4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
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|
7 |
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o pkg/obcs (Stevens BCs): |
8 |
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- fix various problems in the phase speed computations of the Stevens |
9 |
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boundary conditions: |
10 |
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- sign error for western and southern boundaries, |
11 |
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- time tendencies were underestimated by factor of dTracerLev and some just |
12 |
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zero (for multidim advection schemes) -> now estimate time tendencies |
13 |
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from difference between previous (n) time level and the one before (n-1); |
14 |
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this requires storing a field per tracer per boundary, also in the pickup |
15 |
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files. |
16 |
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- replace deltaTmom in cflMer/Zon computation with dTracerLev |
17 |
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- set default phase velocity to cflMer/Zon |
18 |
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- update verification experiment exp4.stevens |
19 |
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o pkg/generic_advdiff (implicit_r): |
20 |
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- fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf |
21 |
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(remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F); |
22 |
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- fix implicit vertical diffusion or advection with NonLin FreeSurf |
23 |
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(was using current recip_hFacC instead of future recip_hFacC): set future |
24 |
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recip_hFac in thermodynamics.F and pass & use it in all vertical implicit |
25 |
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solver S/R ; |
26 |
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- fill diagnostics of vertical advective fluxes (computed from tendency) |
27 |
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when using implicit vert. advection; |
28 |
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- update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion: |
29 |
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global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD), |
30 |
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tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD) |
31 |
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and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5. |
32 |
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o pkg/diagnostics: |
33 |
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- add diags for T & S tendency which goes through Adams-Bashforth. |
34 |
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|
35 |
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checkpoint63f (2011/11/30) |
36 |
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o pkg/obcs/obcs_calc_stevens.F: |
37 |
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- join some loops to reduce number of if-statements |
38 |
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- fix a bug in code for northern and southern boundaries. |
39 |
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o pkg/seaice/seaice_init_varia.F |
40 |
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- undo resetting UVM=0 that has slipped in unnoticed in r1.49 and |
41 |
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caused zero ice-velocities for the B-grid code |
42 |
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o pkg/seaice/seaice_init_fixed.F |
43 |
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- fix a bug in the initialisation of the second metric terms |
44 |
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k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0. |
45 |
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- this affects all seaice configurations with useCurviLinearGrid = .true. |
46 |
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and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms |
47 |
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= .true. (default) |
48 |
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- the only verification experiment affected is global_ocean.cs32x15: |
49 |
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icedyn, seaice, and seaice_dynmix (AD) |
50 |
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o pkg/thsice/thsice_diagnostics_state.F |
51 |
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- only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does |
52 |
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not contain garbage that can lead to surprises in diagstats_calc.F |
53 |
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o model/src: |
54 |
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- move bi,bj loops inside INTEGR_CONTINUITY ; |
55 |
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- call INTEGR_CONTINUITY directly from forward_step.F |
56 |
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(previously called from momentum_correction_step.F) |
57 |
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- call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F, |
58 |
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forward_step.F and pkg/ecco/the_main_loop.F |
59 |
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o model/src/do_oceanic_phys.F: |
60 |
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- reset addMass to zero only if useICEFRONT ; |
61 |
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- separated k-loop for rhoInSitu calculation ; |
62 |
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- add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P) |
63 |
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and at constant T,S (= WdRHOdP); |
64 |
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NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport |
65 |
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of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical |
66 |
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transport of locally-referenced potential density); |
67 |
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to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP) |
68 |
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o gluemnc: |
69 |
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- replace ncrcat with ncks when adding variables to *.glob.nc |
70 |
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- change the way variables without record dimensions are handled so that |
71 |
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files that have variables with and without record variables can be glued: |
72 |
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add a record dimension with a new unique name to be able to differentiate |
73 |
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between variable with and without a-prior record dimensions. Remove |
74 |
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this record dimension before adding the variable to the *.glob.nc file. |
75 |
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This procedure automatically works also for grid.*.nc files that do not |
76 |
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have any record dimension. |
77 |
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o verification/cpl_aim+ocn: |
78 |
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- generate new reference output on baudelaire (gfortran, mpich2) (previously |
79 |
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from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script. |
80 |
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o pkg/obcs/obcs_calc_stevens.F: |
81 |
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- add code for northern and southern boundaries. |
82 |
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- reorder some loops to save some operations and so that drFBar can be scalar |
83 |
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o model/src: |
84 |
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- re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine |
85 |
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truncation) and add diagnostics for Adams-Bashforth tendency increment. |
86 |
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- update test-exp. AD output: |
87 |
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1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl; |
88 |
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and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20, |
89 |
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front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5), |
90 |
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global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4), |
91 |
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matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre, |
92 |
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tutorial_global_oce_in_p, tutorial_global_oce_latlon and |
93 |
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tutorial_plume_on_slope. |
94 |
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o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX |
95 |
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that vectorises. This code uses 3 extra 2D fields, F90 array assignments |
96 |
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and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX |
97 |
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does not even come with an F77 compiler anymore, this should not be |
98 |
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a limitation |
99 |
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|
100 |
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checkpoint63e (2011/11/06) |
101 |
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o pkg/seaice adjoint of LSR: |
102 |
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- substantially rework STORE dirs. |
103 |
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- add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED |
104 |
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this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields |
105 |
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and only perform SOLV_MAX_FIXED adjoint iters. |
106 |
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If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration |
107 |
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always goes to same record, meaning that the last forward field will be |
108 |
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the one used in the adjoint - an approximation. |
109 |
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- now produces non-zero LSR-related gradients, and acceptable gradients for |
110 |
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An's zonal (x-z) test case (to be checked in) |
111 |
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- lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR |
112 |
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(but these are screwed up by the thermodynamics in the first place); |
113 |
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reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution; |
114 |
|
output_adm.txt also reflects changes to seaice_lsr |
115 |
|
- global_ocean.cs32x15: |
116 |
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* the "default" input_ad.seaice has been re-defined to always exclude dynamics |
117 |
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(output_adm.seaice.txt was updated) |
118 |
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* new input_ad.seaice_dynmix tests a forward LSR / backward free-drift |
119 |
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(output_adm.seaice_dynmix.txt) |
120 |
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o test-exp. exp4+stevens: |
121 |
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- switch off pTracers and nonHydrostatic (restart problems with NH); update output |
122 |
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o pkg/seaice (lsr solver): |
123 |
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- put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only); |
124 |
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update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15 |
125 |
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- fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD) |
126 |
|
- new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution |
127 |
|
into initial guess for linearised solver; use weight ~ (1/err)^2,4. |
128 |
|
- compute (with new S/R) and print initial (+ free-driff sol. if available) |
129 |
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and final residual of linearised system. |
130 |
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o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity |
131 |
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(requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F) |
132 |
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o pkg/obcs: Stevens BCs (still only for east and west) |
133 |
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- fix Stevens BCs by using intermediate velocities of previous |
134 |
|
time step as "baroclinic" contribution rather velocity of one grid cell |
135 |
|
inside the boundaries; more consistent but makes the entire treatment |
136 |
|
more complicated, requires new pickup files and two new S/Rs: |
137 |
|
obcs_copy_uv_n and obcs_save_uv_n |
138 |
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keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY |
139 |
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(undefined by default) |
140 |
|
- silently move computation of some grid factors into separate loops to |
141 |
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save some recomputations |
142 |
|
- add a hack for non-linear free surface |
143 |
|
- add a verification experiment to exp4 that tests this code |
144 |
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o make gluemnc/xplodemnc work with (moron) non-GNU shell tools |
145 |
|
|
146 |
|
checkpoint63d (2011/10/25) |
147 |
|
o pkg/obcs + seaice-dynamics: |
148 |
|
- new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before |
149 |
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solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB |
150 |
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values (consistent with an implicit method). |
151 |
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- add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to |
152 |
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return to older implementation (same results as before); note that none of |
153 |
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the "experimental" OBCS_SEAICE options are implemented in the new version. |
154 |
|
- switch test exp. seaice_obcs to use new version (update output). |
155 |
|
o pkg/seaice: |
156 |
|
- add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS) |
157 |
|
- add parenthesis in Water-Ice drag calculations (evp & lsr); |
158 |
|
- in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1; |
159 |
|
and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice) |
160 |
|
- update output of test exp lab_sea that uses evp or lsr (fwd+ad) |
161 |
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and global_ocean.cs32x15 (icedyn & seaice fwd+ad). |
162 |
|
o pkg/layers: |
163 |
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- Include potential density as new coordinate (Thanks to David Munday) |
164 |
|
o pkg/dic: |
165 |
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- Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add |
166 |
|
carbonate computation/output to CALC_PCO2_APPROX |
167 |
|
o pkg/generic_advdiff |
168 |
|
- make TAF generate code that vectorizes: |
169 |
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gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F |
170 |
|
o model/src: |
171 |
|
- improve vectorization also for adjoint code of |
172 |
|
solve_tridiagonal and solve_pentadiagonal. As this requires up to |
173 |
|
5 new 3D-fields, this code is only turned on for the combination of |
174 |
|
ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message |
175 |
|
for singular matrix check (only for TARGET_NEC_SX). |
176 |
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- remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to |
177 |
|
ALLOW_AUTODIFF. This flag now needs to be set outside of |
178 |
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solve_tri/pentadiagonal.F |
179 |
|
o pkg/exf: |
180 |
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- fix previous modif in exf_readparms.F (revision 1.66: treatment of |
181 |
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optional namelist EXF_NML_OBCS). |
182 |
|
- add many debug-print (to trace down where pkg/cal error msg comes from) |
183 |
|
o pkg/mom_vecinv/mom_vi_hdissip.F |
184 |
|
- rearrange loops so that vectorization is improved and in particular |
185 |
|
the adjoint routine vectorizes. The code is a little longer now, but I |
186 |
|
think easier to read. |
187 |
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Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested. |
188 |
|
o pkg/seaice: |
189 |
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- allow to specify initial seaice velocity from files (uIceFile,vIceFile) |
190 |
|
o pkg/exch2: |
191 |
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- alternative code (without tile x tile matrix) for cumulated (global) sum; |
192 |
|
used as default; keep using matrix version in adjustment.cs-32x32x1. |
193 |
|
o tools/build_options: |
194 |
|
- after merging some MPI and/or multi-threads specific optfiles so that |
195 |
|
the modified default optfile support both built (using genmake2 -mpi |
196 |
|
for the MPI built, using genmake2 -omp for OpenMP built), |
197 |
|
move now obsolete optfiles to tools/build_options/unsupported/ |
198 |
|
(add copy of email sent to support list in doc/optfiles_changes.txt) |
199 |
|
|
200 |
|
checkpoint63c (2011/09/28) |
201 |
|
o pkg/ebm: |
202 |
|
- fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of |
203 |
|
test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d) |
204 |
|
o pkg/seaice (SItracer pickup) |
205 |
|
* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER) |
206 |
|
To be done: |
207 |
|
- thorough testing of missing fields in S/R seaice_read_pickup |
208 |
|
- thorough matching between generic tracers and specific fields used |
209 |
|
(e.g. volume-weighted age, area-weighted age, salinity, ...) |
210 |
|
o pkg/grdchk: |
211 |
|
- all procs calculate and print finite-difference gradient (for testreport) |
212 |
|
- change description output used by testreport; |
213 |
|
- AD testing: also compare and report Finite-difference gradient; |
214 |
|
=> update all output_adm*.txt |
215 |
|
o test exp. global_ocean_ebm: |
216 |
|
- switch back useRealFreshWaterFlux (no problem anymore with run-off); |
217 |
|
and turn on exactConserve; update (fwd) output. |
218 |
|
o pkg/seaice (LSR): |
219 |
|
- print to STDOUT number of solver iterations at SEAICE_monFreq interval. |
220 |
|
- modify solver to deal cleanly with u/v switch at face edges (CS-grid): |
221 |
|
* identical results with non-CS topology (but save up to half of EXCH calls) |
222 |
|
* no much changes in cs-32 verification tests since no ice at face edges |
223 |
|
(differences due to convergence criteria, since nb of iterations changed) |
224 |
|
* expect some differences on lat-lon-cap grid. |
225 |
|
update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice) |
226 |
|
o pkg/exch2: |
227 |
|
- add new CPP option to disable Cumul-Sum matrix (to save storage when using |
228 |
|
many tiles); until alternative coding is added, just add a stop. |
229 |
|
o pkg/kpp: |
230 |
|
- move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F |
231 |
|
to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list). |
232 |
|
o optfiles: |
233 |
|
- merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles |
234 |
|
into corresponding standard one, which now support different build: |
235 |
|
(when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built) |
236 |
|
- add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael) |
237 |
|
o pkg/obcs (seaice): |
238 |
|
- add missing EXCH for uIce,vIce after applying OBCS; |
239 |
|
- remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding |
240 |
|
argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R |
241 |
|
EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F; |
242 |
|
- fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared) |
243 |
|
- verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi |
244 |
|
and eedata.mth for MPI and mutlti-threaded testing. |
245 |
|
o pkg/flt: |
246 |
|
- make FLT EXCH working with multi-threads (and MPI + multi-threads); |
247 |
|
- use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h; |
248 |
|
- fix pickup and trajectories + profiles output with multi-threads; |
249 |
|
- add parameter to select group of fields to write along trajectory and |
250 |
|
profile (default unchanged); |
251 |
|
- only call PORT_RAND* function when flt_noise <> 0; |
252 |
|
- add multi-threaded test for verification exp. flt_example. |
253 |
|
o eesupp/src: |
254 |
|
- fix S/R ALL_PROC_DIE for MPI+multi-threads. |
255 |
|
- USE_OMP_THREADING: check that number of threads (from eedata) matches |
256 |
|
actual number (from env.var. setting). |
257 |
|
o pkg/ebm: |
258 |
|
- fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file. |
259 |
|
- add multi-threaded test for verification exp. global_ocean_ebm |
260 |
|
|
261 |
|
checkpoint63b (2011/08/29) |
262 |
|
o pkg/ebm: |
263 |
|
- fix sign of runoff; |
264 |
|
- update directly forcing fields (Qnet,EmPmR) to use standard |
265 |
|
external_forcing_surf.F (remove ebm_forcing_surf.F); |
266 |
|
- avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F); |
267 |
|
- set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm) |
268 |
|
and apply relaxation towards corresponding SST field (2-D map or ZonAver). |
269 |
|
- update global_ocean_ebm parameters file data and update output (fwd+ad). |
270 |
|
o verification/matrix_example: |
271 |
|
- split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for |
272 |
|
MPI and mutlti-threaded testing. |
273 |
|
o pkg/matrix: |
274 |
|
- change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ; |
275 |
|
- fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter); |
276 |
|
- fix for multi-threaded (remove DATA statement); |
277 |
|
- use standard DIFFERENT_MULTIPLE function; |
278 |
|
- add MATRIX_OPTIONS.h |
279 |
|
o verification/matrix_example: |
280 |
|
To allow to split the domain in several tiles, change the domain size |
281 |
|
from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on |
282 |
|
Western side) of land points. |
283 |
|
o (*_)write_pickup: |
284 |
|
- fix few bugs in mypackage_read/write_pickup.F |
285 |
|
- in MDS_WR_METAFILES calls, replace "myTime" by a local copy into |
286 |
|
array of length 1 (was caught by compiler syntax-check). |
287 |
|
o pkg/diagnostics (velocity potential solver): |
288 |
|
- fix initialisation of main diagonal matrix (for overlap values) |
289 |
|
o tools/build_options: |
290 |
|
- towards single optfile for MPI and non-MPI built: merge few +mpi optfile |
291 |
|
into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11) |
292 |
|
- linux_amd64_gfortran: merge +mpi_generic version into standard optfile: |
293 |
|
* move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ; |
294 |
|
* FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list; |
295 |
|
and use "-devel" testreport option for standard testing on baudelaire. |
296 |
|
o pkg/grdchk: |
297 |
|
- Assume that all gradient-check position are within the same tile |
298 |
|
corresponding to global indices (iGloTile,jGloTile) and that |
299 |
|
positions (i,j indices or nbeg) are local to this tile; |
300 |
|
- set tile local-indices and proc. number according to tile global-indices; |
301 |
|
- remove grdchkwhichproc from namelist (retired param); |
302 |
|
- send adjoint gradient to all procs so that all procs print it to STDOUT; |
303 |
|
- switch on MPI test for global_ocean.90x40x15 AD test experiment. |
304 |
|
o adding package bbl (Bottom Boundary Layer) |
305 |
|
description in MITgcm/pkg/bbl/bbl_description.tex |
306 |
|
example/test experiment in MITgcm_contrib/bbl |
307 |
|
o adjoint verifications |
308 |
|
- changed 5 experiments to multi-tiles |
309 |
|
* global_ocean.90x40x15 |
310 |
|
* obcs_ctrl |
311 |
|
* offline_exf_seaice |
312 |
|
* tutorial_dic_adjoffline |
313 |
|
* tutorial_tracer_adjsens |
314 |
|
changed reference output for those that crossed tile boundaries |
315 |
|
(changed choices of gradient check positions) |
316 |
|
- with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi) |
317 |
|
- temporary bug fix in grdchk_loc.F for obcs |
318 |
|
o genmake2 & testreport |
319 |
|
- add target "obj" (just for OBJFILES files) to Makefile; |
320 |
|
- add option to specify FEXTRAFLAGS on command line. |
321 |
|
o pkg/mypackage: |
322 |
|
- remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS |
323 |
|
|
324 |
|
checkpoint63a (2011/08/02) |
325 |
|
o pkg/diagnostics (velocity potential): |
326 |
|
- fix velocity-potential calculation when using OBCS: balance net inflow |
327 |
|
at each level (new S/R OBCS_DIAG_BALANCE). |
328 |
|
- fix some of the problems with OBCS in stream-function calculation. |
329 |
|
o pkg/exf/exf_readparms.F |
330 |
|
- make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF, |
331 |
|
EXF_NML_OBCS) more consistent, so that you need not have these lists |
332 |
|
in data.exf when they are not used. |
333 |
|
o optim/optim_readdata.F: |
334 |
|
- add some output about obcs variables that might help debugging |
335 |
|
- add a check about nvarlength |
336 |
|
o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec |
337 |
|
o pkg/diagnostics (velocity potential): |
338 |
|
- fix mask for OBCS (still problems in stream-function with OBCS); |
339 |
|
- add specific parameter (default = main code CG2D params) for solver; |
340 |
|
- in case of poor convergence, use solution corresponding to lowest residual. |
341 |
|
o pkg/seaice/seaice_growth.F: small changes that permit vectorizable |
342 |
|
adjoint code. In general statements like tmpscal=fld(i,j) are problematic |
343 |
|
and should be avoided where possible. |
344 |
|
o model/src (rStar): |
345 |
|
- include r* effect on reference-state (PhiRef) in totPhiHyd |
346 |
|
(so that it's really the potential anomaly at the cell center); |
347 |
|
affect solution only if z* with full pressure in EOS. |
348 |
|
- test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and |
349 |
|
update output (because of z* in totPhiHyd and viscA4 changes); |
350 |
|
- keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly |
351 |
|
@ constant r) until interpolation at constant r is implemented. |
352 |
|
o pkg/diagnostics |
353 |
|
- fix RCENTER diagnostics in case cell center is not at interface middle |
354 |
|
o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use |
355 |
|
this eos with eosType = 'TEOS10', in data (PARM01). This eos implies |
356 |
|
that THETA and SALT are "conservative temperature" and "absolute |
357 |
|
salinity" |
358 |
|
o pkg/ctrl |
359 |
|
- fix computation of endrec in s/r ctrl_init_rec |
360 |
|
- ctrl_pack/unpack_*: remove unused variables and some obsolete code |
361 |
|
o pkg/seaice/seaice_growth.F |
362 |
|
- fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code, |
363 |
|
remove then obsolete STORE directives |
364 |
|
- fix STORE directives for tice and tices, so that only the |
365 |
|
appropriate part of the fields are stored (and not the entire |
366 |
|
field); update global_ocean.cs32x15.seaice AD output. |
367 |
|
- cosmetic changes: adjust CPP flags and indentation for better |
368 |
|
legibilty |
369 |
|
o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by |
370 |
|
Chris Wilson) |
371 |
|
o pkg/gmredi: |
372 |
|
Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF), |
373 |
|
and test it in verification exp. "front_relax.bvp" (update output.bvp.txt) |
374 |
|
|
375 |
|
checkpoint63 (2011/07/11) |
376 |
|
o pkg/exch2: |
377 |
|
- rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h |
378 |
|
- exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the |
379 |
|
(2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y |
380 |
|
increments, calculates Cumul-Sum @ tile origin and sends results to each tile. |
381 |
|
o pkg/diagnostics: |
382 |
|
- deal with pairs of post-processed diags which are computed together; in |
383 |
|
particular, re-order list of diags within 1 file to save 2nd computation. |
384 |
|
- add S/R to compute velocity stream-function (called after velocity-potential |
385 |
|
calculation) from divergence free transport -> new diagnostics "PsiVEL". |
386 |
|
- add parameter to select grid-point location where PsiVEL == 0. |
387 |
|
o eesupp/src: |
388 |
|
new S/R to calculate cumulated sum on tiled array, corner grid-cell location |
389 |
|
(specific S/R needed with exch2 topology - for now, just print an error msg) |
390 |
|
o pkg/shelfice |
391 |
|
- Implement friction velocity-dependent transfer coefficients following |
392 |
|
Holland and Jenkins, JPO, 1999 |
393 |
|
Original code by M. Losch with small modifs. |
394 |
|
Enable with CPP option SHI_ALLOW_GAMMAFRICT |
395 |
|
and runtime flag SHELFICEuseGammaFrict |
396 |
|
o verification lab_sea & global_ocean.cs32x15: |
397 |
|
- use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local): |
398 |
|
does not miss some dependencies (but is slower) and also works with many files |
399 |
|
(default makedepend limitation for AD built). |
400 |
|
- use cyrus_makedepend in adjustment.128x64x1 (so that it still tested). |
401 |
|
o pkg/diagnostics: |
402 |
|
- add run-time parameter "useMissingValue" (def=False) to fill land-point |
403 |
|
(i.e., where mask=0) with MissingValue ; used only in MNC output file. |
404 |
|
This replaces CPP-option DIAGNOSTICS_MISSING_VALUE. |
405 |
|
- Extend the use of "missing_value" setting from data.diagnostics for the case |
406 |
|
of counter-diagnostics (where fraction-weight is zero). This applies both to |
407 |
|
MNC and MDS output files. |
408 |
|
o pkg/seaice/seaice_growth.F: |
409 |
|
- add 'a priori' cap of latent heat flux based on actual mass considerations |
410 |
|
when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the |
411 |
|
non-legacy seaice_solve4temp. |
412 |
|
- add diagnostic of the residual sublimation freshwater flux (the freshwater |
413 |
|
flux taken from the ocean if the total actual latent heat fluxes exceed |
414 |
|
the maximum) |
415 |
|
- remove the CPP switch around the *_FWbySublim unit change and move diagnostic |
416 |
|
fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F. |
417 |
|
- add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef |
418 |
|
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim). |
419 |
|
- bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET. |
420 |
|
- bug fix : missing part to Martin's r_FWbySublim pathological case fix. |
421 |
|
o verification 1D_ocean_ice_column: |
422 |
|
made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet |
423 |
|
update results |
424 |
|
o pkg/diagnostics: |
425 |
|
- Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P') |
426 |
|
which are not filled-up but computed from other diags ; In this case, the mate |
427 |
|
diag points to the primary (filled-up) diag to used for post processing. |
428 |
|
- Update Velocity-potential computation using post-processed diag framework. |
429 |
|
==> Change the ordering of fields and time-periods in MDS output file |
430 |
|
when using periodic averaging: now writes one time record with the full set |
431 |
|
of fields for this time period, then the next time reccord (it used to be |
432 |
|
one field with the full set of time records then the next field). |
433 |
|
Note: this is now similar to NetCDF (MNC) output file. <== |
434 |
|
|
435 |
|
checkpoint62z (2011/06/21) |
436 |
|
o adjoint monitor: |
437 |
|
- Add adjoint monitor output for packages exf, seaice |
438 |
|
and update relevant testreport output |
439 |
|
o pkg/seaice: |
440 |
|
- re-order diags inits so that they appear in order in available_diagnostics.log |
441 |
|
- added diags: hsnow thermo. rates of change, area preceeding ridiging process, |
442 |
|
area/heff/hsnow preceeding thermodynamic growth/melt. |
443 |
|
- modified diag: SIdA; output actual effect, as the description states. |
444 |
|
- modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. |
445 |
|
- retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. |
446 |
|
(SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; |
447 |
|
and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) |
448 |
|
- modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. |
449 |
|
- added diagnostics for seaice generic tracers (SItr*). |
450 |
|
- added SItrUnit and SItrNameLong run time param (for SItr* diags). |
451 |
|
- in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. |
452 |
|
I. Fenty: 18-Jun-2011: |
453 |
|
Minor changes to seaice package: |
454 |
|
1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and |
455 |
|
added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) |
456 |
|
- Differentiated "regularization variables" from "floor variables" |
457 |
|
* areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor |
458 |
|
* hiceMin became SEAICE_hice_reg (old hiceMin) |
459 |
|
(with _reg meaning regularization variable) |
460 |
|
- SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion |
461 |
|
so as to ensure energy conservation when going between phases |
462 |
|
- A22 was not used anywhere |
463 |
|
2) Changed regularization procedure for heffActual and hsnowActual to ensure |
464 |
|
well-boundedness and smooth adjoint in seaice_growth.F |
465 |
|
3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells |
466 |
|
because the old regularization always set heffActual >= 0.05 cm |
467 |
|
4) Changed the model so that the default behavior is to put a small (10^-5) "floor" |
468 |
|
on AREA when HEFF > 0. |
469 |
|
- went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to |
470 |
|
requiring that DISABLE_AREA_FLOOR *not* be defined |
471 |
|
Affected verifications: |
472 |
|
- 1D_ocean_ice_column (output.txt output_adm.txt) |
473 |
|
- global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) |
474 |
|
o pkg/diagnostics: |
475 |
|
- move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). |
476 |
|
- rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument |
477 |
|
(was _RL, now integer) with option = 0 to retrieve all levels. |
478 |
|
- add pieces of code to compute velocity potential at each level (new diagnostics |
479 |
|
PhiVEL, works only when UVELMASS & VVELMASS are also turned on); |
480 |
|
for now, using same params as CG2D (target-resisual, max Nb of iter ...). |
481 |
|
- fix few issues with counter diagnostics in diagnostics_setdiag.F & |
482 |
|
diagstats_setdiag.F (if diagnostic counter is itself a counter diag) |
483 |
|
and in diagnostics_fract_fill.F (do not need a valid pointer for the |
484 |
|
diagnostics counter-mate); check that definition of counter-diagnostic |
485 |
|
includes a valid counter-mate (in diagnostics_set_levels.F). |
486 |
|
o model/src (rStar): |
487 |
|
- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
488 |
|
affect solution only if z* with full pressure in EOS; |
489 |
|
update output of test-exp global_ocean.90x40x15. |
490 |
|
o pkg/seaice: |
491 |
|
- introduce siEps=1e-5 parameter |
492 |
|
- use areaMax in AREA update (part 4), consistent with ridging step (part 2.5). |
493 |
|
- re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code. |
494 |
|
- introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer. |
495 |
|
For now it covers, and was tested for, ice salinity and age (attached to HEFF), |
496 |
|
as well as ice cover age and ridging index (attached to AREA). |
497 |
|
For now the run time parameters (in data.seaice/SEAICE_PARM03) are |
498 |
|
SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA'). |
499 |
|
Up to SItrMaxNum=3 tracers can be used simultaneously. |
500 |
|
o pkg/salt_plume: |
501 |
|
-introduce SPsalFRAC run time parameter that sets the fraction of the |
502 |
|
salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically) |
503 |
|
that gets vertically redistributed (fluxed down) by pkg/salt_plume. |
504 |
|
o model debug options: |
505 |
|
- Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored |
506 |
|
in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h). |
507 |
|
- Refine debug-msg printing selection (3 new levels): |
508 |
|
debugMode : controls printing of debug messages (sequence of S/R calls). |
509 |
|
debugLevel : controls printing of algorithm-relevant auxiliary/debug messages |
510 |
|
debLevZero = 0 ; /* level of disabled aux. msg printing */ |
511 |
|
debLevA = 1 ; /* level of minimum aux. msg printing */ |
512 |
|
debLevB = 2 ; /* level of low aux. print (report read-file opening)*/ |
513 |
|
debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */ |
514 |
|
debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */ |
515 |
|
debLevE = 5 ; /* level of extensive debug printing */ |
516 |
|
New debugLevel default: with default debugMode value (=F), |
517 |
|
= 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.; |
518 |
|
and if debugMode=T, default debugLevel = 4 (debLevD). |
519 |
|
Relation with previous settings: |
520 |
|
debLevB (=2) corresponds to former debLevA (=1) |
521 |
|
debLevD (=4) corresponds to former debLevB (=2) |
522 |
|
Note: |
523 |
|
a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before); |
524 |
|
b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs); |
525 |
|
to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5) |
526 |
|
- Add new parameter (printResidualFreq, read from PARM02 namelist) to print |
527 |
|
detailed CG solvers convergence; off (=0) by default, except if debugLevel=5. |
528 |
|
o pkg/obcs: |
529 |
|
- change OBCSfixTopo default from True to False (should not change the results); |
530 |
|
keep OBCSfixTopo=T in verification-exp. seaice_obcs. |
531 |
|
o pkg/thsice: |
532 |
|
- fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in |
533 |
|
2nd layer seaice sublimation (unlikely to happen) |
534 |
|
- use Interior mask for OBCS in thsice_advection.F (similar to what is |
535 |
|
done in gad_advection & seaice_advection). |
536 |
|
o adjoint: |
537 |
|
bug fix spotted by Gael Forget: |
538 |
|
seaice_advection and thsice_advection still had |
539 |
|
legacy CPP options to avoid CS corner updates for adjoint |
540 |
|
o pkg/seaice: |
541 |
|
=> Change some of the defaults (2011/05/29): |
542 |
|
- change SEAICEuseFluxForm default (from False to True) |
543 |
|
- change DIFF1 default (from 0.004 m/s to 0. m/s) |
544 |
|
And print warnings if DIFF1 is not set in data.seaice and centered |
545 |
|
avection scheme is used without any diffusion. |
546 |
|
also: |
547 |
|
- fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F; |
548 |
|
- set SEAICEdiffKh[] default in the same way as SEAICEadvSch[] |
549 |
|
- stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any |
550 |
|
other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with |
551 |
|
#undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE. |
552 |
|
update results of test exp.: |
553 |
|
lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20) |
554 |
|
output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200) |
555 |
|
output_adm.noseaicedyn (SEAICEuseFluxForm=T) |
556 |
|
offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T) |
557 |
|
seaice_obcs: output (SEAICEuseFluxForm=T) |
558 |
|
and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004) |
559 |
|
for standard fwd & AD lab_sea tests (to keep the same output). |
560 |
|
o pkg/seaice/seaice_growth.F: |
561 |
|
- use Ian Fenty's capping formulas for actual ice |
562 |
|
thickness thoughout EVOLUTION branch. |
563 |
|
- put treatment pathological case #2) in CPP brackets |
564 |
|
(ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). |
565 |
|
- update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. |
566 |
|
o pkg/seaice: |
567 |
|
- seaice_diffusion.F : remove the min(DX,DY) factor permanently; |
568 |
|
pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter; |
569 |
|
also pass fac as a param, which can be 1. (to update the tendency |
570 |
|
field) or the time step (to update the field itself). |
571 |
|
- seaice_advdiff.F: for multidim, call seaice_diffusion with |
572 |
|
e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call |
573 |
|
seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. |
574 |
|
- SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : |
575 |
|
hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
576 |
|
o pkg/seaice: |
577 |
|
diffusion with centered advection scheme (diffus.F & advect.F): |
578 |
|
- simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) |
579 |
|
to just compute the laplacian of input-field. |
580 |
|
- unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call. |
581 |
|
- fix flux-form version in diffus.F to conserve tracer. |
582 |
|
update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects |
583 |
|
machine truncation) and lab_sea.salt_plume (conservative flux-form modif) |
584 |
|
|
585 |
|
checkpoint62y (2011/05/26) |
586 |
|
o pkg/seaice: |
587 |
|
- seaice_growth.F : in EVOLUTION branch, always include |
588 |
|
a_QSWbyATM_cover in qnet (as it should be). |
589 |
|
- verification/global_ocean.cs32x15 : update results accordingly |
590 |
|
(output.seaice.txt output_adm.seaice.txt). |
591 |
|
o pkg/seaice + obcs: |
592 |
|
- use maskInW & maskInS in multi-dim advection and biharmonic diffusion: |
593 |
|
equivalent of assuming no tracer gradient outside the OB region. |
594 |
|
update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion) |
595 |
|
- remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed |
596 |
|
after changes above); |
597 |
|
- obcs+seaice cleaning: apply seaice-tracer OB values to tracer field |
598 |
|
only at OB location (instead of over a band of OLx width). |
599 |
|
o pkg/seaice: |
600 |
|
- fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F |
601 |
|
(dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid) |
602 |
|
o pkg/obcs: |
603 |
|
- split header file "OBCS.h" into 4 separated files: |
604 |
|
OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h |
605 |
|
Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h |
606 |
|
(contain no conditional statement which depends on OBCS options). |
607 |
|
- move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h) |
608 |
|
to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h). |
609 |
|
o ctrl, cost, grdchk & autodiff pkgs: |
610 |
|
- make options file more standard (like other {PKG}_OPTIONS.h file but |
611 |
|
with AD_CONFIG.h); clean-up some of the included header files. |
612 |
|
o pkg/obcs: |
613 |
|
- do not mask tracer when applying OB (tracer == 0 could generate problems) |
614 |
|
- apply tracer OB values to tracer field only at OB location (instead of |
615 |
|
over a band of OLx width) |
616 |
|
- clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R) |
617 |
|
- remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove |
618 |
|
obcs_apply_tloc.F & obcs_apply_sloc.F |
619 |
|
o obcs in model/src: |
620 |
|
- call OBCS_APPLY_W only if NonHydrostatic. |
621 |
|
- call OBCS_APPLY_ETA only if NonLinFreeSurf. |
622 |
|
- reset dEtaHdt and wVel to zero outside OB interior region ; |
623 |
|
- leave tracer unchanged outside OB interior region: This has no effect |
624 |
|
on the solution but just to prevent unrealistic tracer value outside OB. |
625 |
|
- zero out velocity outside OB interior region: This has no effect on |
626 |
|
the solution but just to prevent unrealistic velocity outside OB. |
627 |
|
o obcs and non-lin free-surf: |
628 |
|
move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F |
629 |
|
and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F |
630 |
|
+ add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR: |
631 |
|
this fixes missing EXCH + get consistent eta OB value (+ fix restart). |
632 |
|
update results of test-exp. exp4(nlfs). |
633 |
|
o exp4 (nlfs) test-exp: |
634 |
|
use OBC for Eta at Western & Eastern OB (to test prescribing Eta |
635 |
|
with NonLin-FreeSurf); update output.nlfs.txt |
636 |
|
o obcs and 2d/3d solver norm: |
637 |
|
use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB |
638 |
|
and outside OB interior region (will allow to place OB further inside the |
639 |
|
domain). Depending on the domain, can affects cg2d-Norm (previous |
640 |
|
cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl, |
641 |
|
and cg3d-Norm (previous Norm was computed before canceling OB terms), |
642 |
|
e.g. in tutorial_plume_on_slope. |
643 |
|
- update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope. |
644 |
|
o pkg rbcs: |
645 |
|
- split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h |
646 |
|
- add capability to apply relaxation to horizontal velocity uVel & vVel. |
647 |
|
o pkg/grdchk: add gradient check for control variable xx_shifwflx |
648 |
|
o pkg/shelfice/shelfice_init_fixed.F |
649 |
|
fix CPP-flag combinations |
650 |
|
o pkg/seaice: Merge iceage code of Pierre Rampal |
651 |
|
* update/change/correct ice age calculations |
652 |
|
* add age updates for pathological cases |
653 |
|
Probably needs more testing... |
654 |
|
|
655 |
|
checkpoint62x (2011/05/13) |
656 |
|
o pkg/mom_vecinv: |
657 |
|
high-order vorticity scheme: use interior masks (maskInW & S) |
658 |
|
to zero-out (outside OB) gradient of vorticity. |
659 |
|
o verification exp.: |
660 |
|
turn on "useEnergyConservingCoriolis" (better discretisation) in exp. |
661 |
|
hs94.128x64x5 and seaice_obcs ; update results. |
662 |
|
o pkg/obcs: |
663 |
|
fix bug in OBeta for YZ sections in obcs_exf_load.F |
664 |
|
o pkg/ctrl, pkg/shelfice, and optim: |
665 |
|
- add new control variable xx_shifwflx (fresh water flux underneath ice |
666 |
|
shelves). This is almost as tedious as obcs-ctrl, because the |
667 |
|
variables needs its own mask. |
668 |
|
- add a cost function term that penalizes the deviation of xx_shifwflx |
669 |
|
from the first guess (zero) in analogy to other control variables |
670 |
|
o pkg/shelfice: |
671 |
|
- start basic adjoint |
672 |
|
o pkg/ctrl: |
673 |
|
- remove extra 2D field "for good measure" when initializing in |
674 |
|
ctrl_set_globfld_[xy/xz/yz].F |
675 |
|
- replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec |
676 |
|
- improve error messages in ctrl_set_unpack_* |
677 |
|
o OBC implementation in momentum: |
678 |
|
use interior masks (maskInC,W & S) in momentum S/R: |
679 |
|
- multiply divergence, tension and some del^i.u or del^j.v by maskInC |
680 |
|
- multiply del2u,del2v by maskInW/S (biharmonic viscosity) |
681 |
|
- multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) |
682 |
|
- multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) |
683 |
|
Motivation: fix/clean implementation of OBC with biharmonic-viscosity |
684 |
|
(and also with Leith/Smagorinsky harmonic-viscosity). |
685 |
|
Update output of experiment dome and exp4 (+nlfs). |
686 |
|
o exp4 test-exp: |
687 |
|
- turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) |
688 |
|
and prescribe time-varying OB (without pkg/exf) for zonal-velocity |
689 |
|
at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
690 |
|
time-varying OB at Western-side for wVel (NonHyd); update output. |
691 |
|
- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
692 |
|
and biharmonic-viscosity ; also use prescribed time varying OB. |
693 |
|
o pkg/obcs: |
694 |
|
fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
695 |
|
o model/src: |
696 |
|
- fix startTime setting when baseTime<>0 & nIter0=0 are specified ; |
697 |
|
- initialise startTime & nIter0 with unlikely values: allows to set one |
698 |
|
from the other without ambiguity. |
699 |
|
o seaice_obcs test-exp.: |
700 |
|
add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output. |
701 |
|
o pkg/obcs: |
702 |
|
- remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: |
703 |
|
no longer needed with maskInC,W,S in pkg/generic_advdiff. |
704 |
|
o pkg/seaice: |
705 |
|
- retired SEAICE_SALINITY and SEAICE_salinity in favor of |
706 |
|
SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively. |
707 |
|
- fixed bug in the initialization of sea ice salinity variable HSALT |
708 |
|
in seaice_init_varia.F (removed dependence on ICE2WATR) |
709 |
|
o fizhi-cs test exp.: |
710 |
|
switch reference output convention for these 2 non-standard test-exp, |
711 |
|
from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5) |
712 |
|
to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11) |
713 |
|
reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran |
714 |
|
o model/inc: |
715 |
|
- change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4") |
716 |
|
of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS) |
717 |
|
o pkg/seaice: |
718 |
|
- fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY |
719 |
|
o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15 |
720 |
|
- updated output*.txt files due to bug fixes in salt, saltPlumeFlux, |
721 |
|
and initial HSALT |
722 |
|
|
723 |
|
checkpoint62w (2011/04/26) |
724 |
|
o pkg/mom_fluxform: |
725 |
|
- fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf. |
726 |
|
- use parameter "sideDragFactor" in no-slip BC side-drag part. |
727 |
|
- update output of exp. global_ocean.90x40x15 |
728 |
|
o pkg/mom_vecinv: |
729 |
|
mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform) |
730 |
|
o update seaice exp.: |
731 |
|
use more consistent parameter values (remove "backward compatability only": |
732 |
|
ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh) |
733 |
|
related to thermodynamics seaice. Update output (fwd+AD) of exp.: |
734 |
|
1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs |
735 |
|
o update test-exp global_ocean.90x40x15: |
736 |
|
o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis). |
737 |
|
o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.) |
738 |
|
o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params) |
739 |
|
o turn on zStar & viscA4 in standard set-up (dir input/) |
740 |
|
and update output files: output.txt & output.dwnslp.txt |
741 |
|
o new AD-test experiment: obcs_ctrl |
742 |
|
(From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector. |
743 |
|
o pkg/dic: |
744 |
|
fix two bugs in handling water vapour pressure in carbonate chemistry |
745 |
|
and air-sea fluxes. Found by Val Bennington and Galen McKinley |
746 |
|
(add DIC Option = WATERVAP_BUG to recover old results) |
747 |
|
update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline |
748 |
|
o adding allowInteriorFreezing option to check for water below freezing point |
749 |
|
at depth and bring the negative heat anomaly to the surface level |
750 |
|
o pkgs _fields_load: |
751 |
|
- extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs) |
752 |
|
- use new S/R GET_PERIODIC_INTERVAL in pkgs: |
753 |
|
bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and |
754 |
|
rbcs to get interpolation weights and time reccord number. |
755 |
|
- fix multi-threading in aim_fields_load.F |
756 |
|
- apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F |
757 |
|
o external_fields_load: |
758 |
|
new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear |
759 |
|
interpolation weights) to use in a periodic time-series ; do not divide by |
760 |
|
time-step to convert to integer: |
761 |
|
- this fixes case where externForcingPeriod is not multiple of time-step |
762 |
|
(Thanks to Christopher L. Wolfe) |
763 |
|
- this fixes case where externForcingPeriod is an odd multiple of time-step |
764 |
|
(was wrong by half of time-step); update results of tutorial_global_oce_in_p. |
765 |
|
store index of time-record which is currently loaded: |
766 |
|
- works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ; |
767 |
|
- needed for the adjoint but not yet used because of extensive recomputations; |
768 |
|
(to be fixed soon) |
769 |
|
|
770 |
|
checkpoint62v (2011/04/02) |
771 |
|
o verification/1D_ocean_ice_column added to test Ian Fenty's |
772 |
|
pkg/seaice_growth.F modifications for improving sea ice code differentiability |
773 |
|
o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope |
774 |
|
(new velocity statistics after changing maskInW & maskInS definition) |
775 |
|
o pkg/generic_advdiff with OBCS: |
776 |
|
use maksInW & maskInS in advective flux and in biharmonic diffusion calculation: |
777 |
|
equivalent to assumption of no tracer gradient outside the OB region. |
778 |
|
This will affect the results if using obcs+biharmonic diffusion. |
779 |
|
update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc) |
780 |
|
o pkg/obcs: |
781 |
|
change definition of maskInW & maskInS: leave OB edges inside (maskIn=1) |
782 |
|
(e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still |
783 |
|
in Interior region. No impact on solution but affects Velocity monitor stats. |
784 |
|
o pkg/ptracers (adjoint) |
785 |
|
New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate |
786 |
|
tape file for each tracer |
787 |
|
o model/inc/src and pkg/autodiff: add parameters that allow to turn |
788 |
|
of parts of the adjoint code at run time. For now, there are only |
789 |
|
useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These |
790 |
|
parameters are set in data.pkg. |
791 |
|
This is the lazy coward's version of doing this, but still useful for |
792 |
|
debugging. In order to do it right, everything needs to be moved to |
793 |
|
pkg/autodiff. |
794 |
|
o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at |
795 |
|
the end; this fixes the adjoint balancing code for open boundaries. |
796 |
|
o pkg/ctrl: |
797 |
|
- change behavior of xx_${varname}period to be analogous to exf-conventions: |
798 |
|
xx_${varname}period = 0., means time-independent control part |
799 |
|
xx_${varname}period = -12., means one-year-periodic monthly control part |
800 |
|
- introduce helper routine ctrl_init_rec (part of ctrl_init.F) to |
801 |
|
clean up ctrl_init a little, remove unused variables |
802 |
|
- ctrl_init: fixed the handling of the start/endrec for obcs-variables |
803 |
|
- move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec |
804 |
|
|
805 |
|
checkpoint62u (2011/03/15) |
806 |
|
o model/src: |
807 |
|
- for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in |
808 |
|
h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ; |
809 |
|
- in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to |
810 |
|
INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF. |
811 |
|
o pkg/ctrl/obcs/ecco: |
812 |
|
- remove obsolete, unused, and partially broken code: |
813 |
|
ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within |
814 |
|
ALLOW_CTRL_OBCS_BALANCE |
815 |
|
- put a stop statement into ecco/cost_obcsvol.F, but also add |
816 |
|
cost_obcsvol to ecco_ad_diff.list |
817 |
|
o pkg/ecco: fix counting cost function contributions for obcs (code |
818 |
|
by Matt M.) and diffkr for diagnostics |
819 |
|
o pkg/ecco, pkg/ctrl, pkg/grdchk: |
820 |
|
add cost penalty terms for initial uvel, vvel, eta controls |
821 |
|
and I/O for prior error files |
822 |
|
o pkg/mdsio: |
823 |
|
move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option |
824 |
|
(new argument) to check for tiled file in mdsioLocalDir : this fix the |
825 |
|
restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir. |
826 |
|
o pkg/ctrl: |
827 |
|
- ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by |
828 |
|
ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove |
829 |
|
unused and superfluous variables |
830 |
|
- ctrl_get_gen_rec.F: catch the case of xx_genperiod=0. |
831 |
|
o pkg/ecco |
832 |
|
- enable adjoint of Stevens OB |
833 |
|
o pkg/ctrl/ecco/grdchk: |
834 |
|
- remove global declaration of tmpfldx/yz and tmpfldx/yz2. |
835 |
|
Fortunately, we do not have any tests for the numerous cpp-flagged |
836 |
|
option of "obcs as control parameters" so we will never know |
837 |
|
if this is an improvement (but at least now things compile). |
838 |
|
- remove an obsolete initialization from ecco_cost_init_barfiles.F |
839 |
|
- fix some problems within never used ifdefs to make the code compile |
840 |
|
o pkg/obcs: |
841 |
|
- Refine Interior mask definition to work with more complex OB (e.g. |
842 |
|
if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to |
843 |
|
read in Interior mask from file. Check if Interior mask is consistent |
844 |
|
with OB list of indices. |
845 |
|
o pkg/seaice |
846 |
|
- beginning code for a seaice tracer package, |
847 |
|
but currently only used for seaice age: SEAICE_AGE |
848 |
|
SEAICE_num = 4 |
849 |
|
iTracer = 1: area-weighted ice age |
850 |
|
= 2: volume-weighted ice age |
851 |
|
= 3, 4: template for one-year vs. multi-year ice |
852 |
|
data.seaice has new namelist SEAICE_PARM03 for arrays related to |
853 |
|
SEAICE_num |
854 |
|
|
855 |
|
checkpoint62t (2011/03/05) |
856 |
|
o pkg/obcs: |
857 |
|
- obcs_apply_uv.F: change to a 2 steps method, first tangential component; |
858 |
|
then normal component. This ensures that the normal component is set |
859 |
|
correctly even when it conficts with tangential setting from an other OB. |
860 |
|
Affects results of test-experiment seaice_obcs: update the output.txt |
861 |
|
o pkg/obcs: |
862 |
|
- add code to monitor statistics of dynamical fields at OB. |
863 |
|
- take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW : |
864 |
|
- fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection). |
865 |
|
- change default: balance the Net inflow through all OB (instead of balancing |
866 |
|
each OB separately); keep the old method if setting OBC_balanceFacX < 0. |
867 |
|
- switch on useOBCSbalance in dome experiment: only correct Western OB outflow |
868 |
|
to match Nortern OB inflow (OBCS_balanceFacN=0). |
869 |
|
o pkg/seaice: |
870 |
|
- redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL |
871 |
|
o pkg/seaice (seaice_growth v 1.113): |
872 |
|
- reverting seaice_growth to v 1.111 in order to have code with exact bit |
873 |
|
compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge |
874 |
|
CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced |
875 |
|
runtime flag SEAICEareaFormula is kept but is inactive |
876 |
|
o model/src: |
877 |
|
- add new param to scale curvilinear grid distance and area when using |
878 |
|
a different sphere radius from the grid-files. |
879 |
|
- test/check multi-threads EXCH applied to local variable (cg2d_x) |
880 |
|
o adjoint: |
881 |
|
- enable adjoint of Stevens OB |
882 |
|
- add dummy_in_dynamics to enable extraction of ADJrhoinsitu |
883 |
|
(a bit delicate because of potentially modified adj. common block structure; |
884 |
|
current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later) |
885 |
|
|
886 |
|
checkpoint62s (2011/02/15) |
887 |
|
o pkg/seaice (seaice_growth v 1.112): |
888 |
|
- introduce SEAICEareaFormula run time parameter, which selects the recipe for |
889 |
|
computing the ice cover tendency from effective thickness tendencies. Include |
890 |
|
Ian Fenty's formula. |
891 |
|
- remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using |
892 |
|
SEAICEareaFormula. |
893 |
|
- simplify notations for the various d_HEFF/d_AREA terms. |
894 |
|
o pkg/gmredi: |
895 |
|
- add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code |
896 |
|
from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative; |
897 |
|
add a verification test-run (front_relax.bvp) to test GM_useBVP. |
898 |
|
o pkg/seaice (seaice_growth v 1.111): |
899 |
|
- for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's. |
900 |
|
- the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to |
901 |
|
also melt ice. |
902 |
|
o pkg/seaice: |
903 |
|
- McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty). |
904 |
|
- can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h |
905 |
|
o pkg/cheapaml: |
906 |
|
- from Nico Wienders: New version of this package. |
907 |
|
o pkg/flt: |
908 |
|
- add CPP options to prevent floats to re-enter the opposite side of |
909 |
|
a periodic domain (default: keep periodicity) |
910 |
|
o pkg/gmredi: |
911 |
|
- apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners |
912 |
|
(needed for multi-dim advection). |
913 |
|
- switch on GM Advective form in global_ocean.cs32x15 and update output.txt |
914 |
|
o model/src: |
915 |
|
- fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run. |
916 |
|
o tutorial_tracer_adjsens |
917 |
|
- extend to NLFS and replace maskC by hFacC |
918 |
|
(change reference output accordingly) |
919 |
|
|
920 |
|
checkpoint62r (2011/01/24) |
921 |
|
o testreport: |
922 |
|
- add option -deloutp (-do) to remove output file after successful run |
923 |
|
- add option -mfile (-mf) for MPI machile-file and for each test-exp, |
924 |
|
extract exact list of procs from this file ; adjust COMMAND by |
925 |
|
replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs. |
926 |
|
o pkg/ecco: replace old ineffective way of penalizing deviations from |
927 |
|
first guess (of obcs) with code by Matt Mazloff |
928 |
|
o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without |
929 |
|
exf/cal |
930 |
|
- ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl |
931 |
|
and handle case of obcs?period == 0 |
932 |
|
Not affected by these changes: There is still an inconsistency in |
933 |
|
the computation of start/endrec for the obcs variables for ALLOW_CAL |
934 |
|
defined (see comment by Menemenlis, 7-Mar-2003) |
935 |
|
- make S/R ctrl_get_gen_rec return something meaningful even if |
936 |
|
ALLOW_CAL is not defined |
937 |
|
- ctrl_getobcs?: simplify code so that it does not need to use |
938 |
|
S/R exf_swapfields |
939 |
|
o testreport: |
940 |
|
allow to test MPI with different number of processors for each experiment: |
941 |
|
create file "SIZE.h.mpi" in each build dir. |
942 |
|
Note: update of "-command" argument not yet implemented. |
943 |
|
o model/src, pkg/autodiff, pkg/ecco, pkg/seaice: |
944 |
|
alleviate the need for additional 3D tapes when using |
945 |
|
the non-inear free surface in the adjoint. This is done |
946 |
|
by adding an 'update' of hfacc etc. to their current |
947 |
|
value at the beginning of forward_step.F. |
948 |
|
o pkg/seaice |
949 |
|
seaice_lsr: move stress-divergence computations out of outer pseudo- |
950 |
|
timestepping loop |
951 |
|
o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD' |
952 |
|
up, so that the calls of the ctrl_* subroutines are really at the end |
953 |
|
of the routine. |
954 |
|
o pkg/gmredi: |
955 |
|
allow to specify a 2-D horizontal map and a 1-D vertical profil |
956 |
|
as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity. |
957 |
|
o pkg/seaice: |
958 |
|
move lsr iterations from seaice_dynsolver to seaice_lsr. |
959 |
|
o pkg/seaice: |
960 |
|
reduce memory footprint of seaice mutldim advection tapes, |
961 |
|
by using a 2D tape independent of the generic_advdiff ones, |
962 |
|
and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc. |
963 |
|
|
964 |
|
checkpoint62q (2010/12/29) |
965 |
|
o model/src: |
966 |
|
- check horizontal grid-spacing for unset or zero/negative values. |
967 |
|
- change AD test hs94.1x64x5 to be truly a 2-D set-up. |
968 |
|
o pkg/flt: |
969 |
|
- use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR |
970 |
|
- precision of input and output files set according to readBinaryPrec |
971 |
|
and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits. |
972 |
|
- initial float position from tiled file was not converted to index space |
973 |
|
(looks like a bug): fixed to make it similar to initial pos. global file. |
974 |
|
o global_ocean.cs32x15: |
975 |
|
change SIZE.h of AD set-up to get same tiling as with MPI. |
976 |
|
Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11) |
977 |
|
o model/src: |
978 |
|
add flag to control printing of domain fields (bathymetry, hFac ...) in |
979 |
|
ini_mask_etc (call to plot_fieds_xy*). |
980 |
|
o pkg/thsice: |
981 |
|
if useEXF, some forcing fields are not valid in overlap: fixed by computing |
982 |
|
over the interior only + apply EXCH at the end (like with SEAICE advection). |
983 |
|
o pkg/mdsio: |
984 |
|
- add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer |
985 |
|
to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS. |
986 |
|
- change barrier call for safe multi-threads access to 3-D shared buffer. |
987 |
|
- MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones) |
988 |
|
- replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and |
989 |
|
remove the 4 S/R MDS_PASS_WH_R4/8toRL/S. |
990 |
|
o pkg/flt: |
991 |
|
- add fourth-order Runge-Kutta integration |
992 |
|
- add basic exch2 support (only 1 facet supported so far!) |
993 |
|
o pkg/mdsio+rw: |
994 |
|
new S/R to read local (or tile independent) vector (read counterpart of |
995 |
|
mds_writevec_loc, and front-end write_glvec_rl/rs). |
996 |
|
o global_ocean.cs32x15: additional input_ad.seaice experiment |
997 |
|
that uses pkg/seaice rather than pkg/thsice. |
998 |
|
(using multidim advection for seaice) |
999 |
|
o towards more F95 syntax for array specification in namelist: |
1000 |
|
- change "data.diagnostics" (data.ptracers was changed before checkpoint62p) |
1001 |
|
of all verification experiments. |
1002 |
|
e.g.: line: fields(1,3)='ETAN ','ETANSQ ', |
1003 |
|
was changed to: fields(1:2,3)='ETAN ','ETANSQ ', |
1004 |
|
- finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles |
1005 |
|
o global_ocean.cs32x15: additional input.seaice experiment |
1006 |
|
that uses pkg/seaice rather than pkg/thsice. |
1007 |
|
|
1008 |
|
checkpoint62p (2010/12/17) |
1009 |
|
o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it |
1010 |
|
to THSICE_SIZE.h to avoid conflict with pkg/seaice. |
1011 |
|
o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint. |
1012 |
|
allow for use of multim. advection in seaice adjoint. |
1013 |
|
o pkg/seaice: add diagnostics for snow precipitation and sublimation flux |
1014 |
|
- first attempt to close budgets by taking into account the freshwater |
1015 |
|
flux implied by the sublimation of snow and ice. So far only the |
1016 |
|
volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag |
1017 |
|
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET |
1018 |
|
o eesupp/src: |
1019 |
|
new S/R with new option (NML_EXTENDED_F77) to change array specification |
1020 |
|
from F95 standard to commonly accepted extended F77 form. |
1021 |
|
This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5) |
1022 |
|
and to revert back to the original syntax (with -DNML_EXTENDED_F77) |
1023 |
|
for less tolerant f77 compiler (e.g., pgf77, g77). |
1024 |
|
o globalFiles: |
1025 |
|
commented out in parameter file "data" since it's not safe with MPI |
1026 |
|
(e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much |
1027 |
|
in this case); no longer commented out in restart test (tst_2+2). |
1028 |
|
o add adTapeDir to specify a special directory where adjoint tapes are |
1029 |
|
written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05 |
1030 |
|
and cannot be used together with mdsioLocalDir. |
1031 |
|
o nesting pkgs: |
1032 |
|
- packages_init_variables : put call to OBCS_INIT_VARIABLES in last position |
1033 |
|
- update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) |
1034 |
|
- add parameter files + utils dir + output from short run on beagle. |
1035 |
|
o pkg/seaice: |
1036 |
|
fix seaice_growth.F store directives; update results of exp. lab_sea.ad |
1037 |
|
o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid |
1038 |
|
unnecessary copying in adjoint code, requires new parameter NMAX_ITER |
1039 |
|
|
1040 |
|
checkpoint62o (2010/11/25) |
1041 |
|
o pkg/exf: |
1042 |
|
- change CPP option EXF_VERBOSE to run-time logical param exf_verbose. |
1043 |
|
o pkg/seaice: |
1044 |
|
- seaice_ocean_stress: split a loop for better vectorization of the |
1045 |
|
adjoint code |
1046 |
|
- seaice_growth.F: fix bug in conservation of freshwater connected to |
1047 |
|
capping of heff, put contribution into d_HEFFbyNEG |
1048 |
|
- replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat |
1049 |
|
by something more sensible (parameters that are what their name implies) |
1050 |
|
- change some defaults, so that by default exf-parameters are used for |
1051 |
|
things like rhoAir, cpAir,latent/sensible heat parameters, in order |
1052 |
|
to reproduce the old results, many data.seaice now contain funny values |
1053 |
|
for cpAir and latent heat of sublimation |
1054 |
|
o packages_readparms.F: move exf_readparms up in line so that |
1055 |
|
exf-parameters are visible for other packages (e.g. seaice) |
1056 |
|
o debugMode & debugLevel=2: |
1057 |
|
- differentiate between debugMode & debugLevel=2: |
1058 |
|
debugMode: controls printing of debug messages (sequence of S/R calls). |
1059 |
|
debugLevel: controls printing of algorithm intermediate results and stats. |
1060 |
|
- remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2"; |
1061 |
|
=> allows to print debug-stats without all sequence of call messages. |
1062 |
|
- switch control of debug print from debugLevel to debugMode in many S/R. |
1063 |
|
o pkg/obcs (obcs-sponge): |
1064 |
|
fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the |
1065 |
|
call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge) |
1066 |
|
o pkg/generic_advdiff: |
1067 |
|
- record overlap minimum size for each advection scheme; |
1068 |
|
- refine criteria on overlap minimum size; |
1069 |
|
- check and stop (in gad_check) if overlap size is too small. |
1070 |
|
o pkg/obcs: |
1071 |
|
- with ptracers: remove multiple calls to obcs_apply_ptracer (only done |
1072 |
|
once, in ptracers_implicit.F) |
1073 |
|
- with seaice: remove test on empty file name in obcs_apply_seaice (always |
1074 |
|
apply OB values when tile has OB) |
1075 |
|
o model/src, coriolis setting: |
1076 |
|
- integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical |
1077 |
|
useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from |
1078 |
|
files (selectCoriMap=3) with any grid. |
1079 |
|
- add parameter "fPrime" for constant second Coriolis coeff (default=0). |
1080 |
|
o pkg/seaice/seaice_growth.F: |
1081 |
|
a few cosmetic changes that reduce the number of lines of code |
1082 |
|
o pkg/obcs: add boundary conditions following Stevens (1990) |
1083 |
|
- the code follows old MOM/NAOSIM code |
1084 |
|
- so far it is only implemented for the eastern and western boundaries |
1085 |
|
and NOT for pTracers |
1086 |
|
o pkg/rbcs: |
1087 |
|
- replace rbcsInIter by rbcsForcingOffset, the time in seconds at the |
1088 |
|
beginning of the first rbcs forcing period. |
1089 |
|
- add option rbcsSingleTimeFiles that makes rbcs read forcing data like the |
1090 |
|
offline package, i.e., one file per time, labeled by iteration number; |
1091 |
|
deltaTrbcs sets the timestep with which the data was generated; |
1092 |
|
rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset. |
1093 |
|
- rbcsForcingCycle=0 makes forcing non-cyclic. |
1094 |
|
- make arithmetic safe for negative times and odd forcing periods. |
1095 |
|
|
1096 |
|
checkpoint62n (2010/11/09) |
1097 |
|
o pkg/seaice: |
1098 |
|
fix masking in free-drift S/R ; update results of exp. lab_sea.fd |
1099 |
|
o pkg/obcs: |
1100 |
|
New S/R to copy tracer value from the OB location to narrow band region |
1101 |
|
(width = same as overlap) beyond the OB: preserve OB value (needed for |
1102 |
|
high-order scheme) which were overwritten by EXCH call if in overlap |
1103 |
|
region. Applied to theta, salt, ptracer and advected seaice variables. |
1104 |
|
With seaice: use maskInC in similar way as in gad_advection.F, |
1105 |
|
in seaice_advection.F and advect.F. |
1106 |
|
Update output of experiment seaice_obcs and change exp4 to test OBCS with |
1107 |
|
4th order Adv.Scheme. for pasive salt and ptracer. |
1108 |
|
o tools/genmake2: |
1109 |
|
- when looking for an optfile (not specified), only search for Fortran compiler |
1110 |
|
(remove sym-link test + setting of CPP + makedepend check + C-compiler check) |
1111 |
|
- in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm |
1112 |
|
(instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong) |
1113 |
|
- set default for CPP to "cpp -traditional -P" (was the case without specifying |
1114 |
|
an optfile, but otherwise default was just "cpp". |
1115 |
|
- comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from) |
1116 |
|
- when "CC" is not set in the optfile, look for possible C compiler |
1117 |
|
(instead of just setting CC=cc) |
1118 |
|
- put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes: |
1119 |
|
=> add a ".F" to ".o" rule for source files with no "#include" (such as |
1120 |
|
port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS. |
1121 |
|
- move gfortran before g77 in list of possible Fortran compiler (consistent |
1122 |
|
with reference compiler switch from g77 to gfortran) |
1123 |
|
o pkg/seaice: |
1124 |
|
o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to |
1125 |
|
seaice_check that stops the model, when the CPP flag is used. |
1126 |
|
o seaice_growth.F: make capping of ice volume conserving by returning the |
1127 |
|
capped ice as freshwater to EmPmR. This does not change the verification |
1128 |
|
experiments but will change runs where the capping is acutally active |
1129 |
|
o change reference platform+compiler from faulks+g77 to baudelaire+gfortran |
1130 |
|
(except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5, |
1131 |
|
global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD), |
1132 |
|
lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd) |
1133 |
|
o tools/genmake2: |
1134 |
|
- merge genmake_warnings & genmake_errors into 1 log file: "genmake.log") |
1135 |
|
- change DUMPSTATE default to false (can use "-ds" option to switch it to T) |
1136 |
|
- clean previous genmake log files before anything else. |
1137 |
|
- change Makefile to remove testreport log files (*.tr_log) and genmake log |
1138 |
|
files only with "CLEAN" target (instead of "Clean"); |
1139 |
|
o pkg/generic_advdiff: |
1140 |
|
Change OBCS in multiDim advection (gad_advection.F): |
1141 |
|
Use maskInC to prevent intermediate update of tracer-field in OB regions, |
1142 |
|
thus keeping current-time-step OB values; and remove the call to OBCS_APPLY |
1143 |
|
which were applying future time-step OB values. |
1144 |
|
This way, all explicit calculations use current-time-step OB values |
1145 |
|
(simpler and more consistent). |
1146 |
|
Affects results when set-up uses time-varying OBC and multi-dim advection; |
1147 |
|
update output of experiment seaice_obcs. |
1148 |
|
o pkg/seaice: |
1149 |
|
move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h: |
1150 |
|
this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH & |
1151 |
|
SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY. |
1152 |
|
Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY |
1153 |
|
but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp |
1154 |
|
unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h) |
1155 |
o pkg aim (2010/10/26): |
o pkg aim (2010/10/26): |
1156 |
- Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation |
- Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation |
1157 |
formulation with obliquity, eccentricity, ... as run-time parameters, |
formulation with obliquity, eccentricity, ... as run-time parameters, |
1158 |
- Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and |
- Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and |
1159 |
upward shortwave radition at the surface (all-sky and clear-sky). |
upward shortwave radition at the surface (all-sky and clear-sky). |
|
|
|
1160 |
o pkg/obcs: |
o pkg/obcs: |
1161 |
- writing sections with globalFiles=T does not work: switch to tiled-files |
- writing sections with globalFiles=T does not work: switch to tiled-files |
1162 |
when writing sections for OBCS (change pkg/rw/write_rec.F accordingly). |
when writing sections for OBCS (change pkg/rw/write_rec.F accordingly). |