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revision 1.1375 by gforget, Wed Feb 9 12:38:57 2011 UTC revision 1.1444 by jmc, Fri May 27 00:44:49 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/seaice:  o pkg/seaice:
8      diffusion with centered advection scheme (diffus.F & advect.F):
9      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
10        to just compute the laplacian of input-field.
11      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
12      - fix flux-form version in diffus.F to conserve tracer.
13      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
14       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
15    
16    checkpoint62y (2011/05/26)
17    o pkg/seaice:
18     - seaice_growth.F : in EVOLUTION branch, always include
19       a_QSWbyATM_cover in qnet (as it should be).
20     - verification/global_ocean.cs32x15 : update results accordingly
21       (output.seaice.txt output_adm.seaice.txt).
22    o pkg/seaice + obcs:
23     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
24       equivalent of assuming no tracer gradient outside the OB region.
25       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
26     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
27       after changes above);
28     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
29       only at OB location (instead of over a band of OLx width).
30    o pkg/seaice:
31     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
32       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
33    o pkg/obcs:
34      - split header file "OBCS.h" into 4 separated files:
35        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
36       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
37         (contain no conditional statement which depends on OBCS options).
38      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
39        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
40    o ctrl, cost, grdchk & autodiff pkgs:
41      - make options file more standard (like other {PKG}_OPTIONS.h file but
42        with AD_CONFIG.h); clean-up some of the included header files.
43    o pkg/obcs:
44      - do not mask tracer when applying OB (tracer == 0 could generate problems)
45      - apply tracer OB values to tracer field only at OB location (instead of
46        over a band of OLx width)
47      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
48      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
49        obcs_apply_tloc.F & obcs_apply_sloc.F
50    o obcs in model/src:
51      - call OBCS_APPLY_W only if NonHydrostatic.
52      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
53      - reset dEtaHdt and wVel to zero outside OB interior region ;
54      - leave tracer unchanged outside OB interior region: This has no effect
55        on the solution but just to prevent unrealistic tracer value outside OB.
56      - zero out velocity outside OB interior region: This has no effect on
57        the solution but just to prevent unrealistic velocity outside OB.
58    o obcs and non-lin free-surf:
59       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
60       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
61       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
62       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
63       update results of test-exp. exp4(nlfs).
64    o exp4 (nlfs) test-exp:
65       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
66       with NonLin-FreeSurf); update output.nlfs.txt
67    o obcs and 2d/3d solver norm:
68       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
69       and outside OB interior region (will allow to place OB further inside the
70       domain). Depending on the domain, can affects cg2d-Norm (previous
71       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
72       and cg3d-Norm (previous Norm was computed before canceling OB terms),
73       e.g. in tutorial_plume_on_slope.
74      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
75    o pkg rbcs:
76      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
77      - add capability to apply relaxation to horizontal velocity uVel & vVel.
78    o pkg/grdchk: add gradient check for control variable xx_shifwflx
79    o pkg/shelfice/shelfice_init_fixed.F
80      fix CPP-flag combinations
81    o pkg/seaice: Merge iceage code of Pierre Rampal
82      * update/change/correct ice age calculations
83      * add age updates for pathological cases
84      Probably needs more testing...
85    
86    checkpoint62x (2011/05/13)
87    o pkg/mom_vecinv:
88       high-order vorticity scheme: use interior masks (maskInW & S)
89       to zero-out (outside OB) gradient of vorticity.
90    o verification exp.:
91       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
92       hs94.128x64x5 and seaice_obcs ; update results.
93    o pkg/obcs:
94      fix bug in OBeta for YZ sections in obcs_exf_load.F
95    o pkg/ctrl, pkg/shelfice, and optim:
96      - add new control variable xx_shifwflx (fresh water flux underneath ice
97        shelves). This is almost as tedious as obcs-ctrl, because the
98        variables needs its own mask.
99      - add a cost function term that penalizes the deviation of xx_shifwflx
100        from the first guess (zero) in analogy to other control variables
101    o pkg/shelfice:
102      - start basic adjoint
103    o pkg/ctrl:
104      - remove extra 2D field "for good measure" when initializing in
105        ctrl_set_globfld_[xy/xz/yz].F
106      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
107      - improve error messages in ctrl_set_unpack_*
108    o OBC implementation in momentum:
109       use interior masks (maskInC,W & S) in momentum S/R:
110       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
111       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
112       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
113       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
114       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
115        (and also with Leith/Smagorinsky harmonic-viscosity).
116       Update output of experiment dome and exp4 (+nlfs).
117    o exp4 test-exp:
118      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
119        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
120        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
121        time-varying OB at Western-side for wVel (NonHyd); update output.
122      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
123        and biharmonic-viscosity ; also use prescribed time varying OB.
124    o pkg/obcs:
125      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
126    o model/src:
127      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
128      - initialise startTime & nIter0 with unlikely values: allows to set one
129        from the other without ambiguity.
130    o seaice_obcs test-exp.:
131      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
132    o pkg/obcs:
133      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
134        no longer needed with maskInC,W,S in pkg/generic_advdiff.
135    o pkg/seaice:
136      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
137        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
138      - fixed bug in the initialization of sea ice salinity variable HSALT
139        in seaice_init_varia.F  (removed dependence on ICE2WATR)
140    o fizhi-cs test exp.:
141       switch reference output convention for these 2 non-standard test-exp,
142        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
143          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
144       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
145    o model/inc:
146      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
147        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
148    o pkg/seaice:
149      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
150    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
151      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
152        and initial HSALT
153    
154    checkpoint62w (2011/04/26)
155    o pkg/mom_fluxform:
156      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
157      - use parameter "sideDragFactor" in no-slip BC side-drag part.
158      - update output of exp. global_ocean.90x40x15
159    o pkg/mom_vecinv:
160      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
161    o update seaice exp.:
162      use more consistent parameter values (remove "backward compatability only":
163       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
164      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
165       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
166    o update test-exp global_ocean.90x40x15:
167      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
168      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
169      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
170      o turn on zStar & viscA4 in standard set-up (dir input/)
171        and update output files: output.txt & output.dwnslp.txt
172    o new AD-test experiment: obcs_ctrl
173      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
174    o pkg/dic:
175      fix two bugs in handling water vapour pressure in carbonate chemistry
176      and air-sea fluxes. Found by Val Bennington and Galen McKinley
177      (add DIC Option = WATERVAP_BUG to recover old results)
178      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
179    o adding allowInteriorFreezing option to check for water below freezing point
180      at depth and bring the negative heat anomaly to the surface level
181    o pkgs _fields_load:
182      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
183      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
184        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
185        rbcs to get interpolation weights and time reccord number.
186      - fix multi-threading in aim_fields_load.F
187      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
188    o external_fields_load:
189      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
190       interpolation weights) to use in a periodic time-series ; do not divide by
191       time-step to convert to integer:
192       - this fixes case where externForcingPeriod is not multiple of time-step
193          (Thanks to Christopher L. Wolfe)
194       - this fixes case where externForcingPeriod is an odd multiple of time-step
195         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
196      store index of time-record which is currently loaded:
197       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
198       - needed for the adjoint but not yet used because of extensive recomputations;
199         (to be fixed soon)
200    
201    checkpoint62v (2011/04/02)
202    o verification/1D_ocean_ice_column added to test Ian Fenty's
203      pkg/seaice_growth.F modifications for improving sea ice code differentiability
204    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
205      (new velocity statistics after changing maskInW & maskInS definition)
206    o pkg/generic_advdiff with OBCS:
207      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
208      equivalent to assumption of no tracer gradient outside the OB region.
209      This will affect the results if using obcs+biharmonic diffusion.
210      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
211    o pkg/obcs:
212      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
213      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
214      in Interior region. No impact on solution but affects Velocity monitor stats.
215    o pkg/ptracers (adjoint)
216      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
217      tape file for each tracer
218    o model/inc/src and pkg/autodiff: add parameters that allow to turn
219      of parts of the adjoint code at run time. For now, there are only
220      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
221      parameters are set in data.pkg.
222      This is the lazy coward's version of doing this, but still useful for
223      debugging. In order to do it right, everything needs to be moved to
224      pkg/autodiff.
225    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
226      the end; this fixes the adjoint balancing code for open boundaries.
227    o pkg/ctrl:
228      - change behavior of xx_${varname}period to be analogous to exf-conventions:
229        xx_${varname}period =   0.,  means time-independent control part
230        xx_${varname}period = -12., means one-year-periodic monthly control part
231      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
232        clean up ctrl_init a little, remove unused variables
233      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
234      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
235    
236    checkpoint62u (2011/03/15)
237    o model/src:
238      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
239        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
240      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
241        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
242    o pkg/ctrl/obcs/ecco:
243      - remove obsolete, unused, and partially broken code:
244        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
245        ALLOW_CTRL_OBCS_BALANCE
246      - put a stop statement into ecco/cost_obcsvol.F, but also add
247        cost_obcsvol to ecco_ad_diff.list
248    o pkg/ecco: fix counting cost function contributions for obcs (code
249      by Matt M.) and diffkr for diagnostics
250    o pkg/ecco, pkg/ctrl, pkg/grdchk:
251      add cost penalty terms for initial uvel, vvel, eta controls
252      and I/O for prior error files
253    o pkg/mdsio:
254       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
255       (new argument) to check for tiled file in mdsioLocalDir : this fix the
256       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
257    o pkg/ctrl:
258     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
259       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
260       unused and superfluous variables
261     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
262    o pkg/ecco
263     - enable adjoint of Stevens OB
264    o pkg/ctrl/ecco/grdchk:
265      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
266        Fortunately, we do not have any tests for the numerous cpp-flagged
267        option of "obcs as control parameters" so we will never know
268        if this is an improvement (but at least now things compile).
269      - remove an obsolete initialization from ecco_cost_init_barfiles.F
270      - fix some problems within never used ifdefs to make the code compile
271    o pkg/obcs:
272     - Refine Interior mask definition to work with more complex OB (e.g.
273       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
274       read in Interior mask from file. Check if Interior mask is consistent
275       with OB list of indices.
276    o pkg/seaice
277     - beginning code for a seaice tracer package,
278       but currently only used for seaice age: SEAICE_AGE
279       SEAICE_num = 4
280       iTracer = 1: area-weighted ice age
281               = 2: volume-weighted ice age
282               = 3, 4: template for one-year vs. multi-year ice
283       data.seaice has new namelist SEAICE_PARM03 for arrays related to
284       SEAICE_num
285    
286    checkpoint62t (2011/03/05)
287    o pkg/obcs:
288     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
289       then normal component. This ensures that the normal component is set
290       correctly even when it conficts with tangential setting from an other OB.
291       Affects results of test-experiment seaice_obcs: update the output.txt
292    o pkg/obcs:
293     - add code to monitor statistics of dynamical fields at OB.
294     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
295       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
296       - change default: balance the Net inflow through all OB (instead of balancing
297         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
298     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
299       to match Nortern OB inflow (OBCS_balanceFacN=0).
300    o pkg/seaice:
301     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
302    o pkg/seaice (seaice_growth v 1.113):
303     - reverting seaice_growth to v 1.111 in order to have code with exact bit
304       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
305       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
306       runtime flag SEAICEareaFormula is kept but is inactive
307    o model/src:
308     - add new param to scale curvilinear grid distance and area when using
309       a different sphere radius from the grid-files.
310     - test/check multi-threads EXCH applied to local variable (cg2d_x)
311    o adjoint:
312     - enable adjoint of Stevens OB
313     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
314       (a bit delicate because of potentially modified adj. common block structure;
315       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
316    
317    checkpoint62s (2011/02/15)
318    o pkg/seaice (seaice_growth v 1.112):
319     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
320       computing the ice cover tendency from effective thickness tendencies. Include
321       Ian Fenty's formula.
322     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
323       SEAICEareaFormula.
324     - simplify notations for the various d_HEFF/d_AREA terms.
325    o pkg/gmredi:
326     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
327       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
328       add a verification test-run (front_relax.bvp) to test GM_useBVP.
329    o pkg/seaice (seaice_growth v 1.111):
330     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
331     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
332       also melt ice.
333    o pkg/seaice:
334   - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).   - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
335   - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h   - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
336  o pkg/cheapaml:  o pkg/cheapaml:

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