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revision 1.1314 by jmc, Sat Oct 16 17:23:12 2010 UTC revision 1.1383 by jmc, Mon Feb 28 18:36:22 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/obcs:
8     - add code to monitor statistics of dynamical fields at OB.
9     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
10       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
11       - change default: balance the Net inflow through all OB (instead of balancing
12         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
13     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
14       to match Nortern OB inflow (OBCS_balanceFacN=0).
15    o pkg/seaice:
16     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
17    o pkg/seaice (seaice_growth v 1.113):
18     - reverting seaice_growth to v 1.111 in order to have code with exact bit
19       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
20       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
21       runtime flag SEAICEareaFormula is kept but is inactive
22    o model/src:
23     - add new param to scale curvilinear grid distance and area when using
24       a different sphere radius from the grid-files.
25     - test/check multi-threads EXCH applied to local variable (cg2d_x)
26    
27    checkpoint62s (2011/02/15)
28    o pkg/seaice (seaice_growth v 1.112):
29     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
30       computing the ice cover tendency from effective thickness tendencies. Include
31       Ian Fenty's formula.
32     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
33       SEAICEareaFormula.
34     - simplify notations for the various d_HEFF/d_AREA terms.
35    o pkg/gmredi:
36     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
37       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
38       add a verification test-run (front_relax.bvp) to test GM_useBVP.
39    o pkg/seaice (seaice_growth v 1.111):
40     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
41     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
42       also melt ice.
43    o pkg/seaice:
44     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
45     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
46    o pkg/cheapaml:
47     - from Nico Wienders: New version of this package.
48    o pkg/flt:
49     - add CPP options to prevent floats to re-enter the opposite side of
50       a periodic domain (default: keep periodicity)
51    o pkg/gmredi:
52     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
53       (needed for multi-dim advection).
54     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
55    o model/src:
56     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
57    o tutorial_tracer_adjsens
58     - extend to NLFS and replace maskC by hFacC
59       (change reference output accordingly)
60    
61    checkpoint62r (2011/01/24)
62    o testreport:
63     - add option -deloutp (-do) to remove output file after successful run
64     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
65       extract exact list of procs from this file ; adjust COMMAND by
66       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
67    o pkg/ecco: replace old ineffective way of penalizing deviations from
68      first guess (of obcs) with code by Matt Mazloff
69    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
70      exf/cal
71      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
72        and handle case of obcs?period == 0
73        Not affected by these changes: There is still an inconsistency in
74        the computation of start/endrec for the obcs variables for ALLOW_CAL
75        defined (see comment by Menemenlis, 7-Mar-2003)
76      - make S/R ctrl_get_gen_rec return something meaningful even if
77        ALLOW_CAL is not defined
78      - ctrl_getobcs?: simplify code so that it does not need to use
79                       S/R exf_swapfields
80    o testreport:
81       allow to test MPI with different number of processors for each experiment:
82       create file "SIZE.h.mpi" in each build dir.
83       Note: update of "-command" argument not yet implemented.
84    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
85      alleviate the need for additional 3D tapes when using
86      the non-inear free surface in the adjoint. This is done
87      by adding an 'update' of hfacc etc. to their current
88      value at the beginning of forward_step.F.
89    o pkg/seaice
90      seaice_lsr: move stress-divergence computations out of outer pseudo-
91      timestepping loop
92    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
93      up, so that the calls of the ctrl_* subroutines are really at the end
94      of the routine.
95    o pkg/gmredi:
96      allow to specify a 2-D horizontal map and a 1-D vertical profil
97      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
98    o pkg/seaice:
99      move lsr iterations from seaice_dynsolver to seaice_lsr.
100    o pkg/seaice:
101      reduce memory footprint of seaice mutldim advection tapes,
102      by using a 2D tape independent of the generic_advdiff ones,
103      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
104    
105    checkpoint62q (2010/12/29)
106    o model/src:
107      - check horizontal grid-spacing for unset or zero/negative values.
108      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
109    o pkg/flt:
110      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
111      - precision of input and output files set according to readBinaryPrec
112        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
113      - initial float position from tiled file was not converted to index space
114        (looks like a bug): fixed to make it similar to initial pos. global file.
115    o global_ocean.cs32x15:
116       change SIZE.h of AD set-up to get same tiling as with MPI.
117       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
118    o model/src:
119       add flag to control printing of domain fields (bathymetry, hFac ...) in
120       ini_mask_etc (call to plot_fieds_xy*).
121    o pkg/thsice:
122       if useEXF, some forcing fields are not valid in overlap: fixed by computing
123       over the interior only + apply EXCH at the end (like with SEAICE advection).
124    o pkg/mdsio:
125      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
126        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
127      - change barrier call for safe multi-threads access to 3-D shared buffer.
128      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
129      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
130        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
131    o pkg/flt:
132      - add fourth-order Runge-Kutta integration
133      - add basic exch2 support (only 1 facet supported so far!)
134    o pkg/mdsio+rw:
135      new S/R to read local (or tile independent) vector (read counterpart of
136       mds_writevec_loc, and front-end write_glvec_rl/rs).
137    o global_ocean.cs32x15: additional input_ad.seaice experiment
138        that uses pkg/seaice rather than pkg/thsice.
139        (using multidim advection for seaice)
140    o towards more F95 syntax for array specification in namelist:
141      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
142        of all verification experiments.
143           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
144          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
145      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
146    o global_ocean.cs32x15: additional input.seaice experiment
147        that uses pkg/seaice rather than pkg/thsice.
148    
149    checkpoint62p (2010/12/17)
150    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
151        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
152    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
153        allow for use of multim. advection in seaice adjoint.
154    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
155      - first attempt to close budgets by taking into account the freshwater
156        flux implied by the sublimation of snow and ice. So far only the
157        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
158        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
159    o eesupp/src:
160      new S/R with new option (NML_EXTENDED_F77) to change array specification
161      from F95 standard to commonly accepted extended F77 form.
162      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
163      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
164      for less tolerant f77 compiler (e.g., pgf77, g77).
165    o globalFiles:
166      commented out in parameter file "data" since it's not safe with MPI
167      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
168      in this case); no longer commented out in restart test (tst_2+2).
169    o add adTapeDir to specify a special directory where adjoint tapes are
170      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
171      and cannot be used together with mdsioLocalDir.
172    o nesting pkgs:
173      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
174      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
175      - add parameter files + utils dir + output from short run on beagle.
176    o pkg/seaice:
177        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
178    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
179      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
180    
181    checkpoint62o (2010/11/25)
182    o pkg/exf:
183      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
184    o pkg/seaice:
185      - seaice_ocean_stress: split a loop for better vectorization of the
186        adjoint code
187      - seaice_growth.F: fix bug in conservation of freshwater connected to
188        capping of heff, put contribution into d_HEFFbyNEG
189      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
190        by something more sensible (parameters that are what their name implies)
191      - change some defaults, so that by default exf-parameters are used for
192        things like rhoAir, cpAir,latent/sensible heat parameters, in order
193        to reproduce the old results, many data.seaice now contain funny values
194        for cpAir and latent heat of sublimation
195    o packages_readparms.F: move exf_readparms up in line so that
196        exf-parameters are visible for other packages (e.g. seaice)
197    o debugMode & debugLevel=2:
198      - differentiate between debugMode & debugLevel=2:
199        debugMode: controls printing of debug messages (sequence of S/R calls).
200        debugLevel: controls printing of algorithm intermediate results and stats.
201      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
202        => allows to print debug-stats without all sequence of call messages.
203      - switch control of debug print from debugLevel to debugMode in many S/R.
204    o pkg/obcs (obcs-sponge):
205        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
206        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
207    o pkg/generic_advdiff:
208      - record overlap minimum size for each advection scheme;
209      - refine criteria on overlap minimum size;
210      - check and stop (in gad_check) if overlap size is too small.
211    o pkg/obcs:
212      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
213        once, in ptracers_implicit.F)
214      - with seaice: remove test on empty file name in obcs_apply_seaice (always
215        apply OB values when tile has OB)
216    o model/src, coriolis setting:
217      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
218        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
219        files (selectCoriMap=3) with any grid.
220      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
221    o pkg/seaice/seaice_growth.F:
222        a few cosmetic changes that reduce the number of lines of code
223    o pkg/obcs: add boundary conditions following Stevens (1990)
224      - the code follows old MOM/NAOSIM code
225      - so far it is only implemented for the eastern and western boundaries
226        and NOT for pTracers
227    o pkg/rbcs:
228      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
229        beginning of the first rbcs forcing period.
230      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
231        offline package, i.e., one file per time, labeled by iteration number;
232        deltaTrbcs sets the timestep with which the data was generated;
233        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
234      - rbcsForcingCycle=0 makes forcing non-cyclic.
235      - make arithmetic safe for negative times and odd forcing periods.
236    
237    checkpoint62n (2010/11/09)
238    o pkg/seaice:
239        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
240    o pkg/obcs:
241       New S/R to copy tracer value from the OB location to narrow band region
242        (width = same as overlap) beyond the OB: preserve OB value (needed for
243        high-order scheme) which were overwritten by EXCH call if in overlap
244        region. Applied to theta, salt, ptracer and advected seaice variables.
245       With seaice: use maskInC in similar way as in gad_advection.F,
246        in seaice_advection.F and advect.F.
247       Update output of experiment seaice_obcs and change exp4 to test OBCS with
248        4th order Adv.Scheme. for pasive salt and ptracer.
249    o tools/genmake2:
250      - when looking for an optfile (not specified), only search for Fortran compiler
251        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
252      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
253        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
254      - set default for CPP to "cpp -traditional -P" (was the case without specifying
255        an optfile, but otherwise default was just "cpp".
256      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
257      - when "CC" is not set in the optfile, look for possible C compiler
258        (instead of just setting CC=cc)
259      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
260        => add a ".F" to ".o" rule for source files with no "#include" (such as
261           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
262      - move gfortran before g77 in list of possible Fortran compiler (consistent
263        with reference compiler switch from g77 to gfortran)
264    o pkg/seaice:
265      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
266        seaice_check that stops the model, when the CPP flag is used.
267      o seaice_growth.F: make capping of ice volume conserving by returning the
268        capped ice as freshwater to EmPmR. This does not change the verification
269        experiments but will change runs where the capping is acutally active
270    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
271      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
272         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
273         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
274    o tools/genmake2:
275      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
276      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
277      - clean previous genmake log files before anything else.
278      - change Makefile to remove testreport log files (*.tr_log) and genmake log
279        files only with "CLEAN" target (instead of "Clean");
280    o pkg/generic_advdiff:
281      Change OBCS in multiDim advection (gad_advection.F):
282       Use maskInC to prevent intermediate update of tracer-field in OB regions,
283       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
284       which were applying future time-step OB values.
285      This way, all explicit calculations use current-time-step OB values
286       (simpler and more consistent).
287      Affects results when set-up uses time-varying OBC and multi-dim advection;
288       update output of experiment seaice_obcs.
289    o pkg/seaice:
290      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
291       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
292         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
293      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
294       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
295       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
296    o pkg aim (2010/10/26):
297      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
298        formulation with obliquity, eccentricity, ... as run-time parameters,
299      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
300        upward shortwave radition at the surface (all-sky and clear-sky).
301    o pkg/obcs:
302      - writing sections with globalFiles=T does not work: switch to tiled-files
303        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
304      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
305      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
306    
307    checkpoint62m (2010/10/21)
308    o pkg/seaice: vectorize seaice_solve4temp.F
309      - move iterations loops outside of i/j-loops
310      - requires 2D arrays for TB and effConduct
311      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
312        modified in this routine
313      - a little bit of clean up, adjusting indentation, etc.
314      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
315        performance and '**TWO' by '**2' (because TWO is a float),
316        replaced ONE, ZERO
317  o eesupp/src:  o eesupp/src:
318     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
319  o pkg/seaice/seaice_growth.F  o pkg/seaice/seaice_growth.F
# Line 38  o pkg/thsice: Line 348  o pkg/thsice:
348      does not change the verifcation experiment, but will change all      does not change the verifcation experiment, but will change all
349      experiments that have this flag undefined (not tested in verification);      experiments that have this flag undefined (not tested in verification);
350      a little reorganization to save a few 2D fields and recomputations      a little reorganization to save a few 2D fields and recomputations
351      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
352      - 2nd step:  fix some store dirs
353        o seems to work somewhat, i.e. using ifort but not g77
354        o likely cause are incomplete init. or recomputation
355        o start verification/global_ocean.cs32x15/input_ad.thsice
356  o pkg/obcs: add support for exch2  o pkg/obcs: add support for exch2
357    - the position of the boundary and prescribed values are specified using    - the position of the boundary and prescribed values are specified using
358      a global domain with exch2 facets stacked      a global domain with exch2 facets stacked
# Line 399  o tools/build_options: Line 714  o tools/build_options:
714      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
715  o pkg/ecco  o pkg/ecco
716    - allow user defined cost function contributions    - allow user defined cost function contributions
717          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
718          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
719    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
720        the two options are complementary.        the two options are complementary.
721  o pkg/smooth  o pkg/smooth

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