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revision 1.390 by jmc, Sun Nov 21 22:22:31 2004 UTC revision 1.419 by edhill, Fri Dec 17 21:28:26 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 add CF-style coordinate variables to MNC
7      - just a first cut:  numbers are meaningless on the cubesphere and
8        missing along the T axis but otherwise it works!
9    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
10    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
11    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
12      this is based directly on what the model compute, so that the content of
13      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
14    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
15    o clean up build options files for SunOS, in particular
16      - remove -traditional from xmakedepend
17      - change -xarch=v9 to -xarch=native for f77
18      - restore use of make (not gmake)
19      - add CC=gcc if using g77
20    o changes per discussion of AM, JMC, & EH3 today:
21      - move redundant "grid" variables out of "state" -- in preparation of
22        creating proper CF-style coordinate variables and in recognition
23        that any/all grid variables can be easily copied (eg. w/NCO) from
24        the grid files into any of the other NetCDF files
25      - *always* output grid variables with MDSIO (this will eventually be
26        changed)
27      - output MNC grid file if useMNC is true
28    o every instance of _END_MASTER() has been found and replaced with
29      _END_MASTER( myThid ) in order to satisfy certain picky Sun
30      preprocessors
31    o re-arrange diagnostics pkg initialisation:
32     - allow each package to extend the available diagnostics list
33     - add some checking and fix small problems (multi-threaded, ...)
34     - new S/R diagnostics_fill (replace fill_diagnostics):
35       look through the short list of active diag. (instead of the long list)
36       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
37    
38    checkpoint57a_post
39    o this set of changes restores TAMC compatibility
40      tested for global_ocean.90x40x15 adjoint on trough
41      (what a pain)
42    
43    checkpoint57a_pre
44    o some modifs in tools/build_options for sunos
45    o call ctrl_pack for ctrl at end for optimcycle=0
46    
47    checkpoint57
48    o add horizontal bi-harmonic viscosity for vertical velocity
49      - new parameter viscA4W (defaults to viscA4)
50      - affects only non-hydrostatic code
51      - to be done: no-slip lateral boundary conditions
52    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
53    o implement Implicit Vertical advection for pTracers
54    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
55      (implemented also for implicit vertical diffusion & advection)
56    o OBCS: extend application of tracer open boundary conditions
57      to a strip beyond the boundary of width Olx/Oly
58    o add call monitor to TAF set of required calls (flow directives)
59      and include in natl_box_adjoint
60    o untangle a few ifdefs related to cost, ctrl, autodiff
61      untangel a few ALLOW_ECCO_OPTIMIZATION
62    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
63      (theta2, salt2 in ecco_cost_weights)
64    
65    checkpoint56c_post
66    o OBCS as control variables
67      - update ctrl_ad_diff.list, obcs_ad_diff.list
68      - remove balance of obcs controls from default
69      - fix index bug nobcs in ctrl_init
70      - fix dummy fields filen in ctrl_pack
71      - add dummy weights for obcs
72    o lsopt: comment out fort.94 output
73    o optim:
74      - remove unnecessary header files
75      - adjusted namelists
76      - add xerbla.F to Makefile
77    o exf:
78      - multiple modifications of exf_check_range
79      - unit change in exf_init_runoff from [m/year] to [m/s]
80    o mdsio:
81      - i/o-vector change debugLevel from debLevA to debLevB
82    
83    checkpoint56b_post
84    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
85      is called from DO_THE_MODEL_IO
86      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
87      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
88      - clean up PTRACERS_WRITE_TIMEAVE a little
89    o add another verification experiment that tests both the cfc-pkg and
90      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
91      reactive tendencies treated inline with regular timestepping
92    o testreport previously did a lousy job of comparing small numbers, so
93      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
94      implemented in the little c-progam tmp_cmpnum.c which is embedded in
95      testreport.
96    o ptracers_monitor: bug fix for MPI
97    
98    checkpoint56a_post
99    o GCHEM: finish reorganizating the package
100      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
101        (introduces another 3D-array for each passive tracer, but only if
102        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
103        gchemTendency is not needed because the timestep is done separately)
104      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
105      - GCHEM is now---more or less cleanly---separate from PTRACERS
106      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
107        so clear to me how that should be done in a general way.
108    o CFC: improve formatting of output in CFC_ATMOS
109    o PTRACERS:
110      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
111        that ALL experiments with ptracers enable can be checked. This makes
112        GCHEM_MONITOR obsolete.
113      - include a runtime parameter PTRACERS_monitorFreq that defaults to
114        monitorFreq
115      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
116    o add PTRACERS (PTR0[1-5]) to testreport output
117    o exf_check_range:
118      * default changed to .TRUE.
119      * will check values for niter0 if debLevA, every timestep if debLevB
120      * STOP in exf_check_range if 'out of range'
121      * range chosen generous to allow for potential extema
122      TBD: a version with stricter range
123           permitted range would be runtime parameters
124  o GMredi:  o GMredi:
125    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
126    - 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 129  o GCHEM:
129    - 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
130      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
131    - introduced a useGCHEM runtime flag and applied it everywhere.    - introduced a useGCHEM runtime flag and applied it everywhere.
132      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
133        this flag is now only visible within GCHEM-pkg routines.
134      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
135        be replaced by a 3D array that is computed before thermodynamics; for
136        this, the tracer ID iTracer had to be included into the parameter list
137        of ptracers_forcing
138      - set up forward_step to call gchem_forcing, that will replace
139        gchem_forcing_int in ptracers_forcing
140      - cleaning up
141  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
142    
143  checkpoint56  checkpoint56
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