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revision 1.1287 by mlosch, Mon Aug 2 10:34:13 2010 UTC revision 1.1352 by gforget, Fri Dec 17 22:00:37 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.seaice experiment
8        that uses pkg/seaice rather than pkg/thsice.
9    checkpoint62p (2010/12/17)
10    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
11        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
12    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
13        allow for use of multim. advection in seaice adjoint.
14    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
15      - first attempt to close budgets by taking into account the freshwater
16        flux implied by the sublimation of snow and ice. So far only the
17        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
18        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
19    o eesupp/src:
20      new S/R with new option (NML_EXTENDED_F77) to change array specification
21      from F95 standard to commonly accepted extended F77 form.
22      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
23      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
24      for less tolerant f77 compiler (e.g., pgf77, g77).
25    o globalFiles:
26      commented out in parameter file "data" since it's not safe with MPI
27      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
28      in this case); no longer commented out in restart test (tst_2+2).
29    o add adTapeDir to specify a special directory where adjoint tapes are
30      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
31      and cannot be used together with mdsioLocalDir.
32    o nesting pkgs:
33      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
34      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
35      - add parameter files + utils dir + output from short run on beagle.
36    o pkg/seaice:
37        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
38    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
39      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
40    
41    checkpoint62o (2010/11/25)
42    o pkg/exf:
43      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
44    o pkg/seaice:
45      - seaice_ocean_stress: split a loop for better vectorization of the
46        adjoint code
47      - seaice_growth.F: fix bug in conservation of freshwater connected to
48        capping of heff, put contribution into d_HEFFbyNEG
49      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
50        by something more sensible (parameters that are what their name implies)
51      - change some defaults, so that by default exf-parameters are used for
52        things like rhoAir, cpAir,latent/sensible heat parameters, in order
53        to reproduce the old results, many data.seaice now contain funny values
54        for cpAir and latent heat of sublimation
55    o packages_readparms.F: move exf_readparms up in line so that
56        exf-parameters are visible for other packages (e.g. seaice)
57    o debugMode & debugLevel=2:
58      - differentiate between debugMode & debugLevel=2:
59        debugMode: controls printing of debug messages (sequence of S/R calls).
60        debugLevel: controls printing of algorithm intermediate results and stats.
61      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
62        => allows to print debug-stats without all sequence of call messages.
63      - switch control of debug print from debugLevel to debugMode in many S/R.
64    o pkg/obcs (obcs-sponge):
65        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
66        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
67    o pkg/generic_advdiff:
68      - record overlap minimum size for each advection scheme;
69      - refine criteria on overlap minimum size;
70      - check and stop (in gad_check) if overlap size is too small.
71    o pkg/obcs:
72      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
73        once, in ptracers_implicit.F)
74      - with seaice: remove test on empty file name in obcs_apply_seaice (always
75        apply OB values when tile has OB)
76    o model/src, coriolis setting:
77      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
78        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
79        files (selectCoriMap=3) with any grid.
80      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
81    o pkg/seaice/seaice_growth.F:
82        a few cosmetic changes that reduce the number of lines of code
83    o pkg/obcs: add boundary conditions following Stevens (1990)
84      - the code follows old MOM/NAOSIM code
85      - so far it is only implemented for the eastern and western boundaries
86        and NOT for pTracers
87    o pkg/rbcs:
88      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
89        beginning of the first rbcs forcing period.
90      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
91        offline package, i.e., one file per time, labeled by iteration number;
92        deltaTrbcs sets the timestep with which the data was generated;
93        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
94      - rbcsForcingCycle=0 makes forcing non-cyclic.
95      - make arithmetic safe for negative times and odd forcing periods.
96    
97    checkpoint62n (2010/11/09)
98    o pkg/seaice:
99        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
100    o pkg/obcs:
101       New S/R to copy tracer value from the OB location to narrow band region
102        (width = same as overlap) beyond the OB: preserve OB value (needed for
103        high-order scheme) which were overwritten by EXCH call if in overlap
104        region. Applied to theta, salt, ptracer and advected seaice variables.
105       With seaice: use maskInC in similar way as in gad_advection.F,
106        in seaice_advection.F and advect.F.
107       Update output of experiment seaice_obcs and change exp4 to test OBCS with
108        4th order Adv.Scheme. for pasive salt and ptracer.
109    o tools/genmake2:
110      - when looking for an optfile (not specified), only search for Fortran compiler
111        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
112      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
113        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
114      - set default for CPP to "cpp -traditional -P" (was the case without specifying
115        an optfile, but otherwise default was just "cpp".
116      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
117      - when "CC" is not set in the optfile, look for possible C compiler
118        (instead of just setting CC=cc)
119      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
120        => add a ".F" to ".o" rule for source files with no "#include" (such as
121           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
122      - move gfortran before g77 in list of possible Fortran compiler (consistent
123        with reference compiler switch from g77 to gfortran)
124    o pkg/seaice:
125      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
126        seaice_check that stops the model, when the CPP flag is used.
127      o seaice_growth.F: make capping of ice volume conserving by returning the
128        capped ice as freshwater to EmPmR. This does not change the verification
129        experiments but will change runs where the capping is acutally active
130    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
131      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
132         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
133         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
134    o tools/genmake2:
135      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
136      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
137      - clean previous genmake log files before anything else.
138      - change Makefile to remove testreport log files (*.tr_log) and genmake log
139        files only with "CLEAN" target (instead of "Clean");
140    o pkg/generic_advdiff:
141      Change OBCS in multiDim advection (gad_advection.F):
142       Use maskInC to prevent intermediate update of tracer-field in OB regions,
143       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
144       which were applying future time-step OB values.
145      This way, all explicit calculations use current-time-step OB values
146       (simpler and more consistent).
147      Affects results when set-up uses time-varying OBC and multi-dim advection;
148       update output of experiment seaice_obcs.
149    o pkg/seaice:
150      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
151       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
152         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
153      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
154       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
155       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
156    o pkg aim (2010/10/26):
157      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
158        formulation with obliquity, eccentricity, ... as run-time parameters,
159      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
160        upward shortwave radition at the surface (all-sky and clear-sky).
161    o pkg/obcs:
162      - writing sections with globalFiles=T does not work: switch to tiled-files
163        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
164      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
165      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
166    
167    checkpoint62m (2010/10/21)
168    o pkg/seaice: vectorize seaice_solve4temp.F
169      - move iterations loops outside of i/j-loops
170      - requires 2D arrays for TB and effConduct
171      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
172        modified in this routine
173      - a little bit of clean up, adjusting indentation, etc.
174      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
175        performance and '**TWO' by '**2' (because TWO is a float),
176        replaced ONE, ZERO
177    o eesupp/src:
178       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
179    o pkg/seaice/seaice_growth.F
180      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
181      merging process. The merged routine has two branches, and one activates the 'evolution'
182      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
183      In summary, here is what the '10/10 revision' did consist of
184        part 1: seaice_growth.F revisions 1.71 to 1.75
185          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
186            The emphasis here was on improving readability (e.g. by trying to use meaningful
187            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
188        part 1.5:
189          - revising the lab_sea experiment to make it a more useful (i.e. stable
190            and representative of an actual model run). This was done by generating a
191            (winter) pickup to start from, switching back the main experiment dynamic
192            solver from evp to lsr, having one of the experiments use the free drift solution.
193        part 2: seaice_growth.F revisions 1.76 to 1.85
194          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
195          - Sorting out the various fields units and sign (set early on and reset at the end)
196            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
197            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
198          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
199            and simplifying logical expressions to further improve readibility.
200        part 3: seaice_growth.F revisions 1.86 to 1.89
201          - Re-organize the blocks of code more logically.
202          - Merging the '_if.F' pieces that add something new.
203    o pkg/thsice:
204      - vectorize thsice_solve4temp and thsice_get_exf.
205        Problem: thsice_solve4temp has an unvectorizable statement that
206        might also be problematic for TAF
207      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
208        does not change the verifcation experiment, but will change all
209        experiments that have this flag undefined (not tested in verification);
210        a little reorganization to save a few 2D fields and recomputations
211      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
212      - 2nd step:  fix some store dirs
213        o seems to work somewhat, i.e. using ifort but not g77
214        o likely cause are incomplete init. or recomputation
215        o start verification/global_ocean.cs32x15/input_ad.thsice
216    o pkg/obcs: add support for exch2
217      - the position of the boundary and prescribed values are specified using
218        a global domain with exch2 facets stacked
219        - in x for N,S boundaries (like W2_mapIO=-1)
220        - in y for E,W boundaries (so E,W boundaries do not overlap)
221    o pkg/mdsio: add support for writing global sections with exch2
222        file layout is as for obcs described above:
223        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
224        - for y-z sections, facets are stacked in y
225    o pkg/thsice:
226       - change a few routines for better vectorization: thsice_albedo.F,
227         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
228         not affected, but in particular the latter routine has changed
229         dramatically (not necessarily easier to read now).
230       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
231       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
232    o verification/lab_sea:
233      - overhaul of the forward model experiments. The main motivation
234        for this revision is that lab_sea has proven quite fragile (when
235        changing the sea-ice code, and switching platforms) to a point
236        when failures were very hard to attribute to specific code problems.
237      - the suspected reason for this fragility is noise amplification by evp so,
238        to start with, we decided to replace evp with lsr in the main experiment.
239      - the input.lsr experiment thus became obsolete and was removed.
240      - it was replaced with the input.fd experiment that uses an
241        analytical "free drift" solution as the ice velocity field.
242      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
243        will hopefully allow us to discriminate problems due to dynamic solvers
244        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
245        us to test additional options, along with the salt plume package.
246      - Finally a pickup was generated (at the end of a one year run) to
247        make the tests more representative of an actual model run. Previously
248        the tests starting point was a 1m thickness of ice everywhere.
249    o pkg/seaice:
250      - introducing S\R seaice_freedrift.F that compute the
251        analytical solution to an approximate ice momentum
252        equation (i.e. the simple stress/coriolis balance).
253      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
254        of the free drift velocity field, and enable its use.
255        To actually use the free drift solution as the model ice
256        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
257    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
258    
259    checkpoint62l (2010/10/04)
260    o pkg/seaice:
261      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
262      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
263       version (with USE_ORIGINAL_SBI undef);
264    o add hooks for new packages OASIS, the package will follow
265      (hooks exclude the seaice pkg for now)
266    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
267      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
268      rather than mdsio_readvector.F/mdsio_writevector.F, within
269      adread_adwrite.F to read/write adjoint-related tapes to disk.
270    o eesupp and pkg/mdsio: ALLOW_WHIO
271      Option to write/read 2D fields to files including tiles halos.
272      The main purpose is for adjoint related "tape I/O".
273      The secondary purpose is for debugging phases.
274      A word on those rather specifically intended purposes.
275      The code was meant to be stripped down to the bare minimum.
276      Typically, there is a unique and basic mapping to the global
277      buffer (tile by tile, then proc by proc, then level by level), and
278      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
279      meant to generate user friendly outputs of various shapes and forms.
280      Rather it is intended, for the knowledgeabale developers,
281      to be largely independent of the many mdsio options, to allow
282      outputs of tiles+halos in debugging phases and in adjoint runs,
283      and to allow some flexibility in tuning (adoint) I/O depending on each
284      file system behavior. With regard to tuning, most of the potential knobs
285      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
286      to specify directories, to specify the typical size of I/O calls, etc.)
287      are not yet included, and will be added if they prove useful.
288    o pkg/seaice:
289       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
290    o pkg/seaice:
291       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
292       code (seaice_budget_ice_if.F) which enable to recover old standard
293       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
294       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
295    o model/src (rStar):
296       use simple average (not area weighted) of rStarFac at U,V point when using
297       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
298       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
299    
300    checkpoint62k (2010/09/17)
301    o adjoint
302       * changed verification/global_ocean.cs32x15 ; adjoint now tests
303         Adams-Bashforth 3 + NLFS + RSTAR
304       * some more modifs required for ECCO-GODAE v4
305    o pkg/seaice
306       add SEAICE_AGE_VOL option to use volume instead of area for
307       integrating SEAICE_AGE
308    o model/src:
309       first check-in of sigma & hybrid-sigma coordinate code ; also includes
310       non-linear free-surface parts ; but pressure-gradient not yet coded.
311    o pkg/ptracers:
312       option for ptracer to convert Salt Relax into additional EmP.
313        tested in exp. global_ocean.90x40x15.dwnslp (update output)
314    
315    checkpoint62j (2010/08/25)
316    o pkg/ggl90:
317       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
318    o pkg/dic: car_flux.F, phos_flux.F
319      - reduce number of exp-calls in order to improve performance
320      - clean up a little (replace fields by their macros, etc., fix
321        typo in CPP-flag)
322    o pkg/ggl90: minor changes
323      - GGL90diffKrS was removed --> always use GGL90diffKr
324      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
325      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
326        (commented out for now)
327      - change in max/min operations to ensure that smoothing is ok
328      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
329      - always use diffKrNrT as background profile (i.e. never use diffKr field)
330    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
331  o pkg/dic:  o pkg/dic:
332      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
333        vectorization
334    - small bug fix in insol for the unlikely case of a cartesian grid    - small bug fix in insol for the unlikely case of a cartesian grid
335    - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F    - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
336      + now vectorize, which also removes adjoint recomputations;      + now vectorize, which also removes adjoint recomputations;
337      + replace integer maksp1 by _RL maskp1      + replace integer maksp1 by _RL maskp1
338        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
339    
340  checkpoint62i (2010/07/21)  checkpoint62i (2010/07/21)
341  o pkg/flt:  o pkg/flt:
# Line 247  o tools/build_options: Line 574  o tools/build_options:
574      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
575  o pkg/ecco  o pkg/ecco
576    - allow user defined cost function contributions    - allow user defined cost function contributions
577          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
578          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
579    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
580        the two options are complementary.        the two options are complementary.
581  o pkg/smooth  o pkg/smooth

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