/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.390 by jmc, Sun Nov 21 22:22:31 2004 UTC revision 1.509 by heimbach, Sat Jul 2 16:13:50 2005 UTC
# Line 1  Line 1 
1  $Header$  $Header$
2    $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint57k_post
8    o lab_sea now uses diagnostics package and provides a suite of
9      new EXF diagnostics output.
10    
11    checkpoint57j_post
12    o exf
13      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
14        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
15        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
16      * extended diagnostics output
17        - now includes all EXF variables
18        - hs, hl moved to common block
19        - separate S/R for diagnostics, called after ctrl vector is added
20        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
21        - EXFqnet contains true Qnet (i.e. includes qsw)
22      * updated verif. lab_sea, global_with_exf
23      * Rearranging hflux (exf_mapfields -> exf_getforcing)
24        to ensure that diagnostics sees a true EXFqnet
25    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
26    o diagnostics pkg: change pointers so that 1 diagnostic can be used
27      several times with different frequencies.
28    o mnc-ify the thsice package as requested by Daniel Enderton
29      - the monitor--MNC output needs work
30      - many attributes need to be added (most are currently blank)
31    o mnc-ify theaim_v23 package as requested by Daniel Enderton
32      - many attributes need to be added (most are currently blank)
33    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
34    o add Sadourny like discretization to the 4th.O vorticity advection scheme
35    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
36      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
37         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
38    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
39     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
40    
41    checkpoint57i_post
42    o Diagnostics package was changed: diagnostic allocation is now deactivated
43      by setting an empty file name in the namelist (used to be by setting 0 frequency)
44    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
45      add 1rst Order upwind vertical Shear.
46    o add a quick fix for A/B checkpointing in OFFLINE mode
47    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
48      end-run around the C/Fortran linking horror in eesup/src/timers.F
49    o added pkg/runclock: allows user to terminate run based on wall clock
50    o added non-hydrostatic scaling parameter: nh_am2
51    o pkg/my82: futile attempt to make results compiler-independent by adding
52      some "_d 0", etc. no effect.
53    o for mnc output, fill the 'T' coordinate var with myTime and create a
54      separate 'iter' variable for iteration count
55    o pkg/diagnostics:
56      add new capability: output of Global/Regional & per-level statistics ;
57      tested against monitor output (including land & thSIce) on various exp.
58    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
59    
60    checkpoint57h_done
61      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
62      data.diagnostics, data.gchem, data.ptracers) is done.
63    
64    o pkg/diagnostics: prepare for Global/Regional statistics.
65      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
66    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
67      and rename it: DIFFERENT_MULTIPLE
68    
69    checkpoint57h_post
70    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
71    o pkg/diagnostics: change output frequency, now in seconds (instead
72      of Nb of iterations). This requires to change data.diagnostics.
73    checkpoint57h_pre
74    
75    o in mnc, let the user create the output dir if both mnc_outdir_date
76      and mnc_outdir_num are false
77    o add fflags() to pkg/diagnostics which allows one to specify, on a
78      per-file basis, the file precision [default behavior is unchanged]
79    o added diagnostics to pkg/kpp, including computation of mixed layer
80      depth based on a temperature/density criterion
81    o updated verification/natl_box to test the new pkg/kpp diagnostics
82    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
83    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
84    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
85      not mnc -- this mistake was found by JMC and is now corrected
86    
87    checkpoint57g_post
88    o add Adams-Bashforth 3rd Order time stepping:
89      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
90      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
91    checkpoint57g_pre
92    
93    o make lambda[Theta,Salt]ClimRelax spatially varying
94      (default remains spatially uniform constant based on tau)
95    o added new control variables
96      * init. uVel, vVel, etanN
97      * lambda[Theta,Salt]ClimRelax
98    o separate masks used for ctrl_pack/unpack 'from write_grid' output
99      (suggested by G. Forget)
100    
101    checkpoint57f_post
102    o add parameter "baseTime" = model base time = time at iteration zero
103      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
104      account for baseTime shift
105    o move Coriolis arrays from PARAMS.h to GRID.h
106    checkpoint57f_pre
107    
108    o mnc-ifying the seaice package
109    o introduced an alternative length scale calculation for use in the limiting
110      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
111    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
112    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
113      as well as grad(vort3).  Made it compatible with both approximate form
114      for the cubed sphere and full form of these gradients.  Added flag
115      useFullLeith to select between approximate and full form.  
116    o add "d0" in getcon.F to reduce differences between compilers/platforms
117      update output.txt of exp. fizhi-gridalt-hs
118    o change port_rand funtion to allow to set the seed.
119    o fix obscure MNC bug involving conversion between reals and integers
120      - it caused no problems with certain (eg. gcc, ifc) compilers but the
121        new version is now more standards-compliant
122    o adjoint-related modifications
123      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
124      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
125      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
126    
127    checkpoint57e_post
128    o Adding eddy stress controls a la Ferreira et al.
129    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
130    
131    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
132      update output.txt of exp. fizhi-gridalt-hs
133    o add more "Z" dimensions and associated coordinate vars to MNC
134    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
135    o parameter calendarDumps: when set, approximate months (30-31 days) and years
136      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
137      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
138      months and years.  Requires pkg/cal.
139    o diagnostics: add pickup functionality
140      - off by default for backwards compatibility
141      - current version only uses MDSIO -- MNC will be added
142    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
143    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
144    
145    checkpoint57d_post
146    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
147    o modify verification/ideal_2D_oce so that it tests the creation of mnc
148      output from the diagnostics package
149    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
150    o make genmake2 more portable by using ".$FS" instead of ".f" for more
151      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
152    o add coordinate variables to the MNC output from the diagnostics package
153    o change MNC-flags default value: true when useMNC=TRUE
154    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
155      the ability (off by default) to read the grid information using MNC
156    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
157    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
158    o do snap-shot diagnostics at the middle of the time-interval (instead of
159      at the end).
160    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
161      new test for AIM with thSIce + slab-ocean
162    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
163    o move state variable diagnostics to the beginning of the time step ;
164      (note: still needs some work specially for snap-shot diagnostics)
165      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
166    
167    checkpoint57c_post
168    o Change testing option (-ieee) to get closer agreement between g77 & ifort
169    o generate new output.txt files on faulks with g77 & the new -ieee option
170    checkpoint57c_pre
171    
172    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
173      update output.txt of exp. global_ocean.90x40x15
174    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
175      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
176    o add saltFlux(+File) forcing capability with periodicExternalForcing
177    o allow to use pkg diagnostics for GM-Redi & ThSIce output
178    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
179    o improvements for the MNC output from DIAGNOSTICS:
180      - correct handling of the unlimitied dimension
181      - all dims now have associated coordinate variables
182      - variables located at U, V, and Corner ("Z") points are now written
183        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
184        *all* data points are output
185    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
186    o added pkg/seaice/seaice_monitor.F
187    o mdsio_readfield.F can now read files visible only to master MPI process.
188    o pkg/seaice: some test code for ice-modified ocean stress
189    o exf_getffields interpolation defaults to bilinear for all scalar forcing
190      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
191      spurious negative numbers for precipitation and humidity.  Will cause
192      some small numerical differences for integrations using pkg/exf/exf_interp.F.
193    o pkg/ctrl/
194      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
195        May be enabled via doPackDiag
196      *  introduce z-scaling of
197         + gradient (doZscalePack) and
198         + control (doZscaleUnpack)
199    o pkg/mdsio/
200      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
201      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
202    
203    checkpoint57b_post
204    o simplify options in diagnostics_fill arguments (remove weird combinations)
205    o fix MNC coordinate variables so that they now contain per-face index
206      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
207      general, EXCH2 grids are only aligned to a "local" coordinate system
208    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
209    o Implement instantaneous output within pkg diagnostics:
210      setting a negative frequency in data.diagnostics produces
211     "snap-shot" output (as opposed to time-average if freq > 0)
212    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
213      NOTE: change ptracer diagnostics name: use 2 characters to work with
214            more than 9 tracers. Add also diagnostics of advect & diffus flux.
215    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
216      becomes the coordinate variable for the 'T' dimension
217    o add CF-style coordinate variables to MNC
218      - just a first cut:  numbers are meaningless on the cubesphere and
219        missing along the T axis but otherwise it works!
220    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
221    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
222    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
223      this is based directly on what the model compute, so that the content of
224      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
225    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
226    o clean up build options files for SunOS, in particular
227      - remove -traditional from xmakedepend
228      - change -xarch=v9 to -xarch=native for f77
229      - restore use of make (not gmake)
230      - add CC=gcc if using g77
231    o changes per discussion of AM, JMC, & EH3 today:
232      - move redundant "grid" variables out of "state" -- in preparation of
233        creating proper CF-style coordinate variables and in recognition
234        that any/all grid variables can be easily copied (eg. w/NCO) from
235        the grid files into any of the other NetCDF files
236      - *always* output grid variables with MDSIO (this will eventually be
237        changed)
238      - output MNC grid file if useMNC is true
239    o every instance of _END_MASTER() has been found and replaced with
240      _END_MASTER( myThid ) in order to satisfy certain picky Sun
241      preprocessors
242    o re-arrange diagnostics pkg initialisation:
243     - allow each package to extend the available diagnostics list
244     - add some checking and fix small problems (multi-threaded, ...)
245     - new S/R diagnostics_fill (replace fill_diagnostics):
246       look through the short list of active diag. (instead of the long list)
247       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
248    
249    checkpoint57a_post
250    o this set of changes restores TAMC compatibility
251      tested for global_ocean.90x40x15 adjoint on trough
252      (what a pain)
253    
254    checkpoint57a_pre
255    o some modifs in tools/build_options for sunos
256    o call ctrl_pack for ctrl at end for optimcycle=0
257    
258    checkpoint57
259    o add horizontal bi-harmonic viscosity for vertical velocity
260      - new parameter viscA4W (defaults to viscA4)
261      - affects only non-hydrostatic code
262      - to be done: no-slip lateral boundary conditions
263    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
264    o implement Implicit Vertical advection for pTracers
265    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
266      (implemented also for implicit vertical diffusion & advection)
267    o OBCS: extend application of tracer open boundary conditions
268      to a strip beyond the boundary of width Olx/Oly
269    o add call monitor to TAF set of required calls (flow directives)
270      and include in natl_box_adjoint
271    o untangle a few ifdefs related to cost, ctrl, autodiff
272      untangel a few ALLOW_ECCO_OPTIMIZATION
273    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
274      (theta2, salt2 in ecco_cost_weights)
275    
276    checkpoint56c_post
277    o OBCS as control variables
278      - update ctrl_ad_diff.list, obcs_ad_diff.list
279      - remove balance of obcs controls from default
280      - fix index bug nobcs in ctrl_init
281      - fix dummy fields filen in ctrl_pack
282      - add dummy weights for obcs
283    o lsopt: comment out fort.94 output
284    o optim:
285      - remove unnecessary header files
286      - adjusted namelists
287      - add xerbla.F to Makefile
288    o exf:
289      - multiple modifications of exf_check_range
290      - unit change in exf_init_runoff from [m/year] to [m/s]
291    o mdsio:
292      - i/o-vector change debugLevel from debLevA to debLevB
293    
294    checkpoint56b_post
295    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
296      is called from DO_THE_MODEL_IO
297      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
298      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
299      - clean up PTRACERS_WRITE_TIMEAVE a little
300    o add another verification experiment that tests both the cfc-pkg and
301      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
302      reactive tendencies treated inline with regular timestepping
303    o testreport previously did a lousy job of comparing small numbers, so
304      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
305      implemented in the little c-progam tmp_cmpnum.c which is embedded in
306      testreport.
307    o ptracers_monitor: bug fix for MPI
308    
309    checkpoint56a_post
310    o GCHEM: finish reorganizating the package
311      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
312        (introduces another 3D-array for each passive tracer, but only if
313        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
314        gchemTendency is not needed because the timestep is done separately)
315      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
316      - GCHEM is now---more or less cleanly---separate from PTRACERS
317      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
318        so clear to me how that should be done in a general way.
319    o CFC: improve formatting of output in CFC_ATMOS
320    o PTRACERS:
321      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
322        that ALL experiments with ptracers enable can be checked. This makes
323        GCHEM_MONITOR obsolete.
324      - include a runtime parameter PTRACERS_monitorFreq that defaults to
325        monitorFreq
326      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
327    o add PTRACERS (PTR0[1-5]) to testreport output
328    o exf_check_range:
329      * default changed to .TRUE.
330      * will check values for niter0 if debLevA, every timestep if debLevB
331      * STOP in exf_check_range if 'out of range'
332      * range chosen generous to allow for potential extema
333      TBD: a version with stricter range
334           permitted range would be runtime parameters
335  o GMredi:  o GMredi:
336    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
337    - 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 340  o GCHEM:
340    - 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
341      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
342    - introduced a useGCHEM runtime flag and applied it everywhere.    - introduced a useGCHEM runtime flag and applied it everywhere.
343      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
344        this flag is now only visible within GCHEM-pkg routines.
345      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
346        be replaced by a 3D array that is computed before thermodynamics; for
347        this, the tracer ID iTracer had to be included into the parameter list
348        of ptracers_forcing
349      - set up forward_step to call gchem_forcing, that will replace
350        gchem_forcing_int in ptracers_forcing
351      - cleaning up
352  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
353    
354  checkpoint56  checkpoint56

Legend:
Removed from v.1.390  
changed lines
  Added in v.1.509

  ViewVC Help
Powered by ViewVC 1.1.22