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revision 1.337 by jmc, Tue Jul 27 15:56:13 2004 UTC revision 1.422 by jmc, Mon Dec 20 02:42:42 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
7    o Implement instantaneous output within pkg diagnostics:
8      setting a negative frequency in data.diagnostics produces
9     "snap-shot" output (as opposed to time-average if freq > 0)
10    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
11      NOTE: change ptracer diagnostics name: use 2 characters to work with
12            more than 9 tracers. Add also diagnostics of advect & diffus flux.
13    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
14      becomes the coordinate variable for the 'T' dimension
15    o add CF-style coordinate variables to MNC
16      - just a first cut:  numbers are meaningless on the cubesphere and
17        missing along the T axis but otherwise it works!
18    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
19    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
20    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
21      this is based directly on what the model compute, so that the content of
22      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
23    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
24    o clean up build options files for SunOS, in particular
25      - remove -traditional from xmakedepend
26      - change -xarch=v9 to -xarch=native for f77
27      - restore use of make (not gmake)
28      - add CC=gcc if using g77
29    o changes per discussion of AM, JMC, & EH3 today:
30      - move redundant "grid" variables out of "state" -- in preparation of
31        creating proper CF-style coordinate variables and in recognition
32        that any/all grid variables can be easily copied (eg. w/NCO) from
33        the grid files into any of the other NetCDF files
34      - *always* output grid variables with MDSIO (this will eventually be
35        changed)
36      - output MNC grid file if useMNC is true
37    o every instance of _END_MASTER() has been found and replaced with
38      _END_MASTER( myThid ) in order to satisfy certain picky Sun
39      preprocessors
40    o re-arrange diagnostics pkg initialisation:
41     - allow each package to extend the available diagnostics list
42     - add some checking and fix small problems (multi-threaded, ...)
43     - new S/R diagnostics_fill (replace fill_diagnostics):
44       look through the short list of active diag. (instead of the long list)
45       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
46    
47    checkpoint57a_post
48    o this set of changes restores TAMC compatibility
49      tested for global_ocean.90x40x15 adjoint on trough
50      (what a pain)
51    
52    checkpoint57a_pre
53    o some modifs in tools/build_options for sunos
54    o call ctrl_pack for ctrl at end for optimcycle=0
55    
56    checkpoint57
57    o add horizontal bi-harmonic viscosity for vertical velocity
58      - new parameter viscA4W (defaults to viscA4)
59      - affects only non-hydrostatic code
60      - to be done: no-slip lateral boundary conditions
61    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
62    o implement Implicit Vertical advection for pTracers
63    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
64      (implemented also for implicit vertical diffusion & advection)
65    o OBCS: extend application of tracer open boundary conditions
66      to a strip beyond the boundary of width Olx/Oly
67    o add call monitor to TAF set of required calls (flow directives)
68      and include in natl_box_adjoint
69    o untangle a few ifdefs related to cost, ctrl, autodiff
70      untangel a few ALLOW_ECCO_OPTIMIZATION
71    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
72      (theta2, salt2 in ecco_cost_weights)
73    
74    checkpoint56c_post
75    o OBCS as control variables
76      - update ctrl_ad_diff.list, obcs_ad_diff.list
77      - remove balance of obcs controls from default
78      - fix index bug nobcs in ctrl_init
79      - fix dummy fields filen in ctrl_pack
80      - add dummy weights for obcs
81    o lsopt: comment out fort.94 output
82    o optim:
83      - remove unnecessary header files
84      - adjusted namelists
85      - add xerbla.F to Makefile
86    o exf:
87      - multiple modifications of exf_check_range
88      - unit change in exf_init_runoff from [m/year] to [m/s]
89    o mdsio:
90      - i/o-vector change debugLevel from debLevA to debLevB
91    
92    checkpoint56b_post
93    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
94      is called from DO_THE_MODEL_IO
95      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
96      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
97      - clean up PTRACERS_WRITE_TIMEAVE a little
98    o add another verification experiment that tests both the cfc-pkg and
99      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
100      reactive tendencies treated inline with regular timestepping
101    o testreport previously did a lousy job of comparing small numbers, so
102      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
103      implemented in the little c-progam tmp_cmpnum.c which is embedded in
104      testreport.
105    o ptracers_monitor: bug fix for MPI
106    
107    checkpoint56a_post
108    o GCHEM: finish reorganizating the package
109      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
110        (introduces another 3D-array for each passive tracer, but only if
111        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
112        gchemTendency is not needed because the timestep is done separately)
113      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
114      - GCHEM is now---more or less cleanly---separate from PTRACERS
115      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
116        so clear to me how that should be done in a general way.
117    o CFC: improve formatting of output in CFC_ATMOS
118    o PTRACERS:
119      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
120        that ALL experiments with ptracers enable can be checked. This makes
121        GCHEM_MONITOR obsolete.
122      - include a runtime parameter PTRACERS_monitorFreq that defaults to
123        monitorFreq
124      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
125    o add PTRACERS (PTR0[1-5]) to testreport output
126    o exf_check_range:
127      * default changed to .TRUE.
128      * will check values for niter0 if debLevA, every timestep if debLevB
129      * STOP in exf_check_range if 'out of range'
130      * range chosen generous to allow for potential extema
131      TBD: a version with stricter range
132           permitted range would be runtime parameters
133    o GMredi:
134      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
135      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
136      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
137    o GCHEM:
138      - move call to GCHEM_FORCING_SEP, so that it is now called before
139        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
140      - introduced a useGCHEM runtime flag and applied it everywhere.
141      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
142        this flag is now only visible within GCHEM-pkg routines.
143      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
144        be replaced by a 3D array that is computed before thermodynamics; for
145        this, the tracer ID iTracer had to be included into the parameter list
146        of ptracers_forcing
147      - set up forward_step to call gchem_forcing, that will replace
148        gchem_forcing_int in ptracers_forcing
149      - cleaning up
150    o small cleaning of exch2: remove files that are also in eesupp/src
151    
152    checkpoint56
153    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
154    o mnc: cleanup "full" files--fixes out-of-memory problem
155    o ECCO-GODAE
156      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
157      * fully merged and updated from SIO code
158        windstress sign change affects
159        - exf_inscal_[u/v]stress
160        - sign of xx_tau[u/v] adjustments
161        - signs in cost_scat
162      * ctrl_get_gen: avoid update of tau[u/v] for first few days
163      * natl_box_adjoint updated and compressed
164      * 2-level checkpoint switch added
165        (tested in EXP. 1 of natl_box_adjoint)
166      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
167    o SVD
168      * first complete, non-hacked version for SVD calculations
169      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
170        performed via direct access files admtlm_vector.it????
171        (via ctrl_[un]pack)
172      * optimcycle is used for ARPACK iteration counter
173        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
174      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
175        and add linear transforms where necessary
176      * controls are initial/final SST, SSS (can be extended; need to check
177        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
178    o mdsio: filename info to both stderr, stdout
179    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
180      from sign change
181    
182    checkpoint55j_post
183    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
184      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
185    o add consistent build directories and .cvsignore files to verification
186    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
187    o make all subroutines 30 or less characters in length for certain older
188      compilers to work (a thorough search only turns up two routines in
189      pkg/ptracers)
190    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
191      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
192    
193    checkpoint55i_post
194    o change arrays for total vertical diffusivity (2.D if explicit,
195      3.D if implicit) ; each ptracer uses its own background value.
196    o added mnc/NetCDF output capability to ocn_compon_interf
197      - added bits to verification/cpl_aim+ocn so that it can run on
198        ITRDA and other clusters without the mpirun "-wd" option
199    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
200      configuration
201    o give MNC the ability to create additional files rather than
202      exceeding a specified file size limit "MNC_MAX_FILESIZE"
203      - the default is just less than 2GB which is a practical limit
204        on many systems
205    o Compute the non-local term using either KPP vertical diffusivity (=default)
206       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
207    
208    checkpoint55h_post
209    o add verification test "vermix"
210    o remove all the *_ioinc flags and replace with the single global
211      outputTypesInclusive flag
212    o allow to set a vertical profile of vertical diffusivity for T & S
213    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
214    o useMNC moved from data.mnc to data.pkg
215    
216    checkpoint55g_post
217    o Renaming carbon AD experiments to comply with testreport conventions
218    o Updating adjoint of Held-Suarez hs94.1x64x5
219    o Fixing directives for non-ECCO forward_step, after ECCO directives
220      have been fixed to avoid recomp. of do_oceanic_phys
221      Works well for global_ocean.90x40x15,
222      but recomp. issue remains for carbon
223    o Updating adjoint output for natl_box_adjoint after
224      pkg/ecco has been modified (see taga c55d_post)
225    
226    checkpoint55f_post
227    o rename to timeave_init_fixed
228    
229    checkpoint55e_post
230    o some delicate re-shuffle of store directives to avoid one
231      extra call of do_oceanic_physics
232      affects ecco_the_main_loop.F, do_oceanic_physics.F
233      checkpoint_lev1_directives.h
234    o NB: this may break global_ocean adjoint temporarily,
235      but it is clear how to fix it. Will do later, need this now.
236    
237    checkpoint55d_post
238    o ECCO specific cost function terms (up-to-date with 1x1 runs)
239    o ecco_cost_weights is modified to 1x1 runs
240    o modifs to allow observations to be read in as
241      single file or yearly files
242    o enable to read exf forcing fields as either
243      single file or yearly files (flag useExfYearlyFields)
244    checkpoint55d_pre
245    
246    o switch between 2-level and 3-level checkpointing
247    o add ability of MNC to write local and "partial" (eg. 2D slices where
248      the full 3D field is never actually stored) arrays to NetCDF files
249      with the correct (that is, the complete multi-dimensional) set of
250      array indicies
251      - used in mom_vecinv() to write the diagFreq output
252      - tested (demonstrated) in verification/aim.5l_cs
253    o further mnc-ification
254      - add verification/lab_sea to the list with mnc setups
255      - fix undefined mnc v-names in cd_code
256      - add kpp to mnc output (both snapshot and timeave)
257    o non-hydrostatic code
258      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
259        in calc_gw.F
260      - defaults to viscAh
261      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
262        friction or Leith) in non-hydrostatic mode, as long as there is
263        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
264    o pkg/cost
265      extend simple cost functions to treat time mean quantities
266      (T,U,V) via cost_accumulate_state from cost_tile
267    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
268        be 2 times larger than the minimum size the advection scheme requires.
269        now get a perfect conservation of salt in advect_cs test-exp (updated)
270    o GGL90 (Gaspar's TKE mixed layer)
271      - add horizontal diffusion of TKE, requires exchanges in
272        do_fields_blocking_exchanges, horizontal diffusivity is zero by
273        default. In OPA there is no horizontal diffusion of TKE but the
274        mixing coefficients are computed from a horizontal average of TKE of
275        6 points or so. I think that diffusion has a little more physical
276        justification.
277      - clean up ggl90_calc in the hope of reducing memory usage (this hope
278        was in vain)
279      - mask tke-variable in ggl90_init
280    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
281    o fix biharmonic diffusion on CS-grid.
282    o more obcs stuff
283      - added obcs_external_fields_load as an alternative to the EXF-pkg option
284        for reading boundary values. This routine is called from
285        obcs_prescribe_read
286      - updated obcs_check
287      - changed sponge layer relaxation parameter units for days to seconds
288      - turned off sponge layer by default
289      - changed argument list of OBCS_CALC to myTime+deltaTclock
290      - fixed about 35 bugs in obcs_external_fields_load
291    
292    checkpoint55c_post
293    o obcs stuff
294      - new runtime flags useOBCSprescribe, useOBCSbalance
295      - re-arranged obcs_calc
296      - moved exf_getobcs to obcs_prescibe_read
297        obcs_prescibe_read is called after ORLANSKI stuff
298        and independent of it (executable can contain all).
299      - updated obcs_check
300      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
301        These may be necessary only if tangential velocities are
302        prescribed at OB, not sure, needs testing.
303    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
304      which simplifies the calls and passes the ifc check-bounds test
305    
306    checkpoint55b_post
307    o add a 2D scalar, Z location, exchange_2 routine.
308    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
309      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
310      affects advect_cs results (for the wrong reason): update output.txt
311    o use a more standard discretization for biharmonic viscosity ;
312     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
313      affects results of dome set-up: update output.txt
314    o fix gad_advection.F (CubedSphere part), back to version 1.23
315    o fix bug in mom_vi_del2uv.F (CubedSphere part).
316    
317    checkpoint55a_post
318    o merged code to
319      * prescribe/read time-dependent open boundaries
320        (works in conjunction with exf, cal)
321      * sponge layer code for open boundaries
322      * each boundary N/S/E/W now has its own CPP option
323        (healthy for the adjoint)
324    
325    checkpoint55
326    o up-to-date adjoint of previous breaks
327      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
328      - global_ocean_ebm: adjoint still needs fix (TLM ok)
329      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
330      - carbon: * remove tr1-related adjoint verification
331                * add ptracer as control variable
332    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
333      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
334    
335    checkpoint54f_post
336    o in verification/carbin/ remove experiment related to
337      ALLOW_PASSIVE_TRACER (array tr1 etc)
338      code_ad/ input_ad/ results_ad
339    
340    o add two new packages
341      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
342        + subject to optimization (memory)
343      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
344        + subject to reordering (many GOTOs in the original code)
345        + so far opps is called for every (i,j) point, and then operates in
346          the vertical; one may want to reorder the scheme in order operate in
347          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
348          fields)
349    o overhaul of IO so that we now have flags for MDSIO and/or MNC
350      - all verification tests compile and run with linux_ia32_g77
351      - defaults are compatible with current input files--nothing
352        should change if you were not previously using MNC
353      - MNC output has been added in numerous places (eg. timeave)
354        but there are still a few writes not yet do-able with MNC
355        (this is in progress)
356      - flags now allow for either/or/both use of MDSIO and MNC and
357        documentation will soon follow
358      - numerous small formatting cleanups for ProTeX
359    o add version info (via BUILD_INFO.h) to MNC and stdout
360    
361    checkpoint54e_post
362    o add two new packages
363      - pp81 (Packanowski and Philander, 1981), Richardson number and
364        stratification dependent mixing
365      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
366      - these scheme operate in a similar manner as KPP (without ghat, of
367        course), however there is only one diffusivity that is used for both
368        temperature and salinity (and passive tracers)ç
369    o add offline package
370    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
371      provided by Stephanie Dutkiewicz
372    o genmake2: add ability to search for C compilers and cleanup test output
373      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
374    
375  checkpoint54d_post  checkpoint54d_post
376  o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed  o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
377  o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,  o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,

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