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revision 1.1396 by mlosch, Mon Mar 14 17:35:43 2011 UTC revision 1.1433 by jmc, Sat May 14 20:04:53 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o pkg/ctrl/obcs/ecco:  o pkg rbcs:
8      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
9      - add capability to apply relaxation to horizontal velocity uVel & vVel.
10    o pkg/grdchk: add gradient check for control variable xx_shifwflx
11    o pkg/shelfice/shelfice_init_fixed.F
12      fix CPP-flag combinations
13    
14    checkpoint62x (2011/05/13)
15    o pkg/mom_vecinv:
16       high-order vorticity scheme: use interior masks (maskInW & S)
17       to zero-out (outside OB) gradient of vorticity.
18    o verification exp.:
19       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
20       hs94.128x64x5 and seaice_obcs ; update results.
21    o pkg/obcs:
22      fix bug in OBeta for YZ sections in obcs_exf_load.F
23    o pkg/ctrl, pkg/shelfice, and optim:
24      - add new control variable xx_shifwflx (fresh water flux underneath ice
25        shelves). This is almost as tedious as obcs-ctrl, because the
26        variables needs its own mask.
27      - add a cost function term that penalizes the deviation of xx_shifwflx
28        from the first guess (zero) in analogy to other control variables
29    o pkg/shelfice:
30      - start basic adjoint
31    o pkg/ctrl:
32      - remove extra 2D field "for good measure" when initializing in
33        ctrl_set_globfld_[xy/xz/yz].F
34      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
35      - improve error messages in ctrl_set_unpack_*
36    o OBC implementation in momentum:
37       use interior masks (maskInC,W & S) in momentum S/R:
38       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
39       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
40       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
41       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
42       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
43        (and also with Leith/Smagorinsky harmonic-viscosity).
44       Update output of experiment dome and exp4 (+nlfs).
45    o exp4 test-exp:
46      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
47        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
48        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
49        time-varying OB at Western-side for wVel (NonHyd); update output.
50      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
51        and biharmonic-viscosity ; also use prescribed time varying OB.
52    o pkg/obcs:
53      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
54    o model/src:
55      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
56      - initialise startTime & nIter0 with unlikely values: allows to set one
57        from the other without ambiguity.
58    o seaice_obcs test-exp.:
59      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
60    o pkg/obcs:
61      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
62        no longer needed with maskInC,W,S in pkg/generic_advdiff.
63    o pkg/seaice:
64      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
65        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
66      - fixed bug in the initialization of sea ice salinity variable HSALT
67        in seaice_init_varia.F  (removed dependence on ICE2WATR)
68    o fizhi-cs test exp.:
69       switch reference output convention for these 2 non-standard test-exp,
70        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
71          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
72       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
73    o model/inc:
74      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
75        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
76    o pkg/seaice:
77      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
78    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
79      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
80        and initial HSALT
81    
82    checkpoint62w (2011/04/26)
83    o pkg/mom_fluxform:
84      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
85      - use parameter "sideDragFactor" in no-slip BC side-drag part.
86      - update output of exp. global_ocean.90x40x15
87    o pkg/mom_vecinv:
88      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
89    o update seaice exp.:
90      use more consistent parameter values (remove "backward compatability only":
91       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
92      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
93       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
94    o update test-exp global_ocean.90x40x15:
95      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
96      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
97      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
98      o turn on zStar & viscA4 in standard set-up (dir input/)
99        and update output files: output.txt & output.dwnslp.txt
100    o new AD-test experiment: obcs_ctrl
101      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
102    o pkg/dic:
103      fix two bugs in handling water vapour pressure in carbonate chemistry
104      and air-sea fluxes. Found by Val Bennington and Galen McKinley
105      (add DIC Option = WATERVAP_BUG to recover old results)
106      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
107    o adding allowInteriorFreezing option to check for water below freezing point
108      at depth and bring the negative heat anomaly to the surface level
109    o pkgs _fields_load:
110      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
111      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
112        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
113        rbcs to get interpolation weights and time reccord number.
114      - fix multi-threading in aim_fields_load.F
115      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
116    o external_fields_load:
117      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
118       interpolation weights) to use in a periodic time-series ; do not divide by
119       time-step to convert to integer:
120       - this fixes case where externForcingPeriod is not multiple of time-step
121          (Thanks to Christopher L. Wolfe)
122       - this fixes case where externForcingPeriod is an odd multiple of time-step
123         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
124      store index of time-record which is currently loaded:
125       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
126       - needed for the adjoint but not yet used because of extensive recomputations;
127         (to be fixed soon)
128    
129    checkpoint62v (2011/04/02)
130    o verification/1D_ocean_ice_column added to test Ian Fenty's
131      pkg/seaice_growth.F modifications for improving sea ice code differentiability
132    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
133      (new velocity statistics after changing maskInW & maskInS definition)
134    o pkg/generic_advdiff with OBCS:
135      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
136      equivalent to assumption of no tracer gradient outside the OB region.
137      This will affect the results if using obcs+biharmonic diffusion.
138      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
139    o pkg/obcs:
140      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
141      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
142      in Interior region. No impact on solution but affects Velocity monitor stats.
143    o pkg/ptracers (adjoint)
144      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
145      tape file for each tracer
146    o model/inc/src and pkg/autodiff: add parameters that allow to turn
147      of parts of the adjoint code at run time. For now, there are only
148      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
149      parameters are set in data.pkg.
150      This is the lazy coward's version of doing this, but still useful for
151      debugging. In order to do it right, everything needs to be moved to
152      pkg/autodiff.
153    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
154      the end; this fixes the adjoint balancing code for open boundaries.
155    o pkg/ctrl:
156      - change behavior of xx_${varname}period to be analogous to exf-conventions:
157        xx_${varname}period =   0.,  means time-independent control part
158        xx_${varname}period = -12., means one-year-periodic monthly control part
159      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
160        clean up ctrl_init a little, remove unused variables
161      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
162      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
163    
164    checkpoint62u (2011/03/15)
165    o model/src:
166      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
167        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
168      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
169        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
170    o pkg/ctrl/obcs/ecco:
171    - remove obsolete, unused, and partially broken code:    - remove obsolete, unused, and partially broken code:
172      ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within      ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
173      ALLOW_CTRL_OBCS_BALANCE      ALLOW_CTRL_OBCS_BALANCE
174    - put a stop statement into ecco/cost_obcsvol.F, but also add    - put a stop statement into ecco/cost_obcsvol.F, but also add
175      cost_obcsvol to ecco_ad_diff.list      cost_obcsvol to ecco_ad_diff.list
176  o pkg/ecco: fix counting cost function contributions for obcs (code  o pkg/ecco: fix counting cost function contributions for obcs (code
177    by Matt M.) and diffkr for diagnostics    by Matt M.) and diffkr for diagnostics
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