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revision 1.390 by jmc, Sun Nov 21 22:22:31 2004 UTC revision 1.423 by edhill, Mon Dec 20 17:10:27 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 fix MNC coordinate variables so that they now contain per-face index
7      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
8      general, EXCH2 grids are only aligned to a "local" coordinate system
9    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
10    o Implement instantaneous output within pkg diagnostics:
11      setting a negative frequency in data.diagnostics produces
12     "snap-shot" output (as opposed to time-average if freq > 0)
13    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
14      NOTE: change ptracer diagnostics name: use 2 characters to work with
15            more than 9 tracers. Add also diagnostics of advect & diffus flux.
16    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
17      becomes the coordinate variable for the 'T' dimension
18    o add CF-style coordinate variables to MNC
19      - just a first cut:  numbers are meaningless on the cubesphere and
20        missing along the T axis but otherwise it works!
21    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
22    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
23    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
24      this is based directly on what the model compute, so that the content of
25      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
26    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
27    o clean up build options files for SunOS, in particular
28      - remove -traditional from xmakedepend
29      - change -xarch=v9 to -xarch=native for f77
30      - restore use of make (not gmake)
31      - add CC=gcc if using g77
32    o changes per discussion of AM, JMC, & EH3 today:
33      - move redundant "grid" variables out of "state" -- in preparation of
34        creating proper CF-style coordinate variables and in recognition
35        that any/all grid variables can be easily copied (eg. w/NCO) from
36        the grid files into any of the other NetCDF files
37      - *always* output grid variables with MDSIO (this will eventually be
38        changed)
39      - output MNC grid file if useMNC is true
40    o every instance of _END_MASTER() has been found and replaced with
41      _END_MASTER( myThid ) in order to satisfy certain picky Sun
42      preprocessors
43    o re-arrange diagnostics pkg initialisation:
44     - allow each package to extend the available diagnostics list
45     - add some checking and fix small problems (multi-threaded, ...)
46     - new S/R diagnostics_fill (replace fill_diagnostics):
47       look through the short list of active diag. (instead of the long list)
48       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
49    
50    checkpoint57a_post
51    o this set of changes restores TAMC compatibility
52      tested for global_ocean.90x40x15 adjoint on trough
53      (what a pain)
54    
55    checkpoint57a_pre
56    o some modifs in tools/build_options for sunos
57    o call ctrl_pack for ctrl at end for optimcycle=0
58    
59    checkpoint57
60    o add horizontal bi-harmonic viscosity for vertical velocity
61      - new parameter viscA4W (defaults to viscA4)
62      - affects only non-hydrostatic code
63      - to be done: no-slip lateral boundary conditions
64    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
65    o implement Implicit Vertical advection for pTracers
66    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
67      (implemented also for implicit vertical diffusion & advection)
68    o OBCS: extend application of tracer open boundary conditions
69      to a strip beyond the boundary of width Olx/Oly
70    o add call monitor to TAF set of required calls (flow directives)
71      and include in natl_box_adjoint
72    o untangle a few ifdefs related to cost, ctrl, autodiff
73      untangel a few ALLOW_ECCO_OPTIMIZATION
74    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
75      (theta2, salt2 in ecco_cost_weights)
76    
77    checkpoint56c_post
78    o OBCS as control variables
79      - update ctrl_ad_diff.list, obcs_ad_diff.list
80      - remove balance of obcs controls from default
81      - fix index bug nobcs in ctrl_init
82      - fix dummy fields filen in ctrl_pack
83      - add dummy weights for obcs
84    o lsopt: comment out fort.94 output
85    o optim:
86      - remove unnecessary header files
87      - adjusted namelists
88      - add xerbla.F to Makefile
89    o exf:
90      - multiple modifications of exf_check_range
91      - unit change in exf_init_runoff from [m/year] to [m/s]
92    o mdsio:
93      - i/o-vector change debugLevel from debLevA to debLevB
94    
95    checkpoint56b_post
96    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
97      is called from DO_THE_MODEL_IO
98      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
99      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
100      - clean up PTRACERS_WRITE_TIMEAVE a little
101    o add another verification experiment that tests both the cfc-pkg and
102      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
103      reactive tendencies treated inline with regular timestepping
104    o testreport previously did a lousy job of comparing small numbers, so
105      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
106      implemented in the little c-progam tmp_cmpnum.c which is embedded in
107      testreport.
108    o ptracers_monitor: bug fix for MPI
109    
110    checkpoint56a_post
111    o GCHEM: finish reorganizating the package
112      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
113        (introduces another 3D-array for each passive tracer, but only if
114        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
115        gchemTendency is not needed because the timestep is done separately)
116      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
117      - GCHEM is now---more or less cleanly---separate from PTRACERS
118      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
119        so clear to me how that should be done in a general way.
120    o CFC: improve formatting of output in CFC_ATMOS
121    o PTRACERS:
122      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
123        that ALL experiments with ptracers enable can be checked. This makes
124        GCHEM_MONITOR obsolete.
125      - include a runtime parameter PTRACERS_monitorFreq that defaults to
126        monitorFreq
127      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
128    o add PTRACERS (PTR0[1-5]) to testreport output
129    o exf_check_range:
130      * default changed to .TRUE.
131      * will check values for niter0 if debLevA, every timestep if debLevB
132      * STOP in exf_check_range if 'out of range'
133      * range chosen generous to allow for potential extema
134      TBD: a version with stricter range
135           permitted range would be runtime parameters
136  o GMredi:  o GMredi:
137    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
138    - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.    - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
# Line 11  o GCHEM: Line 141  o GCHEM:
141    - move call to GCHEM_FORCING_SEP, so that it is now called before    - move call to GCHEM_FORCING_SEP, so that it is now called before
142      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
143    - introduced a useGCHEM runtime flag and applied it everywhere.    - introduced a useGCHEM runtime flag and applied it everywhere.
144      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
145        this flag is now only visible within GCHEM-pkg routines.
146      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
147        be replaced by a 3D array that is computed before thermodynamics; for
148        this, the tracer ID iTracer had to be included into the parameter list
149        of ptracers_forcing
150      - set up forward_step to call gchem_forcing, that will replace
151        gchem_forcing_int in ptracers_forcing
152      - cleaning up
153  o small cleaning of exch2: remove files that are also in eesupp/src  o small cleaning of exch2: remove files that are also in eesupp/src
154    
155  checkpoint56  checkpoint56
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