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revision 1.393 by edhill, Tue Nov 23 21:25:24 2004 UTC revision 1.424 by jmc, Mon Dec 20 19:56:15 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint57b_post
7    o simplify options in diagnostics_fill arguments (remove weird combinations)
8    o fix MNC coordinate variables so that they now contain per-face index
9      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
10      general, EXCH2 grids are only aligned to a "local" coordinate system
11    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
12    o Implement instantaneous output within pkg diagnostics:
13      setting a negative frequency in data.diagnostics produces
14     "snap-shot" output (as opposed to time-average if freq > 0)
15    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
16      NOTE: change ptracer diagnostics name: use 2 characters to work with
17            more than 9 tracers. Add also diagnostics of advect & diffus flux.
18    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
19      becomes the coordinate variable for the 'T' dimension
20    o add CF-style coordinate variables to MNC
21      - just a first cut:  numbers are meaningless on the cubesphere and
22        missing along the T axis but otherwise it works!
23    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
24    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
25    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
26      this is based directly on what the model compute, so that the content of
27      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
28    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
29    o clean up build options files for SunOS, in particular
30      - remove -traditional from xmakedepend
31      - change -xarch=v9 to -xarch=native for f77
32      - restore use of make (not gmake)
33      - add CC=gcc if using g77
34    o changes per discussion of AM, JMC, & EH3 today:
35      - move redundant "grid" variables out of "state" -- in preparation of
36        creating proper CF-style coordinate variables and in recognition
37        that any/all grid variables can be easily copied (eg. w/NCO) from
38        the grid files into any of the other NetCDF files
39      - *always* output grid variables with MDSIO (this will eventually be
40        changed)
41      - output MNC grid file if useMNC is true
42    o every instance of _END_MASTER() has been found and replaced with
43      _END_MASTER( myThid ) in order to satisfy certain picky Sun
44      preprocessors
45    o re-arrange diagnostics pkg initialisation:
46     - allow each package to extend the available diagnostics list
47     - add some checking and fix small problems (multi-threaded, ...)
48     - new S/R diagnostics_fill (replace fill_diagnostics):
49       look through the short list of active diag. (instead of the long list)
50       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
51    
52    checkpoint57a_post
53    o this set of changes restores TAMC compatibility
54      tested for global_ocean.90x40x15 adjoint on trough
55      (what a pain)
56    
57    checkpoint57a_pre
58    o some modifs in tools/build_options for sunos
59    o call ctrl_pack for ctrl at end for optimcycle=0
60    
61    checkpoint57
62    o add horizontal bi-harmonic viscosity for vertical velocity
63      - new parameter viscA4W (defaults to viscA4)
64      - affects only non-hydrostatic code
65      - to be done: no-slip lateral boundary conditions
66    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
67    o implement Implicit Vertical advection for pTracers
68    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
69      (implemented also for implicit vertical diffusion & advection)
70    o OBCS: extend application of tracer open boundary conditions
71      to a strip beyond the boundary of width Olx/Oly
72    o add call monitor to TAF set of required calls (flow directives)
73      and include in natl_box_adjoint
74    o untangle a few ifdefs related to cost, ctrl, autodiff
75      untangel a few ALLOW_ECCO_OPTIMIZATION
76    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
77      (theta2, salt2 in ecco_cost_weights)
78    
79    checkpoint56c_post
80    o OBCS as control variables
81      - update ctrl_ad_diff.list, obcs_ad_diff.list
82      - remove balance of obcs controls from default
83      - fix index bug nobcs in ctrl_init
84      - fix dummy fields filen in ctrl_pack
85      - add dummy weights for obcs
86    o lsopt: comment out fort.94 output
87    o optim:
88      - remove unnecessary header files
89      - adjusted namelists
90      - add xerbla.F to Makefile
91    o exf:
92      - multiple modifications of exf_check_range
93      - unit change in exf_init_runoff from [m/year] to [m/s]
94    o mdsio:
95      - i/o-vector change debugLevel from debLevA to debLevB
96    
97    checkpoint56b_post
98    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
99      is called from DO_THE_MODEL_IO
100      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
101      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
102      - clean up PTRACERS_WRITE_TIMEAVE a little
103    o add another verification experiment that tests both the cfc-pkg and
104      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
105      reactive tendencies treated inline with regular timestepping
106    o testreport previously did a lousy job of comparing small numbers, so
107      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
108      implemented in the little c-progam tmp_cmpnum.c which is embedded in
109      testreport.
110    o ptracers_monitor: bug fix for MPI
111    
112    checkpoint56a_post
113    o GCHEM: finish reorganizating the package
114      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
115        (introduces another 3D-array for each passive tracer, but only if
116        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
117        gchemTendency is not needed because the timestep is done separately)
118      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
119      - GCHEM is now---more or less cleanly---separate from PTRACERS
120      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
121        so clear to me how that should be done in a general way.
122    o CFC: improve formatting of output in CFC_ATMOS
123    o PTRACERS:
124      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
125        that ALL experiments with ptracers enable can be checked. This makes
126        GCHEM_MONITOR obsolete.
127      - include a runtime parameter PTRACERS_monitorFreq that defaults to
128        monitorFreq
129      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
130  o add PTRACERS (PTR0[1-5]) to testreport output  o add PTRACERS (PTR0[1-5]) to testreport output
131  o exf_check_range:  o exf_check_range:
132    * default changed to .TRUE.    * default changed to .TRUE.
# Line 25  o GCHEM: Line 149  o GCHEM:
149      be replaced by a 3D array that is computed before thermodynamics; for      be replaced by a 3D array that is computed before thermodynamics; for
150      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
151      of ptracers_forcing      of ptracers_forcing
152    - set up forward_step for a call to gchem_forcing, that will replace    - set up forward_step to call gchem_forcing, that will replace
153      gchem_forcing_int in ptracers_forcing      gchem_forcing_int in ptracers_forcing
154    - cleaning up    - cleaning up
155  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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