
|
and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5. |
494 |
|
o pkg/diagnostics: |
495 |
|
- add diags for T & S tendency which goes through Adams-Bashforth. |
496 |
|
|
497 |
|
checkpoint63f (2011/11/30) |
498 |
|
o pkg/obcs/obcs_calc_stevens.F: |
499 |
|
- join some loops to reduce number of if-statements |
500 |
|
- fix a bug in code for northern and southern boundaries. |
501 |
|
o pkg/seaice/seaice_init_varia.F |
502 |
|
- undo resetting UVM=0 that has slipped in unnoticed in r1.49 and |
503 |
|
caused zero ice-velocities for the B-grid code |
504 |
|
o pkg/seaice/seaice_init_fixed.F |
505 |
|
- fix a bug in the initialisation of the second metric terms |
506 |
|
k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0. |
507 |
|
- this affects all seaice configurations with useCurviLinearGrid = .true. |
508 |
|
and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms |
509 |
|
= .true. (default) |
510 |
|
- the only verification experiment affected is global_ocean.cs32x15: |
511 |
|
icedyn, seaice, and seaice_dynmix (AD) |
512 |
|
o pkg/thsice/thsice_diagnostics_state.F |
513 |
|
- only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does |
514 |
|
not contain garbage that can lead to surprises in diagstats_calc.F |
515 |
|
o model/src: |
516 |
|
- move bi,bj loops inside INTEGR_CONTINUITY ; |
517 |
|
- call INTEGR_CONTINUITY directly from forward_step.F |
518 |
|
(previously called from momentum_correction_step.F) |
519 |
|
- call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F, |
520 |
|
forward_step.F and pkg/ecco/the_main_loop.F |
521 |
|
o model/src/do_oceanic_phys.F: |
522 |
|
- reset addMass to zero only if useICEFRONT ; |
523 |
|
- separated k-loop for rhoInSitu calculation ; |
524 |
|
- add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P) |
525 |
|
and at constant T,S (= WdRHOdP); |
526 |
|
NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport |
527 |
|
of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical |
528 |
|
transport of locally-referenced potential density); |
529 |
|
to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP) |
530 |
|
o gluemnc: |
531 |
|
- replace ncrcat with ncks when adding variables to *.glob.nc |
532 |
|
- change the way variables without record dimensions are handled so that |
533 |
|
files that have variables with and without record variables can be glued: |
534 |
|
add a record dimension with a new unique name to be able to differentiate |
535 |
|
between variable with and without a-prior record dimensions. Remove |
536 |
|
this record dimension before adding the variable to the *.glob.nc file. |
537 |
|
This procedure automatically works also for grid.*.nc files that do not |
538 |
|
have any record dimension. |
539 |
|
o verification/cpl_aim+ocn: |
540 |
|
- generate new reference output on baudelaire (gfortran, mpich2) (previously |
541 |
|
from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script. |
542 |
|
o pkg/obcs/obcs_calc_stevens.F: |
543 |
|
- add code for northern and southern boundaries. |
544 |
|
- reorder some loops to save some operations and so that drFBar can be scalar |
545 |
|
o model/src: |
546 |
|
- re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine |
547 |
|
truncation) and add diagnostics for Adams-Bashforth tendency increment. |
548 |
|
- update test-exp. AD output: |
549 |
|
1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl; |
550 |
|
and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20, |
551 |
|
front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5), |
552 |
|
global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4), |
553 |
|
matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre, |
554 |
|
tutorial_global_oce_in_p, tutorial_global_oce_latlon and |
555 |
|
tutorial_plume_on_slope. |
556 |
|
o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX |
557 |
|
that vectorises. This code uses 3 extra 2D fields, F90 array assignments |
558 |
|
and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX |
559 |
|
does not even come with an F77 compiler anymore, this should not be |
560 |
|
a limitation |
561 |
|
|
562 |
|
checkpoint63e (2011/11/06) |
563 |
|
o pkg/seaice adjoint of LSR: |
564 |
|
- substantially rework STORE dirs. |
565 |
|
- add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED |
566 |
|
this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields |
567 |
|
and only perform SOLV_MAX_FIXED adjoint iters. |
568 |
|
If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration |
569 |
|
always goes to same record, meaning that the last forward field will be |
570 |
|
the one used in the adjoint - an approximation. |
571 |
|
- now produces non-zero LSR-related gradients, and acceptable gradients for |
572 |
|
An's zonal (x-z) test case (to be checked in) |
573 |
|
- lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR |
574 |
|
(but these are screwed up by the thermodynamics in the first place); |
575 |
|
reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution; |
576 |
|
output_adm.txt also reflects changes to seaice_lsr |
577 |
|
- global_ocean.cs32x15: |
578 |
|
* the "default" input_ad.seaice has been re-defined to always exclude dynamics |
579 |
|
(output_adm.seaice.txt was updated) |
580 |
|
* new input_ad.seaice_dynmix tests a forward LSR / backward free-drift |
581 |
|
(output_adm.seaice_dynmix.txt) |
582 |
|
o test-exp. exp4+stevens: |
583 |
|
- switch off pTracers and nonHydrostatic (restart problems with NH); update output |
584 |
|
o pkg/seaice (lsr solver): |
585 |
|
- put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only); |
586 |
|
update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15 |
587 |
|
- fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD) |
588 |
|
- new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution |
589 |
|
into initial guess for linearised solver; use weight ~ (1/err)^2,4. |
590 |
|
- compute (with new S/R) and print initial (+ free-driff sol. if available) |
591 |
|
and final residual of linearised system. |
592 |
|
o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity |
593 |
|
(requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F) |
594 |
|
o pkg/obcs: Stevens BCs (still only for east and west) |
595 |
|
- fix Stevens BCs by using intermediate velocities of previous |
596 |
|
time step as "baroclinic" contribution rather velocity of one grid cell |
597 |
|
inside the boundaries; more consistent but makes the entire treatment |
598 |
|
more complicated, requires new pickup files and two new S/Rs: |
599 |
|
obcs_copy_uv_n and obcs_save_uv_n |
600 |
|
keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY |
601 |
|
(undefined by default) |
602 |
|
- silently move computation of some grid factors into separate loops to |
603 |
|
save some recomputations |
604 |
|
- add a hack for non-linear free surface |
605 |
|
- add a verification experiment to exp4 that tests this code |
606 |
|
o make gluemnc/xplodemnc work with (moron) non-GNU shell tools |
607 |
|
|
608 |
|
checkpoint63d (2011/10/25) |
609 |
|
o pkg/obcs + seaice-dynamics: |
610 |
|
- new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before |
611 |
|
solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB |
612 |
|
values (consistent with an implicit method). |
613 |
|
- add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to |
614 |
|
return to older implementation (same results as before); note that none of |
615 |
|
the "experimental" OBCS_SEAICE options are implemented in the new version. |
616 |
|
- switch test exp. seaice_obcs to use new version (update output). |
617 |
|
o pkg/seaice: |
618 |
|
- add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS) |
619 |
|
- add parenthesis in Water-Ice drag calculations (evp & lsr); |
620 |
|
- in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1; |
621 |
|
and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice) |
622 |
|
- update output of test exp lab_sea that uses evp or lsr (fwd+ad) |
623 |
|
and global_ocean.cs32x15 (icedyn & seaice fwd+ad). |
624 |
|
o pkg/layers: |
625 |
|
- Include potential density as new coordinate (Thanks to David Munday) |
626 |
|
o pkg/dic: |
627 |
|
- Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add |
628 |
|
carbonate computation/output to CALC_PCO2_APPROX |
629 |
|
o pkg/generic_advdiff |
630 |
|
- make TAF generate code that vectorizes: |
631 |
|
gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F |
632 |
|
o model/src: |
633 |
|
- improve vectorization also for adjoint code of |
634 |
|
solve_tridiagonal and solve_pentadiagonal. As this requires up to |
635 |
|
5 new 3D-fields, this code is only turned on for the combination of |
636 |
|
ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message |
637 |
|
for singular matrix check (only for TARGET_NEC_SX). |
638 |
|
- remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to |
639 |
|
ALLOW_AUTODIFF. This flag now needs to be set outside of |
640 |
|
solve_tri/pentadiagonal.F |
641 |
|
o pkg/exf: |
642 |
|
- fix previous modif in exf_readparms.F (revision 1.66: treatment of |
643 |
|
optional namelist EXF_NML_OBCS). |
644 |
|
- add many debug-print (to trace down where pkg/cal error msg comes from) |
645 |
|
o pkg/mom_vecinv/mom_vi_hdissip.F |
646 |
|
- rearrange loops so that vectorization is improved and in particular |
647 |
|
the adjoint routine vectorizes. The code is a little longer now, but I |
648 |
|
think easier to read. |
649 |
|
Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested. |
650 |
|
o pkg/seaice: |
651 |
|
- allow to specify initial seaice velocity from files (uIceFile,vIceFile) |
652 |
|
o pkg/exch2: |
653 |
|
- alternative code (without tile x tile matrix) for cumulated (global) sum; |
654 |
|
used as default; keep using matrix version in adjustment.cs-32x32x1. |
655 |
|
o tools/build_options: |
656 |
|
- after merging some MPI and/or multi-threads specific optfiles so that |
657 |
|
the modified default optfile support both built (using genmake2 -mpi |
658 |
|
for the MPI built, using genmake2 -omp for OpenMP built), |
659 |
|
move now obsolete optfiles to tools/build_options/unsupported/ |
660 |
|
(add copy of email sent to support list in doc/optfiles_changes.txt) |
661 |
|
|
662 |
|
checkpoint63c (2011/09/28) |
663 |
|
o pkg/ebm: |
664 |
|
- fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of |
665 |
|
test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d) |
666 |
|
o pkg/seaice (SItracer pickup) |
667 |
|
* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER) |
668 |
|
To be done: |
669 |
|
- thorough testing of missing fields in S/R seaice_read_pickup |
670 |
|
- thorough matching between generic tracers and specific fields used |
671 |
|
(e.g. volume-weighted age, area-weighted age, salinity, ...) |
672 |
|
o pkg/grdchk: |
673 |
|
- all procs calculate and print finite-difference gradient (for testreport) |
674 |
|
- change description output used by testreport; |
675 |
|
- AD testing: also compare and report Finite-difference gradient; |
676 |
|
=> update all output_adm*.txt |
677 |
|
o test exp. global_ocean_ebm: |
678 |
|
- switch back useRealFreshWaterFlux (no problem anymore with run-off); |
679 |
|
and turn on exactConserve; update (fwd) output. |
680 |
|
o pkg/seaice (LSR): |
681 |
|
- print to STDOUT number of solver iterations at SEAICE_monFreq interval. |
682 |
|
- modify solver to deal cleanly with u/v switch at face edges (CS-grid): |
683 |
|
* identical results with non-CS topology (but save up to half of EXCH calls) |
684 |
|
* no much changes in cs-32 verification tests since no ice at face edges |
685 |
|
(differences due to convergence criteria, since nb of iterations changed) |
686 |
|
* expect some differences on lat-lon-cap grid. |
687 |
|
update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice) |
688 |
|
o pkg/exch2: |
689 |
|
- add new CPP option to disable Cumul-Sum matrix (to save storage when using |
690 |
|
many tiles); until alternative coding is added, just add a stop. |
691 |
|
o pkg/kpp: |
692 |
|
- move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F |
693 |
|
to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list). |
694 |
|
o optfiles: |
695 |
|
- merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles |
696 |
|
into corresponding standard one, which now support different build: |
697 |
|
(when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built) |
698 |
|
- add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael) |
699 |
|
o pkg/obcs (seaice): |
700 |
|
- add missing EXCH for uIce,vIce after applying OBCS; |
701 |
|
- remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding |
702 |
|
argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R |
703 |
|
EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F; |
704 |
|
- fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared) |
705 |
|
- verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi |
706 |
|
and eedata.mth for MPI and mutlti-threaded testing. |
707 |
|
o pkg/flt: |
708 |
|
- make FLT EXCH working with multi-threads (and MPI + multi-threads); |
709 |
|
- use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h; |
710 |
|
- fix pickup and trajectories + profiles output with multi-threads; |
711 |
|
- add parameter to select group of fields to write along trajectory and |
712 |
|
profile (default unchanged); |
713 |
|
- only call PORT_RAND* function when flt_noise <> 0; |
714 |
|
- add multi-threaded test for verification exp. flt_example. |
715 |
|
o eesupp/src: |
716 |
|
- fix S/R ALL_PROC_DIE for MPI+multi-threads. |
717 |
|
- USE_OMP_THREADING: check that number of threads (from eedata) matches |
718 |
|
actual number (from env.var. setting). |
719 |
|
o pkg/ebm: |
720 |
|
- fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file. |
721 |
|
- add multi-threaded test for verification exp. global_ocean_ebm |
722 |
|
|
723 |
|
checkpoint63b (2011/08/29) |
724 |
|
o pkg/ebm: |
725 |
|
- fix sign of runoff; |
726 |
|
- update directly forcing fields (Qnet,EmPmR) to use standard |
727 |
|
external_forcing_surf.F (remove ebm_forcing_surf.F); |
728 |
|
- avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F); |
729 |
|
- set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm) |
730 |
|
and apply relaxation towards corresponding SST field (2-D map or ZonAver). |
731 |
|
- update global_ocean_ebm parameters file data and update output (fwd+ad). |
732 |
|
o verification/matrix_example: |
733 |
|
- split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for |
734 |
|
MPI and mutlti-threaded testing. |
735 |
|
o pkg/matrix: |
736 |
|
- change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ; |
737 |
|
- fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter); |
738 |
|
- fix for multi-threaded (remove DATA statement); |
739 |
|
- use standard DIFFERENT_MULTIPLE function; |
740 |
|
- add MATRIX_OPTIONS.h |
741 |
|
o verification/matrix_example: |
742 |
|
To allow to split the domain in several tiles, change the domain size |
743 |
|
from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on |
744 |
|
Western side) of land points. |
745 |
|
o (*_)write_pickup: |
746 |
|
- fix few bugs in mypackage_read/write_pickup.F |
747 |
|
- in MDS_WR_METAFILES calls, replace "myTime" by a local copy into |
748 |
|
array of length 1 (was caught by compiler syntax-check). |
749 |
|
o pkg/diagnostics (velocity potential solver): |
750 |
|
- fix initialisation of main diagonal matrix (for overlap values) |
751 |
|
o tools/build_options: |
752 |
|
- towards single optfile for MPI and non-MPI built: merge few +mpi optfile |
753 |
|
into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11) |
754 |
|
- linux_amd64_gfortran: merge +mpi_generic version into standard optfile: |
755 |
|
* move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ; |
756 |
|
* FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list; |
757 |
|
and use "-devel" testreport option for standard testing on baudelaire. |
758 |
|
o pkg/grdchk: |
759 |
|
- Assume that all gradient-check position are within the same tile |
760 |
|
corresponding to global indices (iGloTile,jGloTile) and that |
761 |
|
positions (i,j indices or nbeg) are local to this tile; |
762 |
|
- set tile local-indices and proc. number according to tile global-indices; |
763 |
|
- remove grdchkwhichproc from namelist (retired param); |
764 |
|
- send adjoint gradient to all procs so that all procs print it to STDOUT; |
765 |
|
- switch on MPI test for global_ocean.90x40x15 AD test experiment. |
766 |
|
o adding package bbl (Bottom Boundary Layer) |
767 |
|
description in MITgcm/pkg/bbl/bbl_description.tex |
768 |
|
example/test experiment in MITgcm_contrib/bbl |
769 |
|
o adjoint verifications |
770 |
|
- changed 5 experiments to multi-tiles |
771 |
|
* global_ocean.90x40x15 |
772 |
|
* obcs_ctrl |
773 |
|
* offline_exf_seaice |
774 |
|
* tutorial_dic_adjoffline |
775 |
|
* tutorial_tracer_adjsens |
776 |
|
changed reference output for those that crossed tile boundaries |
777 |
|
(changed choices of gradient check positions) |
778 |
|
- with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi) |
779 |
|
- temporary bug fix in grdchk_loc.F for obcs |
780 |
|
o genmake2 & testreport |
781 |
|
- add target "obj" (just for OBJFILES files) to Makefile; |
782 |
|
- add option to specify FEXTRAFLAGS on command line. |
783 |
|
o pkg/mypackage: |
784 |
|
- remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS |
785 |
|
|
786 |
|
checkpoint63a (2011/08/02) |
787 |
|
o pkg/diagnostics (velocity potential): |
788 |
|
- fix velocity-potential calculation when using OBCS: balance net inflow |
789 |
|
at each level (new S/R OBCS_DIAG_BALANCE). |
790 |
|
- fix some of the problems with OBCS in stream-function calculation. |
791 |
|
o pkg/exf/exf_readparms.F |
792 |
|
- make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF, |
793 |
|
EXF_NML_OBCS) more consistent, so that you need not have these lists |
794 |
|
in data.exf when they are not used. |
795 |
|
o optim/optim_readdata.F: |
796 |
|
- add some output about obcs variables that might help debugging |
797 |
|
- add a check about nvarlength |
798 |
|
o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec |
799 |
|
o pkg/diagnostics (velocity potential): |
800 |
|
- fix mask for OBCS (still problems in stream-function with OBCS); |
801 |
|
- add specific parameter (default = main code CG2D params) for solver; |
802 |
|
- in case of poor convergence, use solution corresponding to lowest residual. |
803 |
|
o pkg/seaice/seaice_growth.F: small changes that permit vectorizable |
804 |
|
adjoint code. In general statements like tmpscal=fld(i,j) are problematic |
805 |
|
and should be avoided where possible. |
806 |
|
o model/src (rStar): |
807 |
|
- include r* effect on reference-state (PhiRef) in totPhiHyd |
808 |
|
(so that it's really the potential anomaly at the cell center); |
809 |
|
affect solution only if z* with full pressure in EOS. |
810 |
|
- test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and |
811 |
|
update output (because of z* in totPhiHyd and viscA4 changes); |
812 |
|
- keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly |
813 |
|
@ constant r) until interpolation at constant r is implemented. |
814 |
|
o pkg/diagnostics |
815 |
|
- fix RCENTER diagnostics in case cell center is not at interface middle |
816 |
|
o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use |
817 |
|
this eos with eosType = 'TEOS10', in data (PARM01). This eos implies |
818 |
|
that THETA and SALT are "conservative temperature" and "absolute |
819 |
|
salinity" |
820 |
|
o pkg/ctrl |
821 |
|
- fix computation of endrec in s/r ctrl_init_rec |
822 |
|
- ctrl_pack/unpack_*: remove unused variables and some obsolete code |
823 |
|
o pkg/seaice/seaice_growth.F |
824 |
|
- fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code, |
825 |
|
remove then obsolete STORE directives |
826 |
|
- fix STORE directives for tice and tices, so that only the |
827 |
|
appropriate part of the fields are stored (and not the entire |
828 |
|
field); update global_ocean.cs32x15.seaice AD output. |
829 |
|
- cosmetic changes: adjust CPP flags and indentation for better |
830 |
|
legibilty |
831 |
|
o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by |
832 |
|
Chris Wilson) |
833 |
|
o pkg/gmredi: |
834 |
|
Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF), |
835 |
|
and test it in verification exp. "front_relax.bvp" (update output.bvp.txt) |
836 |
|
|
837 |
|
checkpoint63 (2011/07/11) |
838 |
|
o pkg/exch2: |
839 |
|
- rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h |
840 |
|
- exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the |
841 |
|
(2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y |
842 |
|
increments, calculates Cumul-Sum @ tile origin and sends results to each tile. |
843 |
|
o pkg/diagnostics: |
844 |
|
- deal with pairs of post-processed diags which are computed together; in |
845 |
|
particular, re-order list of diags within 1 file to save 2nd computation. |
846 |
|
- add S/R to compute velocity stream-function (called after velocity-potential |
847 |
|
calculation) from divergence free transport -> new diagnostics "PsiVEL". |
848 |
|
- add parameter to select grid-point location where PsiVEL == 0. |
849 |
|
o eesupp/src: |
850 |
|
new S/R to calculate cumulated sum on tiled array, corner grid-cell location |
851 |
|
(specific S/R needed with exch2 topology - for now, just print an error msg) |
852 |
|
o pkg/shelfice |
853 |
|
- Implement friction velocity-dependent transfer coefficients following |
854 |
|
Holland and Jenkins, JPO, 1999 |
855 |
|
Original code by M. Losch with small modifs. |
856 |
|
Enable with CPP option SHI_ALLOW_GAMMAFRICT |
857 |
|
and runtime flag SHELFICEuseGammaFrict |
858 |
|
o verification lab_sea & global_ocean.cs32x15: |
859 |
|
- use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local): |
860 |
|
does not miss some dependencies (but is slower) and also works with many files |
861 |
|
(default makedepend limitation for AD built). |
862 |
|
- use cyrus_makedepend in adjustment.128x64x1 (so that it still tested). |
863 |
|
o pkg/diagnostics: |
864 |
|
- add run-time parameter "useMissingValue" (def=False) to fill land-point |
865 |
|
(i.e., where mask=0) with MissingValue ; used only in MNC output file. |
866 |
|
This replaces CPP-option DIAGNOSTICS_MISSING_VALUE. |
867 |
|
- Extend the use of "missing_value" setting from data.diagnostics for the case |
868 |
|
of counter-diagnostics (where fraction-weight is zero). This applies both to |
869 |
|
MNC and MDS output files. |
870 |
|
o pkg/seaice/seaice_growth.F: |
871 |
|
- add 'a priori' cap of latent heat flux based on actual mass considerations |
872 |
|
when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the |
873 |
|
non-legacy seaice_solve4temp. |
874 |
|
- add diagnostic of the residual sublimation freshwater flux (the freshwater |
875 |
|
flux taken from the ocean if the total actual latent heat fluxes exceed |
876 |
|
the maximum) |
877 |
|
- remove the CPP switch around the *_FWbySublim unit change and move diagnostic |
878 |
|
fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F. |
879 |
|
- add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef |
880 |
|
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim). |
881 |
|
- bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET. |
882 |
|
- bug fix : missing part to Martin's r_FWbySublim pathological case fix. |
883 |
|
o verification 1D_ocean_ice_column: |
884 |
|
made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet |
885 |
|
update results |
886 |
|
o pkg/diagnostics: |
887 |
|
- Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P') |
888 |
|
which are not filled-up but computed from other diags ; In this case, the mate |
889 |
|
diag points to the primary (filled-up) diag to used for post processing. |
890 |
|
- Update Velocity-potential computation using post-processed diag framework. |
891 |
|
==> Change the ordering of fields and time-periods in MDS output file |
892 |
|
when using periodic averaging: now writes one time record with the full set |
893 |
|
of fields for this time period, then the next time reccord (it used to be |
894 |
|
one field with the full set of time records then the next field). |
895 |
|
Note: this is now similar to NetCDF (MNC) output file. <== |
896 |
|
|
897 |
|
checkpoint62z (2011/06/21) |
898 |
|
o adjoint monitor: |
899 |
|
- Add adjoint monitor output for packages exf, seaice |
900 |
|
and update relevant testreport output |
901 |
|
o pkg/seaice: |
902 |
|
- re-order diags inits so that they appear in order in available_diagnostics.log |
903 |
|
- added diags: hsnow thermo. rates of change, area preceeding ridiging process, |
904 |
|
area/heff/hsnow preceeding thermodynamic growth/melt. |
905 |
|
- modified diag: SIdA; output actual effect, as the description states. |
906 |
|
- modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. |
907 |
|
- retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. |
908 |
|
(SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; |
909 |
|
and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) |
910 |
|
- modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. |
911 |
|
- added diagnostics for seaice generic tracers (SItr*). |
912 |
|
- added SItrUnit and SItrNameLong run time param (for SItr* diags). |
913 |
|
- in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. |
914 |
|
I. Fenty: 18-Jun-2011: |
915 |
|
Minor changes to seaice package: |
916 |
|
1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and |
917 |
|
added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) |
918 |
|
- Differentiated "regularization variables" from "floor variables" |
919 |
|
* areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor |
920 |
|
* hiceMin became SEAICE_hice_reg (old hiceMin) |
921 |
|
(with _reg meaning regularization variable) |
922 |
|
- SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion |
923 |
|
so as to ensure energy conservation when going between phases |
924 |
|
- A22 was not used anywhere |
925 |
|
2) Changed regularization procedure for heffActual and hsnowActual to ensure |
926 |
|
well-boundedness and smooth adjoint in seaice_growth.F |
927 |
|
3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells |
928 |
|
because the old regularization always set heffActual >= 0.05 cm |
929 |
|
4) Changed the model so that the default behavior is to put a small (10^-5) "floor" |
930 |
|
on AREA when HEFF > 0. |
931 |
|
- went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to |
932 |
|
requiring that DISABLE_AREA_FLOOR *not* be defined |
933 |
|
Affected verifications: |
934 |
|
- 1D_ocean_ice_column (output.txt output_adm.txt) |
935 |
|
- global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) |
936 |
|
o pkg/diagnostics: |
937 |
|
- move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). |
938 |
|
- rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument |
939 |
|
(was _RL, now integer) with option = 0 to retrieve all levels. |
940 |
|
- add pieces of code to compute velocity potential at each level (new diagnostics |
941 |
|
PhiVEL, works only when UVELMASS & VVELMASS are also turned on); |
942 |
|
for now, using same params as CG2D (target-resisual, max Nb of iter ...). |
943 |
|
- fix few issues with counter diagnostics in diagnostics_setdiag.F & |
944 |
|
diagstats_setdiag.F (if diagnostic counter is itself a counter diag) |
945 |
|
and in diagnostics_fract_fill.F (do not need a valid pointer for the |
946 |
|
diagnostics counter-mate); check that definition of counter-diagnostic |
947 |
|
includes a valid counter-mate (in diagnostics_set_levels.F). |
948 |
|
o model/src (rStar): |
949 |
|
- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
950 |
|
affect solution only if z* with full pressure in EOS; |
951 |
|
update output of test-exp global_ocean.90x40x15. |
952 |
|
o pkg/seaice: |
953 |
|
- introduce siEps=1e-5 parameter |
954 |
|
- use areaMax in AREA update (part 4), consistent with ridging step (part 2.5). |
955 |
|
- re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code. |
956 |
|
- introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer. |
957 |
|
For now it covers, and was tested for, ice salinity and age (attached to HEFF), |
958 |
|
as well as ice cover age and ridging index (attached to AREA). |
959 |
|
For now the run time parameters (in data.seaice/SEAICE_PARM03) are |
960 |
|
SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA'). |
961 |
|
Up to SItrMaxNum=3 tracers can be used simultaneously. |
962 |
|
o pkg/salt_plume: |
963 |
|
-introduce SPsalFRAC run time parameter that sets the fraction of the |
964 |
|
salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically) |
965 |
|
that gets vertically redistributed (fluxed down) by pkg/salt_plume. |
966 |
|
o model debug options: |
967 |
|
- Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored |
968 |
|
in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h). |
969 |
|
- Refine debug-msg printing selection (3 new levels): |
970 |
|
debugMode : controls printing of debug messages (sequence of S/R calls). |
971 |
|
debugLevel : controls printing of algorithm-relevant auxiliary/debug messages |
972 |
|
debLevZero = 0 ; /* level of disabled aux. msg printing */ |
973 |
|
debLevA = 1 ; /* level of minimum aux. msg printing */ |
974 |
|
debLevB = 2 ; /* level of low aux. print (report read-file opening)*/ |
975 |
|
debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */ |
976 |
|
debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */ |
977 |
|
debLevE = 5 ; /* level of extensive debug printing */ |
978 |
|
New debugLevel default: with default debugMode value (=F), |
979 |
|
= 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.; |
980 |
|
and if debugMode=T, default debugLevel = 4 (debLevD). |
981 |
|
Relation with previous settings: |
982 |
|
debLevB (=2) corresponds to former debLevA (=1) |
983 |
|
debLevD (=4) corresponds to former debLevB (=2) |
984 |
|
Note: |
985 |
|
a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before); |
986 |
|
b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs); |
987 |
|
to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5) |
988 |
|
- Add new parameter (printResidualFreq, read from PARM02 namelist) to print |
989 |
|
detailed CG solvers convergence; off (=0) by default, except if debugLevel=5. |
990 |
|
o pkg/obcs: |
991 |
|
- change OBCSfixTopo default from True to False (should not change the results); |
992 |
|
keep OBCSfixTopo=T in verification-exp. seaice_obcs. |
993 |
|
o pkg/thsice: |
994 |
|
- fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in |
995 |
|
2nd layer seaice sublimation (unlikely to happen) |
996 |
|
- use Interior mask for OBCS in thsice_advection.F (similar to what is |
997 |
|
done in gad_advection & seaice_advection). |
998 |
|
o adjoint: |
999 |
|
bug fix spotted by Gael Forget: |
1000 |
|
seaice_advection and thsice_advection still had |
1001 |
|
legacy CPP options to avoid CS corner updates for adjoint |
1002 |
|
o pkg/seaice: |
1003 |
|
=> Change some of the defaults (2011/05/29): |
1004 |
|
- change SEAICEuseFluxForm default (from False to True) |
1005 |
|
- change DIFF1 default (from 0.004 m/s to 0. m/s) |
1006 |
|
And print warnings if DIFF1 is not set in data.seaice and centered |
1007 |
|
avection scheme is used without any diffusion. |
1008 |
|
also: |
1009 |
|
- fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F; |
1010 |
|
- set SEAICEdiffKh[] default in the same way as SEAICEadvSch[] |
1011 |
|
- stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any |
1012 |
|
other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with |
1013 |
|
#undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE. |
1014 |
|
update results of test exp.: |
1015 |
|
lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20) |
1016 |
|
output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200) |
1017 |
|
output_adm.noseaicedyn (SEAICEuseFluxForm=T) |
1018 |
|
offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T) |
1019 |
|
seaice_obcs: output (SEAICEuseFluxForm=T) |
1020 |
|
and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004) |
1021 |
|
for standard fwd & AD lab_sea tests (to keep the same output). |
1022 |
|
o pkg/seaice/seaice_growth.F: |
1023 |
|
- use Ian Fenty's capping formulas for actual ice |
1024 |
|
thickness thoughout EVOLUTION branch. |
1025 |
|
- put treatment pathological case #2) in CPP brackets |
1026 |
|
(ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). |
1027 |
|
- update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. |
1028 |
|
o pkg/seaice: |
1029 |
|
- seaice_diffusion.F : remove the min(DX,DY) factor permanently; |
1030 |
|
pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter; |
1031 |
|
also pass fac as a param, which can be 1. (to update the tendency |
1032 |
|
field) or the time step (to update the field itself). |
1033 |
|
- seaice_advdiff.F: for multidim, call seaice_diffusion with |
1034 |
|
e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call |
1035 |
|
seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. |
1036 |
|
- SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : |
1037 |
|
hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
1038 |
|
o pkg/seaice: |
1039 |
|
diffusion with centered advection scheme (diffus.F & advect.F): |
1040 |
|
- simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) |
1041 |
|
to just compute the laplacian of input-field. |
1042 |
|
- unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call. |
1043 |
|
- fix flux-form version in diffus.F to conserve tracer. |
1044 |
|
update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects |
1045 |
|
machine truncation) and lab_sea.salt_plume (conservative flux-form modif) |
1046 |
|
|
1047 |
|
checkpoint62y (2011/05/26) |
1048 |
|
o pkg/seaice: |
1049 |
|
- seaice_growth.F : in EVOLUTION branch, always include |
1050 |
|
a_QSWbyATM_cover in qnet (as it should be). |
1051 |
|
- verification/global_ocean.cs32x15 : update results accordingly |
1052 |
|
(output.seaice.txt output_adm.seaice.txt). |
1053 |
|
o pkg/seaice + obcs: |
1054 |
|
- use maskInW & maskInS in multi-dim advection and biharmonic diffusion: |
1055 |
|
equivalent of assuming no tracer gradient outside the OB region. |
1056 |
|
update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion) |
1057 |
|
- remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed |
1058 |
|
after changes above); |
1059 |
|
- obcs+seaice cleaning: apply seaice-tracer OB values to tracer field |
1060 |
|
only at OB location (instead of over a band of OLx width). |
1061 |
|
o pkg/seaice: |
1062 |
|
- fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F |
1063 |
|
(dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid) |
1064 |
|
o pkg/obcs: |
1065 |
|
- split header file "OBCS.h" into 4 separated files: |
1066 |
|
OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h |
1067 |
|
Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h |
1068 |
|
(contain no conditional statement which depends on OBCS options). |
1069 |
|
- move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h) |
1070 |
|
to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h). |
1071 |
|
o ctrl, cost, grdchk & autodiff pkgs: |
1072 |
|
- make options file more standard (like other {PKG}_OPTIONS.h file but |
1073 |
|
with AD_CONFIG.h); clean-up some of the included header files. |
1074 |
|
o pkg/obcs: |
1075 |
|
- do not mask tracer when applying OB (tracer == 0 could generate problems) |
1076 |
|
- apply tracer OB values to tracer field only at OB location (instead of |
1077 |
|
over a band of OLx width) |
1078 |
|
- clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R) |
1079 |
|
- remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove |
1080 |
|
obcs_apply_tloc.F & obcs_apply_sloc.F |
1081 |
|
o obcs in model/src: |
1082 |
|
- call OBCS_APPLY_W only if NonHydrostatic. |
1083 |
|
- call OBCS_APPLY_ETA only if NonLinFreeSurf. |
1084 |
|
- reset dEtaHdt and wVel to zero outside OB interior region ; |
1085 |
|
- leave tracer unchanged outside OB interior region: This has no effect |
1086 |
|
on the solution but just to prevent unrealistic tracer value outside OB. |
1087 |
|
- zero out velocity outside OB interior region: This has no effect on |
1088 |
|
the solution but just to prevent unrealistic velocity outside OB. |
1089 |
|
o obcs and non-lin free-surf: |
1090 |
|
move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F |
1091 |
|
and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F |
1092 |
|
+ add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR: |
1093 |
|
this fixes missing EXCH + get consistent eta OB value (+ fix restart). |
1094 |
|
update results of test-exp. exp4(nlfs). |
1095 |
|
o exp4 (nlfs) test-exp: |
1096 |
|
use OBC for Eta at Western & Eastern OB (to test prescribing Eta |
1097 |
|
with NonLin-FreeSurf); update output.nlfs.txt |
1098 |
|
o obcs and 2d/3d solver norm: |
1099 |
|
use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB |
1100 |
|
and outside OB interior region (will allow to place OB further inside the |
1101 |
|
domain). Depending on the domain, can affects cg2d-Norm (previous |
1102 |
|
cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl, |
1103 |
|
and cg3d-Norm (previous Norm was computed before canceling OB terms), |
1104 |
|
e.g. in tutorial_plume_on_slope. |
1105 |
|
- update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope. |
1106 |
|
o pkg rbcs: |
1107 |
|
- split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h |
1108 |
|
- add capability to apply relaxation to horizontal velocity uVel & vVel. |
1109 |
|
o pkg/grdchk: add gradient check for control variable xx_shifwflx |
1110 |
|
o pkg/shelfice/shelfice_init_fixed.F |
1111 |
|
fix CPP-flag combinations |
1112 |
|
o pkg/seaice: Merge iceage code of Pierre Rampal |
1113 |
|
* update/change/correct ice age calculations |
1114 |
|
* add age updates for pathological cases |
1115 |
|
Probably needs more testing... |
1116 |
|
|
1117 |
|
checkpoint62x (2011/05/13) |
1118 |
|
o pkg/mom_vecinv: |
1119 |
|
high-order vorticity scheme: use interior masks (maskInW & S) |
1120 |
|
to zero-out (outside OB) gradient of vorticity. |
1121 |
|
o verification exp.: |
1122 |
|
turn on "useEnergyConservingCoriolis" (better discretisation) in exp. |
1123 |
|
hs94.128x64x5 and seaice_obcs ; update results. |
1124 |
|
o pkg/obcs: |
1125 |
|
fix bug in OBeta for YZ sections in obcs_exf_load.F |
1126 |
|
o pkg/ctrl, pkg/shelfice, and optim: |
1127 |
|
- add new control variable xx_shifwflx (fresh water flux underneath ice |
1128 |
|
shelves). This is almost as tedious as obcs-ctrl, because the |
1129 |
|
variables needs its own mask. |
1130 |
|
- add a cost function term that penalizes the deviation of xx_shifwflx |
1131 |
|
from the first guess (zero) in analogy to other control variables |
1132 |
|
o pkg/shelfice: |
1133 |
|
- start basic adjoint |
1134 |
|
o pkg/ctrl: |
1135 |
|
- remove extra 2D field "for good measure" when initializing in |
1136 |
|
ctrl_set_globfld_[xy/xz/yz].F |
1137 |
|
- replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec |
1138 |
|
- improve error messages in ctrl_set_unpack_* |
1139 |
|
o OBC implementation in momentum: |
1140 |
|
use interior masks (maskInC,W & S) in momentum S/R: |
1141 |
|
- multiply divergence, tension and some del^i.u or del^j.v by maskInC |
1142 |
|
- multiply del2u,del2v by maskInW/S (biharmonic viscosity) |
1143 |
|
- multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) |
1144 |
|
- multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) |
1145 |
|
Motivation: fix/clean implementation of OBC with biharmonic-viscosity |
1146 |
|
(and also with Leith/Smagorinsky harmonic-viscosity). |
1147 |
|
Update output of experiment dome and exp4 (+nlfs). |
1148 |
|
o exp4 test-exp: |
1149 |
|
- turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) |
1150 |
|
and prescribe time-varying OB (without pkg/exf) for zonal-velocity |
1151 |
|
at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
1152 |
|
time-varying OB at Western-side for wVel (NonHyd); update output. |
1153 |
|
- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
1154 |
|
and biharmonic-viscosity ; also use prescribed time varying OB. |
1155 |
|
o pkg/obcs: |
1156 |
|
fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
1157 |
|
o model/src: |
1158 |
|
- fix startTime setting when baseTime<>0 & nIter0=0 are specified ; |
1159 |
|
- initialise startTime & nIter0 with unlikely values: allows to set one |
1160 |
|
from the other without ambiguity. |
1161 |
|
o seaice_obcs test-exp.: |
1162 |
|
add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output. |
1163 |
|
o pkg/obcs: |
1164 |
|
- remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: |
1165 |
|
no longer needed with maskInC,W,S in pkg/generic_advdiff. |
1166 |
|
o pkg/seaice: |
1167 |
|
- retired SEAICE_SALINITY and SEAICE_salinity in favor of |
1168 |
|
SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively. |
1169 |
|
- fixed bug in the initialization of sea ice salinity variable HSALT |
1170 |
|
in seaice_init_varia.F (removed dependence on ICE2WATR) |
1171 |
|
o fizhi-cs test exp.: |
1172 |
|
switch reference output convention for these 2 non-standard test-exp, |
1173 |
|
from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5) |
1174 |
|
to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11) |
1175 |
|
reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran |
1176 |
|
o model/inc: |
1177 |
|
- change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4") |
1178 |
|
of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS) |
1179 |
|
o pkg/seaice: |
1180 |
|
- fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY |
1181 |
|
o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15 |
1182 |
|
- updated output*.txt files due to bug fixes in salt, saltPlumeFlux, |
1183 |
|
and initial HSALT |
1184 |
|
|
1185 |
|
checkpoint62w (2011/04/26) |
1186 |
|
o pkg/mom_fluxform: |
1187 |
|
- fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf. |
1188 |
|
- use parameter "sideDragFactor" in no-slip BC side-drag part. |
1189 |
|
- update output of exp. global_ocean.90x40x15 |
1190 |
|
o pkg/mom_vecinv: |
1191 |
|
mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform) |
1192 |
|
o update seaice exp.: |
1193 |
|
use more consistent parameter values (remove "backward compatability only": |
1194 |
|
ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh) |
1195 |
|
related to thermodynamics seaice. Update output (fwd+AD) of exp.: |
1196 |
|
1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs |
1197 |
|
o update test-exp global_ocean.90x40x15: |
1198 |
|
o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis). |
1199 |
|
o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.) |
1200 |
|
o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params) |
1201 |
|
o turn on zStar & viscA4 in standard set-up (dir input/) |
1202 |
|
and update output files: output.txt & output.dwnslp.txt |
1203 |
|
o new AD-test experiment: obcs_ctrl |
1204 |
|
(From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector. |
1205 |
|
o pkg/dic: |
1206 |
|
fix two bugs in handling water vapour pressure in carbonate chemistry |
1207 |
|
and air-sea fluxes. Found by Val Bennington and Galen McKinley |
1208 |
|
(add DIC Option = WATERVAP_BUG to recover old results) |
1209 |
|
update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline |
1210 |
|
o adding allowInteriorFreezing option to check for water below freezing point |
1211 |
|
at depth and bring the negative heat anomaly to the surface level |
1212 |
|
o pkgs _fields_load: |
1213 |
|
- extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs) |
1214 |
|
- use new S/R GET_PERIODIC_INTERVAL in pkgs: |
1215 |
|
bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and |
1216 |
|
rbcs to get interpolation weights and time reccord number. |
1217 |
|
- fix multi-threading in aim_fields_load.F |
1218 |
|
- apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F |
1219 |
|
o external_fields_load: |
1220 |
|
new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear |
1221 |
|
interpolation weights) to use in a periodic time-series ; do not divide by |
1222 |
|
time-step to convert to integer: |
1223 |
|
- this fixes case where externForcingPeriod is not multiple of time-step |
1224 |
|
(Thanks to Christopher L. Wolfe) |
1225 |
|
- this fixes case where externForcingPeriod is an odd multiple of time-step |
1226 |
|
(was wrong by half of time-step); update results of tutorial_global_oce_in_p. |
1227 |
|
store index of time-record which is currently loaded: |
1228 |
|
- works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ; |
1229 |
|
- needed for the adjoint but not yet used because of extensive recomputations; |
1230 |
|
(to be fixed soon) |
1231 |
|
|
1232 |
|
checkpoint62v (2011/04/02) |
1233 |
|
o verification/1D_ocean_ice_column added to test Ian Fenty's |
1234 |
|
pkg/seaice_growth.F modifications for improving sea ice code differentiability |
1235 |
|
o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope |
1236 |
|
(new velocity statistics after changing maskInW & maskInS definition) |
1237 |
|
o pkg/generic_advdiff with OBCS: |
1238 |
|
use maksInW & maskInS in advective flux and in biharmonic diffusion calculation: |
1239 |
|
equivalent to assumption of no tracer gradient outside the OB region. |
1240 |
|
This will affect the results if using obcs+biharmonic diffusion. |
1241 |
|
update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc) |
1242 |
|
o pkg/obcs: |
1243 |
|
change definition of maskInW & maskInS: leave OB edges inside (maskIn=1) |
1244 |
|
(e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still |
1245 |
|
in Interior region. No impact on solution but affects Velocity monitor stats. |
1246 |
|
o pkg/ptracers (adjoint) |
1247 |
|
New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate |
1248 |
|
tape file for each tracer |
1249 |
|
o model/inc/src and pkg/autodiff: add parameters that allow to turn |
1250 |
|
of parts of the adjoint code at run time. For now, there are only |
1251 |
|
useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These |
1252 |
|
parameters are set in data.pkg. |
1253 |
|
This is the lazy coward's version of doing this, but still useful for |
1254 |
|
debugging. In order to do it right, everything needs to be moved to |
1255 |
|
pkg/autodiff. |
1256 |
|
o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at |
1257 |
|
the end; this fixes the adjoint balancing code for open boundaries. |
1258 |
|
o pkg/ctrl: |
1259 |
|
- change behavior of xx_${varname}period to be analogous to exf-conventions: |
1260 |
|
xx_${varname}period = 0., means time-independent control part |
1261 |
|
xx_${varname}period = -12., means one-year-periodic monthly control part |
1262 |
|
- introduce helper routine ctrl_init_rec (part of ctrl_init.F) to |
1263 |
|
clean up ctrl_init a little, remove unused variables |
1264 |
|
- ctrl_init: fixed the handling of the start/endrec for obcs-variables |
1265 |
|
- move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec |
1266 |
|
|
1267 |
|
checkpoint62u (2011/03/15) |
1268 |
|
o model/src: |
1269 |
|
- for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in |
1270 |
|
h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ; |
1271 |
|
- in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to |
1272 |
|
INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF. |
1273 |
|
o pkg/ctrl/obcs/ecco: |
1274 |
|
- remove obsolete, unused, and partially broken code: |
1275 |
|
ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within |
1276 |
|
ALLOW_CTRL_OBCS_BALANCE |
1277 |
|
- put a stop statement into ecco/cost_obcsvol.F, but also add |
1278 |
|
cost_obcsvol to ecco_ad_diff.list |
1279 |
|
o pkg/ecco: fix counting cost function contributions for obcs (code |
1280 |
|
by Matt M.) and diffkr for diagnostics |
1281 |
|
o pkg/ecco, pkg/ctrl, pkg/grdchk: |
1282 |
|
add cost penalty terms for initial uvel, vvel, eta controls |
1283 |
|
and I/O for prior error files |
1284 |
|
o pkg/mdsio: |
1285 |
|
move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option |
1286 |
|
(new argument) to check for tiled file in mdsioLocalDir : this fix the |
1287 |
|
restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir. |
1288 |
|
o pkg/ctrl: |
1289 |
|
- ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by |
1290 |
|
ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove |
1291 |
|
unused and superfluous variables |
1292 |
|
- ctrl_get_gen_rec.F: catch the case of xx_genperiod=0. |
1293 |
|
o pkg/ecco |
1294 |
|
- enable adjoint of Stevens OB |
1295 |
|
o pkg/ctrl/ecco/grdchk: |
1296 |
|
- remove global declaration of tmpfldx/yz and tmpfldx/yz2. |
1297 |
|
Fortunately, we do not have any tests for the numerous cpp-flagged |
1298 |
|
option of "obcs as control parameters" so we will never know |
1299 |
|
if this is an improvement (but at least now things compile). |
1300 |
|
- remove an obsolete initialization from ecco_cost_init_barfiles.F |
1301 |
|
- fix some problems within never used ifdefs to make the code compile |
1302 |
|
o pkg/obcs: |
1303 |
|
- Refine Interior mask definition to work with more complex OB (e.g. |
1304 |
|
if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to |
1305 |
|
read in Interior mask from file. Check if Interior mask is consistent |
1306 |
|
with OB list of indices. |
1307 |
|
o pkg/seaice |
1308 |
|
- beginning code for a seaice tracer package, |
1309 |
|
but currently only used for seaice age: SEAICE_AGE |
1310 |
|
SEAICE_num = 4 |
1311 |
|
iTracer = 1: area-weighted ice age |
1312 |
|
= 2: volume-weighted ice age |
1313 |
|
= 3, 4: template for one-year vs. multi-year ice |
1314 |
|
data.seaice has new namelist SEAICE_PARM03 for arrays related to |
1315 |
|
SEAICE_num |
1316 |
|
|
1317 |
|
checkpoint62t (2011/03/05) |
1318 |
|
o pkg/obcs: |
1319 |
|
- obcs_apply_uv.F: change to a 2 steps method, first tangential component; |
1320 |
|
then normal component. This ensures that the normal component is set |
1321 |
|
correctly even when it conficts with tangential setting from an other OB. |
1322 |
|
Affects results of test-experiment seaice_obcs: update the output.txt |
1323 |
|
o pkg/obcs: |
1324 |
|
- add code to monitor statistics of dynamical fields at OB. |
1325 |
|
- take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW : |
1326 |
|
- fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection). |
1327 |
|
- change default: balance the Net inflow through all OB (instead of balancing |
1328 |
|
each OB separately); keep the old method if setting OBC_balanceFacX < 0. |
1329 |
|
- switch on useOBCSbalance in dome experiment: only correct Western OB outflow |
1330 |
|
to match Nortern OB inflow (OBCS_balanceFacN=0). |
1331 |
|
o pkg/seaice: |
1332 |
|
- redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL |
1333 |
|
o pkg/seaice (seaice_growth v 1.113): |
1334 |
|
- reverting seaice_growth to v 1.111 in order to have code with exact bit |
1335 |
|
compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge |
1336 |
|
CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced |
1337 |
|
runtime flag SEAICEareaFormula is kept but is inactive |
1338 |
|
o model/src: |
1339 |
|
- add new param to scale curvilinear grid distance and area when using |
1340 |
|
a different sphere radius from the grid-files. |
1341 |
|
- test/check multi-threads EXCH applied to local variable (cg2d_x) |
1342 |
|
o adjoint: |
1343 |
|
- enable adjoint of Stevens OB |
1344 |
|
- add dummy_in_dynamics to enable extraction of ADJrhoinsitu |
1345 |
|
(a bit delicate because of potentially modified adj. common block structure; |
1346 |
|
current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later) |
1347 |
|
|
1348 |
|
checkpoint62s (2011/02/15) |
1349 |
|
o pkg/seaice (seaice_growth v 1.112): |
1350 |
|
- introduce SEAICEareaFormula run time parameter, which selects the recipe for |
1351 |
|
computing the ice cover tendency from effective thickness tendencies. Include |
1352 |
|
Ian Fenty's formula. |
1353 |
|
- remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using |
1354 |
|
SEAICEareaFormula. |
1355 |
|
- simplify notations for the various d_HEFF/d_AREA terms. |
1356 |
|
o pkg/gmredi: |
1357 |
|
- add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code |
1358 |
|
from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative; |
1359 |
|
add a verification test-run (front_relax.bvp) to test GM_useBVP. |
1360 |
|
o pkg/seaice (seaice_growth v 1.111): |
1361 |
|
- for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's. |
1362 |
|
- the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to |
1363 |
|
also melt ice. |
1364 |
|
o pkg/seaice: |
1365 |
|
- McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty). |
1366 |
|
- can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h |
1367 |
|
o pkg/cheapaml: |
1368 |
|
- from Nico Wienders: New version of this package. |
1369 |
|
o pkg/flt: |
1370 |
|
- add CPP options to prevent floats to re-enter the opposite side of |
1371 |
|
a periodic domain (default: keep periodicity) |
1372 |
|
o pkg/gmredi: |
1373 |
|
- apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners |
1374 |
|
(needed for multi-dim advection). |
1375 |
|
- switch on GM Advective form in global_ocean.cs32x15 and update output.txt |
1376 |
|
o model/src: |
1377 |
|
- fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run. |
1378 |
|
o tutorial_tracer_adjsens |
1379 |
|
- extend to NLFS and replace maskC by hFacC |
1380 |
|
(change reference output accordingly) |
1381 |
|
|
1382 |
|
checkpoint62r (2011/01/24) |
1383 |
|
o testreport: |
1384 |
|
- add option -deloutp (-do) to remove output file after successful run |
1385 |
|
- add option -mfile (-mf) for MPI machile-file and for each test-exp, |
1386 |
|
extract exact list of procs from this file ; adjust COMMAND by |
1387 |
|
replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs. |
1388 |
|
o pkg/ecco: replace old ineffective way of penalizing deviations from |
1389 |
|
first guess (of obcs) with code by Matt Mazloff |
1390 |
|
o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without |
1391 |
|
exf/cal |
1392 |
|
- ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl |
1393 |
|
and handle case of obcs?period == 0 |
1394 |
|
Not affected by these changes: There is still an inconsistency in |
1395 |
|
the computation of start/endrec for the obcs variables for ALLOW_CAL |
1396 |
|
defined (see comment by Menemenlis, 7-Mar-2003) |
1397 |
|
- make S/R ctrl_get_gen_rec return something meaningful even if |
1398 |
|
ALLOW_CAL is not defined |
1399 |
|
- ctrl_getobcs?: simplify code so that it does not need to use |
1400 |
|
S/R exf_swapfields |
1401 |
|
o testreport: |
1402 |
|
allow to test MPI with different number of processors for each experiment: |
1403 |
|
create file "SIZE.h.mpi" in each build dir. |
1404 |
|
Note: update of "-command" argument not yet implemented. |
1405 |
|
o model/src, pkg/autodiff, pkg/ecco, pkg/seaice: |
1406 |
|
alleviate the need for additional 3D tapes when using |
1407 |
|
the non-inear free surface in the adjoint. This is done |
1408 |
|
by adding an 'update' of hfacc etc. to their current |
1409 |
|
value at the beginning of forward_step.F. |
1410 |
|
o pkg/seaice |
1411 |
|
seaice_lsr: move stress-divergence computations out of outer pseudo- |
1412 |
|
timestepping loop |
1413 |
|
o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD' |
1414 |
|
up, so that the calls of the ctrl_* subroutines are really at the end |
1415 |
|
of the routine. |
1416 |
|
o pkg/gmredi: |
1417 |
|
allow to specify a 2-D horizontal map and a 1-D vertical profil |
1418 |
|
as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity. |
1419 |
|
o pkg/seaice: |
1420 |
|
move lsr iterations from seaice_dynsolver to seaice_lsr. |
1421 |
|
o pkg/seaice: |
1422 |
|
reduce memory footprint of seaice mutldim advection tapes, |
1423 |
|
by using a 2D tape independent of the generic_advdiff ones, |
1424 |
|
and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc. |
1425 |
|
|
1426 |
|
checkpoint62q (2010/12/29) |
1427 |
|
o model/src: |
1428 |
|
- check horizontal grid-spacing for unset or zero/negative values. |
1429 |
|
- change AD test hs94.1x64x5 to be truly a 2-D set-up. |
1430 |
|
o pkg/flt: |
1431 |
|
- use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR |
1432 |
|
- precision of input and output files set according to readBinaryPrec |
1433 |
|
and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits. |
1434 |
|
- initial float position from tiled file was not converted to index space |
1435 |
|
(looks like a bug): fixed to make it similar to initial pos. global file. |
1436 |
|
o global_ocean.cs32x15: |
1437 |
|
change SIZE.h of AD set-up to get same tiling as with MPI. |
1438 |
|
Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11) |
1439 |
|
o model/src: |
1440 |
|
add flag to control printing of domain fields (bathymetry, hFac ...) in |
1441 |
|
ini_mask_etc (call to plot_fieds_xy*). |
1442 |
|
o pkg/thsice: |
1443 |
|
if useEXF, some forcing fields are not valid in overlap: fixed by computing |
1444 |
|
over the interior only + apply EXCH at the end (like with SEAICE advection). |
1445 |
|
o pkg/mdsio: |
1446 |
|
- add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer |
1447 |
|
to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS. |
1448 |
|
- change barrier call for safe multi-threads access to 3-D shared buffer. |
1449 |
|
- MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones) |
1450 |
|
- replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and |
1451 |
|
remove the 4 S/R MDS_PASS_WH_R4/8toRL/S. |
1452 |
|
o pkg/flt: |
1453 |
|
- add fourth-order Runge-Kutta integration |
1454 |
|
- add basic exch2 support (only 1 facet supported so far!) |
1455 |
|
o pkg/mdsio+rw: |
1456 |
|
new S/R to read local (or tile independent) vector (read counterpart of |
1457 |
|
mds_writevec_loc, and front-end write_glvec_rl/rs). |
1458 |
|
o global_ocean.cs32x15: additional input_ad.seaice experiment |
1459 |
|
that uses pkg/seaice rather than pkg/thsice. |
1460 |
|
(using multidim advection for seaice) |
1461 |
|
o towards more F95 syntax for array specification in namelist: |
1462 |
|
- change "data.diagnostics" (data.ptracers was changed before checkpoint62p) |
1463 |
|
of all verification experiments. |
1464 |
|
e.g.: line: fields(1,3)='ETAN ','ETANSQ ', |
1465 |
|
was changed to: fields(1:2,3)='ETAN ','ETANSQ ', |
1466 |
|
- finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles |
1467 |
|
o global_ocean.cs32x15: additional input.seaice experiment |
1468 |
|
that uses pkg/seaice rather than pkg/thsice. |
1469 |
|
|
1470 |
|
checkpoint62p (2010/12/17) |
1471 |
|
o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it |
1472 |
|
to THSICE_SIZE.h to avoid conflict with pkg/seaice. |
1473 |
|
o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint. |
1474 |
|
allow for use of multim. advection in seaice adjoint. |
1475 |
|
o pkg/seaice: add diagnostics for snow precipitation and sublimation flux |
1476 |
|
- first attempt to close budgets by taking into account the freshwater |
1477 |
|
flux implied by the sublimation of snow and ice. So far only the |
1478 |
|
volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag |
1479 |
|
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET |
1480 |
|
o eesupp/src: |
1481 |
|
new S/R with new option (NML_EXTENDED_F77) to change array specification |
1482 |
|
from F95 standard to commonly accepted extended F77 form. |
1483 |
|
This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5) |
1484 |
|
and to revert back to the original syntax (with -DNML_EXTENDED_F77) |
1485 |
|
for less tolerant f77 compiler (e.g., pgf77, g77). |
1486 |
|
o globalFiles: |
1487 |
|
commented out in parameter file "data" since it's not safe with MPI |
1488 |
|
(e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much |
1489 |
|
in this case); no longer commented out in restart test (tst_2+2). |
1490 |
|
o add adTapeDir to specify a special directory where adjoint tapes are |
1491 |
|
written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05 |
1492 |
|
and cannot be used together with mdsioLocalDir. |
1493 |
|
o nesting pkgs: |
1494 |
|
- packages_init_variables : put call to OBCS_INIT_VARIABLES in last position |
1495 |
|
- update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) |
1496 |
|
- add parameter files + utils dir + output from short run on beagle. |
1497 |
|
o pkg/seaice: |
1498 |
|
fix seaice_growth.F store directives; update results of exp. lab_sea.ad |
1499 |
|
o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid |
1500 |
|
unnecessary copying in adjoint code, requires new parameter NMAX_ITER |
1501 |
|
|
1502 |
|
checkpoint62o (2010/11/25) |
1503 |
|
o pkg/exf: |
1504 |
|
- change CPP option EXF_VERBOSE to run-time logical param exf_verbose. |
1505 |
|
o pkg/seaice: |
1506 |
|
- seaice_ocean_stress: split a loop for better vectorization of the |
1507 |
|
adjoint code |
1508 |
|
- seaice_growth.F: fix bug in conservation of freshwater connected to |
1509 |
|
capping of heff, put contribution into d_HEFFbyNEG |
1510 |
|
- replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat |
1511 |
|
by something more sensible (parameters that are what their name implies) |
1512 |
|
- change some defaults, so that by default exf-parameters are used for |
1513 |
|
things like rhoAir, cpAir,latent/sensible heat parameters, in order |
1514 |
|
to reproduce the old results, many data.seaice now contain funny values |
1515 |
|
for cpAir and latent heat of sublimation |
1516 |
|
o packages_readparms.F: move exf_readparms up in line so that |
1517 |
|
exf-parameters are visible for other packages (e.g. seaice) |
1518 |
|
o debugMode & debugLevel=2: |
1519 |
|
- differentiate between debugMode & debugLevel=2: |
1520 |
|
debugMode: controls printing of debug messages (sequence of S/R calls). |
1521 |
|
debugLevel: controls printing of algorithm intermediate results and stats. |
1522 |
|
- remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2"; |
1523 |
|
=> allows to print debug-stats without all sequence of call messages. |
1524 |
|
- switch control of debug print from debugLevel to debugMode in many S/R. |
1525 |
|
o pkg/obcs (obcs-sponge): |
1526 |
|
fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the |
1527 |
|
call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge) |
1528 |
|
o pkg/generic_advdiff: |
1529 |
|
- record overlap minimum size for each advection scheme; |
1530 |
|
- refine criteria on overlap minimum size; |
1531 |
|
- check and stop (in gad_check) if overlap size is too small. |
1532 |
|
o pkg/obcs: |
1533 |
|
- with ptracers: remove multiple calls to obcs_apply_ptracer (only done |
1534 |
|
once, in ptracers_implicit.F) |
1535 |
|
- with seaice: remove test on empty file name in obcs_apply_seaice (always |
1536 |
|
apply OB values when tile has OB) |
1537 |
|
o model/src, coriolis setting: |
1538 |
|
- integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical |
1539 |
|
useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from |
1540 |
|
files (selectCoriMap=3) with any grid. |
1541 |
|
- add parameter "fPrime" for constant second Coriolis coeff (default=0). |
1542 |
|
o pkg/seaice/seaice_growth.F: |
1543 |
|
a few cosmetic changes that reduce the number of lines of code |
1544 |
|
o pkg/obcs: add boundary conditions following Stevens (1990) |
1545 |
|
- the code follows old MOM/NAOSIM code |
1546 |
|
- so far it is only implemented for the eastern and western boundaries |
1547 |
|
and NOT for pTracers |
1548 |
|
o pkg/rbcs: |
1549 |
|
- replace rbcsInIter by rbcsForcingOffset, the time in seconds at the |
1550 |
|
beginning of the first rbcs forcing period. |
1551 |
|
- add option rbcsSingleTimeFiles that makes rbcs read forcing data like the |
1552 |
|
offline package, i.e., one file per time, labeled by iteration number; |
1553 |
|
deltaTrbcs sets the timestep with which the data was generated; |
1554 |
|
rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset. |
1555 |
|
- rbcsForcingCycle=0 makes forcing non-cyclic. |
1556 |
|
- make arithmetic safe for negative times and odd forcing periods. |
1557 |
|
|
1558 |
|
checkpoint62n (2010/11/09) |
1559 |
|
o pkg/seaice: |
1560 |
|
fix masking in free-drift S/R ; update results of exp. lab_sea.fd |
1561 |
|
o pkg/obcs: |
1562 |
|
New S/R to copy tracer value from the OB location to narrow band region |
1563 |
|
(width = same as overlap) beyond the OB: preserve OB value (needed for |
1564 |
|
high-order scheme) which were overwritten by EXCH call if in overlap |
1565 |
|
region. Applied to theta, salt, ptracer and advected seaice variables. |
1566 |
|
With seaice: use maskInC in similar way as in gad_advection.F, |
1567 |
|
in seaice_advection.F and advect.F. |
1568 |
|
Update output of experiment seaice_obcs and change exp4 to test OBCS with |
1569 |
|
4th order Adv.Scheme. for pasive salt and ptracer. |
1570 |
|
o tools/genmake2: |
1571 |
|
- when looking for an optfile (not specified), only search for Fortran compiler |
1572 |
|
(remove sym-link test + setting of CPP + makedepend check + C-compiler check) |
1573 |
|
- in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm |
1574 |
|
(instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong) |
1575 |
|
- set default for CPP to "cpp -traditional -P" (was the case without specifying |
1576 |
|
an optfile, but otherwise default was just "cpp". |
1577 |
|
- comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from) |
1578 |
|
- when "CC" is not set in the optfile, look for possible C compiler |
1579 |
|
(instead of just setting CC=cc) |
1580 |
|
- put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes: |
1581 |
|
=> add a ".F" to ".o" rule for source files with no "#include" (such as |
1582 |
|
port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS. |
1583 |
|
- move gfortran before g77 in list of possible Fortran compiler (consistent |
1584 |
|
with reference compiler switch from g77 to gfortran) |
1585 |
|
o pkg/seaice: |
1586 |
|
o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to |
1587 |
|
seaice_check that stops the model, when the CPP flag is used. |
1588 |
|
o seaice_growth.F: make capping of ice volume conserving by returning the |
1589 |
|
capped ice as freshwater to EmPmR. This does not change the verification |
1590 |
|
experiments but will change runs where the capping is acutally active |
1591 |
|
o change reference platform+compiler from faulks+g77 to baudelaire+gfortran |
1592 |
|
(except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5, |
1593 |
|
global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD), |
1594 |
|
lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd) |
1595 |
|
o tools/genmake2: |
1596 |
|
- merge genmake_warnings & genmake_errors into 1 log file: "genmake.log") |
1597 |
|
- change DUMPSTATE default to false (can use "-ds" option to switch it to T) |
1598 |
|
- clean previous genmake log files before anything else. |
1599 |
|
- change Makefile to remove testreport log files (*.tr_log) and genmake log |
1600 |
|
files only with "CLEAN" target (instead of "Clean"); |
1601 |
|
o pkg/generic_advdiff: |
1602 |
|
Change OBCS in multiDim advection (gad_advection.F): |
1603 |
|
Use maskInC to prevent intermediate update of tracer-field in OB regions, |
1604 |
|
thus keeping current-time-step OB values; and remove the call to OBCS_APPLY |
1605 |
|
which were applying future time-step OB values. |
1606 |
|
This way, all explicit calculations use current-time-step OB values |
1607 |
|
(simpler and more consistent). |
1608 |
|
Affects results when set-up uses time-varying OBC and multi-dim advection; |
1609 |
|
update output of experiment seaice_obcs. |
1610 |
|
o pkg/seaice: |
1611 |
|
move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h: |
1612 |
|
this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH & |
1613 |
|
SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY. |
1614 |
|
Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY |
1615 |
|
but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp |
1616 |
|
unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h) |
1617 |
|
o pkg aim (2010/10/26): |
1618 |
|
- Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation |
1619 |
|
formulation with obliquity, eccentricity, ... as run-time parameters, |
1620 |
|
- Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and |
1621 |
|
upward shortwave radition at the surface (all-sky and clear-sky). |
1622 |
|
o pkg/obcs: |
1623 |
|
- writing sections with globalFiles=T does not work: switch to tiled-files |
1624 |
|
when writing sections for OBCS (change pkg/rw/write_rec.F accordingly). |
1625 |
|
- fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F |
1626 |
|
- apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs |
1627 |
|
|
1628 |
|
checkpoint62m (2010/10/21) |
1629 |
|
o pkg/seaice: vectorize seaice_solve4temp.F |
1630 |
|
- move iterations loops outside of i/j-loops |
1631 |
|
- requires 2D arrays for TB and effConduct |
1632 |
|
- add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is |
1633 |
|
modified in this routine |
1634 |
|
- a little bit of clean up, adjusting indentation, etc. |
1635 |
|
- replaced a few TEN**a by exp(a*log(10.)) in new code for better |
1636 |
|
performance and '**TWO' by '**2' (because TWO is a float), |
1637 |
|
replaced ONE, ZERO |
1638 |
|
o eesupp/src: |
1639 |
|
fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube |
1640 |
|
o pkg/seaice/seaice_growth.F |
1641 |
|
Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and |
1642 |
|
merging process. The merged routine has two branches, and one activates the 'evolution' |
1643 |
|
branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now). |
1644 |
|
In summary, here is what the '10/10 revision' did consist of |
1645 |
|
part 1: seaice_growth.F revisions 1.71 to 1.75 |
1646 |
|
- Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged. |
1647 |
|
The emphasis here was on improving readability (e.g. by trying to use meaningful |
1648 |
|
variable names) and modularity (e.g. by adding arrays to store heff etc. updates). |
1649 |
|
part 1.5: |
1650 |
|
- revising the lab_sea experiment to make it a more useful (i.e. stable |
1651 |
|
and representative of an actual model run). This was done by generating a |
1652 |
|
(winter) pickup to start from, switching back the main experiment dynamic |
1653 |
|
solver from evp to lsr, having one of the experiments use the free drift solution. |
1654 |
|
part 2: seaice_growth.F revisions 1.76 to 1.85 |
1655 |
|
- Sorting out hard-coded constants that prevented heat and fresh water conservation. |
1656 |
|
- Sorting out the various fields units and sign (set early on and reset at the end) |
1657 |
|
to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and |
1658 |
|
fresh water stock is 'effective ice meters', and >0 implies more ice/snow. |
1659 |
|
- Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks, |
1660 |
|
and simplifying logical expressions to further improve readibility. |
1661 |
|
part 3: seaice_growth.F revisions 1.86 to 1.89 |
1662 |
|
- Re-organize the blocks of code more logically. |
1663 |
|
- Merging the '_if.F' pieces that add something new. |
1664 |
|
o pkg/thsice: |
1665 |
|
- vectorize thsice_solve4temp and thsice_get_exf. |
1666 |
|
Problem: thsice_solve4temp has an unvectorizable statement that |
1667 |
|
might also be problematic for TAF |
1668 |
|
- thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This |
1669 |
|
does not change the verifcation experiment, but will change all |
1670 |
|
experiments that have this flag undefined (not tested in verification); |
1671 |
|
a little reorganization to save a few 2D fields and recomputations |
1672 |
|
- 1st step of revisiting thsice adjoint (major recomp. sorted out) |
1673 |
|
- 2nd step: fix some store dirs |
1674 |
|
o seems to work somewhat, i.e. using ifort but not g77 |
1675 |
|
o likely cause are incomplete init. or recomputation |
1676 |
|
o start verification/global_ocean.cs32x15/input_ad.thsice |
1677 |
|
o pkg/obcs: add support for exch2 |
1678 |
|
- the position of the boundary and prescribed values are specified using |
1679 |
|
a global domain with exch2 facets stacked |
1680 |
|
- in x for N,S boundaries (like W2_mapIO=-1) |
1681 |
|
- in y for E,W boundaries (so E,W boundaries do not overlap) |
1682 |
|
o pkg/mdsio: add support for writing global sections with exch2 |
1683 |
|
file layout is as for obcs described above: |
1684 |
|
- for x-z sections, facets are stacked in x (like W2_mapIO=-1) |
1685 |
|
- for y-z sections, facets are stacked in y |
1686 |
|
o pkg/thsice: |
1687 |
|
- change a few routines for better vectorization: thsice_albedo.F, |
1688 |
|
thsice_step_temp.F, and in thsice_calc_thickn.F. Results are |
1689 |
|
not affected, but in particular the latter routine has changed |
1690 |
|
dramatically (not necessarily easier to read now). |
1691 |
|
- re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops |
1692 |
|
iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF. |
1693 |
|
o verification/lab_sea: |
1694 |
|
- overhaul of the forward model experiments. The main motivation |
1695 |
|
for this revision is that lab_sea has proven quite fragile (when |
1696 |
|
changing the sea-ice code, and switching platforms) to a point |
1697 |
|
when failures were very hard to attribute to specific code problems. |
1698 |
|
- the suspected reason for this fragility is noise amplification by evp so, |
1699 |
|
to start with, we decided to replace evp with lsr in the main experiment. |
1700 |
|
- the input.lsr experiment thus became obsolete and was removed. |
1701 |
|
- it was replaced with the input.fd experiment that uses an |
1702 |
|
analytical "free drift" solution as the ice velocity field. |
1703 |
|
- Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp) |
1704 |
|
will hopefully allow us to discriminate problems due to dynamic solvers |
1705 |
|
from problems due to the thermodynamic code. input.salt_plume (lsr) allows |
1706 |
|
us to test additional options, along with the salt plume package. |
1707 |
|
- Finally a pickup was generated (at the end of a one year run) to |
1708 |
|
make the tests more representative of an actual model run. Previously |
1709 |
|
the tests starting point was a 1m thickness of ice everywhere. |
1710 |
|
o pkg/seaice: |
1711 |
|
- introducing S\R seaice_freedrift.F that compute the |
1712 |
|
analytical solution to an approximate ice momentum |
1713 |
|
equation (i.e. the simple stress/coriolis balance). |
1714 |
|
- define SEAICE_ALLOW_FREEDRIFT to trigger the computation |
1715 |
|
of the free drift velocity field, and enable its use. |
1716 |
|
To actually use the free drift solution as the model ice |
1717 |
|
velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice. |
1718 |
|
o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata" |
1719 |
|
|
1720 |
|
checkpoint62l (2010/10/04) |
1721 |
|
o pkg/seaice: |
1722 |
|
-fix the USE_ORIGINAL_SBI version (for variable freezing point); |
1723 |
|
-use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new |
1724 |
|
version (with USE_ORIGINAL_SBI undef); |
1725 |
|
o add hooks for new packages OASIS, the package will follow |
1726 |
|
(hooks exclude the seaice pkg for now) |
1727 |
|
o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO |
1728 |
|
Option to use mdsio_read_whalos.F/mdsio_write_whalos.F, |
1729 |
|
rather than mdsio_readvector.F/mdsio_writevector.F, within |
1730 |
|
adread_adwrite.F to read/write adjoint-related tapes to disk. |
1731 |
|
o eesupp and pkg/mdsio: ALLOW_WHIO |
1732 |
|
Option to write/read 2D fields to files including tiles halos. |
1733 |
|
The main purpose is for adjoint related "tape I/O". |
1734 |
|
The secondary purpose is for debugging phases. |
1735 |
|
A word on those rather specifically intended purposes. |
1736 |
|
The code was meant to be stripped down to the bare minimum. |
1737 |
|
Typically, there is a unique and basic mapping to the global |
1738 |
|
buffer (tile by tile, then proc by proc, then level by level), and |
1739 |
|
byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not |
1740 |
|
meant to generate user friendly outputs of various shapes and forms. |
1741 |
|
Rather it is intended, for the knowledgeabale developers, |
1742 |
|
to be largely independent of the many mdsio options, to allow |
1743 |
|
outputs of tiles+halos in debugging phases and in adjoint runs, |
1744 |
|
and to allow some flexibility in tuning (adoint) I/O depending on each |
1745 |
|
file system behavior. With regard to tuning, most of the potential knobs |
1746 |
|
(to leave files open, to allocate the I/O indep. of usesinglecpuio, |
1747 |
|
to specify directories, to specify the typical size of I/O calls, etc.) |
1748 |
|
are not yet included, and will be added if they prove useful. |
1749 |
|
o pkg/seaice: |
1750 |
|
fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F |
1751 |
|
o pkg/seaice: |
1752 |
|
new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty |
1753 |
|
code (seaice_budget_ice_if.F) which enable to recover old standard |
1754 |
|
code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined. |
1755 |
|
temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F. |
1756 |
|
o model/src (rStar): |
1757 |
|
use simple average (not area weighted) of rStarFac at U,V point when using |
1758 |
|
vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection) |
1759 |
|
update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20. |
1760 |
|
|
1761 |
|
checkpoint62k (2010/09/17) |
1762 |
|
o adjoint |
1763 |
|
* changed verification/global_ocean.cs32x15 ; adjoint now tests |
1764 |
|
Adams-Bashforth 3 + NLFS + RSTAR |
1765 |
|
* some more modifs required for ECCO-GODAE v4 |
1766 |
|
o pkg/seaice |
1767 |
|
add SEAICE_AGE_VOL option to use volume instead of area for |
1768 |
|
integrating SEAICE_AGE |
1769 |
|
o model/src: |
1770 |
|
first check-in of sigma & hybrid-sigma coordinate code ; also includes |
1771 |
|
non-linear free-surface parts ; but pressure-gradient not yet coded. |
1772 |
|
o pkg/ptracers: |
1773 |
|
option for ptracer to convert Salt Relax into additional EmP. |
1774 |
|
tested in exp. global_ocean.90x40x15.dwnslp (update output) |
1775 |
|
|
1776 |
|
checkpoint62j (2010/08/25) |
1777 |
|
o pkg/ggl90: |
1778 |
|
other minor changes: remove 3-D temp array gTKE (+ add argument myIter) |
1779 |
|
o pkg/dic: car_flux.F, phos_flux.F |
1780 |
|
- reduce number of exp-calls in order to improve performance |
1781 |
|
- clean up a little (replace fields by their macros, etc., fix |
1782 |
|
typo in CPP-flag) |
1783 |
|
o pkg/ggl90: minor changes |
1784 |
|
- GGL90diffKrS was removed --> always use GGL90diffKr |
1785 |
|
- GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV |
1786 |
|
- hack of mxlMaxFlag=2 --> ensure mixing between first and second level |
1787 |
|
(commented out for now) |
1788 |
|
- change in max/min operations to ensure that smoothing is ok |
1789 |
|
- smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr) |
1790 |
|
- always use diffKrNrT as background profile (i.e. never use diffKr field) |
1791 |
|
o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj) |
1792 |
|
o pkg/dic: |
1793 |
|
- model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better |
1794 |
|
vectorization |
1795 |
|
- small bug fix in insol for the unlikely case of a cartesian grid |
1796 |
|
- towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F |
1797 |
|
+ now vectorize, which also removes adjoint recomputations; |
1798 |
|
+ replace integer maksp1 by _RL maskp1 |
1799 |
|
+ replace a**x by exp(x*log(a)) in phos_flux.F for speed |
1800 |
|
|
1801 |
|
checkpoint62i (2010/07/21) |
1802 |
|
o pkg/flt: |
1803 |
|
- with OBCS: stop floats which enter the OB region |
1804 |
|
o model/src: |
1805 |
|
- use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones) |
1806 |
|
for implicit vertical advection. |
1807 |
|
o pkg/seaice: |
1808 |
|
- account for melting in seaice age evolution. |
1809 |
|
- remove double counting of seaice ridging effect on seaice age. |
1810 |
|
|
1811 |
|
checkpoint62h (2010/06/18) |
1812 |
|
o pkg/exch2: |
1813 |
|
- remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1). |
1814 |
|
o tools/genmake2 |
1815 |
|
- remove "-pdefault" option: redundant with the use of "packages.conf"; |
1816 |
|
- remove file pkg/pkg_default : set the default as a pkg group |
1817 |
|
("default_pkg_list") defined in pkg/pkg_groups; |
1818 |
|
- fix for case pkg/pkg_depend is missing (was hanging before); |
1819 |
|
- add option "-pgroups" to specify a different pkg_groups than the default. |
1820 |
|
o verification/adjustment.cs-32x32x1: |
1821 |
|
add a "minimal" set-up test (code_min & input_min) which only compiles |
1822 |
|
eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc. |
1823 |
|
o tools/genmake2 |
1824 |
|
- extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg])) |
1825 |
|
- fix details of checking for mnc & profile pkg when NetCDF is unavailable. |
1826 |
|
o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these |
1827 |
|
files are nearly the same anyway. |
1828 |
|
Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04: |
1829 |
|
- redefinition of tau(i,i) (by a factor of ustar) |
1830 |
|
- 1./exf(Const/T) -> exf(-Const/T) (big change in the results) |
1831 |
|
- replace rhonil by rhoConstFresh in computation of evap (bug fix) |
1832 |
|
- replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results) |
1833 |
|
- replace |
1834 |
|
rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh ) |
1835 |
|
shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j) |
1836 |
|
by |
1837 |
|
shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh ) |
1838 |
|
(changes results) |
1839 |
|
-> exf_bulkformulae v1.22, |
1840 |
|
update verification experiments lab_sea, offline_exf_seaice, seaice_obcs |
1841 |
|
(lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13, |
1842 |
|
output.txt 1.63 |
1843 |
|
offline_exf_seaice: output.seaicetd.txt 1.7 |
1844 |
|
seaice_obcs: output.txt 1.10) |
1845 |
|
Step 2: do the actual merge and remove exf_bulk_largeyeager04.F |
1846 |
|
-> exf_bulkformulae v1.23, |
1847 |
|
unfortunately requires updating lab_sea.salt_plume (6 matching digits), |
1848 |
|
and global_ocean.cs32x15.icedyn (only 11 matching digits) |
1849 |
|
Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice. |
1850 |
|
o adjoint of exch-1: |
1851 |
|
- pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list) |
1852 |
|
(note: was already like this when using EXCH-2) and remove flow dir |
1853 |
|
and hand-written AD version of high-level EXCH S/R (pkg/autodiff); |
1854 |
|
- provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow); |
1855 |
|
- update pkg/exch2 diff list. |
1856 |
|
|
1857 |
|
checkpoint62g (2010/05/19) |
1858 |
|
o eesupp/src (exch-1): |
1859 |
|
- split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F) |
1860 |
|
and remove argument "simulationMode"; same thing for all exch_*rx_cube.F |
1861 |
|
(renamed to exch1_*rx_cube.F). |
1862 |
|
- change accordingly exch_*_rx.template and AD version in pkg/autodiff |
1863 |
|
to call new exch1 S/R ; update Makefile and .cvsignore. |
1864 |
|
- replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove |
1865 |
|
exch2_xy_rx later) |
1866 |
|
Note: after updating your code, need to run "make clean" in eesupp/src |
1867 |
|
o test experiment bottom_ctrl_5x5: |
1868 |
|
new output_adm.txt with fewer grdchk & less monitor output. |
1869 |
|
o model/src: |
1870 |
|
remove the call to ini_cori in initialise_varia.F (just keep the usual one |
1871 |
|
in initialise_fixed.F). More consistent with coriolis & horizontal grid |
1872 |
|
beeing treated in the same way (ini_grid is not called a 2nd time). |
1873 |
|
o pkg/exf: |
1874 |
|
- rewrite exf_bulk_largeyeager04.F for better vectorization, changes |
1875 |
|
global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated |
1876 |
|
- fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now) |
1877 |
|
- cosmetic changes to exf_bulkformulae.F to make it look more like |
1878 |
|
exf_bulk_largeyeager04.F |
1879 |
|
o eesupp/src (exch-1): |
1880 |
|
- Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1). |
1881 |
|
- Separate buffer filling and MPI sending: allow EXCH-1 to work for local |
1882 |
|
array (non-shared) when using MPI+MTH. Also reduces number of BARRIER |
1883 |
|
(even without using MPI). |
1884 |
|
- Message mode: move RecvAck setting (indicator of buffer being ready) |
1885 |
|
from send_put to recv_get S/R (was useless before, but not sure if |
1886 |
|
it's much more useful now); |
1887 |
|
- Switch the order of sync: MPI-proc 1rst and then threads; |
1888 |
|
- take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead. |
1889 |
|
- fix AD code for communication mode ='get' (but not used). |
1890 |
|
o model/src: |
1891 |
|
initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does |
1892 |
|
not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp). |
1893 |
|
o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API |
1894 |
|
o pkg/ctrl: require a specific set of control variables and exf-flags for |
1895 |
|
adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied) |
1896 |
|
o model/src: |
1897 |
|
a) 1rst version of a new driver S/R to turn-off output freq and flags after the |
1898 |
|
1rst forward sweep, to avoid over-writing output files during recomputations |
1899 |
|
recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?) |
1900 |
|
b) 2nd version: |
1901 |
|
- add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO); |
1902 |
|
- switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast, |
1903 |
|
writePickupAtEnd) + seaice & ptracers output; |
1904 |
|
- do not switch off MNC flags (otherwise, won't get admonitor netcdf file) |
1905 |
o model/src: |
o model/src: |
1906 |
- new S/R rotate_uv2en_rl (..._rs) that rotates vector fields. |
- new S/R rotate_uv2en_rl (..._rs) that rotates vector fields. |
1907 |
o pkg/exch2: |
o pkg/exch2: |
1908 |
- remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ; |
- remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ; |
1909 |
- add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch). |
- add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch). |
1910 |
o pkg/autodiff & exch2: |
o pkg/autodiff & exch2: |
1911 |
process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF |
process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF |
1912 |
(for now, only if ALLOW_EXCH2 is defined). |
(for now, only if ALLOW_EXCH2 is defined). |
1913 |
o pkg/autodiff: |
o pkg/autodiff: |
1914 |
- include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F |
- include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F |
1915 |
(not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly. |
(not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly. |
1916 |
+ clean-up comments (_RS is not always real*4) |
+ clean-up comments (_RS is not always real*4) |
1917 |
- fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R) |
- fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R) |
2035 |
but keep the former optfile for few weeks for smooth transition |
but keep the former optfile for few weeks for smooth transition |
2036 |
o pkg/ecco |
o pkg/ecco |
2037 |
- allow user defined cost function contributions |
- allow user defined cost function contributions |
2038 |
CPP: ALLOW_USERCOST_CONTRIBUTION |
CPP: ALLOW_USERCOST_CONTRIBUTION |
2039 |
USAGE: compute contributions in cost_usercost_all.F |
USAGE: compute contributions in cost_usercost_all.F |
2040 |
- note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. |
- note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. |
2041 |
the two options are complementary. |
the two options are complementary. |
2042 |
o pkg/smooth |
o pkg/smooth |