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revision 1.392 by mlosch, Tue Nov 23 20:22:12 2004 UTC revision 1.425 by dimitri, Mon Dec 20 23:32:52 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 exf_getffields interpolation defaults to bilinear for all scalar forcing
7      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
8      spurious negative numbers for precipitation and humidity.  Will cause
9      some small numerical differences for integrations using pkg/exf/exf_interp.F.
10    
11    checkpoint57b_post
12    o simplify options in diagnostics_fill arguments (remove weird combinations)
13    o fix MNC coordinate variables so that they now contain per-face index
14      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
15      general, EXCH2 grids are only aligned to a "local" coordinate system
16    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
17    o Implement instantaneous output within pkg diagnostics:
18      setting a negative frequency in data.diagnostics produces
19     "snap-shot" output (as opposed to time-average if freq > 0)
20    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
21      NOTE: change ptracer diagnostics name: use 2 characters to work with
22            more than 9 tracers. Add also diagnostics of advect & diffus flux.
23    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
24      becomes the coordinate variable for the 'T' dimension
25    o add CF-style coordinate variables to MNC
26      - just a first cut:  numbers are meaningless on the cubesphere and
27        missing along the T axis but otherwise it works!
28    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
29    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
30    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
31      this is based directly on what the model compute, so that the content of
32      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
33    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
34    o clean up build options files for SunOS, in particular
35      - remove -traditional from xmakedepend
36      - change -xarch=v9 to -xarch=native for f77
37      - restore use of make (not gmake)
38      - add CC=gcc if using g77
39    o changes per discussion of AM, JMC, & EH3 today:
40      - move redundant "grid" variables out of "state" -- in preparation of
41        creating proper CF-style coordinate variables and in recognition
42        that any/all grid variables can be easily copied (eg. w/NCO) from
43        the grid files into any of the other NetCDF files
44      - *always* output grid variables with MDSIO (this will eventually be
45        changed)
46      - output MNC grid file if useMNC is true
47    o every instance of _END_MASTER() has been found and replaced with
48      _END_MASTER( myThid ) in order to satisfy certain picky Sun
49      preprocessors
50    o re-arrange diagnostics pkg initialisation:
51     - allow each package to extend the available diagnostics list
52     - add some checking and fix small problems (multi-threaded, ...)
53     - new S/R diagnostics_fill (replace fill_diagnostics):
54       look through the short list of active diag. (instead of the long list)
55       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
56    
57    checkpoint57a_post
58    o this set of changes restores TAMC compatibility
59      tested for global_ocean.90x40x15 adjoint on trough
60      (what a pain)
61    
62    checkpoint57a_pre
63    o some modifs in tools/build_options for sunos
64    o call ctrl_pack for ctrl at end for optimcycle=0
65    
66    checkpoint57
67    o add horizontal bi-harmonic viscosity for vertical velocity
68      - new parameter viscA4W (defaults to viscA4)
69      - affects only non-hydrostatic code
70      - to be done: no-slip lateral boundary conditions
71    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
72    o implement Implicit Vertical advection for pTracers
73    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
74      (implemented also for implicit vertical diffusion & advection)
75    o OBCS: extend application of tracer open boundary conditions
76      to a strip beyond the boundary of width Olx/Oly
77    o add call monitor to TAF set of required calls (flow directives)
78      and include in natl_box_adjoint
79    o untangle a few ifdefs related to cost, ctrl, autodiff
80      untangel a few ALLOW_ECCO_OPTIMIZATION
81    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
82      (theta2, salt2 in ecco_cost_weights)
83    
84    checkpoint56c_post
85    o OBCS as control variables
86      - update ctrl_ad_diff.list, obcs_ad_diff.list
87      - remove balance of obcs controls from default
88      - fix index bug nobcs in ctrl_init
89      - fix dummy fields filen in ctrl_pack
90      - add dummy weights for obcs
91    o lsopt: comment out fort.94 output
92    o optim:
93      - remove unnecessary header files
94      - adjusted namelists
95      - add xerbla.F to Makefile
96    o exf:
97      - multiple modifications of exf_check_range
98      - unit change in exf_init_runoff from [m/year] to [m/s]
99    o mdsio:
100      - i/o-vector change debugLevel from debLevA to debLevB
101    
102    checkpoint56b_post
103    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
104      is called from DO_THE_MODEL_IO
105      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
106      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
107      - clean up PTRACERS_WRITE_TIMEAVE a little
108    o add another verification experiment that tests both the cfc-pkg and
109      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
110      reactive tendencies treated inline with regular timestepping
111    o testreport previously did a lousy job of comparing small numbers, so
112      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
113      implemented in the little c-progam tmp_cmpnum.c which is embedded in
114      testreport.
115    o ptracers_monitor: bug fix for MPI
116    
117    checkpoint56a_post
118    o GCHEM: finish reorganizating the package
119      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
120        (introduces another 3D-array for each passive tracer, but only if
121        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
122        gchemTendency is not needed because the timestep is done separately)
123      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
124      - GCHEM is now---more or less cleanly---separate from PTRACERS
125      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
126        so clear to me how that should be done in a general way.
127    o CFC: improve formatting of output in CFC_ATMOS
128    o PTRACERS:
129      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
130        that ALL experiments with ptracers enable can be checked. This makes
131        GCHEM_MONITOR obsolete.
132      - include a runtime parameter PTRACERS_monitorFreq that defaults to
133        monitorFreq
134      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
135    o add PTRACERS (PTR0[1-5]) to testreport output
136  o exf_check_range:  o exf_check_range:
137    * default changed to .TRUE.    * default changed to .TRUE.
138    * will check values for niter0 if debLevA, every timestep if debLevB    * will check values for niter0 if debLevA, every timestep if debLevB
# Line 24  o GCHEM: Line 154  o GCHEM:
154      be replaced by a 3D array that is computed before thermodynamics; for      be replaced by a 3D array that is computed before thermodynamics; for
155      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
156      of ptracers_forcing      of ptracers_forcing
157    - set up forward_step for a call to gchem_forcing, that will replace    - set up forward_step to call gchem_forcing, that will replace
158      gchem_forcing_int in ptracers_forcing      gchem_forcing_int in ptracers_forcing
159    - cleaning up    - cleaning up
160  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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