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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o pkg/ctrl, pkg/shelfice, and optim: |
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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 |
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at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
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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 |
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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: |
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no longer needed with maskInC,W,S in pkg/generic_advdiff. |
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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) |
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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) |
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o pkg/seaice: |
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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 |
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- updated output*.txt files due to bug fixes in salt, saltPlumeFlux, |
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and initial HSALT |
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|
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checkpoint62w (2011/04/26) |
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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 |
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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": |
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ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh) |
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related to thermodynamics seaice. Update output (fwd+AD) of exp.: |
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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 |
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in Interior region. No impact on solution but affects Velocity monitor stats. |
127 |
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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 |
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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 |
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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_${varname}period to be analogous to exf-conventions: |
141 |
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xx_${varname}period = 0., means time-independent control part |
142 |
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xx_${varname}period = -12., means one-year-periodic monthly control part |
143 |
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- introduce helper routine ctrl_init_rec (part of ctrl_init.F) to |
144 |
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clean up ctrl_init a little, remove unused variables |
145 |
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- ctrl_init: fixed the handling of the start/endrec for obcs-variables |
146 |
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- move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec |
147 |
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|
148 |
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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 |
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- 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 |
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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 |
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o pkg/mdsio: |
166 |
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move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option |
167 |
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(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 |
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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 |
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iTracer = 1: area-weighted ice age |
193 |
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= 2: volume-weighted ice age |
194 |
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= 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 |
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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 |
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- change default: balance the Net inflow through all OB (instead of balancing |
209 |
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each OB separately); keep the old method if setting OBC_balanceFacX < 0. |
210 |
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- switch on useOBCSbalance in dome experiment: only correct Western OB outflow |
211 |
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to match Nortern OB inflow (OBCS_balanceFacN=0). |
212 |
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o pkg/seaice: |
213 |
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- redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL |
214 |
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o pkg/seaice (seaice_growth v 1.113): |
215 |
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- reverting seaice_growth to v 1.111 in order to have code with exact bit |
216 |
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compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge |
217 |
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CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced |
218 |
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runtime flag SEAICEareaFormula is kept but is inactive |
219 |
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o model/src: |
220 |
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- add new param to scale curvilinear grid distance and area when using |
221 |
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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 |
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o adjoint: |
224 |
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- enable adjoint of Stevens OB |
225 |
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- add dummy_in_dynamics to enable extraction of ADJrhoinsitu |
226 |
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(a bit delicate because of potentially modified adj. common block structure; |
227 |
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current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later) |
228 |
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|
229 |
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checkpoint62s (2011/02/15) |
230 |
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o pkg/seaice (seaice_growth v 1.112): |
231 |
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- introduce SEAICEareaFormula run time parameter, which selects the recipe for |
232 |
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computing the ice cover tendency from effective thickness tendencies. Include |
233 |
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Ian Fenty's formula. |
234 |
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- remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using |
235 |
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SEAICEareaFormula. |
236 |
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- simplify notations for the various d_HEFF/d_AREA terms. |
237 |
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o pkg/gmredi: |
238 |
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- add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code |
239 |
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from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative; |
240 |
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add a verification test-run (front_relax.bvp) to test GM_useBVP. |
241 |
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o pkg/seaice (seaice_growth v 1.111): |
242 |
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- for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's. |
243 |
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- the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to |
244 |
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also melt ice. |
245 |
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o pkg/seaice: |
246 |
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- McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty). |
247 |
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- can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h |
248 |
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o pkg/cheapaml: |
249 |
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- from Nico Wienders: New version of this package. |
250 |
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o pkg/flt: |
251 |
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- add CPP options to prevent floats to re-enter the opposite side of |
252 |
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a periodic domain (default: keep periodicity) |
253 |
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o pkg/gmredi: |
254 |
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- apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners |
255 |
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(needed for multi-dim advection). |
256 |
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- switch on GM Advective form in global_ocean.cs32x15 and update output.txt |
257 |
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o model/src: |
258 |
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- fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run. |
259 |
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o tutorial_tracer_adjsens |
260 |
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- extend to NLFS and replace maskC by hFacC |
261 |
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(change reference output accordingly) |
262 |
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|
263 |
|
checkpoint62r (2011/01/24) |
264 |
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o testreport: |
265 |
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- add option -deloutp (-do) to remove output file after successful run |
266 |
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- add option -mfile (-mf) for MPI machile-file and for each test-exp, |
267 |
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extract exact list of procs from this file ; adjust COMMAND by |
268 |
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replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs. |
269 |
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o pkg/ecco: replace old ineffective way of penalizing deviations from |
270 |
|
first guess (of obcs) with code by Matt Mazloff |
271 |
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o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without |
272 |
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exf/cal |
273 |
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- ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl |
274 |
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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 |
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ALLOW_CAL is not defined |
280 |
|
- ctrl_getobcs?: simplify code so that it does not need to use |
281 |
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S/R exf_swapfields |
282 |
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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 |
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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 |
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seaice_lsr: move stress-divergence computations out of outer pseudo- |
293 |
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timestepping loop |
294 |
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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 |
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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 |
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|
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 |
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- 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: |
o global_ocean.cs32x15: |
318 |
change SIZE.h of AD set-up to get same tiling as with MPI. |
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) |
Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11) |