4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
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7 |
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o pkg/ctrl, pkg/shelfice, and optim: |
8 |
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- add new control variable xx_shifwflx (fresh water flux underneath ice |
9 |
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shelves). This is almost as tedious as obcs-ctrl, because the |
10 |
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variables needs its own mask. |
11 |
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- add a cost function term that penalizes the deviation of xx_shifwflx |
12 |
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from the first guess (zero) in analogy to other control variables |
13 |
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o pkg/shelfice: |
14 |
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- start basic adjoint |
15 |
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o pkg/ctrl: |
16 |
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- remove extra 2D field "for good measure" when initializing in |
17 |
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ctrl_set_globfld_[xy/xz/yz].F |
18 |
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- replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec |
19 |
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- improve error messages in ctrl_set_unpack_* |
20 |
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o OBC implementation in momentum: |
21 |
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use interior masks (maskInC,W & S) in momentum S/R: |
22 |
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- multiply divergence, tension and some del^i.u or del^j.v by maskInC |
23 |
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- multiply del2u,del2v by maskInW/S (biharmonic viscosity) |
24 |
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- multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) |
25 |
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- multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) |
26 |
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Motivation: fix/clean implementation of OBC with biharmonic-viscosity |
27 |
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(and also with Leith/Smagorinsky harmonic-viscosity). |
28 |
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Update output of experiment dome and exp4 (+nlfs). |
29 |
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o exp4 test-exp: |
30 |
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- turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) |
31 |
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and prescribe time-varying OB (without pkg/exf) for zonal-velocity |
32 |
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at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
33 |
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time-varying OB at Western-side for wVel (NonHyd); update output. |
34 |
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- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
35 |
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and biharmonic-viscosity ; also use prescribed time varying OB. |
36 |
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o pkg/obcs: |
37 |
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fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
38 |
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o model/src: |
39 |
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- fix startTime setting when baseTime<>0 & nIter0=0 are specified ; |
40 |
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- initialise startTime & nIter0 with unlikely values: allows to set one |
41 |
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from the other without ambiguity. |
42 |
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o seaice_obcs test-exp.: |
43 |
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add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output. |
44 |
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o pkg/obcs: |
45 |
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- remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: |
46 |
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no longer needed with maskInC,W,S in pkg/generic_advdiff. |
47 |
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o pkg/seaice: |
48 |
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- retired SEAICE_SALINITY and SEAICE_salinity in favor of |
49 |
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SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively. |
50 |
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- fixed bug in the initialization of sea ice salinity variable HSALT |
51 |
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in seaice_init_varia.F (removed dependence on ICE2WATR) |
52 |
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o fizhi-cs test exp.: |
53 |
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switch reference output convention for these 2 non-standard test-exp, |
54 |
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from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5) |
55 |
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to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11) |
56 |
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reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran |
57 |
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o model/inc: |
58 |
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- change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4") |
59 |
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of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS) |
60 |
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o pkg/seaice: |
61 |
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- fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY |
62 |
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o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15 |
63 |
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- updated output*.txt files due to bug fixes in salt, saltPlumeFlux, |
64 |
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and initial HSALT |
65 |
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|
66 |
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checkpoint62w (2011/04/26) |
67 |
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o pkg/mom_fluxform: |
68 |
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- fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf. |
69 |
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- use parameter "sideDragFactor" in no-slip BC side-drag part. |
70 |
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- update output of exp. global_ocean.90x40x15 |
71 |
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o pkg/mom_vecinv: |
72 |
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mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform) |
73 |
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o update seaice exp.: |
74 |
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use more consistent parameter values (remove "backward compatability only": |
75 |
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ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh) |
76 |
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related to thermodynamics seaice. Update output (fwd+AD) of exp.: |
77 |
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1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs |
78 |
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o update test-exp global_ocean.90x40x15: |
79 |
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o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis). |
80 |
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o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.) |
81 |
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o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params) |
82 |
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o turn on zStar & viscA4 in standard set-up (dir input/) |
83 |
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and update output files: output.txt & output.dwnslp.txt |
84 |
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o new AD-test experiment: obcs_ctrl |
85 |
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(From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector. |
86 |
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o pkg/dic: |
87 |
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fix two bugs in handling water vapour pressure in carbonate chemistry |
88 |
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and air-sea fluxes. Found by Val Bennington and Galen McKinley |
89 |
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(add DIC Option = WATERVAP_BUG to recover old results) |
90 |
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update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline |
91 |
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o adding allowInteriorFreezing option to check for water below freezing point |
92 |
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at depth and bring the negative heat anomaly to the surface level |
93 |
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o pkgs _fields_load: |
94 |
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- extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs) |
95 |
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- use new S/R GET_PERIODIC_INTERVAL in pkgs: |
96 |
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bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and |
97 |
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rbcs to get interpolation weights and time reccord number. |
98 |
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- fix multi-threading in aim_fields_load.F |
99 |
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- apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F |
100 |
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o external_fields_load: |
101 |
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new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear |
102 |
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interpolation weights) to use in a periodic time-series ; do not divide by |
103 |
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time-step to convert to integer: |
104 |
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- this fixes case where externForcingPeriod is not multiple of time-step |
105 |
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(Thanks to Christopher L. Wolfe) |
106 |
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- this fixes case where externForcingPeriod is an odd multiple of time-step |
107 |
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(was wrong by half of time-step); update results of tutorial_global_oce_in_p. |
108 |
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store index of time-record which is currently loaded: |
109 |
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- works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ; |
110 |
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- needed for the adjoint but not yet used because of extensive recomputations; |
111 |
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(to be fixed soon) |
112 |
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|
113 |
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checkpoint62v (2011/04/02) |
114 |
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o verification/1D_ocean_ice_column added to test Ian Fenty's |
115 |
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pkg/seaice_growth.F modifications for improving sea ice code differentiability |
116 |
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o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope |
117 |
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(new velocity statistics after changing maskInW & maskInS definition) |
118 |
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o pkg/generic_advdiff with OBCS: |
119 |
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use maksInW & maskInS in advective flux and in biharmonic diffusion calculation: |
120 |
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equivalent to assumption of no tracer gradient outside the OB region. |
121 |
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This will affect the results if using obcs+biharmonic diffusion. |
122 |
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update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc) |
123 |
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o pkg/obcs: |
124 |
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change definition of maskInW & maskInS: leave OB edges inside (maskIn=1) |
125 |
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(e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still |
126 |
|
in Interior region. No impact on solution but affects Velocity monitor stats. |
127 |
|
o pkg/ptracers (adjoint) |
128 |
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New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate |
129 |
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tape file for each tracer |
130 |
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o model/inc/src and pkg/autodiff: add parameters that allow to turn |
131 |
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of parts of the adjoint code at run time. For now, there are only |
132 |
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useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These |
133 |
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parameters are set in data.pkg. |
134 |
|
This is the lazy coward's version of doing this, but still useful for |
135 |
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debugging. In order to do it right, everything needs to be moved to |
136 |
|
pkg/autodiff. |
137 |
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o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at |
138 |
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the end; this fixes the adjoint balancing code for open boundaries. |
139 |
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o pkg/ctrl: |
140 |
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- change behavior of xx_${varname}period to be analogous to exf-conventions: |
141 |
|
xx_${varname}period = 0., means time-independent control part |
142 |
|
xx_${varname}period = -12., means one-year-periodic monthly control part |
143 |
|
- introduce helper routine ctrl_init_rec (part of ctrl_init.F) to |
144 |
|
clean up ctrl_init a little, remove unused variables |
145 |
|
- ctrl_init: fixed the handling of the start/endrec for obcs-variables |
146 |
|
- move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec |
147 |
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|
148 |
|
checkpoint62u (2011/03/15) |
149 |
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o model/src: |
150 |
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- for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in |
151 |
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h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ; |
152 |
|
- in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to |
153 |
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INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF. |
154 |
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o pkg/ctrl/obcs/ecco: |
155 |
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- remove obsolete, unused, and partially broken code: |
156 |
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ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within |
157 |
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ALLOW_CTRL_OBCS_BALANCE |
158 |
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- put a stop statement into ecco/cost_obcsvol.F, but also add |
159 |
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cost_obcsvol to ecco_ad_diff.list |
160 |
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o pkg/ecco: fix counting cost function contributions for obcs (code |
161 |
|
by Matt M.) and diffkr for diagnostics |
162 |
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o pkg/ecco, pkg/ctrl, pkg/grdchk: |
163 |
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add cost penalty terms for initial uvel, vvel, eta controls |
164 |
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and I/O for prior error files |
165 |
|
o pkg/mdsio: |
166 |
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move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option |
167 |
|
(new argument) to check for tiled file in mdsioLocalDir : this fix the |
168 |
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restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir. |
169 |
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o pkg/ctrl: |
170 |
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- ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by |
171 |
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ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove |
172 |
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unused and superfluous variables |
173 |
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- ctrl_get_gen_rec.F: catch the case of xx_genperiod=0. |
174 |
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o pkg/ecco |
175 |
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- enable adjoint of Stevens OB |
176 |
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o pkg/ctrl/ecco/grdchk: |
177 |
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- remove global declaration of tmpfldx/yz and tmpfldx/yz2. |
178 |
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Fortunately, we do not have any tests for the numerous cpp-flagged |
179 |
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option of "obcs as control parameters" so we will never know |
180 |
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if this is an improvement (but at least now things compile). |
181 |
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- remove an obsolete initialization from ecco_cost_init_barfiles.F |
182 |
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- fix some problems within never used ifdefs to make the code compile |
183 |
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o pkg/obcs: |
184 |
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- Refine Interior mask definition to work with more complex OB (e.g. |
185 |
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if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to |
186 |
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read in Interior mask from file. Check if Interior mask is consistent |
187 |
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with OB list of indices. |
188 |
|
o pkg/seaice |
189 |
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- beginning code for a seaice tracer package, |
190 |
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but currently only used for seaice age: SEAICE_AGE |
191 |
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SEAICE_num = 4 |
192 |
|
iTracer = 1: area-weighted ice age |
193 |
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= 2: volume-weighted ice age |
194 |
|
= 3, 4: template for one-year vs. multi-year ice |
195 |
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data.seaice has new namelist SEAICE_PARM03 for arrays related to |
196 |
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SEAICE_num |
197 |
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|
198 |
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checkpoint62t (2011/03/05) |
199 |
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o pkg/obcs: |
200 |
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- obcs_apply_uv.F: change to a 2 steps method, first tangential component; |
201 |
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then normal component. This ensures that the normal component is set |
202 |
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correctly even when it conficts with tangential setting from an other OB. |
203 |
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Affects results of test-experiment seaice_obcs: update the output.txt |
204 |
|
o pkg/obcs: |
205 |
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- add code to monitor statistics of dynamical fields at OB. |
206 |
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- take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW : |
207 |
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- fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection). |
208 |
|
- change default: balance the Net inflow through all OB (instead of balancing |
209 |
|
each OB separately); keep the old method if setting OBC_balanceFacX < 0. |
210 |
|
- switch on useOBCSbalance in dome experiment: only correct Western OB outflow |
211 |
|
to match Nortern OB inflow (OBCS_balanceFacN=0). |
212 |
|
o pkg/seaice: |
213 |
|
- redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL |
214 |
|
o pkg/seaice (seaice_growth v 1.113): |
215 |
|
- reverting seaice_growth to v 1.111 in order to have code with exact bit |
216 |
|
compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge |
217 |
|
CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced |
218 |
|
runtime flag SEAICEareaFormula is kept but is inactive |
219 |
|
o model/src: |
220 |
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- add new param to scale curvilinear grid distance and area when using |
221 |
|
a different sphere radius from the grid-files. |
222 |
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- test/check multi-threads EXCH applied to local variable (cg2d_x) |
223 |
|
o adjoint: |
224 |
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- enable adjoint of Stevens OB |
225 |
|
- add dummy_in_dynamics to enable extraction of ADJrhoinsitu |
226 |
|
(a bit delicate because of potentially modified adj. common block structure; |
227 |
|
current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later) |
228 |
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|
229 |
|
checkpoint62s (2011/02/15) |
230 |
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o pkg/seaice (seaice_growth v 1.112): |
231 |
|
- introduce SEAICEareaFormula run time parameter, which selects the recipe for |
232 |
|
computing the ice cover tendency from effective thickness tendencies. Include |
233 |
|
Ian Fenty's formula. |
234 |
|
- remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using |
235 |
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SEAICEareaFormula. |
236 |
|
- simplify notations for the various d_HEFF/d_AREA terms. |
237 |
|
o pkg/gmredi: |
238 |
|
- add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code |
239 |
|
from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative; |
240 |
|
add a verification test-run (front_relax.bvp) to test GM_useBVP. |
241 |
|
o pkg/seaice (seaice_growth v 1.111): |
242 |
|
- for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's. |
243 |
|
- the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to |
244 |
|
also melt ice. |
245 |
|
o pkg/seaice: |
246 |
|
- McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty). |
247 |
|
- can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h |
248 |
|
o pkg/cheapaml: |
249 |
|
- from Nico Wienders: New version of this package. |
250 |
|
o pkg/flt: |
251 |
|
- add CPP options to prevent floats to re-enter the opposite side of |
252 |
|
a periodic domain (default: keep periodicity) |
253 |
|
o pkg/gmredi: |
254 |
|
- apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners |
255 |
|
(needed for multi-dim advection). |
256 |
|
- switch on GM Advective form in global_ocean.cs32x15 and update output.txt |
257 |
|
o model/src: |
258 |
|
- fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run. |
259 |
|
o tutorial_tracer_adjsens |
260 |
|
- extend to NLFS and replace maskC by hFacC |
261 |
|
(change reference output accordingly) |
262 |
|
|
263 |
|
checkpoint62r (2011/01/24) |
264 |
|
o testreport: |
265 |
|
- add option -deloutp (-do) to remove output file after successful run |
266 |
|
- add option -mfile (-mf) for MPI machile-file and for each test-exp, |
267 |
|
extract exact list of procs from this file ; adjust COMMAND by |
268 |
|
replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs. |
269 |
|
o pkg/ecco: replace old ineffective way of penalizing deviations from |
270 |
|
first guess (of obcs) with code by Matt Mazloff |
271 |
|
o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without |
272 |
|
exf/cal |
273 |
|
- ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl |
274 |
|
and handle case of obcs?period == 0 |
275 |
|
Not affected by these changes: There is still an inconsistency in |
276 |
|
the computation of start/endrec for the obcs variables for ALLOW_CAL |
277 |
|
defined (see comment by Menemenlis, 7-Mar-2003) |
278 |
|
- make S/R ctrl_get_gen_rec return something meaningful even if |
279 |
|
ALLOW_CAL is not defined |
280 |
|
- ctrl_getobcs?: simplify code so that it does not need to use |
281 |
|
S/R exf_swapfields |
282 |
|
o testreport: |
283 |
|
allow to test MPI with different number of processors for each experiment: |
284 |
|
create file "SIZE.h.mpi" in each build dir. |
285 |
|
Note: update of "-command" argument not yet implemented. |
286 |
|
o model/src, pkg/autodiff, pkg/ecco, pkg/seaice: |
287 |
|
alleviate the need for additional 3D tapes when using |
288 |
|
the non-inear free surface in the adjoint. This is done |
289 |
|
by adding an 'update' of hfacc etc. to their current |
290 |
|
value at the beginning of forward_step.F. |
291 |
|
o pkg/seaice |
292 |
|
seaice_lsr: move stress-divergence computations out of outer pseudo- |
293 |
|
timestepping loop |
294 |
|
o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD' |
295 |
|
up, so that the calls of the ctrl_* subroutines are really at the end |
296 |
|
of the routine. |
297 |
|
o pkg/gmredi: |
298 |
|
allow to specify a 2-D horizontal map and a 1-D vertical profil |
299 |
|
as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity. |
300 |
|
o pkg/seaice: |
301 |
|
move lsr iterations from seaice_dynsolver to seaice_lsr. |
302 |
|
o pkg/seaice: |
303 |
|
reduce memory footprint of seaice mutldim advection tapes, |
304 |
|
by using a 2D tape independent of the generic_advdiff ones, |
305 |
|
and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc. |
306 |
|
|
307 |
|
checkpoint62q (2010/12/29) |
308 |
|
o model/src: |
309 |
|
- check horizontal grid-spacing for unset or zero/negative values. |
310 |
|
- change AD test hs94.1x64x5 to be truly a 2-D set-up. |
311 |
|
o pkg/flt: |
312 |
|
- use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR |
313 |
|
- precision of input and output files set according to readBinaryPrec |
314 |
|
and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits. |
315 |
|
- initial float position from tiled file was not converted to index space |
316 |
|
(looks like a bug): fixed to make it similar to initial pos. global file. |
317 |
|
o global_ocean.cs32x15: |
318 |
|
change SIZE.h of AD set-up to get same tiling as with MPI. |
319 |
|
Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11) |
320 |
|
o model/src: |
321 |
|
add flag to control printing of domain fields (bathymetry, hFac ...) in |
322 |
|
ini_mask_etc (call to plot_fieds_xy*). |
323 |
|
o pkg/thsice: |
324 |
|
if useEXF, some forcing fields are not valid in overlap: fixed by computing |
325 |
|
over the interior only + apply EXCH at the end (like with SEAICE advection). |
326 |
|
o pkg/mdsio: |
327 |
|
- add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer |
328 |
|
to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS. |
329 |
|
- change barrier call for safe multi-threads access to 3-D shared buffer. |
330 |
|
- MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones) |
331 |
|
- replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and |
332 |
|
remove the 4 S/R MDS_PASS_WH_R4/8toRL/S. |
333 |
|
o pkg/flt: |
334 |
|
- add fourth-order Runge-Kutta integration |
335 |
|
- add basic exch2 support (only 1 facet supported so far!) |
336 |
|
o pkg/mdsio+rw: |
337 |
|
new S/R to read local (or tile independent) vector (read counterpart of |
338 |
|
mds_writevec_loc, and front-end write_glvec_rl/rs). |
339 |
|
o global_ocean.cs32x15: additional input_ad.seaice experiment |
340 |
|
that uses pkg/seaice rather than pkg/thsice. |
341 |
|
(using multidim advection for seaice) |
342 |
|
o towards more F95 syntax for array specification in namelist: |
343 |
|
- change "data.diagnostics" (data.ptracers was changed before checkpoint62p) |
344 |
|
of all verification experiments. |
345 |
|
e.g.: line: fields(1,3)='ETAN ','ETANSQ ', |
346 |
|
was changed to: fields(1:2,3)='ETAN ','ETANSQ ', |
347 |
|
- finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles |
348 |
|
o global_ocean.cs32x15: additional input.seaice experiment |
349 |
|
that uses pkg/seaice rather than pkg/thsice. |
350 |
|
|
351 |
|
checkpoint62p (2010/12/17) |
352 |
|
o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it |
353 |
|
to THSICE_SIZE.h to avoid conflict with pkg/seaice. |
354 |
|
o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint. |
355 |
|
allow for use of multim. advection in seaice adjoint. |
356 |
|
o pkg/seaice: add diagnostics for snow precipitation and sublimation flux |
357 |
|
- first attempt to close budgets by taking into account the freshwater |
358 |
|
flux implied by the sublimation of snow and ice. So far only the |
359 |
|
volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag |
360 |
|
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET |
361 |
|
o eesupp/src: |
362 |
|
new S/R with new option (NML_EXTENDED_F77) to change array specification |
363 |
|
from F95 standard to commonly accepted extended F77 form. |
364 |
|
This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5) |
365 |
|
and to revert back to the original syntax (with -DNML_EXTENDED_F77) |
366 |
|
for less tolerant f77 compiler (e.g., pgf77, g77). |
367 |
|
o globalFiles: |
368 |
|
commented out in parameter file "data" since it's not safe with MPI |
369 |
|
(e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much |
370 |
|
in this case); no longer commented out in restart test (tst_2+2). |
371 |
|
o add adTapeDir to specify a special directory where adjoint tapes are |
372 |
|
written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05 |
373 |
|
and cannot be used together with mdsioLocalDir. |
374 |
|
o nesting pkgs: |
375 |
|
- packages_init_variables : put call to OBCS_INIT_VARIABLES in last position |
376 |
|
- update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) |
377 |
|
- add parameter files + utils dir + output from short run on beagle. |
378 |
|
o pkg/seaice: |
379 |
|
fix seaice_growth.F store directives; update results of exp. lab_sea.ad |
380 |
|
o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid |
381 |
|
unnecessary copying in adjoint code, requires new parameter NMAX_ITER |
382 |
|
|
383 |
|
checkpoint62o (2010/11/25) |
384 |
|
o pkg/exf: |
385 |
|
- change CPP option EXF_VERBOSE to run-time logical param exf_verbose. |
386 |
|
o pkg/seaice: |
387 |
|
- seaice_ocean_stress: split a loop for better vectorization of the |
388 |
|
adjoint code |
389 |
|
- seaice_growth.F: fix bug in conservation of freshwater connected to |
390 |
|
capping of heff, put contribution into d_HEFFbyNEG |
391 |
|
- replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat |
392 |
|
by something more sensible (parameters that are what their name implies) |
393 |
|
- change some defaults, so that by default exf-parameters are used for |
394 |
|
things like rhoAir, cpAir,latent/sensible heat parameters, in order |
395 |
|
to reproduce the old results, many data.seaice now contain funny values |
396 |
|
for cpAir and latent heat of sublimation |
397 |
|
o packages_readparms.F: move exf_readparms up in line so that |
398 |
|
exf-parameters are visible for other packages (e.g. seaice) |
399 |
|
o debugMode & debugLevel=2: |
400 |
|
- differentiate between debugMode & debugLevel=2: |
401 |
|
debugMode: controls printing of debug messages (sequence of S/R calls). |
402 |
|
debugLevel: controls printing of algorithm intermediate results and stats. |
403 |
|
- remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2"; |
404 |
|
=> allows to print debug-stats without all sequence of call messages. |
405 |
|
- switch control of debug print from debugLevel to debugMode in many S/R. |
406 |
|
o pkg/obcs (obcs-sponge): |
407 |
|
fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the |
408 |
|
call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge) |
409 |
|
o pkg/generic_advdiff: |
410 |
|
- record overlap minimum size for each advection scheme; |
411 |
|
- refine criteria on overlap minimum size; |
412 |
|
- check and stop (in gad_check) if overlap size is too small. |
413 |
|
o pkg/obcs: |
414 |
|
- with ptracers: remove multiple calls to obcs_apply_ptracer (only done |
415 |
|
once, in ptracers_implicit.F) |
416 |
|
- with seaice: remove test on empty file name in obcs_apply_seaice (always |
417 |
|
apply OB values when tile has OB) |
418 |
|
o model/src, coriolis setting: |
419 |
|
- integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical |
420 |
|
useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from |
421 |
|
files (selectCoriMap=3) with any grid. |
422 |
|
- add parameter "fPrime" for constant second Coriolis coeff (default=0). |
423 |
|
o pkg/seaice/seaice_growth.F: |
424 |
|
a few cosmetic changes that reduce the number of lines of code |
425 |
|
o pkg/obcs: add boundary conditions following Stevens (1990) |
426 |
|
- the code follows old MOM/NAOSIM code |
427 |
|
- so far it is only implemented for the eastern and western boundaries |
428 |
|
and NOT for pTracers |
429 |
|
o pkg/rbcs: |
430 |
|
- replace rbcsInIter by rbcsForcingOffset, the time in seconds at the |
431 |
|
beginning of the first rbcs forcing period. |
432 |
|
- add option rbcsSingleTimeFiles that makes rbcs read forcing data like the |
433 |
|
offline package, i.e., one file per time, labeled by iteration number; |
434 |
|
deltaTrbcs sets the timestep with which the data was generated; |
435 |
|
rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset. |
436 |
|
- rbcsForcingCycle=0 makes forcing non-cyclic. |
437 |
|
- make arithmetic safe for negative times and odd forcing periods. |
438 |
|
|
439 |
|
checkpoint62n (2010/11/09) |
440 |
|
o pkg/seaice: |
441 |
|
fix masking in free-drift S/R ; update results of exp. lab_sea.fd |
442 |
|
o pkg/obcs: |
443 |
|
New S/R to copy tracer value from the OB location to narrow band region |
444 |
|
(width = same as overlap) beyond the OB: preserve OB value (needed for |
445 |
|
high-order scheme) which were overwritten by EXCH call if in overlap |
446 |
|
region. Applied to theta, salt, ptracer and advected seaice variables. |
447 |
|
With seaice: use maskInC in similar way as in gad_advection.F, |
448 |
|
in seaice_advection.F and advect.F. |
449 |
|
Update output of experiment seaice_obcs and change exp4 to test OBCS with |
450 |
|
4th order Adv.Scheme. for pasive salt and ptracer. |
451 |
|
o tools/genmake2: |
452 |
|
- when looking for an optfile (not specified), only search for Fortran compiler |
453 |
|
(remove sym-link test + setting of CPP + makedepend check + C-compiler check) |
454 |
|
- in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm |
455 |
|
(instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong) |
456 |
|
- set default for CPP to "cpp -traditional -P" (was the case without specifying |
457 |
|
an optfile, but otherwise default was just "cpp". |
458 |
|
- comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from) |
459 |
|
- when "CC" is not set in the optfile, look for possible C compiler |
460 |
|
(instead of just setting CC=cc) |
461 |
|
- put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes: |
462 |
|
=> add a ".F" to ".o" rule for source files with no "#include" (such as |
463 |
|
port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS. |
464 |
|
- move gfortran before g77 in list of possible Fortran compiler (consistent |
465 |
|
with reference compiler switch from g77 to gfortran) |
466 |
|
o pkg/seaice: |
467 |
|
o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to |
468 |
|
seaice_check that stops the model, when the CPP flag is used. |
469 |
|
o seaice_growth.F: make capping of ice volume conserving by returning the |
470 |
|
capped ice as freshwater to EmPmR. This does not change the verification |
471 |
|
experiments but will change runs where the capping is acutally active |
472 |
|
o change reference platform+compiler from faulks+g77 to baudelaire+gfortran |
473 |
|
(except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5, |
474 |
|
global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD), |
475 |
|
lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd) |
476 |
|
o tools/genmake2: |
477 |
|
- merge genmake_warnings & genmake_errors into 1 log file: "genmake.log") |
478 |
|
- change DUMPSTATE default to false (can use "-ds" option to switch it to T) |
479 |
|
- clean previous genmake log files before anything else. |
480 |
|
- change Makefile to remove testreport log files (*.tr_log) and genmake log |
481 |
|
files only with "CLEAN" target (instead of "Clean"); |
482 |
|
o pkg/generic_advdiff: |
483 |
|
Change OBCS in multiDim advection (gad_advection.F): |
484 |
|
Use maskInC to prevent intermediate update of tracer-field in OB regions, |
485 |
|
thus keeping current-time-step OB values; and remove the call to OBCS_APPLY |
486 |
|
which were applying future time-step OB values. |
487 |
|
This way, all explicit calculations use current-time-step OB values |
488 |
|
(simpler and more consistent). |
489 |
|
Affects results when set-up uses time-varying OBC and multi-dim advection; |
490 |
|
update output of experiment seaice_obcs. |
491 |
|
o pkg/seaice: |
492 |
|
move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h: |
493 |
|
this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH & |
494 |
|
SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY. |
495 |
|
Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY |
496 |
|
but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp |
497 |
|
unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h) |
498 |
|
o pkg aim (2010/10/26): |
499 |
|
- Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation |
500 |
|
formulation with obliquity, eccentricity, ... as run-time parameters, |
501 |
|
- Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and |
502 |
|
upward shortwave radition at the surface (all-sky and clear-sky). |
503 |
|
o pkg/obcs: |
504 |
|
- writing sections with globalFiles=T does not work: switch to tiled-files |
505 |
|
when writing sections for OBCS (change pkg/rw/write_rec.F accordingly). |
506 |
|
- fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F |
507 |
|
- apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs |
508 |
|
|
509 |
|
checkpoint62m (2010/10/21) |
510 |
|
o pkg/seaice: vectorize seaice_solve4temp.F |
511 |
|
- move iterations loops outside of i/j-loops |
512 |
|
- requires 2D arrays for TB and effConduct |
513 |
|
- add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is |
514 |
|
modified in this routine |
515 |
|
- a little bit of clean up, adjusting indentation, etc. |
516 |
|
- replaced a few TEN**a by exp(a*log(10.)) in new code for better |
517 |
|
performance and '**TWO' by '**2' (because TWO is a float), |
518 |
|
replaced ONE, ZERO |
519 |
|
o eesupp/src: |
520 |
|
fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube |
521 |
|
o pkg/seaice/seaice_growth.F |
522 |
|
Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and |
523 |
|
merging process. The merged routine has two branches, and one activates the 'evolution' |
524 |
|
branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now). |
525 |
|
In summary, here is what the '10/10 revision' did consist of |
526 |
|
part 1: seaice_growth.F revisions 1.71 to 1.75 |
527 |
|
- Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged. |
528 |
|
The emphasis here was on improving readability (e.g. by trying to use meaningful |
529 |
|
variable names) and modularity (e.g. by adding arrays to store heff etc. updates). |
530 |
|
part 1.5: |
531 |
|
- revising the lab_sea experiment to make it a more useful (i.e. stable |
532 |
|
and representative of an actual model run). This was done by generating a |
533 |
|
(winter) pickup to start from, switching back the main experiment dynamic |
534 |
|
solver from evp to lsr, having one of the experiments use the free drift solution. |
535 |
|
part 2: seaice_growth.F revisions 1.76 to 1.85 |
536 |
|
- Sorting out hard-coded constants that prevented heat and fresh water conservation. |
537 |
|
- Sorting out the various fields units and sign (set early on and reset at the end) |
538 |
|
to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and |
539 |
|
fresh water stock is 'effective ice meters', and >0 implies more ice/snow. |
540 |
|
- Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks, |
541 |
|
and simplifying logical expressions to further improve readibility. |
542 |
|
part 3: seaice_growth.F revisions 1.86 to 1.89 |
543 |
|
- Re-organize the blocks of code more logically. |
544 |
|
- Merging the '_if.F' pieces that add something new. |
545 |
|
o pkg/thsice: |
546 |
|
- vectorize thsice_solve4temp and thsice_get_exf. |
547 |
|
Problem: thsice_solve4temp has an unvectorizable statement that |
548 |
|
might also be problematic for TAF |
549 |
|
- thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This |
550 |
|
does not change the verifcation experiment, but will change all |
551 |
|
experiments that have this flag undefined (not tested in verification); |
552 |
|
a little reorganization to save a few 2D fields and recomputations |
553 |
|
- 1st step of revisiting thsice adjoint (major recomp. sorted out) |
554 |
|
- 2nd step: fix some store dirs |
555 |
|
o seems to work somewhat, i.e. using ifort but not g77 |
556 |
|
o likely cause are incomplete init. or recomputation |
557 |
|
o start verification/global_ocean.cs32x15/input_ad.thsice |
558 |
|
o pkg/obcs: add support for exch2 |
559 |
|
- the position of the boundary and prescribed values are specified using |
560 |
|
a global domain with exch2 facets stacked |
561 |
|
- in x for N,S boundaries (like W2_mapIO=-1) |
562 |
|
- in y for E,W boundaries (so E,W boundaries do not overlap) |
563 |
|
o pkg/mdsio: add support for writing global sections with exch2 |
564 |
|
file layout is as for obcs described above: |
565 |
|
- for x-z sections, facets are stacked in x (like W2_mapIO=-1) |
566 |
|
- for y-z sections, facets are stacked in y |
567 |
|
o pkg/thsice: |
568 |
|
- change a few routines for better vectorization: thsice_albedo.F, |
569 |
|
thsice_step_temp.F, and in thsice_calc_thickn.F. Results are |
570 |
|
not affected, but in particular the latter routine has changed |
571 |
|
dramatically (not necessarily easier to read now). |
572 |
|
- re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops |
573 |
|
iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF. |
574 |
|
o verification/lab_sea: |
575 |
|
- overhaul of the forward model experiments. The main motivation |
576 |
|
for this revision is that lab_sea has proven quite fragile (when |
577 |
|
changing the sea-ice code, and switching platforms) to a point |
578 |
|
when failures were very hard to attribute to specific code problems. |
579 |
|
- the suspected reason for this fragility is noise amplification by evp so, |
580 |
|
to start with, we decided to replace evp with lsr in the main experiment. |
581 |
|
- the input.lsr experiment thus became obsolete and was removed. |
582 |
|
- it was replaced with the input.fd experiment that uses an |
583 |
|
analytical "free drift" solution as the ice velocity field. |
584 |
|
- Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp) |
585 |
|
will hopefully allow us to discriminate problems due to dynamic solvers |
586 |
|
from problems due to the thermodynamic code. input.salt_plume (lsr) allows |
587 |
|
us to test additional options, along with the salt plume package. |
588 |
|
- Finally a pickup was generated (at the end of a one year run) to |
589 |
|
make the tests more representative of an actual model run. Previously |
590 |
|
the tests starting point was a 1m thickness of ice everywhere. |
591 |
|
o pkg/seaice: |
592 |
|
- introducing S\R seaice_freedrift.F that compute the |
593 |
|
analytical solution to an approximate ice momentum |
594 |
|
equation (i.e. the simple stress/coriolis balance). |
595 |
|
- define SEAICE_ALLOW_FREEDRIFT to trigger the computation |
596 |
|
of the free drift velocity field, and enable its use. |
597 |
|
To actually use the free drift solution as the model ice |
598 |
|
velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice. |
599 |
|
o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata" |
600 |
|
|
601 |
|
checkpoint62l (2010/10/04) |
602 |
|
o pkg/seaice: |
603 |
|
-fix the USE_ORIGINAL_SBI version (for variable freezing point); |
604 |
|
-use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new |
605 |
|
version (with USE_ORIGINAL_SBI undef); |
606 |
|
o add hooks for new packages OASIS, the package will follow |
607 |
|
(hooks exclude the seaice pkg for now) |
608 |
|
o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO |
609 |
|
Option to use mdsio_read_whalos.F/mdsio_write_whalos.F, |
610 |
|
rather than mdsio_readvector.F/mdsio_writevector.F, within |
611 |
|
adread_adwrite.F to read/write adjoint-related tapes to disk. |
612 |
|
o eesupp and pkg/mdsio: ALLOW_WHIO |
613 |
|
Option to write/read 2D fields to files including tiles halos. |
614 |
|
The main purpose is for adjoint related "tape I/O". |
615 |
|
The secondary purpose is for debugging phases. |
616 |
|
A word on those rather specifically intended purposes. |
617 |
|
The code was meant to be stripped down to the bare minimum. |
618 |
|
Typically, there is a unique and basic mapping to the global |
619 |
|
buffer (tile by tile, then proc by proc, then level by level), and |
620 |
|
byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not |
621 |
|
meant to generate user friendly outputs of various shapes and forms. |
622 |
|
Rather it is intended, for the knowledgeabale developers, |
623 |
|
to be largely independent of the many mdsio options, to allow |
624 |
|
outputs of tiles+halos in debugging phases and in adjoint runs, |
625 |
|
and to allow some flexibility in tuning (adoint) I/O depending on each |
626 |
|
file system behavior. With regard to tuning, most of the potential knobs |
627 |
|
(to leave files open, to allocate the I/O indep. of usesinglecpuio, |
628 |
|
to specify directories, to specify the typical size of I/O calls, etc.) |
629 |
|
are not yet included, and will be added if they prove useful. |
630 |
|
o pkg/seaice: |
631 |
|
fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F |
632 |
|
o pkg/seaice: |
633 |
|
new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty |
634 |
|
code (seaice_budget_ice_if.F) which enable to recover old standard |
635 |
|
code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined. |
636 |
|
temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F. |
637 |
|
o model/src (rStar): |
638 |
|
use simple average (not area weighted) of rStarFac at U,V point when using |
639 |
|
vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection) |
640 |
|
update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20. |
641 |
|
|
642 |
|
checkpoint62k (2010/09/17) |
643 |
|
o adjoint |
644 |
|
* changed verification/global_ocean.cs32x15 ; adjoint now tests |
645 |
|
Adams-Bashforth 3 + NLFS + RSTAR |
646 |
|
* some more modifs required for ECCO-GODAE v4 |
647 |
|
o pkg/seaice |
648 |
|
add SEAICE_AGE_VOL option to use volume instead of area for |
649 |
|
integrating SEAICE_AGE |
650 |
o model/src: |
o model/src: |
651 |
first check-in of sigma & hybrid-sigma coordinate code ; also includes |
first check-in of sigma & hybrid-sigma coordinate code ; also includes |
652 |
non-linear free-surface parts ; but pressure-gradient not yet coded. |
non-linear free-surface parts ; but pressure-gradient not yet coded. |
916 |
but keep the former optfile for few weeks for smooth transition |
but keep the former optfile for few weeks for smooth transition |
917 |
o pkg/ecco |
o pkg/ecco |
918 |
- allow user defined cost function contributions |
- allow user defined cost function contributions |
919 |
CPP: ALLOW_USERCOST_CONTRIBUTION |
CPP: ALLOW_USERCOST_CONTRIBUTION |
920 |
USAGE: compute contributions in cost_usercost_all.F |
USAGE: compute contributions in cost_usercost_all.F |
921 |
- note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. |
- note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. |
922 |
the two options are complementary. |
the two options are complementary. |
923 |
o pkg/smooth |
o pkg/smooth |