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revision 1.390 by jmc, Sun Nov 21 22:22:31 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
122    o exf_check_range:
123      * default changed to .TRUE.
124      * will check values for niter0 if debLevA, every timestep if debLevB
125      * STOP in exf_check_range if 'out of range'
126      * range chosen generous to allow for potential extema
127      TBD: a version with stricter range
128           permitted range would be runtime parameters
129  o GMredi:  o GMredi:
130    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
131    - 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 134  o GCHEM:
134    - 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
135      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
136    - introduced a useGCHEM runtime flag and applied it everywhere.    - introduced a useGCHEM runtime flag and applied it everywhere.
137      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
138        this flag is now only visible within GCHEM-pkg routines.
139      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
140        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
142        of ptracers_forcing
143      - set up forward_step to call gchem_forcing, that will replace
144        gchem_forcing_int in ptracers_forcing
145      - 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
147    
148  checkpoint56  checkpoint56
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