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revision 1.1404 by jmc, Tue Mar 29 20:11:39 2011 UTC revision 1.1455 by gforget, Wed Jun 15 01:31:34 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:
8     - re-order diags inits so that they appear in order in available_diagnostics.log
9     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
10       area/heff/hsnow preceeding thermodynamic growth/melt.
11     - modified diag: SIdA; output actual effect, as the description states.
12     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
13     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
14       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
15        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
16     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
17     - added diagnostics for seaice genereic tracers (SItr*).
18     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
19     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
20    o pkg/diagnostics:
21      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
22      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
23        (was _RL, now integer) with option = 0 to retrieve all levels.
24      - add pieces of code to compute velocity potential at each level (new diagnostics
25        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
26        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
27    o model/src (rStar):
28      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
29        affect solution only if z* with full pressure in EOS;
30        update output of test-exp global_ocean.90x40x15.
31    o pkg/seaice:
32      - introduce siEps=1e-5 parameter
33      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
34      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
35      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
36        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
37        as well as ice cover age and ridging index (attached to AREA).
38        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
39        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
40        Up to SItrMaxNum=3 tracers can be used simultaneously.
41    o pkg/salt_plume:
42      -introduce SPsalFRAC run time parameter that sets the fraction of the
43       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
44       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
45    o model debug options:
46      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
47        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
48      - Refine debug-msg printing selection (3 new levels):
49        debugMode  : controls printing of debug messages (sequence of S/R calls).
50        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
51         debLevZero =  0 ; /* level of disabled aux. msg printing */
52         debLevA =  1 ; /* level of minimum  aux. msg printing */
53         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
54         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
55         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
56         debLevE =  5 ; /* level of extensive debug printing */
57        New debugLevel default: with default debugMode value (=F),
58          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
59          and if debugMode=T, default debugLevel = 4 (debLevD).
60        Relation with previous settings:
61         debLevB (=2) corresponds to former debLevA (=1)
62         debLevD (=4) corresponds to former debLevB (=2)
63        Note:
64         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
65         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
66            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
67      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
68        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
69    o pkg/obcs:
70      - change OBCSfixTopo default from True to False (should not change the results);
71        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
72    o pkg/thsice:
73      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
74        2nd layer seaice sublimation (unlikely to happen)
75      - use Interior mask for OBCS in thsice_advection.F (similar to what is
76        done in gad_advection & seaice_advection).
77    o adjoint:
78      bug fix spotted by Gael Forget:
79      seaice_advection and thsice_advection still had
80      legacy CPP options to avoid CS corner updates for adjoint
81    o pkg/seaice:
82      => Change some of the defaults (2011/05/29):
83         - change SEAICEuseFluxForm default (from False to True)
84         - change DIFF1 default (from 0.004 m/s to 0. m/s)
85         And print warnings if DIFF1 is not set in data.seaice and centered
86          avection scheme is used without any diffusion.
87      also:
88      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
89      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
90      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
91        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
92        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
93      update results of test exp.:
94         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
95             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
96             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
97         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
98         seaice_obcs: output (SEAICEuseFluxForm=T)
99      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
100          for standard fwd & AD lab_sea tests (to keep the same output).
101    o pkg/seaice/seaice_growth.F:
102      - use Ian Fenty's capping formulas for actual ice
103      thickness thoughout EVOLUTION branch.
104      - put treatment pathological case #2) in CPP brackets
105      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
106      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
107    o pkg/seaice:
108      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
109      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
110      also pass fac as a param, which can be 1. (to update the tendency
111      field) or the time step (to update the field itself).
112      - seaice_advdiff.F: for multidim, call seaice_diffusion with
113      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
114      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
115      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
116      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
117    o pkg/seaice:
118      diffusion with centered advection scheme (diffus.F & advect.F):
119      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
120        to just compute the laplacian of input-field.
121      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
122      - fix flux-form version in diffus.F to conserve tracer.
123      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
124       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
125    
126    checkpoint62y (2011/05/26)
127    o pkg/seaice:
128     - seaice_growth.F : in EVOLUTION branch, always include
129       a_QSWbyATM_cover in qnet (as it should be).
130     - verification/global_ocean.cs32x15 : update results accordingly
131       (output.seaice.txt output_adm.seaice.txt).
132    o pkg/seaice + obcs:
133     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
134       equivalent of assuming no tracer gradient outside the OB region.
135       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
136     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
137       after changes above);
138     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
139       only at OB location (instead of over a band of OLx width).
140    o pkg/seaice:
141     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
142       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
143    o pkg/obcs:
144      - split header file "OBCS.h" into 4 separated files:
145        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
146       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
147         (contain no conditional statement which depends on OBCS options).
148      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
149        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
150    o ctrl, cost, grdchk & autodiff pkgs:
151      - make options file more standard (like other {PKG}_OPTIONS.h file but
152        with AD_CONFIG.h); clean-up some of the included header files.
153    o pkg/obcs:
154      - do not mask tracer when applying OB (tracer == 0 could generate problems)
155      - apply tracer OB values to tracer field only at OB location (instead of
156        over a band of OLx width)
157      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
158      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
159        obcs_apply_tloc.F & obcs_apply_sloc.F
160    o obcs in model/src:
161      - call OBCS_APPLY_W only if NonHydrostatic.
162      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
163      - reset dEtaHdt and wVel to zero outside OB interior region ;
164      - leave tracer unchanged outside OB interior region: This has no effect
165        on the solution but just to prevent unrealistic tracer value outside OB.
166      - zero out velocity outside OB interior region: This has no effect on
167        the solution but just to prevent unrealistic velocity outside OB.
168    o obcs and non-lin free-surf:
169       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
170       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
171       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
172       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
173       update results of test-exp. exp4(nlfs).
174    o exp4 (nlfs) test-exp:
175       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
176       with NonLin-FreeSurf); update output.nlfs.txt
177    o obcs and 2d/3d solver norm:
178       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
179       and outside OB interior region (will allow to place OB further inside the
180       domain). Depending on the domain, can affects cg2d-Norm (previous
181       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
182       and cg3d-Norm (previous Norm was computed before canceling OB terms),
183       e.g. in tutorial_plume_on_slope.
184      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
185    o pkg rbcs:
186      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
187      - add capability to apply relaxation to horizontal velocity uVel & vVel.
188    o pkg/grdchk: add gradient check for control variable xx_shifwflx
189    o pkg/shelfice/shelfice_init_fixed.F
190      fix CPP-flag combinations
191    o pkg/seaice: Merge iceage code of Pierre Rampal
192      * update/change/correct ice age calculations
193      * add age updates for pathological cases
194      Probably needs more testing...
195    
196    checkpoint62x (2011/05/13)
197    o pkg/mom_vecinv:
198       high-order vorticity scheme: use interior masks (maskInW & S)
199       to zero-out (outside OB) gradient of vorticity.
200    o verification exp.:
201       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
202       hs94.128x64x5 and seaice_obcs ; update results.
203    o pkg/obcs:
204      fix bug in OBeta for YZ sections in obcs_exf_load.F
205    o pkg/ctrl, pkg/shelfice, and optim:
206      - add new control variable xx_shifwflx (fresh water flux underneath ice
207        shelves). This is almost as tedious as obcs-ctrl, because the
208        variables needs its own mask.
209      - add a cost function term that penalizes the deviation of xx_shifwflx
210        from the first guess (zero) in analogy to other control variables
211    o pkg/shelfice:
212      - start basic adjoint
213    o pkg/ctrl:
214      - remove extra 2D field "for good measure" when initializing in
215        ctrl_set_globfld_[xy/xz/yz].F
216      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
217      - improve error messages in ctrl_set_unpack_*
218    o OBC implementation in momentum:
219       use interior masks (maskInC,W & S) in momentum S/R:
220       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
221       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
222       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
223       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
224       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
225        (and also with Leith/Smagorinsky harmonic-viscosity).
226       Update output of experiment dome and exp4 (+nlfs).
227    o exp4 test-exp:
228      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
229        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
230        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
231        time-varying OB at Western-side for wVel (NonHyd); update output.
232      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
233        and biharmonic-viscosity ; also use prescribed time varying OB.
234    o pkg/obcs:
235      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
236    o model/src:
237      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
238      - initialise startTime & nIter0 with unlikely values: allows to set one
239        from the other without ambiguity.
240    o seaice_obcs test-exp.:
241      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
242    o pkg/obcs:
243      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
244        no longer needed with maskInC,W,S in pkg/generic_advdiff.
245    o pkg/seaice:
246      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
247        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
248      - fixed bug in the initialization of sea ice salinity variable HSALT
249        in seaice_init_varia.F  (removed dependence on ICE2WATR)
250    o fizhi-cs test exp.:
251       switch reference output convention for these 2 non-standard test-exp,
252        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
253          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
254       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
255    o model/inc:
256      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
257        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
258    o pkg/seaice:
259      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
260    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
261      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
262        and initial HSALT
263    
264    checkpoint62w (2011/04/26)
265    o pkg/mom_fluxform:
266      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
267      - use parameter "sideDragFactor" in no-slip BC side-drag part.
268      - update output of exp. global_ocean.90x40x15
269    o pkg/mom_vecinv:
270      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
271    o update seaice exp.:
272      use more consistent parameter values (remove "backward compatability only":
273       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
274      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
275       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
276    o update test-exp global_ocean.90x40x15:
277      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
278      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
279      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
280      o turn on zStar & viscA4 in standard set-up (dir input/)
281        and update output files: output.txt & output.dwnslp.txt
282    o new AD-test experiment: obcs_ctrl
283      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
284    o pkg/dic:
285      fix two bugs in handling water vapour pressure in carbonate chemistry
286      and air-sea fluxes. Found by Val Bennington and Galen McKinley
287      (add DIC Option = WATERVAP_BUG to recover old results)
288      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
289    o adding allowInteriorFreezing option to check for water below freezing point
290      at depth and bring the negative heat anomaly to the surface level
291    o pkgs _fields_load:
292      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
293      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
294        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
295        rbcs to get interpolation weights and time reccord number.
296      - fix multi-threading in aim_fields_load.F
297      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
298    o external_fields_load:
299      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
300       interpolation weights) to use in a periodic time-series ; do not divide by
301       time-step to convert to integer:
302       - this fixes case where externForcingPeriod is not multiple of time-step
303          (Thanks to Christopher L. Wolfe)
304       - this fixes case where externForcingPeriod is an odd multiple of time-step
305         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
306      store index of time-record which is currently loaded:
307       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
308       - needed for the adjoint but not yet used because of extensive recomputations;
309         (to be fixed soon)
310    
311    checkpoint62v (2011/04/02)
312    o verification/1D_ocean_ice_column added to test Ian Fenty's
313      pkg/seaice_growth.F modifications for improving sea ice code differentiability
314    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
315      (new velocity statistics after changing maskInW & maskInS definition)
316  o pkg/generic_advdiff with OBCS:  o pkg/generic_advdiff with OBCS:
317    use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:    use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
318    equivalent to assumption of no tracer gradient outside the OB region.    equivalent to assumption of no tracer gradient outside the OB region.

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