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revision 1.1314 by jmc, Sat Oct 16 17:23:12 2010 UTC revision 1.1393 by jmc, Mon Mar 14 02:12:53 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/mdsio:
8       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
9       (new argument) to check for tiled file in mdsioLocalDir : this fix the
10       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
11    o pkg/ctrl:
12     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
13       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
14       unused and superfluous variables
15     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
16    o pkg/ecco
17     - enable adjoint of Stevens OB
18    o pkg/ctrl/ecco/grdchk:
19      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
20        Fortunately, we do not have any tests for the numerous cpp-flagged
21        option of "obcs as control parameters" so we will never know
22        if this is an improvement (but at least now things compile).
23      - remove an obsolete initialization from ecco_cost_init_barfiles.F
24      - fix some problems within never used ifdefs to make the code compile
25    o pkg/obcs:
26     - Refine Interior mask definition to work with more complex OB (e.g.
27       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
28       read in Interior mask from file. Check if Interior mask is consistent
29       with OB list of indices.
30    o pkg/seaice
31     - beginning code for a seaice tracer package,
32       but currently only used for seaice age: SEAICE_AGE
33       SEAICE_num = 4
34       iTracer = 1: area-weighted ice age
35               = 2: volume-weighted ice age
36               = 3, 4: template for one-year vs. multi-year ice
37       data.seaice has new namelist SEAICE_PARM03 for arrays related to
38       SEAICE_num
39    
40    checkpoint62t (2011/03/05)
41    o pkg/obcs:
42     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
43       then normal component. This ensures that the normal component is set
44       correctly even when it conficts with tangential setting from an other OB.
45       Affects results of test-experiment seaice_obcs: update the output.txt
46    o pkg/obcs:
47     - add code to monitor statistics of dynamical fields at OB.
48     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
49       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
50       - change default: balance the Net inflow through all OB (instead of balancing
51         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
52     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
53       to match Nortern OB inflow (OBCS_balanceFacN=0).
54    o pkg/seaice:
55     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
56    o pkg/seaice (seaice_growth v 1.113):
57     - reverting seaice_growth to v 1.111 in order to have code with exact bit
58       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
59       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
60       runtime flag SEAICEareaFormula is kept but is inactive
61    o model/src:
62     - add new param to scale curvilinear grid distance and area when using
63       a different sphere radius from the grid-files.
64     - test/check multi-threads EXCH applied to local variable (cg2d_x)
65    o adjoint:
66     - enable adjoint of Stevens OB
67     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
68       (a bit delicate because of potentially modified adj. common block structure;
69       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
70    
71    checkpoint62s (2011/02/15)
72    o pkg/seaice (seaice_growth v 1.112):
73     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
74       computing the ice cover tendency from effective thickness tendencies. Include
75       Ian Fenty's formula.
76     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
77       SEAICEareaFormula.
78     - simplify notations for the various d_HEFF/d_AREA terms.
79    o pkg/gmredi:
80     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
81       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
82       add a verification test-run (front_relax.bvp) to test GM_useBVP.
83    o pkg/seaice (seaice_growth v 1.111):
84     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
85     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
86       also melt ice.
87    o pkg/seaice:
88     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
89     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
90    o pkg/cheapaml:
91     - from Nico Wienders: New version of this package.
92    o pkg/flt:
93     - add CPP options to prevent floats to re-enter the opposite side of
94       a periodic domain (default: keep periodicity)
95    o pkg/gmredi:
96     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
97       (needed for multi-dim advection).
98     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
99    o model/src:
100     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
101    o tutorial_tracer_adjsens
102     - extend to NLFS and replace maskC by hFacC
103       (change reference output accordingly)
104    
105    checkpoint62r (2011/01/24)
106    o testreport:
107     - add option -deloutp (-do) to remove output file after successful run
108     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
109       extract exact list of procs from this file ; adjust COMMAND by
110       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
111    o pkg/ecco: replace old ineffective way of penalizing deviations from
112      first guess (of obcs) with code by Matt Mazloff
113    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
114      exf/cal
115      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
116        and handle case of obcs?period == 0
117        Not affected by these changes: There is still an inconsistency in
118        the computation of start/endrec for the obcs variables for ALLOW_CAL
119        defined (see comment by Menemenlis, 7-Mar-2003)
120      - make S/R ctrl_get_gen_rec return something meaningful even if
121        ALLOW_CAL is not defined
122      - ctrl_getobcs?: simplify code so that it does not need to use
123                       S/R exf_swapfields
124    o testreport:
125       allow to test MPI with different number of processors for each experiment:
126       create file "SIZE.h.mpi" in each build dir.
127       Note: update of "-command" argument not yet implemented.
128    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
129      alleviate the need for additional 3D tapes when using
130      the non-inear free surface in the adjoint. This is done
131      by adding an 'update' of hfacc etc. to their current
132      value at the beginning of forward_step.F.
133    o pkg/seaice
134      seaice_lsr: move stress-divergence computations out of outer pseudo-
135      timestepping loop
136    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
137      up, so that the calls of the ctrl_* subroutines are really at the end
138      of the routine.
139    o pkg/gmredi:
140      allow to specify a 2-D horizontal map and a 1-D vertical profil
141      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
142    o pkg/seaice:
143      move lsr iterations from seaice_dynsolver to seaice_lsr.
144    o pkg/seaice:
145      reduce memory footprint of seaice mutldim advection tapes,
146      by using a 2D tape independent of the generic_advdiff ones,
147      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
148    
149    checkpoint62q (2010/12/29)
150    o model/src:
151      - check horizontal grid-spacing for unset or zero/negative values.
152      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
153    o pkg/flt:
154      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
155      - precision of input and output files set according to readBinaryPrec
156        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
157      - initial float position from tiled file was not converted to index space
158        (looks like a bug): fixed to make it similar to initial pos. global file.
159    o global_ocean.cs32x15:
160       change SIZE.h of AD set-up to get same tiling as with MPI.
161       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
162    o model/src:
163       add flag to control printing of domain fields (bathymetry, hFac ...) in
164       ini_mask_etc (call to plot_fieds_xy*).
165    o pkg/thsice:
166       if useEXF, some forcing fields are not valid in overlap: fixed by computing
167       over the interior only + apply EXCH at the end (like with SEAICE advection).
168    o pkg/mdsio:
169      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
170        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
171      - change barrier call for safe multi-threads access to 3-D shared buffer.
172      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
173      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
174        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
175    o pkg/flt:
176      - add fourth-order Runge-Kutta integration
177      - add basic exch2 support (only 1 facet supported so far!)
178    o pkg/mdsio+rw:
179      new S/R to read local (or tile independent) vector (read counterpart of
180       mds_writevec_loc, and front-end write_glvec_rl/rs).
181    o global_ocean.cs32x15: additional input_ad.seaice experiment
182        that uses pkg/seaice rather than pkg/thsice.
183        (using multidim advection for seaice)
184    o towards more F95 syntax for array specification in namelist:
185      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
186        of all verification experiments.
187           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
188          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
189      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
190    o global_ocean.cs32x15: additional input.seaice experiment
191        that uses pkg/seaice rather than pkg/thsice.
192    
193    checkpoint62p (2010/12/17)
194    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
195        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
196    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
197        allow for use of multim. advection in seaice adjoint.
198    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
199      - first attempt to close budgets by taking into account the freshwater
200        flux implied by the sublimation of snow and ice. So far only the
201        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
202        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
203    o eesupp/src:
204      new S/R with new option (NML_EXTENDED_F77) to change array specification
205      from F95 standard to commonly accepted extended F77 form.
206      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
207      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
208      for less tolerant f77 compiler (e.g., pgf77, g77).
209    o globalFiles:
210      commented out in parameter file "data" since it's not safe with MPI
211      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
212      in this case); no longer commented out in restart test (tst_2+2).
213    o add adTapeDir to specify a special directory where adjoint tapes are
214      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
215      and cannot be used together with mdsioLocalDir.
216    o nesting pkgs:
217      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
218      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
219      - add parameter files + utils dir + output from short run on beagle.
220    o pkg/seaice:
221        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
222    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
223      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
224    
225    checkpoint62o (2010/11/25)
226    o pkg/exf:
227      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
228    o pkg/seaice:
229      - seaice_ocean_stress: split a loop for better vectorization of the
230        adjoint code
231      - seaice_growth.F: fix bug in conservation of freshwater connected to
232        capping of heff, put contribution into d_HEFFbyNEG
233      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
234        by something more sensible (parameters that are what their name implies)
235      - change some defaults, so that by default exf-parameters are used for
236        things like rhoAir, cpAir,latent/sensible heat parameters, in order
237        to reproduce the old results, many data.seaice now contain funny values
238        for cpAir and latent heat of sublimation
239    o packages_readparms.F: move exf_readparms up in line so that
240        exf-parameters are visible for other packages (e.g. seaice)
241    o debugMode & debugLevel=2:
242      - differentiate between debugMode & debugLevel=2:
243        debugMode: controls printing of debug messages (sequence of S/R calls).
244        debugLevel: controls printing of algorithm intermediate results and stats.
245      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
246        => allows to print debug-stats without all sequence of call messages.
247      - switch control of debug print from debugLevel to debugMode in many S/R.
248    o pkg/obcs (obcs-sponge):
249        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
250        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
251    o pkg/generic_advdiff:
252      - record overlap minimum size for each advection scheme;
253      - refine criteria on overlap minimum size;
254      - check and stop (in gad_check) if overlap size is too small.
255    o pkg/obcs:
256      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
257        once, in ptracers_implicit.F)
258      - with seaice: remove test on empty file name in obcs_apply_seaice (always
259        apply OB values when tile has OB)
260    o model/src, coriolis setting:
261      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
262        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
263        files (selectCoriMap=3) with any grid.
264      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
265    o pkg/seaice/seaice_growth.F:
266        a few cosmetic changes that reduce the number of lines of code
267    o pkg/obcs: add boundary conditions following Stevens (1990)
268      - the code follows old MOM/NAOSIM code
269      - so far it is only implemented for the eastern and western boundaries
270        and NOT for pTracers
271    o pkg/rbcs:
272      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
273        beginning of the first rbcs forcing period.
274      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
275        offline package, i.e., one file per time, labeled by iteration number;
276        deltaTrbcs sets the timestep with which the data was generated;
277        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
278      - rbcsForcingCycle=0 makes forcing non-cyclic.
279      - make arithmetic safe for negative times and odd forcing periods.
280    
281    checkpoint62n (2010/11/09)
282    o pkg/seaice:
283        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
284    o pkg/obcs:
285       New S/R to copy tracer value from the OB location to narrow band region
286        (width = same as overlap) beyond the OB: preserve OB value (needed for
287        high-order scheme) which were overwritten by EXCH call if in overlap
288        region. Applied to theta, salt, ptracer and advected seaice variables.
289       With seaice: use maskInC in similar way as in gad_advection.F,
290        in seaice_advection.F and advect.F.
291       Update output of experiment seaice_obcs and change exp4 to test OBCS with
292        4th order Adv.Scheme. for pasive salt and ptracer.
293    o tools/genmake2:
294      - when looking for an optfile (not specified), only search for Fortran compiler
295        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
296      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
297        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
298      - set default for CPP to "cpp -traditional -P" (was the case without specifying
299        an optfile, but otherwise default was just "cpp".
300      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
301      - when "CC" is not set in the optfile, look for possible C compiler
302        (instead of just setting CC=cc)
303      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
304        => add a ".F" to ".o" rule for source files with no "#include" (such as
305           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
306      - move gfortran before g77 in list of possible Fortran compiler (consistent
307        with reference compiler switch from g77 to gfortran)
308    o pkg/seaice:
309      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
310        seaice_check that stops the model, when the CPP flag is used.
311      o seaice_growth.F: make capping of ice volume conserving by returning the
312        capped ice as freshwater to EmPmR. This does not change the verification
313        experiments but will change runs where the capping is acutally active
314    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
315      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
316         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
317         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
318    o tools/genmake2:
319      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
320      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
321      - clean previous genmake log files before anything else.
322      - change Makefile to remove testreport log files (*.tr_log) and genmake log
323        files only with "CLEAN" target (instead of "Clean");
324    o pkg/generic_advdiff:
325      Change OBCS in multiDim advection (gad_advection.F):
326       Use maskInC to prevent intermediate update of tracer-field in OB regions,
327       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
328       which were applying future time-step OB values.
329      This way, all explicit calculations use current-time-step OB values
330       (simpler and more consistent).
331      Affects results when set-up uses time-varying OBC and multi-dim advection;
332       update output of experiment seaice_obcs.
333    o pkg/seaice:
334      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
335       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
336         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
337      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
338       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
339       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
340    o pkg aim (2010/10/26):
341      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
342        formulation with obliquity, eccentricity, ... as run-time parameters,
343      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
344        upward shortwave radition at the surface (all-sky and clear-sky).
345    o pkg/obcs:
346      - writing sections with globalFiles=T does not work: switch to tiled-files
347        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
348      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
349      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
350    
351    checkpoint62m (2010/10/21)
352    o pkg/seaice: vectorize seaice_solve4temp.F
353      - move iterations loops outside of i/j-loops
354      - requires 2D arrays for TB and effConduct
355      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
356        modified in this routine
357      - a little bit of clean up, adjusting indentation, etc.
358      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
359        performance and '**TWO' by '**2' (because TWO is a float),
360        replaced ONE, ZERO
361  o eesupp/src:  o eesupp/src:
362     fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube     fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
363  o pkg/seaice/seaice_growth.F  o pkg/seaice/seaice_growth.F
# Line 38  o pkg/thsice: Line 392  o pkg/thsice:
392      does not change the verifcation experiment, but will change all      does not change the verifcation experiment, but will change all
393      experiments that have this flag undefined (not tested in verification);      experiments that have this flag undefined (not tested in verification);
394      a little reorganization to save a few 2D fields and recomputations      a little reorganization to save a few 2D fields and recomputations
395      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
396      - 2nd step:  fix some store dirs
397        o seems to work somewhat, i.e. using ifort but not g77
398        o likely cause are incomplete init. or recomputation
399        o start verification/global_ocean.cs32x15/input_ad.thsice
400  o pkg/obcs: add support for exch2  o pkg/obcs: add support for exch2
401    - the position of the boundary and prescribed values are specified using    - the position of the boundary and prescribed values are specified using
402      a global domain with exch2 facets stacked      a global domain with exch2 facets stacked
# Line 399  o tools/build_options: Line 758  o tools/build_options:
758      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
759  o pkg/ecco  o pkg/ecco
760    - allow user defined cost function contributions    - allow user defined cost function contributions
761          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
762          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
763    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
764        the two options are complementary.        the two options are complementary.
765  o pkg/smooth  o pkg/smooth

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