4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
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|
7 |
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o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz |
8 |
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- this is an intermediate state of a truely converging EVP that has |
9 |
|
the potential of outperforming implicit VP methods, I do not recommend |
10 |
|
using it yet. |
11 |
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- for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION |
12 |
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and all parameters are hardwired |
13 |
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- for convergence it still requires very smooth regularisations, that means, |
14 |
|
if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is |
15 |
|
different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also |
16 |
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specific averaging appears to be required, still subject to tuning |
17 |
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- still needs cleaning and I need to turn parameter into runtime parameters |
18 |
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- add code to compute and print residuals of iteration, compile with |
19 |
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defining ALLOW_SEAICE_EVP_RESIDUAL to enable it |
20 |
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o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq) |
21 |
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that entered with r1.54 on Sep04, 2015, -> update results |
22 |
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|
23 |
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checkpoint65o (2015/09/14) |
24 |
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o pkg/mom_vecinv & mom_common: |
25 |
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- add deep-atmosphere geometry factor in mom_calc_visc.F + in routines |
26 |
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called from there. |
27 |
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- add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this |
28 |
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allows to use Vector-Invariant form in deep atmos and anelastic formulation |
29 |
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o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015) |
30 |
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and Koenig-Beatty+Holland (2012) |
31 |
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- two new parameters SEAICE_tensilFac and SEAICE_tensilDepth |
32 |
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- global 2D field tensileStrength, computed in seaice_calc_ice_strength |
33 |
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- requires an extra input argument for S/R seaice_calc_viscosities |
34 |
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- tensileStrength's depth dependence is different from Itkin et al. (2015) |
35 |
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(to be changed and played with, for now exponential) |
36 |
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o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.) |
37 |
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- if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice |
38 |
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by AREA according to Connelly et al. (2004), JPO. |
39 |
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- For EVP and the LSR solver, the implicit part of the drag term is |
40 |
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the only non-zero term in the denominator when there is no ice (which |
41 |
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prevented running the model with zero ice-ocean drag). If |
42 |
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SEAICEscaleSurfStress = .TRUE., this results in a division by zero |
43 |
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(or zero main diagonals BU/BV) which need to be caught. A practical |
44 |
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consequence is that for open water, the momentum equation reduce |
45 |
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to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if |
46 |
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they happen to be zero, often leading to a non-zero solution over |
47 |
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open water. |
48 |
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o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more |
49 |
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efficient EVP method. |
50 |
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- introduce area-weighted averages for e12 (analogously to |
51 |
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seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits |
52 |
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remain, but also changing the order of terms in the previous average |
53 |
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changed the results as much) -> update experiment |
54 |
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- add SEAICE_DELTA_SMOOTHREG code |
55 |
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- disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for |
56 |
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TEM-code |
57 |
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- adjust loop bounds so that only required fields are computed |
58 |
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- add new averaging code for zetaZ/deltaZ (again similar to |
59 |
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seaice_calc_viscosities.F), inactive by default for now (will change |
60 |
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results again), but will replace old code eventually |
61 |
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o eesupp/src: |
62 |
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- add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F) |
63 |
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to always cumulate tile local-sum in the same order |
64 |
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(option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h). |
65 |
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Still uses MPI_Allreduce (like standard code) but on array of tiles |
66 |
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and should be faster than GLOBAL_SUM_SEND_RECV code. |
67 |
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- switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV |
68 |
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(defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead. |
69 |
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- add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.: |
70 |
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aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40, |
71 |
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fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example, |
72 |
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natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre, |
73 |
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tutorial_baroclinic_gyre and tutorial_held_suarez_cs. |
74 |
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|
75 |
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checkpoint65n (2015/07/29) |
76 |
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o pkg/thsice: |
77 |
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- add a warning when used with pkg/aim but without updating SST |
78 |
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(stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ). |
79 |
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o pkg/offline: |
80 |
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- change where Offline-Fields are loaded, from load_fields_driver.F to |
81 |
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directly within FORWARD_STEP, just after updating iter number and time; |
82 |
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- move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new |
83 |
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S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS; |
84 |
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These changes allow: |
85 |
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a) to recover exactly on-line results using deltaToffline=deltaTClock, |
86 |
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tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2) |
87 |
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both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous |
88 |
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time-step, both with GM & KPP files and with recomputing these fields; |
89 |
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b) no needs to switch on staggerTimeStep anymore; |
90 |
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c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf. |
91 |
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- update output of experiment tutorial_dic_adjoffline (only 3 digits left). |
92 |
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o pkg/offline: |
93 |
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- change (rarely used) offset-iteration parameter to an offset time (in s): |
94 |
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can easily recover previous offset-iter effect by setting offset-time |
95 |
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(offlineTimeOffset) to offset-iter x deltaToffline; |
96 |
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- do not turn-off Temp & Salinity surface relaxation when using KPP (used |
97 |
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in KPP as part of surface buoyancy forcing) in offline run. |
98 |
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- fix ptracers KPP non-local term in the case where KPP is re-computed. |
99 |
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o OpenAD |
100 |
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- Adding preliminary ggl90 test to OpenAD verification. |
101 |
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Config. with ggl90 currently diverges after 64 time steps |
102 |
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so will need more work to become more stable |
103 |
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- Adding preliminary kpp test to OpenAD verification. |
104 |
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required small tweakes in kpp_routines.F |
105 |
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- Merge and update from Krishna Narayanan's contrib area: |
106 |
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* Add one variable for preliminary OpenAD DIVA |
107 |
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* Add replacement time-stepping for OpenAD DIVA |
108 |
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* genmake2 flag -diva (but only for OpenAD; preliminary) |
109 |
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* required modifs for OAD_support |
110 |
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successful preliminary test for tutorial_global_oce_biogeo/ |
111 |
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o pkg/seaice: |
112 |
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- initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr |
113 |
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- add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising |
114 |
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delta with a smooth function in s/r seaice_calc_viscosity |
115 |
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(no effect on EVP) |
116 |
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- rename local suffix "sqr" into "sq" for more consistent variable names |
117 |
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o pkg/seaice: |
118 |
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add new parameter SEAICE_deltaMin that is used ***only*** |
119 |
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for regularizing Delta (and nothing else, like the parameter |
120 |
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which is also used for all sorts of things SEAICE_EPS). |
121 |
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Defaults to SEAICE_EPS for backward compatibility only. |
122 |
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o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with |
123 |
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the wrong key by inialising it before use -> fixes a recomputation |
124 |
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problem but does not fix the gradient |
125 |
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o pkg/layers: |
126 |
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- move resetting of flux arrays to outside the iLa loop |
127 |
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(this caused layers_diapycnal to not work with more than one layer coord.) |
128 |
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- fix bug in calculation of layers_recip_delta in layers_init_fixed.F |
129 |
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o pkg/layers: |
130 |
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- remove from common block 3D layers fields (used to diagnose transport |
131 |
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in tracer coords) and declare them as local arrays in layers_calc.F |
132 |
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o pkg/seaice: |
133 |
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- Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it |
134 |
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in lab_sea forward experiment (changes results -> updated) |
135 |
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- update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v |
136 |
|
o pkg/seaice: modify seaice_lsr.F in order to improve the gradient |
137 |
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computations; for SEAICE_VECTORIZE_LSR |
138 |
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- move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v) |
139 |
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sweep to the outside, |
140 |
|
- remove store directives and add "CADJ loop sequential" directives |
141 |
|
in analogy to model/src/solve_tridiagonal.F |
142 |
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- replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop |
143 |
|
boundaries to yield more readable code. This has also the charming side |
144 |
|
effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without |
145 |
|
SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in |
146 |
|
seaice_lsr_tridiagu/v now requires either of these flags, vectorization |
147 |
|
still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as |
148 |
|
an additional option) |
149 |
|
The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F |
150 |
|
but the adjoint gradients (which are affected by this change) still explode. |
151 |
|
o coupler (atm & ocn _compon_interf): |
152 |
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- avoid using Exch2 IO mapping if not suitable. |
153 |
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|
154 |
|
checkpoint65m (2015/06/15) |
155 |
|
o pkg/layers: |
156 |
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- clean-up old parameters setting (from Sep 2012): |
157 |
|
+ remove old parameters setting from common block (declared locally); |
158 |
|
+ stop if any old parameter is mixed with new parameters; |
159 |
|
+ check for valid or consistent parameter setting (e.g., layers_name) |
160 |
|
- check that layers_bounds for Pot.Density are in the right range; |
161 |
|
this is supposed to catch un-updated setting after recently shifting |
162 |
|
potential density field "prho" by -1000 (now in "sigma" scale). |
163 |
|
o pkg/layers: |
164 |
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- Added missing call to layers_fill for keeping track of tottend in |
165 |
|
pkg/diagnostics/diagnostics_fill_state.F |
166 |
|
o pkg/layers: |
167 |
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- added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning |
168 |
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of diapycnal fluxes |
169 |
|
o pkg/layers: |
170 |
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- reverted changes to interpolation to previous treatment; there |
171 |
|
was never actually a problem |
172 |
|
o pkg/layers: |
173 |
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- fix interpolation of layers tracers in the presence of partial cells |
174 |
|
- add lots of new functionality to compute water mass transformation |
175 |
|
(enabled by CPP flag LAYERS_THERMODYNAMICS) |
176 |
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- add new calls from main code (diags_oceanic_surf_flux.F, |
177 |
|
thermodynamics.F, impldiff.F) and gad to save the necessary fields |
178 |
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for layers_thermodynamics calculations |
179 |
|
o pkg/ptracers: |
180 |
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- add capability of stepping a passive tracer forward without advection |
181 |
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by setting PTRACERS_advScheme to 0. |
182 |
|
o pkg/diagnostics: |
183 |
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- add few (threads) _BARRIER around any update of "diag_pkgStatus". |
184 |
|
o pkg/layers: |
185 |
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- shift potential density field "prho" by -1000 for density layer averaging so |
186 |
|
that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000); |
187 |
|
Note that density bin boundaries (layers_bounds in data.layers) have |
188 |
|
to be set accordingly (i.e., shifted, in sigma scale). |
189 |
|
o pkg/layers: |
190 |
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- fix snap-shot output of layer thickness @ V.pt and output of pot.density |
191 |
|
- fix calculation of layer non-weighted velocity and layer probability |
192 |
|
- add diagnostics for pot.density used for layer averaging |
193 |
|
o pkg/seaice: |
194 |
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- seaice_calc_viscosity.F: change computation of deltaC**2 to ensure |
195 |
|
positiveness, modify a few comments and improve variable names, |
196 |
|
- the changed computation of deltaC affects most seaice-related |
197 |
|
experiments at the truncation level. |
198 |
|
seaice_itd.thermo is affected by far the most, with |
199 |
|
only 7 digits of agreement remaining; update experiments. |
200 |
|
|
201 |
|
checkpoint65l (2015/05/04) |
202 |
|
o pkg/shelfice: |
203 |
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- in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set |
204 |
|
factor drKp1 to zero where it is negative (ie. do not use |
205 |
|
SHELFICEBoundaryLayer if hFacC>1) |
206 |
|
- the same for factor drLoc in shelfice_forcing.F |
207 |
|
o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem |
208 |
|
with modules in ptracers, when using testreport option "-small_f" |
209 |
|
o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD) |
210 |
|
- replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1)) |
211 |
|
o verification/testreport |
212 |
|
- add new option -small_f |
213 |
|
with this option testreport first makes the target small_f (*.f files) |
214 |
|
before running make (all). This is useful for explicit inlining when |
215 |
|
all sources need to be full available. |
216 |
|
o pkg/exf/exf_interp.F: |
217 |
|
remove previous changes related to reverse (decreasing) input grids latitude |
218 |
|
|
219 |
|
checkpoint65k (2015/04/01) |
220 |
|
o pkg/ecco: |
221 |
|
fix missing cosphi initialization; use eccoiter in place of optimcycle; |
222 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
223 |
|
instead of active read/write |
224 |
|
o pkg/ctrl: |
225 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
226 |
|
instead of active read/write. |
227 |
|
o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F |
228 |
|
return if .NOT.useAUTODIFF |
229 |
|
o pkg/seaice: add CPP brackets (cost function related). |
230 |
|
o model/src: |
231 |
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add useAUTODIFF run time switch. |
232 |
|
o pkg/exf/exf_interp.F: |
233 |
|
add code to allow input grids with latitude starting in the north (i.e. when |
234 |
|
j=1 corresponds to northern edge of field); modify global_with_exf to test |
235 |
|
this feature. |
236 |
|
o verification/testreport: |
237 |
|
- replace "grep -A3" with POSIX conformal sed command, because there are |
238 |
|
implementations of grep that cannot do contextual searches |
239 |
|
- replace "cat -n" by "nl" (two occurrences), because not all implementations |
240 |
|
of "cat" have the option "-n" |
241 |
|
o model/src: |
242 |
|
add new file gsw_teos10.F that contains 3 functions, more or less a copy |
243 |
|
of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to |
244 |
|
convert from conservative to potential temperature. For now they are not |
245 |
|
called anywhere. |
246 |
|
o pkg/ggl90: make "useIDEMIX" useful |
247 |
|
- re-organize code in s/r ggl90_calc a little to move computations that |
248 |
|
are different for idemix into separate loops (changes verification |
249 |
|
experiment idemix at truncation level, 12 digits remain -> updated) |
250 |
|
- requires 2 new 2D fields KappaM, verticalShear |
251 |
|
- make hFacI and recip_hFacI local 3D variables that are passed to |
252 |
|
s/r ggl90_idemix |
253 |
|
- fix and improve some comments |
254 |
|
|
255 |
|
checkpoint65j (2015/02/25) |
256 |
|
o pkg/openad |
257 |
|
- synchronize seawater.F with version in model/src: replace routine |
258 |
|
body of sw_temp by calling sw_ptmp and fix/add a few comments. |
259 |
|
o pkg/mnc: |
260 |
|
- change default value of pickup_read/write_mnc params to FALSE |
261 |
|
(since few features are missing in reading MNC pickup files). |
262 |
|
o model/src: |
263 |
|
- change default (background) vertical diffusivity for salt to be the |
264 |
|
temperature (background) vertical diffusivity. |
265 |
|
- change background vertical diffusivity in vertical mixing pkgs ggl90, |
266 |
|
kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity. |
267 |
|
This makes ptracers default diffusivity (that uses salt diffKr) more |
268 |
|
consistent with vertical mixing schemes. |
269 |
|
o verification/testreport: |
270 |
|
- fix typo in "-pcls" option ; |
271 |
|
- put temp files in /tmp (instead of in local dir) |
272 |
|
- add option "-ncad" to use genmake2 new option "-nocat4ad" |
273 |
|
- allow to use "-j" option (for multi-procs make) for AD, OAD and TLM. |
274 |
|
o pkg/ggl90 (idemix code): |
275 |
|
- apply few fixes ; add some missing "_d 0" ; update output of exp. |
276 |
|
global_ocean.90x40x15.idemix |
277 |
|
o OpenAD |
278 |
|
- enable active file I/O and begin removal of work-around code |
279 |
|
for OpenAD for handling control variables (memory vs. active files) |
280 |
|
- new CPP options file OPENAD_OPTIONS.h |
281 |
|
- revert to genarr2d gradient check for hs94.1x64x5 |
282 |
|
- (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens) |
283 |
|
- gentim2d works for halfpipe_streamice but not yet hs94.1x64x5 |
284 |
|
o tools/genmake2: |
285 |
|
- add option for an alternative Makefile (from Martin) where multiple |
286 |
|
source files are sent to TAF (instead of all in one file). |
287 |
|
o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013) |
288 |
|
- code provided by Carsten Eden as an extension of ggl90 |
289 |
|
- so far the code is turned on within ggl90 by setting a CPP-flag at |
290 |
|
compile time; a runtime flag implementation is not yet complete |
291 |
|
- tested in new verification experiment global_ocean.90x40x15.idemix |
292 |
|
o verification: |
293 |
|
- reduce length of the AD test run by half for experiments |
294 |
|
global_ocean.cs32x15 (std + thsice) and isomip |
295 |
|
- enable active file I/O for OpenAD, adjust verifications accordingly |
296 |
|
- halfpipe_streamice: change gradient check from genarr2d to gentim2d |
297 |
|
o verification/testreport: |
298 |
|
- fix two non-POSIX sed statements so that there are no error messages |
299 |
|
on Mac OS X |
300 |
|
- replace hostname -s with hostname | sed 's/\..*$//' |
301 |
|
o model/src/seawater.F: |
302 |
|
- simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged |
303 |
|
(following the matlab code), which would have avoided the bug caught |
304 |
|
by Matt (see below) in the first place |
305 |
|
o pkg/shelfice: |
306 |
|
- implement alternative discretisation of quadratic drag (selectBotDragQuadr) |
307 |
|
and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag. |
308 |
|
- fix sign of friction tendency (no-slip BC) and fix u,v drag for thin |
309 |
|
ice-shelf case (i.e., within surface level). |
310 |
|
- add config summary in shelfice_check.F |
311 |
|
- remove global variable recip_SHELFICElatentHeat and replace by a local |
312 |
|
variable recip_latentHeat |
313 |
|
- introduce diagnostics for friction velocity uStar (in case of |
314 |
|
SHELFICEuseGammaFrict) |
315 |
|
- change verification experiment isomip.htd: |
316 |
|
+ start from pickup (as input_ad at nIter0=8640) |
317 |
|
+ start from SHELFICEmassFile instead of SHELFICEloadAnomaly file |
318 |
|
+ test SHELFICEuseGammaFrict = .TRUE. |
319 |
|
+ test SHELFICEadvDiffHeatFlux = .TRUE. |
320 |
|
o model/src: |
321 |
|
- fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to |
322 |
|
in-situ Temp) and in routine SW_TEMP (in pkg/openad); |
323 |
|
update output of experiments global_with_exf.yearly and isomip (all 6). |
324 |
|
o pkg/shelfice: |
325 |
|
- change setting of kTopC to also be zero where there is no ice-shelf. |
326 |
|
- zero out surface forcing arrays (for now, for T & S + EmPmR) where |
327 |
|
ice-shelf is. |
328 |
|
- first attempt to get RealFreshWaterFlux effects: for now, only without |
329 |
|
SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping. |
330 |
|
o pkg/seaice: add the option to prescribe a fixed thickness PDF |
331 |
|
for thermodynamic calculations |
332 |
|
- because of divisions of the type 7/7 not exactly equal to 1, this change |
333 |
|
affects results of some verification experiments by up to 4 digits: |
334 |
|
global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume, |
335 |
|
seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides |
336 |
|
adjoint: lab_sea, lab_sea.noseaicedyn |
337 |
|
-> updated |
338 |
|
|
339 |
|
checkpoint65i (2015/01/23) |
340 |
|
o model/src: |
341 |
|
- change units of frictionHeating field from W to W/m^2 |
342 |
|
- fix bug in frictional heating from stratospheric drag in |
343 |
|
S/R ATM_PHYS_TENDENCY_APPLY_V |
344 |
|
- with synchronous time-stepping: move resetting to zero of frictionHeating |
345 |
|
field from load_fields_driver.F to thermodynamics.F ; |
346 |
|
- add diagnostics for frictional heating. |
347 |
|
o model/src & gmredi K3D: |
348 |
|
- add frictionHeating field to pickup-files (for synchronous time-stepping) |
349 |
|
- move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h |
350 |
|
- rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name |
351 |
|
and name in pickup file). |
352 |
|
- fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F |
353 |
|
o model/src: |
354 |
|
- move (from ini_forcing.F) initialisation of all arrays in header file |
355 |
|
FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart |
356 |
|
(since Nov 2012) with option selectAddFluid=1. |
357 |
|
o pkg/shelfice: |
358 |
|
- change units (+ document) of newly added field "shelfIceMassDynTendency" |
359 |
|
- upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays. |
360 |
|
o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers |
361 |
|
o pkg/seaice: two new runtime parameters: |
362 |
|
- SEAICE_cStar replaces the hard wired "20" in the strength formulation, |
363 |
|
long overdue |
364 |
|
- SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012) |
365 |
|
parameterization of tensil stress for fast ice (does not do anything yet) |
366 |
|
o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method |
367 |
|
for LSR: move checking overlaps out of JFNK-if-block |
368 |
|
o pkg/atm_phys: |
369 |
|
- move copy of grid and dynamical fields out of atm_phys_driver.F into |
370 |
|
new S/R ATM_PHYS_DYN2PHYS. |
371 |
|
- fix level height for Linear Free-Surf case (to be consistent with |
372 |
|
fixed-in-time pressure levels). |
373 |
|
o pkg/mom_common (bottomdrag): |
374 |
|
- average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center |
375 |
|
to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG; |
376 |
|
update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag. |
377 |
|
o pkg/shelfice (u/v_drag): |
378 |
|
- add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG; |
379 |
|
- use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F |
380 |
|
(now similar to shelfice_u_drag.F) |
381 |
|
- remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG |
382 |
|
from mom_vecinv.F (similar to mom_fluxform calls). |
383 |
|
o pkg/mom_common (bottomdrag): |
384 |
|
- add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG; |
385 |
|
- add options for alternative discretisation of velocity norm in quadratic |
386 |
|
bottom drag: averaging of grid-cell-center KE to U.point and V.point |
387 |
|
(selectBotDragQuadr=0, original code) can produce noisy patterns; this |
388 |
|
improves when averaging only the other component (e.g. vVel for U bottom |
389 |
|
drag) using wet-point method (selectBotDragQuadr=2) or not (=1). |
390 |
|
- add options (bottomVisc_pCell) to account for partial-cell in bottom |
391 |
|
friction (no-slip BC) thus getting the true distance from the bottom; |
392 |
|
off by default since this also reduces model stability (explicit bottom |
393 |
|
friction). Changes produce different machine truncation with linear-drag |
394 |
|
+ no-slip BC: update output of experiments exp4.stevens (10 digits) and |
395 |
|
front_relax (bvp & mxl, 10 & 11 digits). |
396 |
|
o model/src & mom pkgs: |
397 |
|
- add one more level to vertical viscosity local arrays (Nr+1, previously Nr) |
398 |
|
since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k |
399 |
|
- for now and until vertical mixing scheme are updated to fill up level Nr+1, |
400 |
|
just copy level Nr value to level Nr+1. |
401 |
|
o doc: |
402 |
|
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
403 |
|
o pkg/streamice: |
404 |
|
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
405 |
|
SHELFICE.h: move array shelficemass to init_varia, initialise |
406 |
|
from array shelficemassinit, which is set in init_fixed and |
407 |
|
has option to be set from file; introduce array |
408 |
|
shelficeMassDynTend array, set thru file in init_fixed |
409 |
|
- NEW FILE: shelfice_step_icemass.F: update shelficemass from either |
410 |
|
shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in |
411 |
|
pkg/streamice |
412 |
|
- shelfice_thermodynamics.F: call shelfice_step_icemass if |
413 |
|
SHELFICEMassStepping = .true. |
414 |
|
- shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f |
415 |
|
|
416 |
|
checkpoint65h (2014/12/17) |
417 |
|
o verification/global_ocean.90x40x15, global_ocean_ebm: |
418 |
|
- update to generic controls. |
419 |
|
o pkg/ctrl: |
420 |
|
- ctrl_map_ini_genarr.F: test for igen>0 |
421 |
|
- ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. |
422 |
|
- move gentim2d part of ctrl_map_ini_genarr.F to |
423 |
|
new separate routine : ctrl_map_ini_gentim2d.F |
424 |
|
- ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: |
425 |
|
add time variable weights and cyclic controls (time mean, |
426 |
|
seasonal cycle, etc) capabilities to gentim2d |
427 |
|
o pkg/ecco: |
428 |
|
- move reading of error, conversion to weights from |
429 |
|
ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei) |
430 |
|
o global_oce_llc90, cs32: |
431 |
|
- activte sbo. |
432 |
|
- CTRL_SIZE.h : add maxCtrlProc. |
433 |
|
- activate the new genctrl capabilities. |
434 |
|
- update following reorganization of global_oce_input_fields.tar.gz |
435 |
|
o pkg/ctrl/ctrl_ad_diff.list: |
436 |
|
- add missing ctrl_init_rec.f |
437 |
|
o tools/OAD_support/keepOriginal: |
438 |
|
- add ctrl_init_rec.F |
439 |
|
o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F: |
440 |
|
- avoid recomputations of xx_gentim2d_dummy. |
441 |
|
o momentum diagnostics: |
442 |
|
- move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and |
443 |
|
mom_vecinv.F to timestep.F (to include Smag-3D contribution). |
444 |
|
o pkg/seaice/seaice_lsr.F: |
445 |
|
- fix computation of BU/BV, make sure they are non-zero, only necessary |
446 |
|
for cubed sphere exchanges and SEAICE_OLx/y>0. |
447 |
|
This makes calling s/r fill_cs_corner_rl obsolete (removed). |
448 |
|
o verification/global_ocean.cs32x15/input.seaice |
449 |
|
- add test for strong implicit coupling and restricted addtive Schwarz |
450 |
|
methods for LSR |
451 |
|
- update results/output.seaice.txt |
452 |
|
o verification/tutorial_global_oce_biogeo: |
453 |
|
- AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up) |
454 |
|
and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK); |
455 |
|
update output_adm,_oadm,_tlm.txt |
456 |
|
o pkg/dic: |
457 |
|
- change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h |
458 |
|
- add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn |
459 |
|
for tracer 1 & 2 is set (to avoid double counting of dilution effect). |
460 |
|
o verification/tutorial_global_oce_biogeo: |
461 |
|
- AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since |
462 |
|
dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ; |
463 |
|
update output_adm,_oadm,_tlm.txt |
464 |
|
o eesupp/src: |
465 |
|
- add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F) |
466 |
|
and call it in seaice_lsr when using nonzero SEAICE_OLx/y |
467 |
|
o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing |
468 |
|
LSR (following Hutchings et al. 2004) |
469 |
|
- introduce zetaZ as a global variable (requires adjustments in |
470 |
|
seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ |
471 |
|
in seaice_calc_viscosities.F |
472 |
|
- new flag SEAICEuseStrImpCpl (default off) |
473 |
|
- add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the |
474 |
|
momentum equations |
475 |
|
- JFNK-solver (preconditioner) adjusted to allow using this method |
476 |
|
(where it does not have any positive effect) |
477 |
|
o pkg/seaice |
478 |
|
- add overlap for restrictive additive Schwartz method also to LSR, but |
479 |
|
turn it off by default (because it only seems to work for non-cubed |
480 |
|
sphere/llc topologies) |
481 |
|
o pkg/autodiff |
482 |
|
- add extra exchanges in addummy_in_steppging also for mnc output |
483 |
|
o pkg/seaice: |
484 |
|
- add extra exchanges before dumping adjoint fields in seaice_ad_dump.F |
485 |
|
to avoid stripes in the adjoint output (similar to addummy_in_stepping.F) |
486 |
|
o pkg/obcs: |
487 |
|
- add option to specify domain-connected piece Id along OB though files |
488 |
|
(for now, only used to diagnose PhiVel; default =1 -> global correction) |
489 |
|
- modify obcs_diag_balance.F to process each connected-part separately; |
490 |
|
exclude OB where Id = 0 but keep the full divergence there (-> constant |
491 |
|
Psi along this portion of OB and all inflow derived from grad(Phi)) |
492 |
|
- add example of OB-conect files in verification/so_box_biogeo/input. |
493 |
|
o pkg/diagnostics: |
494 |
|
- improve treatment of Open-Boundaries in Velocity-Potential calculation: |
495 |
|
a) use non zero matrix element across OB and solve for Phi 1 grid point |
496 |
|
outside OB (i.e, where tracer OBCS are applied). |
497 |
|
b) global imbalance of inFlow/outFlow across OB: instead of modifying |
498 |
|
velocity across OB, spread it uniformly along the OB in the RHS. |
499 |
|
|
500 |
|
checkpoint65g (2014/11/19) |
501 |
|
o pkg/diagnostcis: |
502 |
|
- add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param |
503 |
|
o pkg/my82,pp81,kl10: |
504 |
|
- fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D |
505 |
|
field diffKr as background diffusivity to set minimum diffusivity value. |
506 |
|
o pkg/seaice: |
507 |
|
- add new parameter SEAICEuseEVPrev (for revisited EVP by |
508 |
|
Bouillon et al 2013) |
509 |
|
- add SEAICE_evpAlpha/Beta to namelist |
510 |
|
- modify seaice_evp code to able to use SEAICEuseEVPrev. These changes |
511 |
|
involve trivial re-ordering of divisions/multiplications that should not |
512 |
|
have any effects, but ... they do change the results of lab_sea.hb87 so |
513 |
|
that only 2 digits of agreement remain, in line with the general |
514 |
|
instability/fragility of the evp-code. For now, I do not care and just |
515 |
|
update the verification experiment |
516 |
|
o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc) |
517 |
|
- remove xx_genarr2d_numsmooth etc |
518 |
|
- use xx_genarr2d_preproc etc instead |
519 |
|
- carry out smooth_correl2D at initialization stage rather than during |
520 |
|
time stepping. |
521 |
|
- get smoothOpNb from xx_gentim2d_preproc |
522 |
|
o global_oce_cs32 : |
523 |
|
- add test of generic ecco capabilities. |
524 |
|
o pkg/exf/exf_getsurfacefluxes.F : |
525 |
|
- add to tmpUE/tmpVN rather than re-initializing them (conventional behavior). |
526 |
|
o pkg/ctrl,ecco : |
527 |
|
- omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED |
528 |
|
is defined. |
529 |
|
o pkg/seaice: add diagnostics for Delta (deformation parameter) |
530 |
|
o model/src: |
531 |
|
- when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical |
532 |
|
diffusivity (background) is specified but ignored. |
533 |
|
o verification: |
534 |
|
- in testreport, convert hostname to lower case for default output dir name |
535 |
|
o model, pkg : add useCTRL, useECCO parameters (on/off run time switch). |
536 |
|
o pkg/dic: add modifications from Hajoon: |
537 |
|
- add iron sedimentation flux function of the flux of PO4 out of bottom layer |
538 |
|
- light attenuation: add self-shading effect by climatological Chlorophyll |
539 |
|
(read from file). |
540 |
|
o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also |
541 |
|
compiles when SEAICE_ALLOW_DYNAMICS is undefined |
542 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
543 |
|
AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
544 |
|
ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
545 |
|
approach where CPP_OPTIONS.h includes an omnipotent |
546 |
|
ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
547 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
548 |
|
ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
549 |
|
o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
550 |
|
to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
551 |
|
(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
552 |
|
o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
553 |
|
add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
554 |
|
- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
555 |
|
- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
556 |
|
- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
557 |
|
o pkg/ctrl,ecco,exf : |
558 |
|
- remove variables associated with NON-generic costs, |
559 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
560 |
|
- remove NON-generic NON-obcs controls, |
561 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
562 |
|
o pkg/ctrl : added ctrl_local_params.h |
563 |
|
o pkg/ecco : added ecco_local_params.h |
564 |
|
o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
565 |
|
experiments, which will progressively be removed once the |
566 |
|
experiments are revised to use only generic controls/costs. |
567 |
|
|
568 |
|
checkpoint65f (2014/10/13) |
569 |
|
o pkg/ctrl, ecco, seaice : minor changes in headers |
570 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
571 |
|
cost function and control capabilities added since checkpoint65c. |
572 |
|
o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
573 |
|
o pkg/ecco: increase modularity and improve logic |
574 |
|
- ecco_toolbox.F (new) : basic operations that are often used, |
575 |
|
including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk, |
576 |
|
ecco_addcost, ecco_add, ecco_div, ecco_readbar. |
577 |
|
- cost_gencal.F (new) : determine filnames and records. |
578 |
|
- cost_genread.F, cost_generic.F : condense code using ecco_toolbox. |
579 |
|
- cost_generic.F : use spzeroloc rather than hard-coded -9999, |
580 |
|
and exploit the above functions leading to more compact code. |
581 |
|
- cost_genread.F : rm un-necessary arguments, re-arrange args order. |
582 |
|
- ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj, |
583 |
|
using_ers, using_gfo, using_mdt is now only defined within gencost) |
584 |
|
o pkg/ecco: extend generic cost capabilities |
585 |
|
- pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost |
586 |
|
capabilities via gencost_preproc (+ _c,_i,_r related params), |
587 |
|
gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod, |
588 |
|
gencost_outputlevel arguments to cost_generic |
589 |
|
- pkg/ecco/cost_genread.F (new) : interface between cost_generic |
590 |
|
and active_read, making room for gencost_preproc to take effect. |
591 |
|
Added preproc code ('climmon') to replace GENERIC_BAR_MONTH. |
592 |
|
- pkg/ecco/cost_generic.F : |
593 |
|
compute and store misfit maks*(model-data) in localdif that is |
594 |
|
then used in cost and for output, output misfit if outlev.GT.0 |
595 |
|
- pkg/ecco/cost_averagesfields.F : depend on gencost_barskip |
596 |
|
rather gencost_barfile for deciding whether to write barfile |
597 |
|
- pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd |
598 |
|
- pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from |
599 |
|
ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip |
600 |
|
- pkg/ecco/ecco_summary.F : report gencost variables |
601 |
|
- pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs |
602 |
|
o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA |
603 |
|
o pkg/ecco: internal re-organization |
604 |
|
- resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl |
605 |
|
(rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter, |
606 |
|
mv relevant variables definition from ecco_cost.h to ecco.h, |
607 |
|
make sure gencost routines only include ecco.h) |
608 |
|
- throughout : add missing CCP switches, rm unused variables, |
609 |
|
and rm un-necessary CPP switches |
610 |
|
- throughout gencost routines : replace modelstartdate with |
611 |
|
gencost_startdate when needed |
612 |
|
- cost_bp_read.F : use arguments, instead of common blocs |
613 |
|
so that it can be used also by (new) cost_gencost_bpv4.F |
614 |
|
- ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0 |
615 |
|
- ecco_phys.F : compute etanFull |
616 |
|
- ecco_readparms.F : rename using_topex as using_tpj, add |
617 |
|
bpv4-grace to gencost list, initialize added parameters |
618 |
|
- ecco_summary.F : include SIZE.h needed for augmented ecco.h |
619 |
|
|
620 |
|
checkpoint65e (2014/09/28) |
621 |
|
o pkg/obcs: |
622 |
|
- replaced the just-added CPP options with run-time variables |
623 |
|
(see pkg/obcs/OBCS_PARAMS.h for details) |
624 |
|
o pkg/obcs: |
625 |
|
- add additional CPP options for sponge boundary layers |
626 |
|
(see pkg/obcs/OBCS_OPTIONS.h for details) |
627 |
|
o pkg/atm_phys: |
628 |
|
- implement simple (obliquity only, assuming circular planet orbit) |
629 |
|
seasonal cycle for incoming insolation ; used when run-time parameter |
630 |
|
"select_incSW" is set to 1 ; by default (=0), uses old unchanged formula. |
631 |
|
o pkg/exf, pkg/ecco, pkg/ctrl: |
632 |
|
- add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets |
633 |
|
- activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip |
634 |
|
- implement gentim2d for xx_tauu, xx_tauv |
635 |
|
o pkg/ctrl, pkg/ecco : |
636 |
|
- fix and complement the generic controls implementation |
637 |
|
o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F, |
638 |
|
pkg/shelfice/shelfice_thermodynamics.F, |
639 |
|
verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F, |
640 |
|
verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F : |
641 |
|
- add weight in CTRL_GET_GEN calls |
642 |
|
o pkg/ctrl : |
643 |
|
- ctrl_get_gen.F : add weight as input parameter, and apply |
644 |
|
it directly rather than using smooth_correl2Dw (to be retired). |
645 |
|
- ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call |
646 |
|
o pkg/ctrl : |
647 |
|
- introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, |
648 |
|
ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) |
649 |
|
- re-activate ctrl_summary (call in ctrl_init.F) |
650 |
|
o pkg/ctrl/ctrl_cost_gen.F : |
651 |
|
- fix CCP brackets, remove un-necessary myiter, mytime |
652 |
|
o pkg/ecco, pkg/ctrl : |
653 |
|
- remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) |
654 |
|
- remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) |
655 |
|
- add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) |
656 |
|
- add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) |
657 |
|
|
658 |
|
checkpoint65d (2014/09/15) |
659 |
|
o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : |
660 |
|
- add xx_genarr2d_bounds,xx_genarr3d_bounds, |
661 |
|
xx_genarr2d_numsmooth, xx_genarr3d_numsmooth |
662 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : |
663 |
|
- remove compilation failure |
664 |
|
- replace hard coded example |
665 |
|
- use ctrl_map_ini_gen2D, 3D |
666 |
|
o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : |
667 |
|
- on/off switch based upon xx_genarr2d_weight,3d |
668 |
|
o src/packages_init_variables.F : |
669 |
|
- regroup pkg/estimation calls |
670 |
|
- remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
671 |
|
(moved to ctrl_init_variables) |
672 |
|
o cost/cost_init_varia.F : |
673 |
|
- remove ecco_cost_init_varia |
674 |
|
(moved to ecco_init_varia) |
675 |
|
o ctrl/ctrl_init_variables.F : |
676 |
|
- add CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
677 |
|
- add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI |
678 |
|
o ctrl/ctrl_map_ini.F : |
679 |
|
- remove ctrl_map_ini_genarr, seaice_ctrl_map_ini |
680 |
|
(moved to ctrl_init_variables) |
681 |
|
o ctrl/ctrl_map_ini_ecco.F : |
682 |
|
- remove ECCO_PHYS (mv to ecco_init_varia) |
683 |
|
- remove seaice_ctrl_map_ini (mv to ctrl_init_variables) |
684 |
|
o ecco/ecco_ad_diff.list : |
685 |
|
- add ecco_init_varia.f |
686 |
|
o ecco/ecco_init_varia.F |
687 |
|
- new routine |
688 |
|
o pkg/streamice: |
689 |
|
- move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F |
690 |
|
to streamice_init_fixed.F ; fix setting of STREAMICEisOn. |
691 |
|
- from model/src, only call pkg/streamice routines if useStreamIce is TRUE. |
692 |
|
o pkg/generic_advdiff: |
693 |
|
- fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. |
694 |
|
o pkg/exf: |
695 |
|
- exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, |
696 |
|
xxg_precip capability |
697 |
|
- exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch |
698 |
|
o pkg/ctrl: |
699 |
|
- ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d |
700 |
|
o model/src/load_fields_driver.F : |
701 |
|
- move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING |
702 |
|
so xx_gentim2d can be applied to e.g. exf fields in a timely manner. |
703 |
|
o OpenAD verification experiments: |
704 |
|
- Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h |
705 |
|
in src files (to enable to skip the ECCO_CPPOPTIONS.h); |
706 |
|
for now, only in pkgs used in OpenAD verification experiments. |
707 |
|
- Change all except one (halfpipe_streamice) OpenAD experiments to use pkg |
708 |
|
specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) |
709 |
|
instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). |
710 |
|
This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. |
711 |
|
o OpenAD verification tests: |
712 |
|
- finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); |
713 |
|
- finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for |
714 |
|
tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. |
715 |
|
- leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) |
716 |
|
and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). |
717 |
|
o model/src & generic_advdiff: |
718 |
|
- change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S |
719 |
|
forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model |
720 |
|
dynamics requires valid tracer forcing only over tile interior but, for |
721 |
|
some diagnostics, may need to extend it over 1 point in tile halo region. |
722 |
|
- in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid |
723 |
|
tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max |
724 |
|
setting in temp/salt/ptracer_integrate.F |
725 |
|
o pkg/dic: |
726 |
|
- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
727 |
|
gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
728 |
|
in gchem_forcing_sep.F |
729 |
|
o pkg/autodiff & obcs: |
730 |
|
- add storage of current OB values for U & V (was already done for T & S). |
731 |
|
|
732 |
|
checkpoint65c (2014/08/30) |
733 |
|
o pkg/dic: |
734 |
|
- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
735 |
|
and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
736 |
|
AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
737 |
|
o verification: |
738 |
|
- new experiment testing OBCS and DIC pkgs, using params & output from |
739 |
|
tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
740 |
|
passage: take OBCS from the last year of a 2 yrs simulation and initial |
741 |
|
conditions from t=1.yr while keeping the same forcing. |
742 |
|
o model/src: |
743 |
|
- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
744 |
|
(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
745 |
|
o pkg/diagnostics (Stats-Diags): |
746 |
|
- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
747 |
|
a) refine region where stats are computed, excluding where arrhFac=0 ; |
748 |
|
b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
749 |
|
c) extend regional stats over the region edges (for U or V pt location). |
750 |
|
o pkg/gchem: |
751 |
|
- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
752 |
|
pkg/dic is currently changing/updating ptracers values beyond the OB). |
753 |
|
o verification (hs94): |
754 |
|
- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
755 |
|
bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
756 |
|
hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
757 |
|
apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
758 |
|
o pkg/ptracers: |
759 |
|
- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
760 |
|
switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
761 |
|
- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
762 |
|
with AB-2 code (so that it get tested). |
763 |
|
o model/src: |
764 |
|
- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
765 |
|
with AB-2 code (previously only available with AB-3 code). |
766 |
|
Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
767 |
|
to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
768 |
|
there, by calling CYCLE_AB_TRACER). |
769 |
|
o pkg/generic_advdiff: |
770 |
|
- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
771 |
|
GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
772 |
|
+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
773 |
|
S/R temp/salt/ptracers_integrate.F |
774 |
|
o model/src & pkg/ptracers: |
775 |
|
- remove common block variables gT,gS (in DYNVARS.h), except when |
776 |
|
USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
777 |
|
- remove common block variable gPtr. |
778 |
|
o model/src & pkgs: |
779 |
|
- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
780 |
|
ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
781 |
|
IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
782 |
|
GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
783 |
|
+ change accordingly all calling S/R. |
784 |
|
- use local temperature/salinity/ptracer tendency array (without bi,bj) |
785 |
|
in S/R temp/salt/ptracers_integrate.F |
786 |
|
o pkg/seaice: |
787 |
|
- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
788 |
|
to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
789 |
|
- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
790 |
|
in seaice_lsr |
791 |
|
- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
792 |
|
in s/r seaice_lsr_calc_coeffs |
793 |
|
o pkg/mdsio: |
794 |
|
- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
795 |
|
(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
796 |
|
too long (e.g., > MAX_LEN_FNAM/2 ) |
797 |
|
|
798 |
|
checkpoint65b (2014/08/12) |
799 |
|
o pkg/matrix: |
800 |
|
- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
801 |
|
o model/src: |
802 |
|
- fix initialisation of geothermalFile; compile geothermal-flux code in |
803 |
|
natl_box verification experiment. |
804 |
|
o model/src & pkg/down_slope: |
805 |
|
- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
806 |
|
- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
807 |
|
field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
808 |
|
results at machine truncation level: update output of experiments |
809 |
|
global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
810 |
|
o pkg/diagnostics (Stats-Diags): |
811 |
|
- do not cumulate the full volume when DIAGNOSTICS_FILL is |
812 |
|
called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
813 |
|
This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
814 |
|
times (but Min,Max and StD are still wrong). |
815 |
|
o model/src: |
816 |
|
- add geothermal flux forcing: read in ini_forcing.F as time-constant |
817 |
|
field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
818 |
|
o model/src: |
819 |
|
- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
820 |
|
_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
821 |
|
arrays are already updated while adjustments (filters, conv.adjustment) are |
822 |
|
still applied later, in S/R TRACERS_CORRECTION_STEP. |
823 |
|
o model/src: |
824 |
|
- store in common bloc array "rhoInSitu" the virtual potential temperature |
825 |
|
anomaly that is used to compute geopotential: this make the atmos code |
826 |
|
more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
827 |
|
o pkg/seaice/seaice_lsr.F |
828 |
|
- rename integer variable ilcall to ipass (that's what it is called |
829 |
|
in the residual diagnostics |
830 |
|
- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
831 |
|
default) for improved non-linear convergence of the first few steps |
832 |
|
- adjust a few comments and add new ones to explain some of the store |
833 |
|
directives |
834 |
|
o pkg/generic_advdiff (& ptracers): |
835 |
|
- re-work the code to check for valid advection scheme and for minimum |
836 |
|
size of overlap (now stored in local common bloc in gad_advscheme.F) |
837 |
|
o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
838 |
|
- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
839 |
|
- add an auxilliary variable "bet" and fix store directives and keys in |
840 |
|
seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
841 |
|
less exact gradients in my tests); but there are still |
842 |
|
recomputation warning (although gradients are sort of OK), when |
843 |
|
SEAICE_LSR_VECTORIZE is not defined, so this flag and |
844 |
|
SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
845 |
|
- update verification experiments lab_sea. |
846 |
|
- change some comments in S/R seaice_calc_viscosities |
847 |
|
o model/src: |
848 |
|
- if staggerTimeStep=T, always apply exchange to velocity field in |
849 |
|
do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
850 |
|
(independent of using multi-dim advection or not); no effect on FWD run |
851 |
|
but affects AD results (at machine truncation level): update output of |
852 |
|
experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
853 |
|
and isomip (oad: 12.d). |
854 |
|
o pkg/generic_advdiff: |
855 |
|
- stop if doAB_onGtGs is set to FALSE but ignored |
856 |
|
- refine warning related to stability of tracer time-stepping |
857 |
|
regarding internal wave dynamics. |
858 |
|
- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
859 |
|
on staggerTimeStep & implicitIntGravWave (will now get a warning |
860 |
|
if potentially unstable). |
861 |
|
o pkg/kl10: |
862 |
|
- add new pkg "kl10" for mixing due to internal wave breaking, from |
863 |
|
http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
864 |
|
(contribution from Jody Klymak), tested in verification experiment |
865 |
|
verification/internal_wave/input.kl10/ |
866 |
|
o isomip experiment: |
867 |
|
- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
868 |
|
(input.htd) and update the output. |
869 |
|
o cd_code experiments: |
870 |
|
- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
871 |
|
#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
872 |
|
global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
873 |
|
update the corresponding output. |
874 |
|
o pkg/seaice: |
875 |
|
- reduce the number of include files and store directives in |
876 |
|
S/R seaice_lsr_tridiagu/v |
877 |
|
- change the order of loops in one case in S/R seaice_lsr_tridiagv |
878 |
|
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
879 |
|
get rid off one store directive (a TAF bug?) |
880 |
|
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
881 |
|
S/R seaice_lsr_tridiagv to change the loop range for consistency |
882 |
|
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
883 |
|
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
884 |
|
S/R seaice_lsr_tridiagu/v (requires update of |
885 |
|
offline_exf_seaice/input.dyn_jfnk) |
886 |
|
|
887 |
|
checkpoint65a (2014/07/27) |
888 |
|
o model/src: |
889 |
|
- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
890 |
|
surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
891 |
|
(topo in p-coords, ice-shelf in z-coords); update output of experiments |
892 |
|
tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
893 |
|
o model/src: |
894 |
|
- collect momentum forcing tendency into local 2-D array (passed as argument |
895 |
|
to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
896 |
|
parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
897 |
|
affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
898 |
|
- collect T & S forcing tendency into local 2-D array (passed as argument to |
899 |
|
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
900 |
|
affects results at machine truncation level (e.g., ocean: if using |
901 |
|
SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
902 |
|
correction due to vertical advection). |
903 |
|
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
904 |
|
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
905 |
|
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
906 |
|
obcs_ctrl (ad & fwd grd @ 12 & 7). |
907 |
|
o pkg/ptracers & diagnostics: |
908 |
|
- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
909 |
|
title (to avoid some unexpected truncation); sort out ptracers diags units. |
910 |
|
- collect ptracer forcing tendency into local 2-D array (passed as argument |
911 |
|
to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
912 |
|
|
913 |
|
checkpoint65 (2014/07/18) |
914 |
|
o pkg/fizhi: |
915 |
|
- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
916 |
|
affects results at machine truncation level. Update output of experiments |
917 |
|
fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). |
918 |
|
o pkg/seaice: more clean up |
919 |
|
- rename TAF common block tapes to be more consistent and remove |
920 |
|
unnecessary duplicates |
921 |
|
- add store directives to remove more recomputations, but use smaller |
922 |
|
tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. |
923 |
|
The idea behind this flag is to reduce the memory footprint when the |
924 |
|
adjoint of the LSR is not required. As of now, defining the flag |
925 |
|
SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by |
926 |
|
a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). |
927 |
|
For experiment offline_exf_seaice, this means on a linux box with gfortran |
928 |
|
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
929 |
|
this experiment): |
930 |
|
> size mitgcmuv_ad |
931 |
|
text data bss dec hex |
932 |
|
5100659 1216 220458952 225560827 d71c8fb |
933 |
|
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
934 |
|
but only a moderate increase of 36% for global_ocean.cs32x15: |
935 |
|
text data bss dec hex |
936 |
|
6695027 1648 1014578664 1021275339 3cdf6ccb |
937 |
|
6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER) |
938 |
|
- note: there are still recomputations in global_ocean.cs32x15 and |
939 |
|
offline_exf_seaice and the gradient agreement changes (gets a |
940 |
|
little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) |
941 |
|
- in general, the AD gradients still are wrong |
942 |
|
o OpenAD |
943 |
|
- clean up code_oad/ directories somewhat by moving files |
944 |
|
dontCompile, dontTransform, keepOriginal to OAD_support/ |
945 |
o model/src: |
o model/src: |
946 |
- using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F |
- using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F |
947 |
(not currently tested): add dissipation terms before NLFS rescaling of |
(not currently tested): add dissipation terms before NLFS rescaling of |