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revision 1.1349 by mlosch, Thu Dec 16 08:34:01 2010 UTC revision 1.1419 by jmc, Fri Apr 29 21:21:10 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 seaice_obcs test-exp.:
8      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
9    o pkg/obcs:
10      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
11        no longer needed with maskInC,W,S in pkg/generic_advdiff.
12    o pkg/seaice:
13      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
14        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
15      - fixed bug in the initialization of sea ice salinity variable HSALT
16        in seaice_init_varia.F  (removed dependence on ICE2WATR)
17    o fizhi-cs test exp.:
18       switch reference output convention for these 2 non-standard test-exp,
19        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
20          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
21       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
22    o model/inc:
23      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
24        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
25    o pkg/seaice:
26      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
27    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
28      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
29        and initial HSALT
30    
31    checkpoint62w (2011/04/26)
32    o pkg/mom_fluxform:
33      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
34      - use parameter "sideDragFactor" in no-slip BC side-drag part.
35      - update output of exp. global_ocean.90x40x15
36    o pkg/mom_vecinv:
37      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
38    o update seaice exp.:
39      use more consistent parameter values (remove "backward compatability only":
40       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
41      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
42       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
43    o update test-exp global_ocean.90x40x15:
44      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
45      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
46      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
47      o turn on zStar & viscA4 in standard set-up (dir input/)
48        and update output files: output.txt & output.dwnslp.txt
49    o new AD-test experiment: obcs_ctrl
50      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
51    o pkg/dic:
52      fix two bugs in handling water vapour pressure in carbonate chemistry
53      and air-sea fluxes. Found by Val Bennington and Galen McKinley
54      (add DIC Option = WATERVAP_BUG to recover old results)
55      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
56    o adding allowInteriorFreezing option to check for water below freezing point
57      at depth and bring the negative heat anomaly to the surface level
58    o pkgs _fields_load:
59      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
60      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
61        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
62        rbcs to get interpolation weights and time reccord number.
63      - fix multi-threading in aim_fields_load.F
64      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
65    o external_fields_load:
66      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
67       interpolation weights) to use in a periodic time-series ; do not divide by
68       time-step to convert to integer:
69       - this fixes case where externForcingPeriod is not multiple of time-step
70          (Thanks to Christopher L. Wolfe)
71       - this fixes case where externForcingPeriod is an odd multiple of time-step
72         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
73      store index of time-record which is currently loaded:
74       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
75       - needed for the adjoint but not yet used because of extensive recomputations;
76         (to be fixed soon)
77    
78    checkpoint62v (2011/04/02)
79    o verification/1D_ocean_ice_column added to test Ian Fenty's
80      pkg/seaice_growth.F modifications for improving sea ice code differentiability
81    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
82      (new velocity statistics after changing maskInW & maskInS definition)
83    o pkg/generic_advdiff with OBCS:
84      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
85      equivalent to assumption of no tracer gradient outside the OB region.
86      This will affect the results if using obcs+biharmonic diffusion.
87      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
88    o pkg/obcs:
89      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
90      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
91      in Interior region. No impact on solution but affects Velocity monitor stats.
92    o pkg/ptracers (adjoint)
93      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
94      tape file for each tracer
95    o model/inc/src and pkg/autodiff: add parameters that allow to turn
96      of parts of the adjoint code at run time. For now, there are only
97      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
98      parameters are set in data.pkg.
99      This is the lazy coward's version of doing this, but still useful for
100      debugging. In order to do it right, everything needs to be moved to
101      pkg/autodiff.
102    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
103      the end; this fixes the adjoint balancing code for open boundaries.
104    o pkg/ctrl:
105      - change behavior of xx_${varname}period to be analogous to exf-conventions:
106        xx_${varname}period =   0.,  means time-independent control part
107        xx_${varname}period = -12., means one-year-periodic monthly control part
108      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
109        clean up ctrl_init a little, remove unused variables
110      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
111      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
112    
113    checkpoint62u (2011/03/15)
114    o model/src:
115      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
116        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
117      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
118        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
119    o pkg/ctrl/obcs/ecco:
120      - remove obsolete, unused, and partially broken code:
121        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
122        ALLOW_CTRL_OBCS_BALANCE
123      - put a stop statement into ecco/cost_obcsvol.F, but also add
124        cost_obcsvol to ecco_ad_diff.list
125    o pkg/ecco: fix counting cost function contributions for obcs (code
126      by Matt M.) and diffkr for diagnostics
127    o pkg/ecco, pkg/ctrl, pkg/grdchk:
128      add cost penalty terms for initial uvel, vvel, eta controls
129      and I/O for prior error files
130    o pkg/mdsio:
131       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
132       (new argument) to check for tiled file in mdsioLocalDir : this fix the
133       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
134    o pkg/ctrl:
135     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
136       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
137       unused and superfluous variables
138     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
139    o pkg/ecco
140     - enable adjoint of Stevens OB
141    o pkg/ctrl/ecco/grdchk:
142      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
143        Fortunately, we do not have any tests for the numerous cpp-flagged
144        option of "obcs as control parameters" so we will never know
145        if this is an improvement (but at least now things compile).
146      - remove an obsolete initialization from ecco_cost_init_barfiles.F
147      - fix some problems within never used ifdefs to make the code compile
148    o pkg/obcs:
149     - Refine Interior mask definition to work with more complex OB (e.g.
150       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
151       read in Interior mask from file. Check if Interior mask is consistent
152       with OB list of indices.
153    o pkg/seaice
154     - beginning code for a seaice tracer package,
155       but currently only used for seaice age: SEAICE_AGE
156       SEAICE_num = 4
157       iTracer = 1: area-weighted ice age
158               = 2: volume-weighted ice age
159               = 3, 4: template for one-year vs. multi-year ice
160       data.seaice has new namelist SEAICE_PARM03 for arrays related to
161       SEAICE_num
162    
163    checkpoint62t (2011/03/05)
164    o pkg/obcs:
165     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
166       then normal component. This ensures that the normal component is set
167       correctly even when it conficts with tangential setting from an other OB.
168       Affects results of test-experiment seaice_obcs: update the output.txt
169    o pkg/obcs:
170     - add code to monitor statistics of dynamical fields at OB.
171     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
172       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
173       - change default: balance the Net inflow through all OB (instead of balancing
174         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
175     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
176       to match Nortern OB inflow (OBCS_balanceFacN=0).
177    o pkg/seaice:
178     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
179    o pkg/seaice (seaice_growth v 1.113):
180     - reverting seaice_growth to v 1.111 in order to have code with exact bit
181       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
182       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
183       runtime flag SEAICEareaFormula is kept but is inactive
184    o model/src:
185     - add new param to scale curvilinear grid distance and area when using
186       a different sphere radius from the grid-files.
187     - test/check multi-threads EXCH applied to local variable (cg2d_x)
188    o adjoint:
189     - enable adjoint of Stevens OB
190     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
191       (a bit delicate because of potentially modified adj. common block structure;
192       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
193    
194    checkpoint62s (2011/02/15)
195    o pkg/seaice (seaice_growth v 1.112):
196     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
197       computing the ice cover tendency from effective thickness tendencies. Include
198       Ian Fenty's formula.
199     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
200       SEAICEareaFormula.
201     - simplify notations for the various d_HEFF/d_AREA terms.
202    o pkg/gmredi:
203     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
204       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
205       add a verification test-run (front_relax.bvp) to test GM_useBVP.
206    o pkg/seaice (seaice_growth v 1.111):
207     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
208     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
209       also melt ice.
210    o pkg/seaice:
211     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
212     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
213    o pkg/cheapaml:
214     - from Nico Wienders: New version of this package.
215    o pkg/flt:
216     - add CPP options to prevent floats to re-enter the opposite side of
217       a periodic domain (default: keep periodicity)
218    o pkg/gmredi:
219     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
220       (needed for multi-dim advection).
221     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
222    o model/src:
223     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
224    o tutorial_tracer_adjsens
225     - extend to NLFS and replace maskC by hFacC
226       (change reference output accordingly)
227    
228    checkpoint62r (2011/01/24)
229    o testreport:
230     - add option -deloutp (-do) to remove output file after successful run
231     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
232       extract exact list of procs from this file ; adjust COMMAND by
233       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
234    o pkg/ecco: replace old ineffective way of penalizing deviations from
235      first guess (of obcs) with code by Matt Mazloff
236    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
237      exf/cal
238      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
239        and handle case of obcs?period == 0
240        Not affected by these changes: There is still an inconsistency in
241        the computation of start/endrec for the obcs variables for ALLOW_CAL
242        defined (see comment by Menemenlis, 7-Mar-2003)
243      - make S/R ctrl_get_gen_rec return something meaningful even if
244        ALLOW_CAL is not defined
245      - ctrl_getobcs?: simplify code so that it does not need to use
246                       S/R exf_swapfields
247    o testreport:
248       allow to test MPI with different number of processors for each experiment:
249       create file "SIZE.h.mpi" in each build dir.
250       Note: update of "-command" argument not yet implemented.
251    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
252      alleviate the need for additional 3D tapes when using
253      the non-inear free surface in the adjoint. This is done
254      by adding an 'update' of hfacc etc. to their current
255      value at the beginning of forward_step.F.
256    o pkg/seaice
257      seaice_lsr: move stress-divergence computations out of outer pseudo-
258      timestepping loop
259    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
260      up, so that the calls of the ctrl_* subroutines are really at the end
261      of the routine.
262    o pkg/gmredi:
263      allow to specify a 2-D horizontal map and a 1-D vertical profil
264      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
265    o pkg/seaice:
266      move lsr iterations from seaice_dynsolver to seaice_lsr.
267    o pkg/seaice:
268      reduce memory footprint of seaice mutldim advection tapes,
269      by using a 2D tape independent of the generic_advdiff ones,
270      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
271    
272    checkpoint62q (2010/12/29)
273    o model/src:
274      - check horizontal grid-spacing for unset or zero/negative values.
275      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
276    o pkg/flt:
277      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
278      - precision of input and output files set according to readBinaryPrec
279        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
280      - initial float position from tiled file was not converted to index space
281        (looks like a bug): fixed to make it similar to initial pos. global file.
282    o global_ocean.cs32x15:
283       change SIZE.h of AD set-up to get same tiling as with MPI.
284       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
285    o model/src:
286       add flag to control printing of domain fields (bathymetry, hFac ...) in
287       ini_mask_etc (call to plot_fieds_xy*).
288    o pkg/thsice:
289       if useEXF, some forcing fields are not valid in overlap: fixed by computing
290       over the interior only + apply EXCH at the end (like with SEAICE advection).
291    o pkg/mdsio:
292      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
293        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
294      - change barrier call for safe multi-threads access to 3-D shared buffer.
295      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
296      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
297        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
298    o pkg/flt:
299      - add fourth-order Runge-Kutta integration
300      - add basic exch2 support (only 1 facet supported so far!)
301    o pkg/mdsio+rw:
302      new S/R to read local (or tile independent) vector (read counterpart of
303       mds_writevec_loc, and front-end write_glvec_rl/rs).
304    o global_ocean.cs32x15: additional input_ad.seaice experiment
305        that uses pkg/seaice rather than pkg/thsice.
306        (using multidim advection for seaice)
307    o towards more F95 syntax for array specification in namelist:
308      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
309        of all verification experiments.
310           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
311          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
312      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
313    o global_ocean.cs32x15: additional input.seaice experiment
314        that uses pkg/seaice rather than pkg/thsice.
315    
316    checkpoint62p (2010/12/17)
317    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
318        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
319    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
320        allow for use of multim. advection in seaice adjoint.
321  o pkg/seaice: add diagnostics for snow precipitation and sublimation flux  o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
322    - first attempt to close budgets by taking into account the freshwater    - first attempt to close budgets by taking into account the freshwater
323      flux implied by the sublimation of snow and ice. So far only the      flux implied by the sublimation of snow and ice. So far only the
324      volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag      volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
325      SEAICE_ADD_SUBLIMATION_TO_FWBUDGET      SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
326  o eesupp/src:  o eesupp/src:

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