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revision 1.352 by heimbach, Wed Sep 22 21:31:35 2004 UTC revision 1.447 by edhill, Tue Feb 8 20:39:58 2005 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    o add coordinate variables to the MNC output from the diagnostics package
7    o change MNC-flags default value: true when useMNC=TRUE
8    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
9      the ability (off by default) to read the grid information using MNC
10    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
11    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
12    o do snap-shot diagnostics at the middle of the time-interval (instead of
13      at the end).
14    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
15      new test for AIM with thSIce + slab-ocean
16    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
17    o move state variable diagnostics to the beginning of the time step ;
18      (note: still needs some work specially for snap-shot diagnostics)
19      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
20    
21    checkpoint57c_post
22    o Change testing option (-ieee) to get closer agreement between g77 & ifort
23    o generate new output.txt files on faulks with g77 & the new -ieee option
24    checkpoint57c_pre
25    
26    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
27      update output.txt of exp. global_ocean.90x40x15
28    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
29      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
30    o add saltFlux(+File) forcing capability with periodicExternalForcing
31    o allow to use pkg diagnostics for GM-Redi & ThSIce output
32    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
33    o improvements for the MNC output from DIAGNOSTICS:
34      - correct handling of the unlimitied dimension
35      - all dims now have associated coordinate variables
36      - variables located at U, V, and Corner ("Z") points are now written
37        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
38        *all* data points are output
39    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
40    o added pkg/seaice/seaice_monitor.F
41    o mdsio_readfield.F can now read files visible only to master MPI process.
42    o pkg/seaice: some test code for ice-modified ocean stress
43    o exf_getffields interpolation defaults to bilinear for all scalar forcing
44      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
45      spurious negative numbers for precipitation and humidity.  Will cause
46      some small numerical differences for integrations using pkg/exf/exf_interp.F.
47    o pkg/ctrl/
48      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
49        May be enabled via doPackDiag
50      *  introduce z-scaling of
51         + gradient (doZscalePack) and
52         + control (doZscaleUnpack)
53    o pkg/mdsio/
54      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
55      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
56    
57    checkpoint57b_post
58    o simplify options in diagnostics_fill arguments (remove weird combinations)
59    o fix MNC coordinate variables so that they now contain per-face index
60      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
61      general, EXCH2 grids are only aligned to a "local" coordinate system
62    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
63    o Implement instantaneous output within pkg diagnostics:
64      setting a negative frequency in data.diagnostics produces
65     "snap-shot" output (as opposed to time-average if freq > 0)
66    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
67      NOTE: change ptracer diagnostics name: use 2 characters to work with
68            more than 9 tracers. Add also diagnostics of advect & diffus flux.
69    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
70      becomes the coordinate variable for the 'T' dimension
71    o add CF-style coordinate variables to MNC
72      - just a first cut:  numbers are meaningless on the cubesphere and
73        missing along the T axis but otherwise it works!
74    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
75    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
76    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
77      this is based directly on what the model compute, so that the content of
78      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
79    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
80    o clean up build options files for SunOS, in particular
81      - remove -traditional from xmakedepend
82      - change -xarch=v9 to -xarch=native for f77
83      - restore use of make (not gmake)
84      - add CC=gcc if using g77
85    o changes per discussion of AM, JMC, & EH3 today:
86      - move redundant "grid" variables out of "state" -- in preparation of
87        creating proper CF-style coordinate variables and in recognition
88        that any/all grid variables can be easily copied (eg. w/NCO) from
89        the grid files into any of the other NetCDF files
90      - *always* output grid variables with MDSIO (this will eventually be
91        changed)
92      - output MNC grid file if useMNC is true
93    o every instance of _END_MASTER() has been found and replaced with
94      _END_MASTER( myThid ) in order to satisfy certain picky Sun
95      preprocessors
96    o re-arrange diagnostics pkg initialisation:
97     - allow each package to extend the available diagnostics list
98     - add some checking and fix small problems (multi-threaded, ...)
99     - new S/R diagnostics_fill (replace fill_diagnostics):
100       look through the short list of active diag. (instead of the long list)
101       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
102    
103    checkpoint57a_post
104    o this set of changes restores TAMC compatibility
105      tested for global_ocean.90x40x15 adjoint on trough
106      (what a pain)
107    
108    checkpoint57a_pre
109    o some modifs in tools/build_options for sunos
110    o call ctrl_pack for ctrl at end for optimcycle=0
111    
112    checkpoint57
113    o add horizontal bi-harmonic viscosity for vertical velocity
114      - new parameter viscA4W (defaults to viscA4)
115      - affects only non-hydrostatic code
116      - to be done: no-slip lateral boundary conditions
117    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
118    o implement Implicit Vertical advection for pTracers
119    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
120      (implemented also for implicit vertical diffusion & advection)
121    o OBCS: extend application of tracer open boundary conditions
122      to a strip beyond the boundary of width Olx/Oly
123    o add call monitor to TAF set of required calls (flow directives)
124      and include in natl_box_adjoint
125    o untangle a few ifdefs related to cost, ctrl, autodiff
126      untangel a few ALLOW_ECCO_OPTIMIZATION
127    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
128      (theta2, salt2 in ecco_cost_weights)
129    
130    checkpoint56c_post
131    o OBCS as control variables
132      - update ctrl_ad_diff.list, obcs_ad_diff.list
133      - remove balance of obcs controls from default
134      - fix index bug nobcs in ctrl_init
135      - fix dummy fields filen in ctrl_pack
136      - add dummy weights for obcs
137    o lsopt: comment out fort.94 output
138    o optim:
139      - remove unnecessary header files
140      - adjusted namelists
141      - add xerbla.F to Makefile
142    o exf:
143      - multiple modifications of exf_check_range
144      - unit change in exf_init_runoff from [m/year] to [m/s]
145    o mdsio:
146      - i/o-vector change debugLevel from debLevA to debLevB
147    
148    checkpoint56b_post
149    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
150      is called from DO_THE_MODEL_IO
151      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
152      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
153      - clean up PTRACERS_WRITE_TIMEAVE a little
154    o add another verification experiment that tests both the cfc-pkg and
155      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
156      reactive tendencies treated inline with regular timestepping
157    o testreport previously did a lousy job of comparing small numbers, so
158      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
159      implemented in the little c-progam tmp_cmpnum.c which is embedded in
160      testreport.
161    o ptracers_monitor: bug fix for MPI
162    
163    checkpoint56a_post
164    o GCHEM: finish reorganizating the package
165      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
166        (introduces another 3D-array for each passive tracer, but only if
167        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
168        gchemTendency is not needed because the timestep is done separately)
169      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
170      - GCHEM is now---more or less cleanly---separate from PTRACERS
171      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
172        so clear to me how that should be done in a general way.
173    o CFC: improve formatting of output in CFC_ATMOS
174    o PTRACERS:
175      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
176        that ALL experiments with ptracers enable can be checked. This makes
177        GCHEM_MONITOR obsolete.
178      - include a runtime parameter PTRACERS_monitorFreq that defaults to
179        monitorFreq
180      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
181    o add PTRACERS (PTR0[1-5]) to testreport output
182    o exf_check_range:
183      * default changed to .TRUE.
184      * will check values for niter0 if debLevA, every timestep if debLevB
185      * STOP in exf_check_range if 'out of range'
186      * range chosen generous to allow for potential extema
187      TBD: a version with stricter range
188           permitted range would be runtime parameters
189    o GMredi:
190      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
191      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
192      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
193    o GCHEM:
194      - move call to GCHEM_FORCING_SEP, so that it is now called before
195        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
196      - introduced a useGCHEM runtime flag and applied it everywhere.
197      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
198        this flag is now only visible within GCHEM-pkg routines.
199      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
200        be replaced by a 3D array that is computed before thermodynamics; for
201        this, the tracer ID iTracer had to be included into the parameter list
202        of ptracers_forcing
203      - set up forward_step to call gchem_forcing, that will replace
204        gchem_forcing_int in ptracers_forcing
205      - cleaning up
206    o small cleaning of exch2: remove files that are also in eesupp/src
207    
208    checkpoint56
209    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
210    o mnc: cleanup "full" files--fixes out-of-memory problem
211    o ECCO-GODAE
212      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
213      * fully merged and updated from SIO code
214        windstress sign change affects
215        - exf_inscal_[u/v]stress
216        - sign of xx_tau[u/v] adjustments
217        - signs in cost_scat
218      * ctrl_get_gen: avoid update of tau[u/v] for first few days
219      * natl_box_adjoint updated and compressed
220      * 2-level checkpoint switch added
221        (tested in EXP. 1 of natl_box_adjoint)
222      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
223    o SVD
224      * first complete, non-hacked version for SVD calculations
225      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
226        performed via direct access files admtlm_vector.it????
227        (via ctrl_[un]pack)
228      * optimcycle is used for ARPACK iteration counter
229        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
230      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
231        and add linear transforms where necessary
232      * controls are initial/final SST, SSS (can be extended; need to check
233        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
234    o mdsio: filename info to both stderr, stdout
235    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
236      from sign change
237    
238    checkpoint55j_post
239    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
240      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
241    o add consistent build directories and .cvsignore files to verification
242    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
243    o make all subroutines 30 or less characters in length for certain older
244      compilers to work (a thorough search only turns up two routines in
245      pkg/ptracers)
246    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
247      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
248    
249    checkpoint55i_post
250    o change arrays for total vertical diffusivity (2.D if explicit,
251      3.D if implicit) ; each ptracer uses its own background value.
252    o added mnc/NetCDF output capability to ocn_compon_interf
253      - added bits to verification/cpl_aim+ocn so that it can run on
254        ITRDA and other clusters without the mpirun "-wd" option
255    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
256      configuration
257    o give MNC the ability to create additional files rather than
258      exceeding a specified file size limit "MNC_MAX_FILESIZE"
259      - the default is just less than 2GB which is a practical limit
260        on many systems
261    o Compute the non-local term using either KPP vertical diffusivity (=default)
262       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
263    
264    checkpoint55h_post
265    o add verification test "vermix"
266    o remove all the *_ioinc flags and replace with the single global
267      outputTypesInclusive flag
268    o allow to set a vertical profile of vertical diffusivity for T & S
269    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
270    o useMNC moved from data.mnc to data.pkg
271    
272    checkpoint55g_post
273    o Renaming carbon AD experiments to comply with testreport conventions
274    o Updating adjoint of Held-Suarez hs94.1x64x5
275    o Fixing directives for non-ECCO forward_step, after ECCO directives
276      have been fixed to avoid recomp. of do_oceanic_phys
277      Works well for global_ocean.90x40x15,
278      but recomp. issue remains for carbon
279    o Updating adjoint output for natl_box_adjoint after
280      pkg/ecco has been modified (see taga c55d_post)
281    
282    checkpoint55f_post
283    o rename to timeave_init_fixed
284    
285    checkpoint55e_post
286    o some delicate re-shuffle of store directives to avoid one
287      extra call of do_oceanic_physics
288      affects ecco_the_main_loop.F, do_oceanic_physics.F
289      checkpoint_lev1_directives.h
290    o NB: this may break global_ocean adjoint temporarily,
291      but it is clear how to fix it. Will do later, need this now.
292    
293    checkpoint55d_post
294    o ECCO specific cost function terms (up-to-date with 1x1 runs)
295    o ecco_cost_weights is modified to 1x1 runs
296    o modifs to allow observations to be read in as
297      single file or yearly files
298    o enable to read exf forcing fields as either
299      single file or yearly files (flag useExfYearlyFields)
300    checkpoint55d_pre
301    
302    o switch between 2-level and 3-level checkpointing
303    o add ability of MNC to write local and "partial" (eg. 2D slices where
304      the full 3D field is never actually stored) arrays to NetCDF files
305      with the correct (that is, the complete multi-dimensional) set of
306      array indicies
307      - used in mom_vecinv() to write the diagFreq output
308      - tested (demonstrated) in verification/aim.5l_cs
309    o further mnc-ification
310      - add verification/lab_sea to the list with mnc setups
311      - fix undefined mnc v-names in cd_code
312      - add kpp to mnc output (both snapshot and timeave)
313    o non-hydrostatic code
314      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
315        in calc_gw.F
316      - defaults to viscAh
317      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
318        friction or Leith) in non-hydrostatic mode, as long as there is
319        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
320    o pkg/cost
321      extend simple cost functions to treat time mean quantities
322      (T,U,V) via cost_accumulate_state from cost_tile
323    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
324        be 2 times larger than the minimum size the advection scheme requires.
325        now get a perfect conservation of salt in advect_cs test-exp (updated)
326    o GGL90 (Gaspar's TKE mixed layer)
327      - add horizontal diffusion of TKE, requires exchanges in
328        do_fields_blocking_exchanges, horizontal diffusivity is zero by
329        default. In OPA there is no horizontal diffusion of TKE but the
330        mixing coefficients are computed from a horizontal average of TKE of
331        6 points or so. I think that diffusion has a little more physical
332        justification.
333      - clean up ggl90_calc in the hope of reducing memory usage (this hope
334        was in vain)
335      - mask tke-variable in ggl90_init
336    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
337    o fix biharmonic diffusion on CS-grid.
338    o more obcs stuff
339      - added obcs_external_fields_load as an alternative to the EXF-pkg option
340        for reading boundary values. This routine is called from
341        obcs_prescribe_read
342      - updated obcs_check
343      - changed sponge layer relaxation parameter units for days to seconds
344      - turned off sponge layer by default
345      - changed argument list of OBCS_CALC to myTime+deltaTclock
346      - fixed about 35 bugs in obcs_external_fields_load
347    
348    checkpoint55c_post
349  o obcs stuff  o obcs stuff
350    - new runtime flags useOBCSprescribe, useOBCSbalance    - new runtime flags useOBCSprescribe, useOBCSbalance
351    - re-arranged obcs_calc    - re-arranged obcs_calc
# Line 10  o obcs stuff Line 353  o obcs stuff
353      obcs_prescibe_read is called after ORLANSKI stuff      obcs_prescibe_read is called after ORLANSKI stuff
354      and independent of it (executable can contain all).      and independent of it (executable can contain all).
355    - updated obcs_check    - updated obcs_check
356      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
357        These may be necessary only if tangential velocities are
358        prescribed at OB, not sure, needs testing.
359  o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments  o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
360    which simplifies the calls and passes the ifc check-bounds test    which simplifies the calls and passes the ifc check-bounds test
361    

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