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revision 1.332 by jmc, Sun Jul 18 14:20:17 2004 UTC revision 1.417 by jmc, Fri Dec 17 05:03:43 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 pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
7    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
8      this is based directly on what the model compute, so that the content of
9      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
10    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
11    o clean up build options files for SunOS, in particular
12      - remove -traditional from xmakedepend
13      - change -xarch=v9 to -xarch=native for f77
14      - restore use of make (not gmake)
15      - add CC=gcc if using g77
16    o changes per discussion of AM, JMC, & EH3 today:
17      - move redundant "grid" variables out of "state" -- in preparation of
18        creating proper CF-style coordinate variables and in recognition
19        that any/all grid variables can be easily copied (eg. w/NCO) from
20        the grid files into any of the other NetCDF files
21      - *always* output grid variables with MDSIO (this will eventually be
22        changed)
23      - output MNC grid file if useMNC is true
24    o every instance of _END_MASTER() has been found and replaced with
25      _END_MASTER( myThid ) in order to satisfy certain picky Sun
26      preprocessors
27    o re-arrange diagnostics pkg initialisation:
28     - allow each package to extend the available diagnostics list
29     - add some checking and fix small problems (multi-threaded, ...)
30     - new S/R diagnostics_fill (replace fill_diagnostics):
31       look through the short list of active diag. (instead of the long list)
32       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
33    
34    checkpoint57a_post
35    o this set of changes restores TAMC compatibility
36      tested for global_ocean.90x40x15 adjoint on trough
37      (what a pain)
38    
39    checkpoint57a_pre
40    o some modifs in tools/build_options for sunos
41    o call ctrl_pack for ctrl at end for optimcycle=0
42    
43    checkpoint57
44    o add horizontal bi-harmonic viscosity for vertical velocity
45      - new parameter viscA4W (defaults to viscA4)
46      - affects only non-hydrostatic code
47      - to be done: no-slip lateral boundary conditions
48    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
49    o implement Implicit Vertical advection for pTracers
50    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
51      (implemented also for implicit vertical diffusion & advection)
52    o OBCS: extend application of tracer open boundary conditions
53      to a strip beyond the boundary of width Olx/Oly
54    o add call monitor to TAF set of required calls (flow directives)
55      and include in natl_box_adjoint
56    o untangle a few ifdefs related to cost, ctrl, autodiff
57      untangel a few ALLOW_ECCO_OPTIMIZATION
58    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
59      (theta2, salt2 in ecco_cost_weights)
60    
61    checkpoint56c_post
62    o OBCS as control variables
63      - update ctrl_ad_diff.list, obcs_ad_diff.list
64      - remove balance of obcs controls from default
65      - fix index bug nobcs in ctrl_init
66      - fix dummy fields filen in ctrl_pack
67      - add dummy weights for obcs
68    o lsopt: comment out fort.94 output
69    o optim:
70      - remove unnecessary header files
71      - adjusted namelists
72      - add xerbla.F to Makefile
73    o exf:
74      - multiple modifications of exf_check_range
75      - unit change in exf_init_runoff from [m/year] to [m/s]
76    o mdsio:
77      - i/o-vector change debugLevel from debLevA to debLevB
78    
79    checkpoint56b_post
80    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
81      is called from DO_THE_MODEL_IO
82      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
83      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
84      - clean up PTRACERS_WRITE_TIMEAVE a little
85    o add another verification experiment that tests both the cfc-pkg and
86      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
87      reactive tendencies treated inline with regular timestepping
88    o testreport previously did a lousy job of comparing small numbers, so
89      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
90      implemented in the little c-progam tmp_cmpnum.c which is embedded in
91      testreport.
92    o ptracers_monitor: bug fix for MPI
93    
94    checkpoint56a_post
95    o GCHEM: finish reorganizating the package
96      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
97        (introduces another 3D-array for each passive tracer, but only if
98        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
99        gchemTendency is not needed because the timestep is done separately)
100      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
101      - GCHEM is now---more or less cleanly---separate from PTRACERS
102      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
103        so clear to me how that should be done in a general way.
104    o CFC: improve formatting of output in CFC_ATMOS
105    o PTRACERS:
106      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
107        that ALL experiments with ptracers enable can be checked. This makes
108        GCHEM_MONITOR obsolete.
109      - include a runtime parameter PTRACERS_monitorFreq that defaults to
110        monitorFreq
111      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
112    o add PTRACERS (PTR0[1-5]) to testreport output
113    o exf_check_range:
114      * default changed to .TRUE.
115      * will check values for niter0 if debLevA, every timestep if debLevB
116      * STOP in exf_check_range if 'out of range'
117      * range chosen generous to allow for potential extema
118      TBD: a version with stricter range
119           permitted range would be runtime parameters
120    o GMredi:
121      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
122      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
123      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
124    o GCHEM:
125      - move call to GCHEM_FORCING_SEP, so that it is now called before
126        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
127      - introduced a useGCHEM runtime flag and applied it everywhere.
128      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
129        this flag is now only visible within GCHEM-pkg routines.
130      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
131        be replaced by a 3D array that is computed before thermodynamics; for
132        this, the tracer ID iTracer had to be included into the parameter list
133        of ptracers_forcing
134      - set up forward_step to call gchem_forcing, that will replace
135        gchem_forcing_int in ptracers_forcing
136      - cleaning up
137    o small cleaning of exch2: remove files that are also in eesupp/src
138    
139    checkpoint56
140    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
141    o mnc: cleanup "full" files--fixes out-of-memory problem
142    o ECCO-GODAE
143      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
144      * fully merged and updated from SIO code
145        windstress sign change affects
146        - exf_inscal_[u/v]stress
147        - sign of xx_tau[u/v] adjustments
148        - signs in cost_scat
149      * ctrl_get_gen: avoid update of tau[u/v] for first few days
150      * natl_box_adjoint updated and compressed
151      * 2-level checkpoint switch added
152        (tested in EXP. 1 of natl_box_adjoint)
153      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
154    o SVD
155      * first complete, non-hacked version for SVD calculations
156      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
157        performed via direct access files admtlm_vector.it????
158        (via ctrl_[un]pack)
159      * optimcycle is used for ARPACK iteration counter
160        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
161      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
162        and add linear transforms where necessary
163      * controls are initial/final SST, SSS (can be extended; need to check
164        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
165    o mdsio: filename info to both stderr, stdout
166    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
167      from sign change
168    
169    checkpoint55j_post
170    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
171      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
172    o add consistent build directories and .cvsignore files to verification
173    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
174    o make all subroutines 30 or less characters in length for certain older
175      compilers to work (a thorough search only turns up two routines in
176      pkg/ptracers)
177    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
178      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
179    
180    checkpoint55i_post
181    o change arrays for total vertical diffusivity (2.D if explicit,
182      3.D if implicit) ; each ptracer uses its own background value.
183    o added mnc/NetCDF output capability to ocn_compon_interf
184      - added bits to verification/cpl_aim+ocn so that it can run on
185        ITRDA and other clusters without the mpirun "-wd" option
186    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
187      configuration
188    o give MNC the ability to create additional files rather than
189      exceeding a specified file size limit "MNC_MAX_FILESIZE"
190      - the default is just less than 2GB which is a practical limit
191        on many systems
192    o Compute the non-local term using either KPP vertical diffusivity (=default)
193       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
194    
195    checkpoint55h_post
196    o add verification test "vermix"
197    o remove all the *_ioinc flags and replace with the single global
198      outputTypesInclusive flag
199    o allow to set a vertical profile of vertical diffusivity for T & S
200    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
201    o useMNC moved from data.mnc to data.pkg
202    
203    checkpoint55g_post
204    o Renaming carbon AD experiments to comply with testreport conventions
205    o Updating adjoint of Held-Suarez hs94.1x64x5
206    o Fixing directives for non-ECCO forward_step, after ECCO directives
207      have been fixed to avoid recomp. of do_oceanic_phys
208      Works well for global_ocean.90x40x15,
209      but recomp. issue remains for carbon
210    o Updating adjoint output for natl_box_adjoint after
211      pkg/ecco has been modified (see taga c55d_post)
212    
213    checkpoint55f_post
214    o rename to timeave_init_fixed
215    
216    checkpoint55e_post
217    o some delicate re-shuffle of store directives to avoid one
218      extra call of do_oceanic_physics
219      affects ecco_the_main_loop.F, do_oceanic_physics.F
220      checkpoint_lev1_directives.h
221    o NB: this may break global_ocean adjoint temporarily,
222      but it is clear how to fix it. Will do later, need this now.
223    
224    checkpoint55d_post
225    o ECCO specific cost function terms (up-to-date with 1x1 runs)
226    o ecco_cost_weights is modified to 1x1 runs
227    o modifs to allow observations to be read in as
228      single file or yearly files
229    o enable to read exf forcing fields as either
230      single file or yearly files (flag useExfYearlyFields)
231    checkpoint55d_pre
232    
233    o switch between 2-level and 3-level checkpointing
234    o add ability of MNC to write local and "partial" (eg. 2D slices where
235      the full 3D field is never actually stored) arrays to NetCDF files
236      with the correct (that is, the complete multi-dimensional) set of
237      array indicies
238      - used in mom_vecinv() to write the diagFreq output
239      - tested (demonstrated) in verification/aim.5l_cs
240    o further mnc-ification
241      - add verification/lab_sea to the list with mnc setups
242      - fix undefined mnc v-names in cd_code
243      - add kpp to mnc output (both snapshot and timeave)
244    o non-hydrostatic code
245      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
246        in calc_gw.F
247      - defaults to viscAh
248      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
249        friction or Leith) in non-hydrostatic mode, as long as there is
250        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
251    o pkg/cost
252      extend simple cost functions to treat time mean quantities
253      (T,U,V) via cost_accumulate_state from cost_tile
254    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
255        be 2 times larger than the minimum size the advection scheme requires.
256        now get a perfect conservation of salt in advect_cs test-exp (updated)
257    o GGL90 (Gaspar's TKE mixed layer)
258      - add horizontal diffusion of TKE, requires exchanges in
259        do_fields_blocking_exchanges, horizontal diffusivity is zero by
260        default. In OPA there is no horizontal diffusion of TKE but the
261        mixing coefficients are computed from a horizontal average of TKE of
262        6 points or so. I think that diffusion has a little more physical
263        justification.
264      - clean up ggl90_calc in the hope of reducing memory usage (this hope
265        was in vain)
266      - mask tke-variable in ggl90_init
267    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
268    o fix biharmonic diffusion on CS-grid.
269    o more obcs stuff
270      - added obcs_external_fields_load as an alternative to the EXF-pkg option
271        for reading boundary values. This routine is called from
272        obcs_prescribe_read
273      - updated obcs_check
274      - changed sponge layer relaxation parameter units for days to seconds
275      - turned off sponge layer by default
276      - changed argument list of OBCS_CALC to myTime+deltaTclock
277      - fixed about 35 bugs in obcs_external_fields_load
278    
279    checkpoint55c_post
280    o obcs stuff
281      - new runtime flags useOBCSprescribe, useOBCSbalance
282      - re-arranged obcs_calc
283      - moved exf_getobcs to obcs_prescibe_read
284        obcs_prescibe_read is called after ORLANSKI stuff
285        and independent of it (executable can contain all).
286      - updated obcs_check
287      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
288        These may be necessary only if tangential velocities are
289        prescribed at OB, not sure, needs testing.
290    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
291      which simplifies the calls and passes the ifc check-bounds test
292    
293    checkpoint55b_post
294    o add a 2D scalar, Z location, exchange_2 routine.
295    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
296      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
297      affects advect_cs results (for the wrong reason): update output.txt
298    o use a more standard discretization for biharmonic viscosity ;
299     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
300      affects results of dome set-up: update output.txt
301    o fix gad_advection.F (CubedSphere part), back to version 1.23
302    o fix bug in mom_vi_del2uv.F (CubedSphere part).
303    
304    checkpoint55a_post
305    o merged code to
306      * prescribe/read time-dependent open boundaries
307        (works in conjunction with exf, cal)
308      * sponge layer code for open boundaries
309      * each boundary N/S/E/W now has its own CPP option
310        (healthy for the adjoint)
311    
312    checkpoint55
313    o up-to-date adjoint of previous breaks
314      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
315      - global_ocean_ebm: adjoint still needs fix (TLM ok)
316      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
317      - carbon: * remove tr1-related adjoint verification
318                * add ptracer as control variable
319    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
320      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
321    
322    checkpoint54f_post
323    o in verification/carbin/ remove experiment related to
324      ALLOW_PASSIVE_TRACER (array tr1 etc)
325      code_ad/ input_ad/ results_ad
326    
327    o add two new packages
328      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
329        + subject to optimization (memory)
330      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
331        + subject to reordering (many GOTOs in the original code)
332        + so far opps is called for every (i,j) point, and then operates in
333          the vertical; one may want to reorder the scheme in order operate in
334          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
335          fields)
336    o overhaul of IO so that we now have flags for MDSIO and/or MNC
337      - all verification tests compile and run with linux_ia32_g77
338      - defaults are compatible with current input files--nothing
339        should change if you were not previously using MNC
340      - MNC output has been added in numerous places (eg. timeave)
341        but there are still a few writes not yet do-able with MNC
342        (this is in progress)
343      - flags now allow for either/or/both use of MDSIO and MNC and
344        documentation will soon follow
345      - numerous small formatting cleanups for ProTeX
346    o add version info (via BUILD_INFO.h) to MNC and stdout
347    
348    checkpoint54e_post
349    o add two new packages
350      - pp81 (Packanowski and Philander, 1981), Richardson number and
351        stratification dependent mixing
352      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
353      - these scheme operate in a similar manner as KPP (without ghat, of
354        course), however there is only one diffusivity that is used for both
355        temperature and salinity (and passive tracers)ç
356    o add offline package
357    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
358      provided by Stephanie Dutkiewicz
359    o genmake2: add ability to search for C compilers and cleanup test output
360      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
361    
362    checkpoint54d_post
363    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
364    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
365      leading to additional shift by 5 days each year of integration
366       (i.e. leading to considerable offset over the years)
367    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
368    o start with no AB and no initial filtering (staggerTimeStep):
369      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
370    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
371      (external loading & cpl import/export stay in forward_step.F)
372    o update coupling interface to work with new staggerTimeStep
373    o change MDSIO ptracers_pickup.
374    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
375    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
376    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
377    
378  checkpoint54c_post  checkpoint54c_post
379  o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr  o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
380    this affects (truncation error) output.txt of test-exp:    this affects (truncation error) output.txt of test-exp:

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