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revision 1.1392 by mlosch, Thu Mar 10 09:35:14 2011 UTC revision 1.1425 by mlosch, Mon May 9 08:56:59 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:
8      - remove extra 2D field "for good measure" when initializing in
9        ctrl_set_globfld_[xy/xz/yz].F
10      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
11      - improve error messages in ctrl_set_unpack_*
12    o OBC implementation in momentum:
13       use interior masks (maskInC,W & S) in momentum S/R:
14       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
15       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
16       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
17       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
18       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
19        (and also with Leith/Smagorinsky harmonic-viscosity).
20       Update output of experiment dome and exp4 (+nlfs).
21    o exp4 test-exp:
22      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
23        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
24        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
25        time-varying OB at Western-side for wVel (NonHyd); update output.
26      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
27        and biharmonic-viscosity ; also use prescribed time varying OB.
28    o pkg/obcs:
29      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
30    o model/src:
31      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
32      - initialise startTime & nIter0 with unlikely values: allows to set one
33        from the other without ambiguity.
34    o seaice_obcs test-exp.:
35      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
36    o pkg/obcs:
37      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
38        no longer needed with maskInC,W,S in pkg/generic_advdiff.
39    o pkg/seaice:
40      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
41        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
42      - fixed bug in the initialization of sea ice salinity variable HSALT
43        in seaice_init_varia.F  (removed dependence on ICE2WATR)
44    o fizhi-cs test exp.:
45       switch reference output convention for these 2 non-standard test-exp,
46        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
47          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
48       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
49    o model/inc:
50      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
51        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
52    o pkg/seaice:
53      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
54    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
55      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
56        and initial HSALT
57    
58    checkpoint62w (2011/04/26)
59    o pkg/mom_fluxform:
60      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
61      - use parameter "sideDragFactor" in no-slip BC side-drag part.
62      - update output of exp. global_ocean.90x40x15
63    o pkg/mom_vecinv:
64      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
65    o update seaice exp.:
66      use more consistent parameter values (remove "backward compatability only":
67       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
68      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
69       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
70    o update test-exp global_ocean.90x40x15:
71      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
72      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
73      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
74      o turn on zStar & viscA4 in standard set-up (dir input/)
75        and update output files: output.txt & output.dwnslp.txt
76    o new AD-test experiment: obcs_ctrl
77      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
78    o pkg/dic:
79      fix two bugs in handling water vapour pressure in carbonate chemistry
80      and air-sea fluxes. Found by Val Bennington and Galen McKinley
81      (add DIC Option = WATERVAP_BUG to recover old results)
82      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
83    o adding allowInteriorFreezing option to check for water below freezing point
84      at depth and bring the negative heat anomaly to the surface level
85    o pkgs _fields_load:
86      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
87      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
88        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
89        rbcs to get interpolation weights and time reccord number.
90      - fix multi-threading in aim_fields_load.F
91      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
92    o external_fields_load:
93      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
94       interpolation weights) to use in a periodic time-series ; do not divide by
95       time-step to convert to integer:
96       - this fixes case where externForcingPeriod is not multiple of time-step
97          (Thanks to Christopher L. Wolfe)
98       - this fixes case where externForcingPeriod is an odd multiple of time-step
99         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
100      store index of time-record which is currently loaded:
101       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
102       - needed for the adjoint but not yet used because of extensive recomputations;
103         (to be fixed soon)
104    
105    checkpoint62v (2011/04/02)
106    o verification/1D_ocean_ice_column added to test Ian Fenty's
107      pkg/seaice_growth.F modifications for improving sea ice code differentiability
108    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
109      (new velocity statistics after changing maskInW & maskInS definition)
110    o pkg/generic_advdiff with OBCS:
111      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
112      equivalent to assumption of no tracer gradient outside the OB region.
113      This will affect the results if using obcs+biharmonic diffusion.
114      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
115    o pkg/obcs:
116      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
117      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
118      in Interior region. No impact on solution but affects Velocity monitor stats.
119    o pkg/ptracers (adjoint)
120      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
121      tape file for each tracer
122    o model/inc/src and pkg/autodiff: add parameters that allow to turn
123      of parts of the adjoint code at run time. For now, there are only
124      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
125      parameters are set in data.pkg.
126      This is the lazy coward's version of doing this, but still useful for
127      debugging. In order to do it right, everything needs to be moved to
128      pkg/autodiff.
129    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
130      the end; this fixes the adjoint balancing code for open boundaries.
131    o pkg/ctrl:
132      - change behavior of xx_${varname}period to be analogous to exf-conventions:
133        xx_${varname}period =   0.,  means time-independent control part
134        xx_${varname}period = -12., means one-year-periodic monthly control part
135      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
136        clean up ctrl_init a little, remove unused variables
137      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
138      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
139    
140    checkpoint62u (2011/03/15)
141    o model/src:
142      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
143        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
144      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
145        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
146    o pkg/ctrl/obcs/ecco:
147      - remove obsolete, unused, and partially broken code:
148        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
149        ALLOW_CTRL_OBCS_BALANCE
150      - put a stop statement into ecco/cost_obcsvol.F, but also add
151        cost_obcsvol to ecco_ad_diff.list
152    o pkg/ecco: fix counting cost function contributions for obcs (code
153      by Matt M.) and diffkr for diagnostics
154    o pkg/ecco, pkg/ctrl, pkg/grdchk:
155      add cost penalty terms for initial uvel, vvel, eta controls
156      and I/O for prior error files
157    o pkg/mdsio:
158       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
159       (new argument) to check for tiled file in mdsioLocalDir : this fix the
160       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
161  o pkg/ctrl:  o pkg/ctrl:
162   - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by   - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
163     ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove     ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
# Line 11  o pkg/ctrl: Line 165  o pkg/ctrl:
165   - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.   - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
166  o pkg/ecco  o pkg/ecco
167   - enable adjoint of Stevens OB   - enable adjoint of Stevens OB
168  o pkg/ctrl/ecco/grdchk:  o pkg/ctrl/ecco/grdchk:
169    - remove global declaration of tmpfldx/yz and tmpfldx/yz2.    - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
170      Fortunately, we do not have any tests for the numerous cpp-flagged      Fortunately, we do not have any tests for the numerous cpp-flagged
171      option of "obcs as control parameters" so we will never know      option of "obcs as control parameters" so we will never know
172      if this is an improvement (but at least now things compile).      if this is an improvement (but at least now things compile).
173    - remove an obsolete initialization from ecco_cost_init_barfiles.F    - remove an obsolete initialization from ecco_cost_init_barfiles.F
174    - fix some problems within never used ifdefs to make the code compile    - fix some problems within never used ifdefs to make the code compile
175  o pkg/obcs:  o pkg/obcs:
176   - Refine Interior mask definition to work with more complex OB (e.g.   - Refine Interior mask definition to work with more complex OB (e.g.
177     if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to     if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
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