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revision 1.369 by jmc, Sun Oct 17 23:29:14 2004 UTC revision 1.486 by jmc, Sun May 15 04:00:56 2005 UTC
# Line 1  Line 1 
1  $Header$  $Header$
2    $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
8      and rename it: DIFFERENT_MULTIPLE
9    
10    checkpoint57h_post
11    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
12    o pkg/diagnostics: change output frequency, now in seconds (instead
13      of Nb of iterations). This requires to change data.diagnostics.
14    checkpoint57h_pre
15    
16    o in mnc, let the user create the output dir if both mnc_outdir_date
17      and mnc_outdir_num are false
18    o add fflags() to pkg/diagnostics which allows one to specify, on a
19      per-file basis, the file precision [default behavior is unchanged]
20    o added diagnostics to pkg/kpp, including computation of mixed layer
21      depth based on a temperature/density criterion
22    o updated verification/natl_box to test the new pkg/kpp diagnostics
23    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
24    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
25    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
26      not mnc -- this mistake was found by JMC and is now corrected
27    
28    checkpoint57g_post
29    o add Adams-Bashforth 3rd Order time stepping:
30      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
31      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
32    checkpoint57g_pre
33    
34    o make lambda[Theta,Salt]ClimRelax spatially varying
35      (default remains spatially uniform constant based on tau)
36    o added new control variables
37      * init. uVel, vVel, etanN
38      * lambda[Theta,Salt]ClimRelax
39    o separate masks used for ctrl_pack/unpack 'from write_grid' output
40      (suggested by G. Forget)
41    
42    checkpoint57f_post
43    o add parameter "baseTime" = model base time = time at iteration zero
44      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
45      account for baseTime shift
46    o move Coriolis arrays from PARAMS.h to GRID.h
47    checkpoint57f_pre
48    
49    o mnc-ifying the seaice package
50    o introduced an alternative length scale calculation for use in the limiting
51      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
52    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
53    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
54      as well as grad(vort3).  Made it compatible with both approximate form
55      for the cubed sphere and full form of these gradients.  Added flag
56      useFullLeith to select between approximate and full form.  
57    o add "d0" in getcon.F to reduce differences between compilers/platforms
58      update output.txt of exp. fizhi-gridalt-hs
59    o change port_rand funtion to allow to set the seed.
60    o fix obscure MNC bug involving conversion between reals and integers
61      - it caused no problems with certain (eg. gcc, ifc) compilers but the
62        new version is now more standards-compliant
63    o adjoint-related modifications
64      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
65      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
66      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
67    
68    checkpoint57e_post
69    o Adding eddy stress controls a la Ferreira et al.
70    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
71    
72    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
73      update output.txt of exp. fizhi-gridalt-hs
74    o add more "Z" dimensions and associated coordinate vars to MNC
75    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
76    o parameter calendarDumps: when set, approximate months (30-31 days) and years
77      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
78      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
79      months and years.  Requires pkg/cal.
80    o diagnostics: add pickup functionality
81      - off by default for backwards compatibility
82      - current version only uses MDSIO -- MNC will be added
83    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
84    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
85    
86    checkpoint57d_post
87    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
88    o modify verification/ideal_2D_oce so that it tests the creation of mnc
89      output from the diagnostics package
90    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
91    o make genmake2 more portable by using ".$FS" instead of ".f" for more
92      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
93    o add coordinate variables to the MNC output from the diagnostics package
94    o change MNC-flags default value: true when useMNC=TRUE
95    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
96      the ability (off by default) to read the grid information using MNC
97    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
98    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
99    o do snap-shot diagnostics at the middle of the time-interval (instead of
100      at the end).
101    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
102      new test for AIM with thSIce + slab-ocean
103    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
104    o move state variable diagnostics to the beginning of the time step ;
105      (note: still needs some work specially for snap-shot diagnostics)
106      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
107    
108    checkpoint57c_post
109    o Change testing option (-ieee) to get closer agreement between g77 & ifort
110    o generate new output.txt files on faulks with g77 & the new -ieee option
111    checkpoint57c_pre
112    
113    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
114      update output.txt of exp. global_ocean.90x40x15
115    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
116      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
117    o add saltFlux(+File) forcing capability with periodicExternalForcing
118    o allow to use pkg diagnostics for GM-Redi & ThSIce output
119    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
120    o improvements for the MNC output from DIAGNOSTICS:
121      - correct handling of the unlimitied dimension
122      - all dims now have associated coordinate variables
123      - variables located at U, V, and Corner ("Z") points are now written
124        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
125        *all* data points are output
126    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
127    o added pkg/seaice/seaice_monitor.F
128    o mdsio_readfield.F can now read files visible only to master MPI process.
129    o pkg/seaice: some test code for ice-modified ocean stress
130    o exf_getffields interpolation defaults to bilinear for all scalar forcing
131      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
132      spurious negative numbers for precipitation and humidity.  Will cause
133      some small numerical differences for integrations using pkg/exf/exf_interp.F.
134    o pkg/ctrl/
135      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
136        May be enabled via doPackDiag
137      *  introduce z-scaling of
138         + gradient (doZscalePack) and
139         + control (doZscaleUnpack)
140    o pkg/mdsio/
141      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
142      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
143    
144    checkpoint57b_post
145    o simplify options in diagnostics_fill arguments (remove weird combinations)
146    o fix MNC coordinate variables so that they now contain per-face index
147      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
148      general, EXCH2 grids are only aligned to a "local" coordinate system
149    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
150    o Implement instantaneous output within pkg diagnostics:
151      setting a negative frequency in data.diagnostics produces
152     "snap-shot" output (as opposed to time-average if freq > 0)
153    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
154      NOTE: change ptracer diagnostics name: use 2 characters to work with
155            more than 9 tracers. Add also diagnostics of advect & diffus flux.
156    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
157      becomes the coordinate variable for the 'T' dimension
158    o add CF-style coordinate variables to MNC
159      - just a first cut:  numbers are meaningless on the cubesphere and
160        missing along the T axis but otherwise it works!
161    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
162    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
163    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
164      this is based directly on what the model compute, so that the content of
165      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
166    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
167    o clean up build options files for SunOS, in particular
168      - remove -traditional from xmakedepend
169      - change -xarch=v9 to -xarch=native for f77
170      - restore use of make (not gmake)
171      - add CC=gcc if using g77
172    o changes per discussion of AM, JMC, & EH3 today:
173      - move redundant "grid" variables out of "state" -- in preparation of
174        creating proper CF-style coordinate variables and in recognition
175        that any/all grid variables can be easily copied (eg. w/NCO) from
176        the grid files into any of the other NetCDF files
177      - *always* output grid variables with MDSIO (this will eventually be
178        changed)
179      - output MNC grid file if useMNC is true
180    o every instance of _END_MASTER() has been found and replaced with
181      _END_MASTER( myThid ) in order to satisfy certain picky Sun
182      preprocessors
183    o re-arrange diagnostics pkg initialisation:
184     - allow each package to extend the available diagnostics list
185     - add some checking and fix small problems (multi-threaded, ...)
186     - new S/R diagnostics_fill (replace fill_diagnostics):
187       look through the short list of active diag. (instead of the long list)
188       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
189    
190    checkpoint57a_post
191    o this set of changes restores TAMC compatibility
192      tested for global_ocean.90x40x15 adjoint on trough
193      (what a pain)
194    
195    checkpoint57a_pre
196    o some modifs in tools/build_options for sunos
197    o call ctrl_pack for ctrl at end for optimcycle=0
198    
199    checkpoint57
200    o add horizontal bi-harmonic viscosity for vertical velocity
201      - new parameter viscA4W (defaults to viscA4)
202      - affects only non-hydrostatic code
203      - to be done: no-slip lateral boundary conditions
204    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
205    o implement Implicit Vertical advection for pTracers
206    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
207      (implemented also for implicit vertical diffusion & advection)
208    o OBCS: extend application of tracer open boundary conditions
209      to a strip beyond the boundary of width Olx/Oly
210    o add call monitor to TAF set of required calls (flow directives)
211      and include in natl_box_adjoint
212    o untangle a few ifdefs related to cost, ctrl, autodiff
213      untangel a few ALLOW_ECCO_OPTIMIZATION
214    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
215      (theta2, salt2 in ecco_cost_weights)
216    
217    checkpoint56c_post
218    o OBCS as control variables
219      - update ctrl_ad_diff.list, obcs_ad_diff.list
220      - remove balance of obcs controls from default
221      - fix index bug nobcs in ctrl_init
222      - fix dummy fields filen in ctrl_pack
223      - add dummy weights for obcs
224    o lsopt: comment out fort.94 output
225    o optim:
226      - remove unnecessary header files
227      - adjusted namelists
228      - add xerbla.F to Makefile
229    o exf:
230      - multiple modifications of exf_check_range
231      - unit change in exf_init_runoff from [m/year] to [m/s]
232    o mdsio:
233      - i/o-vector change debugLevel from debLevA to debLevB
234    
235    checkpoint56b_post
236    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
237      is called from DO_THE_MODEL_IO
238      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
239      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
240      - clean up PTRACERS_WRITE_TIMEAVE a little
241    o add another verification experiment that tests both the cfc-pkg and
242      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
243      reactive tendencies treated inline with regular timestepping
244    o testreport previously did a lousy job of comparing small numbers, so
245      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
246      implemented in the little c-progam tmp_cmpnum.c which is embedded in
247      testreport.
248    o ptracers_monitor: bug fix for MPI
249    
250    checkpoint56a_post
251    o GCHEM: finish reorganizating the package
252      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
253        (introduces another 3D-array for each passive tracer, but only if
254        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
255        gchemTendency is not needed because the timestep is done separately)
256      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
257      - GCHEM is now---more or less cleanly---separate from PTRACERS
258      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
259        so clear to me how that should be done in a general way.
260    o CFC: improve formatting of output in CFC_ATMOS
261    o PTRACERS:
262      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
263        that ALL experiments with ptracers enable can be checked. This makes
264        GCHEM_MONITOR obsolete.
265      - include a runtime parameter PTRACERS_monitorFreq that defaults to
266        monitorFreq
267      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
268    o add PTRACERS (PTR0[1-5]) to testreport output
269    o exf_check_range:
270      * default changed to .TRUE.
271      * will check values for niter0 if debLevA, every timestep if debLevB
272      * STOP in exf_check_range if 'out of range'
273      * range chosen generous to allow for potential extema
274      TBD: a version with stricter range
275           permitted range would be runtime parameters
276    o GMredi:
277      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
278      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
279      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
280    o GCHEM:
281      - move call to GCHEM_FORCING_SEP, so that it is now called before
282        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
283      - introduced a useGCHEM runtime flag and applied it everywhere.
284      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
285        this flag is now only visible within GCHEM-pkg routines.
286      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
287        be replaced by a 3D array that is computed before thermodynamics; for
288        this, the tracer ID iTracer had to be included into the parameter list
289        of ptracers_forcing
290      - set up forward_step to call gchem_forcing, that will replace
291        gchem_forcing_int in ptracers_forcing
292      - cleaning up
293    o small cleaning of exch2: remove files that are also in eesupp/src
294    
295    checkpoint56
296    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
297    o mnc: cleanup "full" files--fixes out-of-memory problem
298    o ECCO-GODAE
299      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
300      * fully merged and updated from SIO code
301        windstress sign change affects
302        - exf_inscal_[u/v]stress
303        - sign of xx_tau[u/v] adjustments
304        - signs in cost_scat
305      * ctrl_get_gen: avoid update of tau[u/v] for first few days
306      * natl_box_adjoint updated and compressed
307      * 2-level checkpoint switch added
308        (tested in EXP. 1 of natl_box_adjoint)
309      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
310    o SVD
311      * first complete, non-hacked version for SVD calculations
312      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
313        performed via direct access files admtlm_vector.it????
314        (via ctrl_[un]pack)
315      * optimcycle is used for ARPACK iteration counter
316        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
317      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
318        and add linear transforms where necessary
319      * controls are initial/final SST, SSS (can be extended; need to check
320        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
321    o mdsio: filename info to both stderr, stdout
322    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
323      from sign change
324    
325    checkpoint55j_post
326    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
327      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
328    o add consistent build directories and .cvsignore files to verification
329    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
330    o make all subroutines 30 or less characters in length for certain older
331      compilers to work (a thorough search only turns up two routines in
332      pkg/ptracers)
333    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
334      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
335    
336    checkpoint55i_post
337    o change arrays for total vertical diffusivity (2.D if explicit,
338      3.D if implicit) ; each ptracer uses its own background value.
339    o added mnc/NetCDF output capability to ocn_compon_interf
340      - added bits to verification/cpl_aim+ocn so that it can run on
341        ITRDA and other clusters without the mpirun "-wd" option
342    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
343      configuration
344    o give MNC the ability to create additional files rather than
345      exceeding a specified file size limit "MNC_MAX_FILESIZE"
346      - the default is just less than 2GB which is a practical limit
347        on many systems
348    o Compute the non-local term using either KPP vertical diffusivity (=default)
349       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
350    
351    checkpoint55h_post
352    o add verification test "vermix"
353    o remove all the *_ioinc flags and replace with the single global
354      outputTypesInclusive flag
355  o allow to set a vertical profile of vertical diffusivity for T & S  o allow to set a vertical profile of vertical diffusivity for T & S
356    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
357    o useMNC moved from data.mnc to data.pkg
358    
359  checkpoint55g_post  checkpoint55g_post
360  o Renaming carbon AD experiments to comply with testreport conventions  o Renaming carbon AD experiments to comply with testreport conventions

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