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revision 1.393 by edhill, Tue Nov 23 21:25:24 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  o add PTRACERS (PTR0[1-5]) to testreport output
126  o exf_check_range:  o exf_check_range:
127    * default changed to .TRUE.    * default changed to .TRUE.
# Line 25  o GCHEM: Line 144  o GCHEM:
144      be replaced by a 3D array that is computed before thermodynamics; for      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      this, the tracer ID iTracer had to be included into the parameter list
146      of ptracers_forcing      of ptracers_forcing
147    - set up forward_step for a call to gchem_forcing, that will replace    - set up forward_step to call gchem_forcing, that will replace
148      gchem_forcing_int in ptracers_forcing      gchem_forcing_int in ptracers_forcing
149    - cleaning up    - cleaning up
150  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
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