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revision 1.1335 by jmc, Tue Nov 16 17:53:33 2010 UTC revision 1.1411 by jmc, Mon Apr 25 20:57:56 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/mom_vecinv:
8      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
9    o update test-exp global_ocean.90x40x15:
10      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
11      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
12      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
13      o turn on zStar & viscA4 in standard set-up (dir input/)
14        and update output files: output.txt & output.dwnslp.txt
15    o new AD-test experiment: obcs_ctrl
16      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
17    o pkg/dic:
18      fix two bugs in handling water vapour pressure in carbonate chemistry
19      and air-sea fluxes. Found by Val Bennington and Galen McKinley
20      (add DIC Option = WATERVAP_BUG to recover old results)
21      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
22    o adding allowInteriorFreezing option to check for water below freezing point
23      at depth and bring the negative heat anomaly to the surface level
24    o pkgs _fields_load:
25      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
26      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
27        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
28        rbcs to get interpolation weights and time reccord number.
29      - fix multi-threading in aim_fields_load.F
30      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
31    o external_fields_load:
32      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
33       interpolation weights) to use in a periodic time-series ; do not divide by
34       time-step to convert to integer:
35       - this fixes case where externForcingPeriod is not multiple of time-step
36          (Thanks to Christopher L. Wolfe)
37       - this fixes case where externForcingPeriod is an odd multiple of time-step
38         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
39      store index of time-record which is currently loaded:
40       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
41       - needed for the adjoint but not yet used because of extensive recomputations;
42         (to be fixed soon)
43    
44    checkpoint62v (2011/04/02)
45    o verification/1D_ocean_ice_column added to test Ian Fenty's
46      pkg/seaice_growth.F modifications for improving sea ice code differentiability
47    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
48      (new velocity statistics after changing maskInW & maskInS definition)
49    o pkg/generic_advdiff with OBCS:
50      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
51      equivalent to assumption of no tracer gradient outside the OB region.
52      This will affect the results if using obcs+biharmonic diffusion.
53      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
54    o pkg/obcs:
55      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
56      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
57      in Interior region. No impact on solution but affects Velocity monitor stats.
58    o pkg/ptracers (adjoint)
59      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
60      tape file for each tracer
61    o model/inc/src and pkg/autodiff: add parameters that allow to turn
62      of parts of the adjoint code at run time. For now, there are only
63      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
64      parameters are set in data.pkg.
65      This is the lazy coward's version of doing this, but still useful for
66      debugging. In order to do it right, everything needs to be moved to
67      pkg/autodiff.
68    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
69      the end; this fixes the adjoint balancing code for open boundaries.
70    o pkg/ctrl:
71      - change behavior of xx_${varname}period to be analogous to exf-conventions:
72        xx_${varname}period =   0.,  means time-independent control part
73        xx_${varname}period = -12., means one-year-periodic monthly control part
74      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
75        clean up ctrl_init a little, remove unused variables
76      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
77      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
78    
79    checkpoint62u (2011/03/15)
80    o model/src:
81      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
82        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
83      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
84        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
85    o pkg/ctrl/obcs/ecco:
86      - remove obsolete, unused, and partially broken code:
87        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
88        ALLOW_CTRL_OBCS_BALANCE
89      - put a stop statement into ecco/cost_obcsvol.F, but also add
90        cost_obcsvol to ecco_ad_diff.list
91    o pkg/ecco: fix counting cost function contributions for obcs (code
92      by Matt M.) and diffkr for diagnostics
93    o pkg/ecco, pkg/ctrl, pkg/grdchk:
94      add cost penalty terms for initial uvel, vvel, eta controls
95      and I/O for prior error files
96    o pkg/mdsio:
97       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
98       (new argument) to check for tiled file in mdsioLocalDir : this fix the
99       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
100    o pkg/ctrl:
101     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
102       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
103       unused and superfluous variables
104     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
105    o pkg/ecco
106     - enable adjoint of Stevens OB
107    o pkg/ctrl/ecco/grdchk:
108      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
109        Fortunately, we do not have any tests for the numerous cpp-flagged
110        option of "obcs as control parameters" so we will never know
111        if this is an improvement (but at least now things compile).
112      - remove an obsolete initialization from ecco_cost_init_barfiles.F
113      - fix some problems within never used ifdefs to make the code compile
114    o pkg/obcs:
115     - Refine Interior mask definition to work with more complex OB (e.g.
116       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
117       read in Interior mask from file. Check if Interior mask is consistent
118       with OB list of indices.
119    o pkg/seaice
120     - beginning code for a seaice tracer package,
121       but currently only used for seaice age: SEAICE_AGE
122       SEAICE_num = 4
123       iTracer = 1: area-weighted ice age
124               = 2: volume-weighted ice age
125               = 3, 4: template for one-year vs. multi-year ice
126       data.seaice has new namelist SEAICE_PARM03 for arrays related to
127       SEAICE_num
128    
129    checkpoint62t (2011/03/05)
130    o pkg/obcs:
131     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
132       then normal component. This ensures that the normal component is set
133       correctly even when it conficts with tangential setting from an other OB.
134       Affects results of test-experiment seaice_obcs: update the output.txt
135    o pkg/obcs:
136     - add code to monitor statistics of dynamical fields at OB.
137     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
138       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
139       - change default: balance the Net inflow through all OB (instead of balancing
140         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
141     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
142       to match Nortern OB inflow (OBCS_balanceFacN=0).
143    o pkg/seaice:
144     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
145    o pkg/seaice (seaice_growth v 1.113):
146     - reverting seaice_growth to v 1.111 in order to have code with exact bit
147       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
148       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
149       runtime flag SEAICEareaFormula is kept but is inactive
150    o model/src:
151     - add new param to scale curvilinear grid distance and area when using
152       a different sphere radius from the grid-files.
153     - test/check multi-threads EXCH applied to local variable (cg2d_x)
154    o adjoint:
155     - enable adjoint of Stevens OB
156     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
157       (a bit delicate because of potentially modified adj. common block structure;
158       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
159    
160    checkpoint62s (2011/02/15)
161    o pkg/seaice (seaice_growth v 1.112):
162     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
163       computing the ice cover tendency from effective thickness tendencies. Include
164       Ian Fenty's formula.
165     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
166       SEAICEareaFormula.
167     - simplify notations for the various d_HEFF/d_AREA terms.
168    o pkg/gmredi:
169     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
170       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
171       add a verification test-run (front_relax.bvp) to test GM_useBVP.
172    o pkg/seaice (seaice_growth v 1.111):
173     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
174     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
175       also melt ice.
176    o pkg/seaice:
177     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
178     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
179    o pkg/cheapaml:
180     - from Nico Wienders: New version of this package.
181    o pkg/flt:
182     - add CPP options to prevent floats to re-enter the opposite side of
183       a periodic domain (default: keep periodicity)
184    o pkg/gmredi:
185     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
186       (needed for multi-dim advection).
187     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
188    o model/src:
189     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
190    o tutorial_tracer_adjsens
191     - extend to NLFS and replace maskC by hFacC
192       (change reference output accordingly)
193    
194    checkpoint62r (2011/01/24)
195    o testreport:
196     - add option -deloutp (-do) to remove output file after successful run
197     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
198       extract exact list of procs from this file ; adjust COMMAND by
199       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
200    o pkg/ecco: replace old ineffective way of penalizing deviations from
201      first guess (of obcs) with code by Matt Mazloff
202    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
203      exf/cal
204      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
205        and handle case of obcs?period == 0
206        Not affected by these changes: There is still an inconsistency in
207        the computation of start/endrec for the obcs variables for ALLOW_CAL
208        defined (see comment by Menemenlis, 7-Mar-2003)
209      - make S/R ctrl_get_gen_rec return something meaningful even if
210        ALLOW_CAL is not defined
211      - ctrl_getobcs?: simplify code so that it does not need to use
212                       S/R exf_swapfields
213    o testreport:
214       allow to test MPI with different number of processors for each experiment:
215       create file "SIZE.h.mpi" in each build dir.
216       Note: update of "-command" argument not yet implemented.
217    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
218      alleviate the need for additional 3D tapes when using
219      the non-inear free surface in the adjoint. This is done
220      by adding an 'update' of hfacc etc. to their current
221      value at the beginning of forward_step.F.
222    o pkg/seaice
223      seaice_lsr: move stress-divergence computations out of outer pseudo-
224      timestepping loop
225    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
226      up, so that the calls of the ctrl_* subroutines are really at the end
227      of the routine.
228    o pkg/gmredi:
229      allow to specify a 2-D horizontal map and a 1-D vertical profil
230      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
231    o pkg/seaice:
232      move lsr iterations from seaice_dynsolver to seaice_lsr.
233    o pkg/seaice:
234      reduce memory footprint of seaice mutldim advection tapes,
235      by using a 2D tape independent of the generic_advdiff ones,
236      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
237    
238    checkpoint62q (2010/12/29)
239    o model/src:
240      - check horizontal grid-spacing for unset or zero/negative values.
241      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
242    o pkg/flt:
243      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
244      - precision of input and output files set according to readBinaryPrec
245        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
246      - initial float position from tiled file was not converted to index space
247        (looks like a bug): fixed to make it similar to initial pos. global file.
248    o global_ocean.cs32x15:
249       change SIZE.h of AD set-up to get same tiling as with MPI.
250       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
251    o model/src:
252       add flag to control printing of domain fields (bathymetry, hFac ...) in
253       ini_mask_etc (call to plot_fieds_xy*).
254    o pkg/thsice:
255       if useEXF, some forcing fields are not valid in overlap: fixed by computing
256       over the interior only + apply EXCH at the end (like with SEAICE advection).
257    o pkg/mdsio:
258      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
259        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
260      - change barrier call for safe multi-threads access to 3-D shared buffer.
261      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
262      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
263        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
264    o pkg/flt:
265      - add fourth-order Runge-Kutta integration
266      - add basic exch2 support (only 1 facet supported so far!)
267    o pkg/mdsio+rw:
268      new S/R to read local (or tile independent) vector (read counterpart of
269       mds_writevec_loc, and front-end write_glvec_rl/rs).
270    o global_ocean.cs32x15: additional input_ad.seaice experiment
271        that uses pkg/seaice rather than pkg/thsice.
272        (using multidim advection for seaice)
273    o towards more F95 syntax for array specification in namelist:
274      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
275        of all verification experiments.
276           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
277          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
278      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
279    o global_ocean.cs32x15: additional input.seaice experiment
280        that uses pkg/seaice rather than pkg/thsice.
281    
282    checkpoint62p (2010/12/17)
283    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
284        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
285    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
286        allow for use of multim. advection in seaice adjoint.
287    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
288      - first attempt to close budgets by taking into account the freshwater
289        flux implied by the sublimation of snow and ice. So far only the
290        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
291        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
292    o eesupp/src:
293      new S/R with new option (NML_EXTENDED_F77) to change array specification
294      from F95 standard to commonly accepted extended F77 form.
295      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
296      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
297      for less tolerant f77 compiler (e.g., pgf77, g77).
298    o globalFiles:
299      commented out in parameter file "data" since it's not safe with MPI
300      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
301      in this case); no longer commented out in restart test (tst_2+2).
302    o add adTapeDir to specify a special directory where adjoint tapes are
303      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
304      and cannot be used together with mdsioLocalDir.
305    o nesting pkgs:
306      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
307      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
308      - add parameter files + utils dir + output from short run on beagle.
309    o pkg/seaice:
310        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
311    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
312      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
313    
314    checkpoint62o (2010/11/25)
315    o pkg/exf:
316      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
317    o pkg/seaice:
318      - seaice_ocean_stress: split a loop for better vectorization of the
319        adjoint code
320      - seaice_growth.F: fix bug in conservation of freshwater connected to
321        capping of heff, put contribution into d_HEFFbyNEG
322      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
323        by something more sensible (parameters that are what their name implies)
324      - change some defaults, so that by default exf-parameters are used for
325        things like rhoAir, cpAir,latent/sensible heat parameters, in order
326        to reproduce the old results, many data.seaice now contain funny values
327        for cpAir and latent heat of sublimation
328    o packages_readparms.F: move exf_readparms up in line so that
329        exf-parameters are visible for other packages (e.g. seaice)
330    o debugMode & debugLevel=2:
331      - differentiate between debugMode & debugLevel=2:
332        debugMode: controls printing of debug messages (sequence of S/R calls).
333        debugLevel: controls printing of algorithm intermediate results and stats.
334      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
335        => allows to print debug-stats without all sequence of call messages.
336      - switch control of debug print from debugLevel to debugMode in many S/R.
337    o pkg/obcs (obcs-sponge):
338        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
339        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
340  o pkg/generic_advdiff:  o pkg/generic_advdiff:
341    - record overlap minimum size for each advection scheme;    - record overlap minimum size for each advection scheme;
342    - refine criteria on overlap minimum size;    - refine criteria on overlap minimum size;

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