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revision 1.359 by heimbach, Mon Sep 27 14:56:42 2004 UTC revision 1.461 by heimbach, Mon Feb 28 17:47:35 2005 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint57e_post
7    o Adding eddy stress controls a la Ferreira et al.
8    checkpoint57e_pre
9    
10    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
11      update output.txt of exp. fizhi-gridalt-hs
12    o add more "Z" dimensions and associated coordinate vars to MNC
13    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
14    o parameter calendarDumps: when set, approximate months (30-31 days) and years
15      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
16      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
17      months and years.  Requires pkg/cal.
18    o diagnostics: add pickup functionality
19      - off by default for backwards compatibility
20      - current version only uses MDSIO -- MNC will be added
21    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
22    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
23    
24    checkpoint57d_post
25    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
26    o modify verification/ideal_2D_oce so that it tests the creation of mnc
27      output from the diagnostics package
28    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
29    o make genmake2 more portable by using ".$FS" instead of ".f" for more
30      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
31    o add coordinate variables to the MNC output from the diagnostics package
32    o change MNC-flags default value: true when useMNC=TRUE
33    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
34      the ability (off by default) to read the grid information using MNC
35    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
36    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
37    o do snap-shot diagnostics at the middle of the time-interval (instead of
38      at the end).
39    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
40      new test for AIM with thSIce + slab-ocean
41    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
42    o move state variable diagnostics to the beginning of the time step ;
43      (note: still needs some work specially for snap-shot diagnostics)
44      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
45    
46    checkpoint57c_post
47    o Change testing option (-ieee) to get closer agreement between g77 & ifort
48    o generate new output.txt files on faulks with g77 & the new -ieee option
49    checkpoint57c_pre
50    
51    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
52      update output.txt of exp. global_ocean.90x40x15
53    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
54      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
55    o add saltFlux(+File) forcing capability with periodicExternalForcing
56    o allow to use pkg diagnostics for GM-Redi & ThSIce output
57    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
58    o improvements for the MNC output from DIAGNOSTICS:
59      - correct handling of the unlimitied dimension
60      - all dims now have associated coordinate variables
61      - variables located at U, V, and Corner ("Z") points are now written
62        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
63        *all* data points are output
64    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
65    o added pkg/seaice/seaice_monitor.F
66    o mdsio_readfield.F can now read files visible only to master MPI process.
67    o pkg/seaice: some test code for ice-modified ocean stress
68    o exf_getffields interpolation defaults to bilinear for all scalar forcing
69      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
70      spurious negative numbers for precipitation and humidity.  Will cause
71      some small numerical differences for integrations using pkg/exf/exf_interp.F.
72    o pkg/ctrl/
73      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
74        May be enabled via doPackDiag
75      *  introduce z-scaling of
76         + gradient (doZscalePack) and
77         + control (doZscaleUnpack)
78    o pkg/mdsio/
79      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
80      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
81    
82    checkpoint57b_post
83    o simplify options in diagnostics_fill arguments (remove weird combinations)
84    o fix MNC coordinate variables so that they now contain per-face index
85      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
86      general, EXCH2 grids are only aligned to a "local" coordinate system
87    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
88    o Implement instantaneous output within pkg diagnostics:
89      setting a negative frequency in data.diagnostics produces
90     "snap-shot" output (as opposed to time-average if freq > 0)
91    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
92      NOTE: change ptracer diagnostics name: use 2 characters to work with
93            more than 9 tracers. Add also diagnostics of advect & diffus flux.
94    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
95      becomes the coordinate variable for the 'T' dimension
96    o add CF-style coordinate variables to MNC
97      - just a first cut:  numbers are meaningless on the cubesphere and
98        missing along the T axis but otherwise it works!
99    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
100    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
101    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
102      this is based directly on what the model compute, so that the content of
103      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
104    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
105    o clean up build options files for SunOS, in particular
106      - remove -traditional from xmakedepend
107      - change -xarch=v9 to -xarch=native for f77
108      - restore use of make (not gmake)
109      - add CC=gcc if using g77
110    o changes per discussion of AM, JMC, & EH3 today:
111      - move redundant "grid" variables out of "state" -- in preparation of
112        creating proper CF-style coordinate variables and in recognition
113        that any/all grid variables can be easily copied (eg. w/NCO) from
114        the grid files into any of the other NetCDF files
115      - *always* output grid variables with MDSIO (this will eventually be
116        changed)
117      - output MNC grid file if useMNC is true
118    o every instance of _END_MASTER() has been found and replaced with
119      _END_MASTER( myThid ) in order to satisfy certain picky Sun
120      preprocessors
121    o re-arrange diagnostics pkg initialisation:
122     - allow each package to extend the available diagnostics list
123     - add some checking and fix small problems (multi-threaded, ...)
124     - new S/R diagnostics_fill (replace fill_diagnostics):
125       look through the short list of active diag. (instead of the long list)
126       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
127    
128    checkpoint57a_post
129    o this set of changes restores TAMC compatibility
130      tested for global_ocean.90x40x15 adjoint on trough
131      (what a pain)
132    
133    checkpoint57a_pre
134    o some modifs in tools/build_options for sunos
135    o call ctrl_pack for ctrl at end for optimcycle=0
136    
137    checkpoint57
138    o add horizontal bi-harmonic viscosity for vertical velocity
139      - new parameter viscA4W (defaults to viscA4)
140      - affects only non-hydrostatic code
141      - to be done: no-slip lateral boundary conditions
142    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
143    o implement Implicit Vertical advection for pTracers
144    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
145      (implemented also for implicit vertical diffusion & advection)
146    o OBCS: extend application of tracer open boundary conditions
147      to a strip beyond the boundary of width Olx/Oly
148    o add call monitor to TAF set of required calls (flow directives)
149      and include in natl_box_adjoint
150    o untangle a few ifdefs related to cost, ctrl, autodiff
151      untangel a few ALLOW_ECCO_OPTIMIZATION
152    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
153      (theta2, salt2 in ecco_cost_weights)
154    
155    checkpoint56c_post
156    o OBCS as control variables
157      - update ctrl_ad_diff.list, obcs_ad_diff.list
158      - remove balance of obcs controls from default
159      - fix index bug nobcs in ctrl_init
160      - fix dummy fields filen in ctrl_pack
161      - add dummy weights for obcs
162    o lsopt: comment out fort.94 output
163    o optim:
164      - remove unnecessary header files
165      - adjusted namelists
166      - add xerbla.F to Makefile
167    o exf:
168      - multiple modifications of exf_check_range
169      - unit change in exf_init_runoff from [m/year] to [m/s]
170    o mdsio:
171      - i/o-vector change debugLevel from debLevA to debLevB
172    
173    checkpoint56b_post
174    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
175      is called from DO_THE_MODEL_IO
176      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
177      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
178      - clean up PTRACERS_WRITE_TIMEAVE a little
179    o add another verification experiment that tests both the cfc-pkg and
180      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
181      reactive tendencies treated inline with regular timestepping
182    o testreport previously did a lousy job of comparing small numbers, so
183      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
184      implemented in the little c-progam tmp_cmpnum.c which is embedded in
185      testreport.
186    o ptracers_monitor: bug fix for MPI
187    
188    checkpoint56a_post
189    o GCHEM: finish reorganizating the package
190      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
191        (introduces another 3D-array for each passive tracer, but only if
192        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
193        gchemTendency is not needed because the timestep is done separately)
194      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
195      - GCHEM is now---more or less cleanly---separate from PTRACERS
196      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
197        so clear to me how that should be done in a general way.
198    o CFC: improve formatting of output in CFC_ATMOS
199    o PTRACERS:
200      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
201        that ALL experiments with ptracers enable can be checked. This makes
202        GCHEM_MONITOR obsolete.
203      - include a runtime parameter PTRACERS_monitorFreq that defaults to
204        monitorFreq
205      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
206    o add PTRACERS (PTR0[1-5]) to testreport output
207    o exf_check_range:
208      * default changed to .TRUE.
209      * will check values for niter0 if debLevA, every timestep if debLevB
210      * STOP in exf_check_range if 'out of range'
211      * range chosen generous to allow for potential extema
212      TBD: a version with stricter range
213           permitted range would be runtime parameters
214    o GMredi:
215      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
216      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
217      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
218    o GCHEM:
219      - move call to GCHEM_FORCING_SEP, so that it is now called before
220        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
221      - introduced a useGCHEM runtime flag and applied it everywhere.
222      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
223        this flag is now only visible within GCHEM-pkg routines.
224      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
225        be replaced by a 3D array that is computed before thermodynamics; for
226        this, the tracer ID iTracer had to be included into the parameter list
227        of ptracers_forcing
228      - set up forward_step to call gchem_forcing, that will replace
229        gchem_forcing_int in ptracers_forcing
230      - cleaning up
231    o small cleaning of exch2: remove files that are also in eesupp/src
232    
233    checkpoint56
234    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
235    o mnc: cleanup "full" files--fixes out-of-memory problem
236    o ECCO-GODAE
237      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
238      * fully merged and updated from SIO code
239        windstress sign change affects
240        - exf_inscal_[u/v]stress
241        - sign of xx_tau[u/v] adjustments
242        - signs in cost_scat
243      * ctrl_get_gen: avoid update of tau[u/v] for first few days
244      * natl_box_adjoint updated and compressed
245      * 2-level checkpoint switch added
246        (tested in EXP. 1 of natl_box_adjoint)
247      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
248    o SVD
249      * first complete, non-hacked version for SVD calculations
250      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
251        performed via direct access files admtlm_vector.it????
252        (via ctrl_[un]pack)
253      * optimcycle is used for ARPACK iteration counter
254        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
255      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
256        and add linear transforms where necessary
257      * controls are initial/final SST, SSS (can be extended; need to check
258        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
259    o mdsio: filename info to both stderr, stdout
260    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
261      from sign change
262    
263    checkpoint55j_post
264    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
265      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
266    o add consistent build directories and .cvsignore files to verification
267    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
268    o make all subroutines 30 or less characters in length for certain older
269      compilers to work (a thorough search only turns up two routines in
270      pkg/ptracers)
271    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
272      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
273    
274    checkpoint55i_post
275    o change arrays for total vertical diffusivity (2.D if explicit,
276      3.D if implicit) ; each ptracer uses its own background value.
277    o added mnc/NetCDF output capability to ocn_compon_interf
278      - added bits to verification/cpl_aim+ocn so that it can run on
279        ITRDA and other clusters without the mpirun "-wd" option
280    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
281      configuration
282    o give MNC the ability to create additional files rather than
283      exceeding a specified file size limit "MNC_MAX_FILESIZE"
284      - the default is just less than 2GB which is a practical limit
285        on many systems
286    o Compute the non-local term using either KPP vertical diffusivity (=default)
287       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
288    
289    checkpoint55h_post
290    o add verification test "vermix"
291    o remove all the *_ioinc flags and replace with the single global
292      outputTypesInclusive flag
293    o allow to set a vertical profile of vertical diffusivity for T & S
294    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
295    o useMNC moved from data.mnc to data.pkg
296    
297    checkpoint55g_post
298    o Renaming carbon AD experiments to comply with testreport conventions
299    o Updating adjoint of Held-Suarez hs94.1x64x5
300    o Fixing directives for non-ECCO forward_step, after ECCO directives
301      have been fixed to avoid recomp. of do_oceanic_phys
302      Works well for global_ocean.90x40x15,
303      but recomp. issue remains for carbon
304    o Updating adjoint output for natl_box_adjoint after
305      pkg/ecco has been modified (see taga c55d_post)
306    
307    checkpoint55f_post
308    o rename to timeave_init_fixed
309    
310    checkpoint55e_post
311    o some delicate re-shuffle of store directives to avoid one
312      extra call of do_oceanic_physics
313      affects ecco_the_main_loop.F, do_oceanic_physics.F
314      checkpoint_lev1_directives.h
315    o NB: this may break global_ocean adjoint temporarily,
316      but it is clear how to fix it. Will do later, need this now.
317    
318    checkpoint55d_post
319    o ECCO specific cost function terms (up-to-date with 1x1 runs)
320    o ecco_cost_weights is modified to 1x1 runs
321    o modifs to allow observations to be read in as
322      single file or yearly files
323    o enable to read exf forcing fields as either
324      single file or yearly files (flag useExfYearlyFields)
325    checkpoint55d_pre
326    
327    o switch between 2-level and 3-level checkpointing
328    o add ability of MNC to write local and "partial" (eg. 2D slices where
329      the full 3D field is never actually stored) arrays to NetCDF files
330      with the correct (that is, the complete multi-dimensional) set of
331      array indicies
332      - used in mom_vecinv() to write the diagFreq output
333      - tested (demonstrated) in verification/aim.5l_cs
334    o further mnc-ification
335      - add verification/lab_sea to the list with mnc setups
336      - fix undefined mnc v-names in cd_code
337      - add kpp to mnc output (both snapshot and timeave)
338    o non-hydrostatic code
339      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
340        in calc_gw.F
341      - defaults to viscAh
342      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
343        friction or Leith) in non-hydrostatic mode, as long as there is
344        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
345    o pkg/cost
346      extend simple cost functions to treat time mean quantities
347      (T,U,V) via cost_accumulate_state from cost_tile
348  o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to  o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
349      be 2 times larger than the minimum size the advection scheme requires.      be 2 times larger than the minimum size the advection scheme requires.
350      now get a perfect conservation of salt in advect_cs test-exp (updated)      now get a perfect conservation of salt in advect_cs test-exp (updated)
# Line 26  o more obcs stuff Line 368  o more obcs stuff
368    - changed sponge layer relaxation parameter units for days to seconds    - changed sponge layer relaxation parameter units for days to seconds
369    - turned off sponge layer by default    - turned off sponge layer by default
370    - changed argument list of OBCS_CALC to myTime+deltaTclock    - changed argument list of OBCS_CALC to myTime+deltaTclock
371      - fixed about 35 bugs in obcs_external_fields_load
372    
373  checkpoint55c_post  checkpoint55c_post
374  o obcs stuff  o obcs stuff

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