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revision 1.393 by edhill, Tue Nov 23 21:25:24 2004 UTC revision 1.421 by jmc, Sun Dec 19 00:59:16 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 move out off EQUIVALENCE all diagnostics that fizhi does not use ;
7      NOTE: change ptracer diagnostics name: use 2 characters to work with
8            more than 9 tracers. Add also diagnostics of advect & diffus flux.
9    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
10      becomes the coordinate variable for the 'T' dimension
11    o add CF-style coordinate variables to MNC
12      - just a first cut:  numbers are meaningless on the cubesphere and
13        missing along the T axis but otherwise it works!
14    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
15    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
16    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
17      this is based directly on what the model compute, so that the content of
18      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
19    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
20    o clean up build options files for SunOS, in particular
21      - remove -traditional from xmakedepend
22      - change -xarch=v9 to -xarch=native for f77
23      - restore use of make (not gmake)
24      - add CC=gcc if using g77
25    o changes per discussion of AM, JMC, & EH3 today:
26      - move redundant "grid" variables out of "state" -- in preparation of
27        creating proper CF-style coordinate variables and in recognition
28        that any/all grid variables can be easily copied (eg. w/NCO) from
29        the grid files into any of the other NetCDF files
30      - *always* output grid variables with MDSIO (this will eventually be
31        changed)
32      - output MNC grid file if useMNC is true
33    o every instance of _END_MASTER() has been found and replaced with
34      _END_MASTER( myThid ) in order to satisfy certain picky Sun
35      preprocessors
36    o re-arrange diagnostics pkg initialisation:
37     - allow each package to extend the available diagnostics list
38     - add some checking and fix small problems (multi-threaded, ...)
39     - new S/R diagnostics_fill (replace fill_diagnostics):
40       look through the short list of active diag. (instead of the long list)
41       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
42    
43    checkpoint57a_post
44    o this set of changes restores TAMC compatibility
45      tested for global_ocean.90x40x15 adjoint on trough
46      (what a pain)
47    
48    checkpoint57a_pre
49    o some modifs in tools/build_options for sunos
50    o call ctrl_pack for ctrl at end for optimcycle=0
51    
52    checkpoint57
53    o add horizontal bi-harmonic viscosity for vertical velocity
54      - new parameter viscA4W (defaults to viscA4)
55      - affects only non-hydrostatic code
56      - to be done: no-slip lateral boundary conditions
57    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
58    o implement Implicit Vertical advection for pTracers
59    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
60      (implemented also for implicit vertical diffusion & advection)
61    o OBCS: extend application of tracer open boundary conditions
62      to a strip beyond the boundary of width Olx/Oly
63    o add call monitor to TAF set of required calls (flow directives)
64      and include in natl_box_adjoint
65    o untangle a few ifdefs related to cost, ctrl, autodiff
66      untangel a few ALLOW_ECCO_OPTIMIZATION
67    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
68      (theta2, salt2 in ecco_cost_weights)
69    
70    checkpoint56c_post
71    o OBCS as control variables
72      - update ctrl_ad_diff.list, obcs_ad_diff.list
73      - remove balance of obcs controls from default
74      - fix index bug nobcs in ctrl_init
75      - fix dummy fields filen in ctrl_pack
76      - add dummy weights for obcs
77    o lsopt: comment out fort.94 output
78    o optim:
79      - remove unnecessary header files
80      - adjusted namelists
81      - add xerbla.F to Makefile
82    o exf:
83      - multiple modifications of exf_check_range
84      - unit change in exf_init_runoff from [m/year] to [m/s]
85    o mdsio:
86      - i/o-vector change debugLevel from debLevA to debLevB
87    
88    checkpoint56b_post
89    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
90      is called from DO_THE_MODEL_IO
91      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
92      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
93      - clean up PTRACERS_WRITE_TIMEAVE a little
94    o add another verification experiment that tests both the cfc-pkg and
95      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
96      reactive tendencies treated inline with regular timestepping
97    o testreport previously did a lousy job of comparing small numbers, so
98      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
99      implemented in the little c-progam tmp_cmpnum.c which is embedded in
100      testreport.
101    o ptracers_monitor: bug fix for MPI
102    
103    checkpoint56a_post
104    o GCHEM: finish reorganizating the package
105      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
106        (introduces another 3D-array for each passive tracer, but only if
107        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
108        gchemTendency is not needed because the timestep is done separately)
109      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
110      - GCHEM is now---more or less cleanly---separate from PTRACERS
111      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
112        so clear to me how that should be done in a general way.
113    o CFC: improve formatting of output in CFC_ATMOS
114    o PTRACERS:
115      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
116        that ALL experiments with ptracers enable can be checked. This makes
117        GCHEM_MONITOR obsolete.
118      - include a runtime parameter PTRACERS_monitorFreq that defaults to
119        monitorFreq
120      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
121  o add PTRACERS (PTR0[1-5]) to testreport output  o add PTRACERS (PTR0[1-5]) to testreport output
122  o exf_check_range:  o exf_check_range:
123    * default changed to .TRUE.    * default changed to .TRUE.
# Line 25  o GCHEM: Line 140  o GCHEM:
140      be replaced by a 3D array that is computed before thermodynamics; for      be replaced by a 3D array that is computed before thermodynamics; for
141      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
142      of ptracers_forcing      of ptracers_forcing
143    - set up forward_step for a call to gchem_forcing, that will replace    - set up forward_step to call gchem_forcing, that will replace
144      gchem_forcing_int in ptracers_forcing      gchem_forcing_int in ptracers_forcing
145    - cleaning up    - cleaning up
146  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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