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revision 1.1290 by gforget, Fri Aug 6 18:45:41 2010 UTC revision 1.1354 by gforget, Tue Dec 21 23:36:55 2010 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o global_ocean.cs32x15: additional input_ad.seaice experiment
8        that uses pkg/seaice rather than pkg/thsice.
9        (using multidim advection for seaice)
10    o towards more F95 syntax for array specification in namelist:
11      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
12        of all verification experiments.
13           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
14          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
15      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
16    o global_ocean.cs32x15: additional input.seaice experiment
17        that uses pkg/seaice rather than pkg/thsice.
18    
19    checkpoint62p (2010/12/17)
20    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
21        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
22    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
23        allow for use of multim. advection in seaice adjoint.
24    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
25      - first attempt to close budgets by taking into account the freshwater
26        flux implied by the sublimation of snow and ice. So far only the
27        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
28        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
29    o eesupp/src:
30      new S/R with new option (NML_EXTENDED_F77) to change array specification
31      from F95 standard to commonly accepted extended F77 form.
32      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
33      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
34      for less tolerant f77 compiler (e.g., pgf77, g77).
35    o globalFiles:
36      commented out in parameter file "data" since it's not safe with MPI
37      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
38      in this case); no longer commented out in restart test (tst_2+2).
39    o add adTapeDir to specify a special directory where adjoint tapes are
40      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
41      and cannot be used together with mdsioLocalDir.
42    o nesting pkgs:
43      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
44      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
45      - add parameter files + utils dir + output from short run on beagle.
46    o pkg/seaice:
47        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
48    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
49      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
50    
51    checkpoint62o (2010/11/25)
52    o pkg/exf:
53      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
54    o pkg/seaice:
55      - seaice_ocean_stress: split a loop for better vectorization of the
56        adjoint code
57      - seaice_growth.F: fix bug in conservation of freshwater connected to
58        capping of heff, put contribution into d_HEFFbyNEG
59      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
60        by something more sensible (parameters that are what their name implies)
61      - change some defaults, so that by default exf-parameters are used for
62        things like rhoAir, cpAir,latent/sensible heat parameters, in order
63        to reproduce the old results, many data.seaice now contain funny values
64        for cpAir and latent heat of sublimation
65    o packages_readparms.F: move exf_readparms up in line so that
66        exf-parameters are visible for other packages (e.g. seaice)
67    o debugMode & debugLevel=2:
68      - differentiate between debugMode & debugLevel=2:
69        debugMode: controls printing of debug messages (sequence of S/R calls).
70        debugLevel: controls printing of algorithm intermediate results and stats.
71      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
72        => allows to print debug-stats without all sequence of call messages.
73      - switch control of debug print from debugLevel to debugMode in many S/R.
74    o pkg/obcs (obcs-sponge):
75        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
76        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
77    o pkg/generic_advdiff:
78      - record overlap minimum size for each advection scheme;
79      - refine criteria on overlap minimum size;
80      - check and stop (in gad_check) if overlap size is too small.
81    o pkg/obcs:
82      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
83        once, in ptracers_implicit.F)
84      - with seaice: remove test on empty file name in obcs_apply_seaice (always
85        apply OB values when tile has OB)
86    o model/src, coriolis setting:
87      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
88        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
89        files (selectCoriMap=3) with any grid.
90      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
91    o pkg/seaice/seaice_growth.F:
92        a few cosmetic changes that reduce the number of lines of code
93    o pkg/obcs: add boundary conditions following Stevens (1990)
94      - the code follows old MOM/NAOSIM code
95      - so far it is only implemented for the eastern and western boundaries
96        and NOT for pTracers
97    o pkg/rbcs:
98      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
99        beginning of the first rbcs forcing period.
100      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
101        offline package, i.e., one file per time, labeled by iteration number;
102        deltaTrbcs sets the timestep with which the data was generated;
103        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
104      - rbcsForcingCycle=0 makes forcing non-cyclic.
105      - make arithmetic safe for negative times and odd forcing periods.
106    
107    checkpoint62n (2010/11/09)
108    o pkg/seaice:
109        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
110    o pkg/obcs:
111       New S/R to copy tracer value from the OB location to narrow band region
112        (width = same as overlap) beyond the OB: preserve OB value (needed for
113        high-order scheme) which were overwritten by EXCH call if in overlap
114        region. Applied to theta, salt, ptracer and advected seaice variables.
115       With seaice: use maskInC in similar way as in gad_advection.F,
116        in seaice_advection.F and advect.F.
117       Update output of experiment seaice_obcs and change exp4 to test OBCS with
118        4th order Adv.Scheme. for pasive salt and ptracer.
119    o tools/genmake2:
120      - when looking for an optfile (not specified), only search for Fortran compiler
121        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
122      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
123        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
124      - set default for CPP to "cpp -traditional -P" (was the case without specifying
125        an optfile, but otherwise default was just "cpp".
126      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
127      - when "CC" is not set in the optfile, look for possible C compiler
128        (instead of just setting CC=cc)
129      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
130        => add a ".F" to ".o" rule for source files with no "#include" (such as
131           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
132      - move gfortran before g77 in list of possible Fortran compiler (consistent
133        with reference compiler switch from g77 to gfortran)
134    o pkg/seaice:
135      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
136        seaice_check that stops the model, when the CPP flag is used.
137      o seaice_growth.F: make capping of ice volume conserving by returning the
138        capped ice as freshwater to EmPmR. This does not change the verification
139        experiments but will change runs where the capping is acutally active
140    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
141      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
142         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
143         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
144    o tools/genmake2:
145      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
146      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
147      - clean previous genmake log files before anything else.
148      - change Makefile to remove testreport log files (*.tr_log) and genmake log
149        files only with "CLEAN" target (instead of "Clean");
150    o pkg/generic_advdiff:
151      Change OBCS in multiDim advection (gad_advection.F):
152       Use maskInC to prevent intermediate update of tracer-field in OB regions,
153       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
154       which were applying future time-step OB values.
155      This way, all explicit calculations use current-time-step OB values
156       (simpler and more consistent).
157      Affects results when set-up uses time-varying OBC and multi-dim advection;
158       update output of experiment seaice_obcs.
159    o pkg/seaice:
160      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
161       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
162         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
163      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
164       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
165       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
166    o pkg aim (2010/10/26):
167      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
168        formulation with obliquity, eccentricity, ... as run-time parameters,
169      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
170        upward shortwave radition at the surface (all-sky and clear-sky).
171    o pkg/obcs:
172      - writing sections with globalFiles=T does not work: switch to tiled-files
173        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
174      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
175      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
176    
177    checkpoint62m (2010/10/21)
178    o pkg/seaice: vectorize seaice_solve4temp.F
179      - move iterations loops outside of i/j-loops
180      - requires 2D arrays for TB and effConduct
181      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
182        modified in this routine
183      - a little bit of clean up, adjusting indentation, etc.
184      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
185        performance and '**TWO' by '**2' (because TWO is a float),
186        replaced ONE, ZERO
187    o eesupp/src:
188       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
189    o pkg/seaice/seaice_growth.F
190      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
191      merging process. The merged routine has two branches, and one activates the 'evolution'
192      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
193      In summary, here is what the '10/10 revision' did consist of
194        part 1: seaice_growth.F revisions 1.71 to 1.75
195          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
196            The emphasis here was on improving readability (e.g. by trying to use meaningful
197            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
198        part 1.5:
199          - revising the lab_sea experiment to make it a more useful (i.e. stable
200            and representative of an actual model run). This was done by generating a
201            (winter) pickup to start from, switching back the main experiment dynamic
202            solver from evp to lsr, having one of the experiments use the free drift solution.
203        part 2: seaice_growth.F revisions 1.76 to 1.85
204          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
205          - Sorting out the various fields units and sign (set early on and reset at the end)
206            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
207            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
208          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
209            and simplifying logical expressions to further improve readibility.
210        part 3: seaice_growth.F revisions 1.86 to 1.89
211          - Re-organize the blocks of code more logically.
212          - Merging the '_if.F' pieces that add something new.
213    o pkg/thsice:
214      - vectorize thsice_solve4temp and thsice_get_exf.
215        Problem: thsice_solve4temp has an unvectorizable statement that
216        might also be problematic for TAF
217      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
218        does not change the verifcation experiment, but will change all
219        experiments that have this flag undefined (not tested in verification);
220        a little reorganization to save a few 2D fields and recomputations
221      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
222      - 2nd step:  fix some store dirs
223        o seems to work somewhat, i.e. using ifort but not g77
224        o likely cause are incomplete init. or recomputation
225        o start verification/global_ocean.cs32x15/input_ad.thsice
226    o pkg/obcs: add support for exch2
227      - the position of the boundary and prescribed values are specified using
228        a global domain with exch2 facets stacked
229        - in x for N,S boundaries (like W2_mapIO=-1)
230        - in y for E,W boundaries (so E,W boundaries do not overlap)
231    o pkg/mdsio: add support for writing global sections with exch2
232        file layout is as for obcs described above:
233        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
234        - for y-z sections, facets are stacked in y
235    o pkg/thsice:
236       - change a few routines for better vectorization: thsice_albedo.F,
237         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
238         not affected, but in particular the latter routine has changed
239         dramatically (not necessarily easier to read now).
240       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
241       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
242    o verification/lab_sea:
243      - overhaul of the forward model experiments. The main motivation
244        for this revision is that lab_sea has proven quite fragile (when
245        changing the sea-ice code, and switching platforms) to a point
246        when failures were very hard to attribute to specific code problems.
247      - the suspected reason for this fragility is noise amplification by evp so,
248        to start with, we decided to replace evp with lsr in the main experiment.
249      - the input.lsr experiment thus became obsolete and was removed.
250      - it was replaced with the input.fd experiment that uses an
251        analytical "free drift" solution as the ice velocity field.
252      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
253        will hopefully allow us to discriminate problems due to dynamic solvers
254        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
255        us to test additional options, along with the salt plume package.
256      - Finally a pickup was generated (at the end of a one year run) to
257        make the tests more representative of an actual model run. Previously
258        the tests starting point was a 1m thickness of ice everywhere.
259    o pkg/seaice:
260      - introducing S\R seaice_freedrift.F that compute the
261        analytical solution to an approximate ice momentum
262        equation (i.e. the simple stress/coriolis balance).
263      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
264        of the free drift velocity field, and enable its use.
265        To actually use the free drift solution as the model ice
266        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
267    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
268    
269    checkpoint62l (2010/10/04)
270    o pkg/seaice:
271      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
272      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
273       version (with USE_ORIGINAL_SBI undef);
274    o add hooks for new packages OASIS, the package will follow
275      (hooks exclude the seaice pkg for now)
276    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
277      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
278      rather than mdsio_readvector.F/mdsio_writevector.F, within
279      adread_adwrite.F to read/write adjoint-related tapes to disk.
280    o eesupp and pkg/mdsio: ALLOW_WHIO
281      Option to write/read 2D fields to files including tiles halos.
282      The main purpose is for adjoint related "tape I/O".
283      The secondary purpose is for debugging phases.
284      A word on those rather specifically intended purposes.
285      The code was meant to be stripped down to the bare minimum.
286      Typically, there is a unique and basic mapping to the global
287      buffer (tile by tile, then proc by proc, then level by level), and
288      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
289      meant to generate user friendly outputs of various shapes and forms.
290      Rather it is intended, for the knowledgeabale developers,
291      to be largely independent of the many mdsio options, to allow
292      outputs of tiles+halos in debugging phases and in adjoint runs,
293      and to allow some flexibility in tuning (adoint) I/O depending on each
294      file system behavior. With regard to tuning, most of the potential knobs
295      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
296      to specify directories, to specify the typical size of I/O calls, etc.)
297      are not yet included, and will be added if they prove useful.
298    o pkg/seaice:
299       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
300    o pkg/seaice:
301       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
302       code (seaice_budget_ice_if.F) which enable to recover old standard
303       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
304       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
305    o model/src (rStar):
306       use simple average (not area weighted) of rStarFac at U,V point when using
307       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
308       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
309    
310    checkpoint62k (2010/09/17)
311    o adjoint
312       * changed verification/global_ocean.cs32x15 ; adjoint now tests
313         Adams-Bashforth 3 + NLFS + RSTAR
314       * some more modifs required for ECCO-GODAE v4
315    o pkg/seaice
316       add SEAICE_AGE_VOL option to use volume instead of area for
317       integrating SEAICE_AGE
318    o model/src:
319       first check-in of sigma & hybrid-sigma coordinate code ; also includes
320       non-linear free-surface parts ; but pressure-gradient not yet coded.
321    o pkg/ptracers:
322       option for ptracer to convert Salt Relax into additional EmP.
323        tested in exp. global_ocean.90x40x15.dwnslp (update output)
324    
325    checkpoint62j (2010/08/25)
326    o pkg/ggl90:
327       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
328    o pkg/dic: car_flux.F, phos_flux.F
329      - reduce number of exp-calls in order to improve performance
330      - clean up a little (replace fields by their macros, etc., fix
331        typo in CPP-flag)
332  o pkg/ggl90: minor changes  o pkg/ggl90: minor changes
333    - GGL90diffKrS was removed --> always use GGL90diffKr    - GGL90diffKrS was removed --> always use GGL90diffKr
334    - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV    - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
335    - hack of mxlMaxFlag=2 --> ensure mixing between first and second level (commented out for now)    - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
336        (commented out for now)
337    - change in max/min operations to ensure that smoothing is ok    - change in max/min operations to ensure that smoothing is ok
338    - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)    - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
339    - always use diffKrNrT as background profile (i.e. never use diffKr field)    - always use diffKrNrT as background profile (i.e. never use diffKr field)
# Line 258  o tools/build_options: Line 584  o tools/build_options:
584      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
585  o pkg/ecco  o pkg/ecco
586    - allow user defined cost function contributions    - allow user defined cost function contributions
587          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
588          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
589    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
590        the two options are complementary.        the two options are complementary.
591  o pkg/smooth  o pkg/smooth

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