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revision 1.1346 by jmc, Thu Dec 9 19:12:17 2010 UTC revision 1.1421 by jmc, Mon May 2 21:14:28 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 exp4 test-exp:
8      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
9        and biharmonic-viscosity ; prescribe time varying OB but without pkg/exf.
10    o pkg/obcs:
11      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
12    o model/src:
13      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
14      - initialise startTime & nIter0 with unlikely values: allows to set one
15        from the other without ambiguity.
16    o seaice_obcs test-exp.:
17      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
18    o pkg/obcs:
19      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
20        no longer needed with maskInC,W,S in pkg/generic_advdiff.
21    o pkg/seaice:
22      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
23        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
24      - fixed bug in the initialization of sea ice salinity variable HSALT
25        in seaice_init_varia.F  (removed dependence on ICE2WATR)
26    o fizhi-cs test exp.:
27       switch reference output convention for these 2 non-standard test-exp,
28        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
29          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
30       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
31    o model/inc:
32      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
33        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
34    o pkg/seaice:
35      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
36    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
37      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
38        and initial HSALT
39    
40    checkpoint62w (2011/04/26)
41    o pkg/mom_fluxform:
42      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
43      - use parameter "sideDragFactor" in no-slip BC side-drag part.
44      - update output of exp. global_ocean.90x40x15
45    o pkg/mom_vecinv:
46      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
47    o update seaice exp.:
48      use more consistent parameter values (remove "backward compatability only":
49       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
50      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
51       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
52    o update test-exp global_ocean.90x40x15:
53      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
54      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
55      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
56      o turn on zStar & viscA4 in standard set-up (dir input/)
57        and update output files: output.txt & output.dwnslp.txt
58    o new AD-test experiment: obcs_ctrl
59      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
60    o pkg/dic:
61      fix two bugs in handling water vapour pressure in carbonate chemistry
62      and air-sea fluxes. Found by Val Bennington and Galen McKinley
63      (add DIC Option = WATERVAP_BUG to recover old results)
64      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
65    o adding allowInteriorFreezing option to check for water below freezing point
66      at depth and bring the negative heat anomaly to the surface level
67    o pkgs _fields_load:
68      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
69      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
70        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
71        rbcs to get interpolation weights and time reccord number.
72      - fix multi-threading in aim_fields_load.F
73      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
74    o external_fields_load:
75      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
76       interpolation weights) to use in a periodic time-series ; do not divide by
77       time-step to convert to integer:
78       - this fixes case where externForcingPeriod is not multiple of time-step
79          (Thanks to Christopher L. Wolfe)
80       - this fixes case where externForcingPeriod is an odd multiple of time-step
81         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
82      store index of time-record which is currently loaded:
83       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
84       - needed for the adjoint but not yet used because of extensive recomputations;
85         (to be fixed soon)
86    
87    checkpoint62v (2011/04/02)
88    o verification/1D_ocean_ice_column added to test Ian Fenty's
89      pkg/seaice_growth.F modifications for improving sea ice code differentiability
90    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
91      (new velocity statistics after changing maskInW & maskInS definition)
92    o pkg/generic_advdiff with OBCS:
93      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
94      equivalent to assumption of no tracer gradient outside the OB region.
95      This will affect the results if using obcs+biharmonic diffusion.
96      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
97    o pkg/obcs:
98      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
99      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
100      in Interior region. No impact on solution but affects Velocity monitor stats.
101    o pkg/ptracers (adjoint)
102      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
103      tape file for each tracer
104    o model/inc/src and pkg/autodiff: add parameters that allow to turn
105      of parts of the adjoint code at run time. For now, there are only
106      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
107      parameters are set in data.pkg.
108      This is the lazy coward's version of doing this, but still useful for
109      debugging. In order to do it right, everything needs to be moved to
110      pkg/autodiff.
111    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
112      the end; this fixes the adjoint balancing code for open boundaries.
113    o pkg/ctrl:
114      - change behavior of xx_${varname}period to be analogous to exf-conventions:
115        xx_${varname}period =   0.,  means time-independent control part
116        xx_${varname}period = -12., means one-year-periodic monthly control part
117      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
118        clean up ctrl_init a little, remove unused variables
119      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
120      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
121    
122    checkpoint62u (2011/03/15)
123    o model/src:
124      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
125        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
126      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
127        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
128    o pkg/ctrl/obcs/ecco:
129      - remove obsolete, unused, and partially broken code:
130        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
131        ALLOW_CTRL_OBCS_BALANCE
132      - put a stop statement into ecco/cost_obcsvol.F, but also add
133        cost_obcsvol to ecco_ad_diff.list
134    o pkg/ecco: fix counting cost function contributions for obcs (code
135      by Matt M.) and diffkr for diagnostics
136    o pkg/ecco, pkg/ctrl, pkg/grdchk:
137      add cost penalty terms for initial uvel, vvel, eta controls
138      and I/O for prior error files
139    o pkg/mdsio:
140       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
141       (new argument) to check for tiled file in mdsioLocalDir : this fix the
142       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
143    o pkg/ctrl:
144     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
145       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
146       unused and superfluous variables
147     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
148    o pkg/ecco
149     - enable adjoint of Stevens OB
150    o pkg/ctrl/ecco/grdchk:
151      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
152        Fortunately, we do not have any tests for the numerous cpp-flagged
153        option of "obcs as control parameters" so we will never know
154        if this is an improvement (but at least now things compile).
155      - remove an obsolete initialization from ecco_cost_init_barfiles.F
156      - fix some problems within never used ifdefs to make the code compile
157    o pkg/obcs:
158     - Refine Interior mask definition to work with more complex OB (e.g.
159       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
160       read in Interior mask from file. Check if Interior mask is consistent
161       with OB list of indices.
162    o pkg/seaice
163     - beginning code for a seaice tracer package,
164       but currently only used for seaice age: SEAICE_AGE
165       SEAICE_num = 4
166       iTracer = 1: area-weighted ice age
167               = 2: volume-weighted ice age
168               = 3, 4: template for one-year vs. multi-year ice
169       data.seaice has new namelist SEAICE_PARM03 for arrays related to
170       SEAICE_num
171    
172    checkpoint62t (2011/03/05)
173    o pkg/obcs:
174     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
175       then normal component. This ensures that the normal component is set
176       correctly even when it conficts with tangential setting from an other OB.
177       Affects results of test-experiment seaice_obcs: update the output.txt
178    o pkg/obcs:
179     - add code to monitor statistics of dynamical fields at OB.
180     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
181       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
182       - change default: balance the Net inflow through all OB (instead of balancing
183         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
184     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
185       to match Nortern OB inflow (OBCS_balanceFacN=0).
186    o pkg/seaice:
187     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
188    o pkg/seaice (seaice_growth v 1.113):
189     - reverting seaice_growth to v 1.111 in order to have code with exact bit
190       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
191       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
192       runtime flag SEAICEareaFormula is kept but is inactive
193    o model/src:
194     - add new param to scale curvilinear grid distance and area when using
195       a different sphere radius from the grid-files.
196     - test/check multi-threads EXCH applied to local variable (cg2d_x)
197    o adjoint:
198     - enable adjoint of Stevens OB
199     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
200       (a bit delicate because of potentially modified adj. common block structure;
201       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
202    
203    checkpoint62s (2011/02/15)
204    o pkg/seaice (seaice_growth v 1.112):
205     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
206       computing the ice cover tendency from effective thickness tendencies. Include
207       Ian Fenty's formula.
208     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
209       SEAICEareaFormula.
210     - simplify notations for the various d_HEFF/d_AREA terms.
211    o pkg/gmredi:
212     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
213       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
214       add a verification test-run (front_relax.bvp) to test GM_useBVP.
215    o pkg/seaice (seaice_growth v 1.111):
216     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
217     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
218       also melt ice.
219    o pkg/seaice:
220     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
221     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
222    o pkg/cheapaml:
223     - from Nico Wienders: New version of this package.
224    o pkg/flt:
225     - add CPP options to prevent floats to re-enter the opposite side of
226       a periodic domain (default: keep periodicity)
227    o pkg/gmredi:
228     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
229       (needed for multi-dim advection).
230     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
231    o model/src:
232     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
233    o tutorial_tracer_adjsens
234     - extend to NLFS and replace maskC by hFacC
235       (change reference output accordingly)
236    
237    checkpoint62r (2011/01/24)
238    o testreport:
239     - add option -deloutp (-do) to remove output file after successful run
240     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
241       extract exact list of procs from this file ; adjust COMMAND by
242       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
243    o pkg/ecco: replace old ineffective way of penalizing deviations from
244      first guess (of obcs) with code by Matt Mazloff
245    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
246      exf/cal
247      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
248        and handle case of obcs?period == 0
249        Not affected by these changes: There is still an inconsistency in
250        the computation of start/endrec for the obcs variables for ALLOW_CAL
251        defined (see comment by Menemenlis, 7-Mar-2003)
252      - make S/R ctrl_get_gen_rec return something meaningful even if
253        ALLOW_CAL is not defined
254      - ctrl_getobcs?: simplify code so that it does not need to use
255                       S/R exf_swapfields
256    o testreport:
257       allow to test MPI with different number of processors for each experiment:
258       create file "SIZE.h.mpi" in each build dir.
259       Note: update of "-command" argument not yet implemented.
260    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
261      alleviate the need for additional 3D tapes when using
262      the non-inear free surface in the adjoint. This is done
263      by adding an 'update' of hfacc etc. to their current
264      value at the beginning of forward_step.F.
265    o pkg/seaice
266      seaice_lsr: move stress-divergence computations out of outer pseudo-
267      timestepping loop
268    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
269      up, so that the calls of the ctrl_* subroutines are really at the end
270      of the routine.
271    o pkg/gmredi:
272      allow to specify a 2-D horizontal map and a 1-D vertical profil
273      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
274    o pkg/seaice:
275      move lsr iterations from seaice_dynsolver to seaice_lsr.
276    o pkg/seaice:
277      reduce memory footprint of seaice mutldim advection tapes,
278      by using a 2D tape independent of the generic_advdiff ones,
279      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
280    
281    checkpoint62q (2010/12/29)
282    o model/src:
283      - check horizontal grid-spacing for unset or zero/negative values.
284      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
285    o pkg/flt:
286      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
287      - precision of input and output files set according to readBinaryPrec
288        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
289      - initial float position from tiled file was not converted to index space
290        (looks like a bug): fixed to make it similar to initial pos. global file.
291    o global_ocean.cs32x15:
292       change SIZE.h of AD set-up to get same tiling as with MPI.
293       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
294    o model/src:
295       add flag to control printing of domain fields (bathymetry, hFac ...) in
296       ini_mask_etc (call to plot_fieds_xy*).
297    o pkg/thsice:
298       if useEXF, some forcing fields are not valid in overlap: fixed by computing
299       over the interior only + apply EXCH at the end (like with SEAICE advection).
300    o pkg/mdsio:
301      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
302        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
303      - change barrier call for safe multi-threads access to 3-D shared buffer.
304      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
305      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
306        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
307    o pkg/flt:
308      - add fourth-order Runge-Kutta integration
309      - add basic exch2 support (only 1 facet supported so far!)
310    o pkg/mdsio+rw:
311      new S/R to read local (or tile independent) vector (read counterpart of
312       mds_writevec_loc, and front-end write_glvec_rl/rs).
313    o global_ocean.cs32x15: additional input_ad.seaice experiment
314        that uses pkg/seaice rather than pkg/thsice.
315        (using multidim advection for seaice)
316    o towards more F95 syntax for array specification in namelist:
317      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
318        of all verification experiments.
319           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
320          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
321      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
322    o global_ocean.cs32x15: additional input.seaice experiment
323        that uses pkg/seaice rather than pkg/thsice.
324    
325    checkpoint62p (2010/12/17)
326    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
327        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
328    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
329        allow for use of multim. advection in seaice adjoint.
330    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
331      - first attempt to close budgets by taking into account the freshwater
332        flux implied by the sublimation of snow and ice. So far only the
333        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
334        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
335    o eesupp/src:
336      new S/R with new option (NML_EXTENDED_F77) to change array specification
337      from F95 standard to commonly accepted extended F77 form.
338      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
339      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
340      for less tolerant f77 compiler (e.g., pgf77, g77).
341  o globalFiles:  o globalFiles:
342    commented out in parameter file "data" since it's not safe with MPI    commented out in parameter file "data" since it's not safe with MPI
343    (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much    (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much

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