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revision 1.1327 by mlosch, Fri Nov 5 08:13:29 2010 UTC revision 1.1398 by mlosch, Tue Mar 15 16:12:52 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint62u (2011/03/15)
8    o model/src:
9      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
10        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
11      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
12        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
13    o pkg/ctrl/obcs/ecco:
14      - remove obsolete, unused, and partially broken code:
15        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
16        ALLOW_CTRL_OBCS_BALANCE
17      - put a stop statement into ecco/cost_obcsvol.F, but also add
18        cost_obcsvol to ecco_ad_diff.list
19    o pkg/ecco: fix counting cost function contributions for obcs (code
20      by Matt M.) and diffkr for diagnostics
21    o pkg/ecco, pkg/ctrl, pkg/grdchk:
22      add cost penalty terms for initial uvel, vvel, eta controls
23      and I/O for prior error files
24    o pkg/mdsio:
25       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
26       (new argument) to check for tiled file in mdsioLocalDir : this fix the
27       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
28    o pkg/ctrl:
29     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
30       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
31       unused and superfluous variables
32     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
33    o pkg/ecco
34     - enable adjoint of Stevens OB
35    o pkg/ctrl/ecco/grdchk:
36      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
37        Fortunately, we do not have any tests for the numerous cpp-flagged
38        option of "obcs as control parameters" so we will never know
39        if this is an improvement (but at least now things compile).
40      - remove an obsolete initialization from ecco_cost_init_barfiles.F
41      - fix some problems within never used ifdefs to make the code compile
42    o pkg/obcs:
43     - Refine Interior mask definition to work with more complex OB (e.g.
44       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
45       read in Interior mask from file. Check if Interior mask is consistent
46       with OB list of indices.
47    o pkg/seaice
48     - beginning code for a seaice tracer package,
49       but currently only used for seaice age: SEAICE_AGE
50       SEAICE_num = 4
51       iTracer = 1: area-weighted ice age
52               = 2: volume-weighted ice age
53               = 3, 4: template for one-year vs. multi-year ice
54       data.seaice has new namelist SEAICE_PARM03 for arrays related to
55       SEAICE_num
56    
57    checkpoint62t (2011/03/05)
58    o pkg/obcs:
59     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
60       then normal component. This ensures that the normal component is set
61       correctly even when it conficts with tangential setting from an other OB.
62       Affects results of test-experiment seaice_obcs: update the output.txt
63    o pkg/obcs:
64     - add code to monitor statistics of dynamical fields at OB.
65     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
66       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
67       - change default: balance the Net inflow through all OB (instead of balancing
68         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
69     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
70       to match Nortern OB inflow (OBCS_balanceFacN=0).
71    o pkg/seaice:
72     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
73    o pkg/seaice (seaice_growth v 1.113):
74     - reverting seaice_growth to v 1.111 in order to have code with exact bit
75       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
76       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
77       runtime flag SEAICEareaFormula is kept but is inactive
78    o model/src:
79     - add new param to scale curvilinear grid distance and area when using
80       a different sphere radius from the grid-files.
81     - test/check multi-threads EXCH applied to local variable (cg2d_x)
82    o adjoint:
83     - enable adjoint of Stevens OB
84     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
85       (a bit delicate because of potentially modified adj. common block structure;
86       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
87    
88    checkpoint62s (2011/02/15)
89    o pkg/seaice (seaice_growth v 1.112):
90     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
91       computing the ice cover tendency from effective thickness tendencies. Include
92       Ian Fenty's formula.
93     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
94       SEAICEareaFormula.
95     - simplify notations for the various d_HEFF/d_AREA terms.
96    o pkg/gmredi:
97     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
98       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
99       add a verification test-run (front_relax.bvp) to test GM_useBVP.
100    o pkg/seaice (seaice_growth v 1.111):
101     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
102     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
103       also melt ice.
104    o pkg/seaice:
105     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
106     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
107    o pkg/cheapaml:
108     - from Nico Wienders: New version of this package.
109    o pkg/flt:
110     - add CPP options to prevent floats to re-enter the opposite side of
111       a periodic domain (default: keep periodicity)
112    o pkg/gmredi:
113     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
114       (needed for multi-dim advection).
115     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
116    o model/src:
117     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
118    o tutorial_tracer_adjsens
119     - extend to NLFS and replace maskC by hFacC
120       (change reference output accordingly)
121    
122    checkpoint62r (2011/01/24)
123    o testreport:
124     - add option -deloutp (-do) to remove output file after successful run
125     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
126       extract exact list of procs from this file ; adjust COMMAND by
127       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
128    o pkg/ecco: replace old ineffective way of penalizing deviations from
129      first guess (of obcs) with code by Matt Mazloff
130    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
131      exf/cal
132      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
133        and handle case of obcs?period == 0
134        Not affected by these changes: There is still an inconsistency in
135        the computation of start/endrec for the obcs variables for ALLOW_CAL
136        defined (see comment by Menemenlis, 7-Mar-2003)
137      - make S/R ctrl_get_gen_rec return something meaningful even if
138        ALLOW_CAL is not defined
139      - ctrl_getobcs?: simplify code so that it does not need to use
140                       S/R exf_swapfields
141    o testreport:
142       allow to test MPI with different number of processors for each experiment:
143       create file "SIZE.h.mpi" in each build dir.
144       Note: update of "-command" argument not yet implemented.
145    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
146      alleviate the need for additional 3D tapes when using
147      the non-inear free surface in the adjoint. This is done
148      by adding an 'update' of hfacc etc. to their current
149      value at the beginning of forward_step.F.
150    o pkg/seaice
151      seaice_lsr: move stress-divergence computations out of outer pseudo-
152      timestepping loop
153    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
154      up, so that the calls of the ctrl_* subroutines are really at the end
155      of the routine.
156    o pkg/gmredi:
157      allow to specify a 2-D horizontal map and a 1-D vertical profil
158      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
159    o pkg/seaice:
160      move lsr iterations from seaice_dynsolver to seaice_lsr.
161    o pkg/seaice:
162      reduce memory footprint of seaice mutldim advection tapes,
163      by using a 2D tape independent of the generic_advdiff ones,
164      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
165    
166    checkpoint62q (2010/12/29)
167    o model/src:
168      - check horizontal grid-spacing for unset or zero/negative values.
169      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
170    o pkg/flt:
171      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
172      - precision of input and output files set according to readBinaryPrec
173        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
174      - initial float position from tiled file was not converted to index space
175        (looks like a bug): fixed to make it similar to initial pos. global file.
176    o global_ocean.cs32x15:
177       change SIZE.h of AD set-up to get same tiling as with MPI.
178       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
179    o model/src:
180       add flag to control printing of domain fields (bathymetry, hFac ...) in
181       ini_mask_etc (call to plot_fieds_xy*).
182    o pkg/thsice:
183       if useEXF, some forcing fields are not valid in overlap: fixed by computing
184       over the interior only + apply EXCH at the end (like with SEAICE advection).
185    o pkg/mdsio:
186      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
187        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
188      - change barrier call for safe multi-threads access to 3-D shared buffer.
189      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
190      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
191        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
192    o pkg/flt:
193      - add fourth-order Runge-Kutta integration
194      - add basic exch2 support (only 1 facet supported so far!)
195    o pkg/mdsio+rw:
196      new S/R to read local (or tile independent) vector (read counterpart of
197       mds_writevec_loc, and front-end write_glvec_rl/rs).
198    o global_ocean.cs32x15: additional input_ad.seaice experiment
199        that uses pkg/seaice rather than pkg/thsice.
200        (using multidim advection for seaice)
201    o towards more F95 syntax for array specification in namelist:
202      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
203        of all verification experiments.
204           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
205          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
206      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
207    o global_ocean.cs32x15: additional input.seaice experiment
208        that uses pkg/seaice rather than pkg/thsice.
209    
210    checkpoint62p (2010/12/17)
211    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
212        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
213    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
214        allow for use of multim. advection in seaice adjoint.
215    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
216      - first attempt to close budgets by taking into account the freshwater
217        flux implied by the sublimation of snow and ice. So far only the
218        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
219        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
220    o eesupp/src:
221      new S/R with new option (NML_EXTENDED_F77) to change array specification
222      from F95 standard to commonly accepted extended F77 form.
223      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
224      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
225      for less tolerant f77 compiler (e.g., pgf77, g77).
226    o globalFiles:
227      commented out in parameter file "data" since it's not safe with MPI
228      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
229      in this case); no longer commented out in restart test (tst_2+2).
230    o add adTapeDir to specify a special directory where adjoint tapes are
231      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
232      and cannot be used together with mdsioLocalDir.
233    o nesting pkgs:
234      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
235      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
236      - add parameter files + utils dir + output from short run on beagle.
237    o pkg/seaice:
238        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
239    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
240      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
241    
242    checkpoint62o (2010/11/25)
243    o pkg/exf:
244      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
245    o pkg/seaice:
246      - seaice_ocean_stress: split a loop for better vectorization of the
247        adjoint code
248      - seaice_growth.F: fix bug in conservation of freshwater connected to
249        capping of heff, put contribution into d_HEFFbyNEG
250      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
251        by something more sensible (parameters that are what their name implies)
252      - change some defaults, so that by default exf-parameters are used for
253        things like rhoAir, cpAir,latent/sensible heat parameters, in order
254        to reproduce the old results, many data.seaice now contain funny values
255        for cpAir and latent heat of sublimation
256    o packages_readparms.F: move exf_readparms up in line so that
257        exf-parameters are visible for other packages (e.g. seaice)
258    o debugMode & debugLevel=2:
259      - differentiate between debugMode & debugLevel=2:
260        debugMode: controls printing of debug messages (sequence of S/R calls).
261        debugLevel: controls printing of algorithm intermediate results and stats.
262      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
263        => allows to print debug-stats without all sequence of call messages.
264      - switch control of debug print from debugLevel to debugMode in many S/R.
265    o pkg/obcs (obcs-sponge):
266        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
267        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
268    o pkg/generic_advdiff:
269      - record overlap minimum size for each advection scheme;
270      - refine criteria on overlap minimum size;
271      - check and stop (in gad_check) if overlap size is too small.
272    o pkg/obcs:
273      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
274        once, in ptracers_implicit.F)
275      - with seaice: remove test on empty file name in obcs_apply_seaice (always
276        apply OB values when tile has OB)
277    o model/src, coriolis setting:
278      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
279        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
280        files (selectCoriMap=3) with any grid.
281      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
282    o pkg/seaice/seaice_growth.F:
283        a few cosmetic changes that reduce the number of lines of code
284    o pkg/obcs: add boundary conditions following Stevens (1990)
285      - the code follows old MOM/NAOSIM code
286      - so far it is only implemented for the eastern and western boundaries
287        and NOT for pTracers
288    o pkg/rbcs:
289      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
290        beginning of the first rbcs forcing period.
291      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
292        offline package, i.e., one file per time, labeled by iteration number;
293        deltaTrbcs sets the timestep with which the data was generated;
294        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
295      - rbcsForcingCycle=0 makes forcing non-cyclic.
296      - make arithmetic safe for negative times and odd forcing periods.
297    
298    checkpoint62n (2010/11/09)
299    o pkg/seaice:
300        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
301    o pkg/obcs:
302       New S/R to copy tracer value from the OB location to narrow band region
303        (width = same as overlap) beyond the OB: preserve OB value (needed for
304        high-order scheme) which were overwritten by EXCH call if in overlap
305        region. Applied to theta, salt, ptracer and advected seaice variables.
306       With seaice: use maskInC in similar way as in gad_advection.F,
307        in seaice_advection.F and advect.F.
308       Update output of experiment seaice_obcs and change exp4 to test OBCS with
309        4th order Adv.Scheme. for pasive salt and ptracer.
310    o tools/genmake2:
311      - when looking for an optfile (not specified), only search for Fortran compiler
312        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
313      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
314        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
315      - set default for CPP to "cpp -traditional -P" (was the case without specifying
316        an optfile, but otherwise default was just "cpp".
317      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
318      - when "CC" is not set in the optfile, look for possible C compiler
319        (instead of just setting CC=cc)
320      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
321        => add a ".F" to ".o" rule for source files with no "#include" (such as
322           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
323      - move gfortran before g77 in list of possible Fortran compiler (consistent
324        with reference compiler switch from g77 to gfortran)
325  o pkg/seaice:  o pkg/seaice:
326    o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to    o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
327      seaice_check that stops the model, when the CPP flag is used.      seaice_check that stops the model, when the CPP flag is used.
328    o seaice_growth.F: make capping of ice volume conserving by returning the    o seaice_growth.F: make capping of ice volume conserving by returning the
329      capped ice as freshwater to EmPmR. This does not change the verification      capped ice as freshwater to EmPmR. This does not change the verification
# Line 36  o pkg/seaice: Line 354  o pkg/seaice:
354    Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY    Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
355     but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp     but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
356     unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)     unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
   For OBCS, close southern and western boundaries for sea ice solver  
    based on myYGlobalLo and myXGlobalLo instead of OB_Js and OB_Iw.  
357  o pkg aim (2010/10/26):  o pkg aim (2010/10/26):
358    - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation    - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
359      formulation with obliquity, eccentricity, ... as run-time parameters,      formulation with obliquity, eccentricity, ... as run-time parameters,

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