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revision 1.1374 by jmc, Sun Feb 6 00:24:40 2011 UTC revision 1.1443 by jmc, Thu May 26 13:55:50 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint62y (2011/05/26)
8    o pkg/seaice:
9     - seaice_growth.F : in EVOLUTION branch, always include
10       a_QSWbyATM_cover in qnet (as it should be).
11     - verification/global_ocean.cs32x15 : update results accordingly
12       (output.seaice.txt output_adm.seaice.txt).
13    o pkg/seaice + obcs:
14     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
15       equivalent of assuming no tracer gradient outside the OB region.
16       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
17     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
18       after changes above);
19     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
20       only at OB location (instead of over a band of OLx width).
21    o pkg/seaice:
22     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
23       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
24    o pkg/obcs:
25      - split header file "OBCS.h" into 4 separated files:
26        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
27       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
28         (contain no conditional statement which depends on OBCS options).
29      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
30        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
31    o ctrl, cost, grdchk & autodiff pkgs:
32      - make options file more standard (like other {PKG}_OPTIONS.h file but
33        with AD_CONFIG.h); clean-up some of the included header files.
34    o pkg/obcs:
35      - do not mask tracer when applying OB (tracer == 0 could generate problems)
36      - apply tracer OB values to tracer field only at OB location (instead of
37        over a band of OLx width)
38      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
39      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
40        obcs_apply_tloc.F & obcs_apply_sloc.F
41    o obcs in model/src:
42      - call OBCS_APPLY_W only if NonHydrostatic.
43      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
44      - reset dEtaHdt and wVel to zero outside OB interior region ;
45      - leave tracer unchanged outside OB interior region: This has no effect
46        on the solution but just to prevent unrealistic tracer value outside OB.
47      - zero out velocity outside OB interior region: This has no effect on
48        the solution but just to prevent unrealistic velocity outside OB.
49    o obcs and non-lin free-surf:
50       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
51       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
52       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
53       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
54       update results of test-exp. exp4(nlfs).
55    o exp4 (nlfs) test-exp:
56       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
57       with NonLin-FreeSurf); update output.nlfs.txt
58    o obcs and 2d/3d solver norm:
59       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
60       and outside OB interior region (will allow to place OB further inside the
61       domain). Depending on the domain, can affects cg2d-Norm (previous
62       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
63       and cg3d-Norm (previous Norm was computed before canceling OB terms),
64       e.g. in tutorial_plume_on_slope.
65      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
66    o pkg rbcs:
67      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
68      - add capability to apply relaxation to horizontal velocity uVel & vVel.
69    o pkg/grdchk: add gradient check for control variable xx_shifwflx
70    o pkg/shelfice/shelfice_init_fixed.F
71      fix CPP-flag combinations
72    o pkg/seaice: Merge iceage code of Pierre Rampal
73      * update/change/correct ice age calculations
74      * add age updates for pathological cases
75      Probably needs more testing...
76    
77    checkpoint62x (2011/05/13)
78    o pkg/mom_vecinv:
79       high-order vorticity scheme: use interior masks (maskInW & S)
80       to zero-out (outside OB) gradient of vorticity.
81    o verification exp.:
82       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
83       hs94.128x64x5 and seaice_obcs ; update results.
84    o pkg/obcs:
85      fix bug in OBeta for YZ sections in obcs_exf_load.F
86    o pkg/ctrl, pkg/shelfice, and optim:
87      - add new control variable xx_shifwflx (fresh water flux underneath ice
88        shelves). This is almost as tedious as obcs-ctrl, because the
89        variables needs its own mask.
90      - add a cost function term that penalizes the deviation of xx_shifwflx
91        from the first guess (zero) in analogy to other control variables
92    o pkg/shelfice:
93      - start basic adjoint
94    o pkg/ctrl:
95      - remove extra 2D field "for good measure" when initializing in
96        ctrl_set_globfld_[xy/xz/yz].F
97      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
98      - improve error messages in ctrl_set_unpack_*
99    o OBC implementation in momentum:
100       use interior masks (maskInC,W & S) in momentum S/R:
101       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
102       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
103       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
104       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
105       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
106        (and also with Leith/Smagorinsky harmonic-viscosity).
107       Update output of experiment dome and exp4 (+nlfs).
108    o exp4 test-exp:
109      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
110        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
111        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
112        time-varying OB at Western-side for wVel (NonHyd); update output.
113      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
114        and biharmonic-viscosity ; also use prescribed time varying OB.
115    o pkg/obcs:
116      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
117    o model/src:
118      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
119      - initialise startTime & nIter0 with unlikely values: allows to set one
120        from the other without ambiguity.
121    o seaice_obcs test-exp.:
122      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
123    o pkg/obcs:
124      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
125        no longer needed with maskInC,W,S in pkg/generic_advdiff.
126    o pkg/seaice:
127      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
128        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
129      - fixed bug in the initialization of sea ice salinity variable HSALT
130        in seaice_init_varia.F  (removed dependence on ICE2WATR)
131    o fizhi-cs test exp.:
132       switch reference output convention for these 2 non-standard test-exp,
133        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
134          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
135       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
136    o model/inc:
137      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
138        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
139    o pkg/seaice:
140      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
141    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
142      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
143        and initial HSALT
144    
145    checkpoint62w (2011/04/26)
146    o pkg/mom_fluxform:
147      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
148      - use parameter "sideDragFactor" in no-slip BC side-drag part.
149      - update output of exp. global_ocean.90x40x15
150    o pkg/mom_vecinv:
151      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
152    o update seaice exp.:
153      use more consistent parameter values (remove "backward compatability only":
154       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
155      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
156       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
157    o update test-exp global_ocean.90x40x15:
158      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
159      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
160      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
161      o turn on zStar & viscA4 in standard set-up (dir input/)
162        and update output files: output.txt & output.dwnslp.txt
163    o new AD-test experiment: obcs_ctrl
164      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
165    o pkg/dic:
166      fix two bugs in handling water vapour pressure in carbonate chemistry
167      and air-sea fluxes. Found by Val Bennington and Galen McKinley
168      (add DIC Option = WATERVAP_BUG to recover old results)
169      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
170    o adding allowInteriorFreezing option to check for water below freezing point
171      at depth and bring the negative heat anomaly to the surface level
172    o pkgs _fields_load:
173      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
174      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
175        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
176        rbcs to get interpolation weights and time reccord number.
177      - fix multi-threading in aim_fields_load.F
178      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
179    o external_fields_load:
180      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
181       interpolation weights) to use in a periodic time-series ; do not divide by
182       time-step to convert to integer:
183       - this fixes case where externForcingPeriod is not multiple of time-step
184          (Thanks to Christopher L. Wolfe)
185       - this fixes case where externForcingPeriod is an odd multiple of time-step
186         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
187      store index of time-record which is currently loaded:
188       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
189       - needed for the adjoint but not yet used because of extensive recomputations;
190         (to be fixed soon)
191    
192    checkpoint62v (2011/04/02)
193    o verification/1D_ocean_ice_column added to test Ian Fenty's
194      pkg/seaice_growth.F modifications for improving sea ice code differentiability
195    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
196      (new velocity statistics after changing maskInW & maskInS definition)
197    o pkg/generic_advdiff with OBCS:
198      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
199      equivalent to assumption of no tracer gradient outside the OB region.
200      This will affect the results if using obcs+biharmonic diffusion.
201      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
202    o pkg/obcs:
203      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
204      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
205      in Interior region. No impact on solution but affects Velocity monitor stats.
206    o pkg/ptracers (adjoint)
207      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
208      tape file for each tracer
209    o model/inc/src and pkg/autodiff: add parameters that allow to turn
210      of parts of the adjoint code at run time. For now, there are only
211      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
212      parameters are set in data.pkg.
213      This is the lazy coward's version of doing this, but still useful for
214      debugging. In order to do it right, everything needs to be moved to
215      pkg/autodiff.
216    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
217      the end; this fixes the adjoint balancing code for open boundaries.
218    o pkg/ctrl:
219      - change behavior of xx_${varname}period to be analogous to exf-conventions:
220        xx_${varname}period =   0.,  means time-independent control part
221        xx_${varname}period = -12., means one-year-periodic monthly control part
222      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
223        clean up ctrl_init a little, remove unused variables
224      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
225      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
226    
227    checkpoint62u (2011/03/15)
228    o model/src:
229      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
230        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
231      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
232        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
233    o pkg/ctrl/obcs/ecco:
234      - remove obsolete, unused, and partially broken code:
235        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
236        ALLOW_CTRL_OBCS_BALANCE
237      - put a stop statement into ecco/cost_obcsvol.F, but also add
238        cost_obcsvol to ecco_ad_diff.list
239    o pkg/ecco: fix counting cost function contributions for obcs (code
240      by Matt M.) and diffkr for diagnostics
241    o pkg/ecco, pkg/ctrl, pkg/grdchk:
242      add cost penalty terms for initial uvel, vvel, eta controls
243      and I/O for prior error files
244    o pkg/mdsio:
245       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
246       (new argument) to check for tiled file in mdsioLocalDir : this fix the
247       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
248    o pkg/ctrl:
249     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
250       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
251       unused and superfluous variables
252     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
253    o pkg/ecco
254     - enable adjoint of Stevens OB
255    o pkg/ctrl/ecco/grdchk:
256      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
257        Fortunately, we do not have any tests for the numerous cpp-flagged
258        option of "obcs as control parameters" so we will never know
259        if this is an improvement (but at least now things compile).
260      - remove an obsolete initialization from ecco_cost_init_barfiles.F
261      - fix some problems within never used ifdefs to make the code compile
262    o pkg/obcs:
263     - Refine Interior mask definition to work with more complex OB (e.g.
264       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
265       read in Interior mask from file. Check if Interior mask is consistent
266       with OB list of indices.
267    o pkg/seaice
268     - beginning code for a seaice tracer package,
269       but currently only used for seaice age: SEAICE_AGE
270       SEAICE_num = 4
271       iTracer = 1: area-weighted ice age
272               = 2: volume-weighted ice age
273               = 3, 4: template for one-year vs. multi-year ice
274       data.seaice has new namelist SEAICE_PARM03 for arrays related to
275       SEAICE_num
276    
277    checkpoint62t (2011/03/05)
278    o pkg/obcs:
279     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
280       then normal component. This ensures that the normal component is set
281       correctly even when it conficts with tangential setting from an other OB.
282       Affects results of test-experiment seaice_obcs: update the output.txt
283    o pkg/obcs:
284     - add code to monitor statistics of dynamical fields at OB.
285     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
286       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
287       - change default: balance the Net inflow through all OB (instead of balancing
288         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
289     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
290       to match Nortern OB inflow (OBCS_balanceFacN=0).
291    o pkg/seaice:
292     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
293    o pkg/seaice (seaice_growth v 1.113):
294     - reverting seaice_growth to v 1.111 in order to have code with exact bit
295       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
296       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
297       runtime flag SEAICEareaFormula is kept but is inactive
298    o model/src:
299     - add new param to scale curvilinear grid distance and area when using
300       a different sphere radius from the grid-files.
301     - test/check multi-threads EXCH applied to local variable (cg2d_x)
302    o adjoint:
303     - enable adjoint of Stevens OB
304     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
305       (a bit delicate because of potentially modified adj. common block structure;
306       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
307    
308    checkpoint62s (2011/02/15)
309    o pkg/seaice (seaice_growth v 1.112):
310     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
311       computing the ice cover tendency from effective thickness tendencies. Include
312       Ian Fenty's formula.
313     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
314       SEAICEareaFormula.
315     - simplify notations for the various d_HEFF/d_AREA terms.
316    o pkg/gmredi:
317     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
318       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
319       add a verification test-run (front_relax.bvp) to test GM_useBVP.
320    o pkg/seaice (seaice_growth v 1.111):
321     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
322     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
323       also melt ice.
324    o pkg/seaice:
325     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
326     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
327  o pkg/cheapaml:  o pkg/cheapaml:
328   - from Nico Wienders: New version of this package.   - from Nico Wienders: New version of this package.
329  o pkg/flt:  o pkg/flt:

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