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revision 1.390 by jmc, Sun Nov 21 22:22:31 2004 UTC revision 1.511 by jmc, Sun Jul 10 01:30:46 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    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
8          and/or using a fraction-weight field.
9    o fix aim_diagnostics_init.F mate numbers.
10    o add mnc output capability to diagnostics/diagstat and update
11      our cvsignore files for the ACSII output generated
12    
13    checkpoint57k_post
14    o lab_sea now uses diagnostics package and provides a suite of
15      new EXF diagnostics output.
16    
17    checkpoint57j_post
18    o exf
19      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
20        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
21        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
22      * extended diagnostics output
23        - now includes all EXF variables
24        - hs, hl moved to common block
25        - separate S/R for diagnostics, called after ctrl vector is added
26        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
27        - EXFqnet contains true Qnet (i.e. includes qsw)
28      * updated verif. lab_sea, global_with_exf
29      * Rearranging hflux (exf_mapfields -> exf_getforcing)
30        to ensure that diagnostics sees a true EXFqnet
31    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
32    o diagnostics pkg: change pointers so that 1 diagnostic can be used
33      several times with different frequencies.
34    o mnc-ify the thsice package as requested by Daniel Enderton
35      - the monitor--MNC output needs work
36      - many attributes need to be added (most are currently blank)
37    o mnc-ify theaim_v23 package as requested by Daniel Enderton
38      - many attributes need to be added (most are currently blank)
39    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
40    o add Sadourny like discretization to the 4th.O vorticity advection scheme
41    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
42      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
43         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
44    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
45     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
46    
47    checkpoint57i_post
48    o Diagnostics package was changed: diagnostic allocation is now deactivated
49      by setting an empty file name in the namelist (used to be by setting 0 frequency)
50    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
51      add 1rst Order upwind vertical Shear.
52    o add a quick fix for A/B checkpointing in OFFLINE mode
53    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
54      end-run around the C/Fortran linking horror in eesup/src/timers.F
55    o added pkg/runclock: allows user to terminate run based on wall clock
56    o added non-hydrostatic scaling parameter: nh_am2
57    o pkg/my82: futile attempt to make results compiler-independent by adding
58      some "_d 0", etc. no effect.
59    o for mnc output, fill the 'T' coordinate var with myTime and create a
60      separate 'iter' variable for iteration count
61    o pkg/diagnostics:
62      add new capability: output of Global/Regional & per-level statistics ;
63      tested against monitor output (including land & thSIce) on various exp.
64    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
65    
66    checkpoint57h_done
67      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
68      data.diagnostics, data.gchem, data.ptracers) is done.
69    
70    o pkg/diagnostics: prepare for Global/Regional statistics.
71      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
72    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
73      and rename it: DIFFERENT_MULTIPLE
74    
75    checkpoint57h_post
76    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
77    o pkg/diagnostics: change output frequency, now in seconds (instead
78      of Nb of iterations). This requires to change data.diagnostics.
79    checkpoint57h_pre
80    
81    o in mnc, let the user create the output dir if both mnc_outdir_date
82      and mnc_outdir_num are false
83    o add fflags() to pkg/diagnostics which allows one to specify, on a
84      per-file basis, the file precision [default behavior is unchanged]
85    o added diagnostics to pkg/kpp, including computation of mixed layer
86      depth based on a temperature/density criterion
87    o updated verification/natl_box to test the new pkg/kpp diagnostics
88    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
89    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
90    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
91      not mnc -- this mistake was found by JMC and is now corrected
92    
93    checkpoint57g_post
94    o add Adams-Bashforth 3rd Order time stepping:
95      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
96      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
97    checkpoint57g_pre
98    
99    o make lambda[Theta,Salt]ClimRelax spatially varying
100      (default remains spatially uniform constant based on tau)
101    o added new control variables
102      * init. uVel, vVel, etanN
103      * lambda[Theta,Salt]ClimRelax
104    o separate masks used for ctrl_pack/unpack 'from write_grid' output
105      (suggested by G. Forget)
106    
107    checkpoint57f_post
108    o add parameter "baseTime" = model base time = time at iteration zero
109      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
110      account for baseTime shift
111    o move Coriolis arrays from PARAMS.h to GRID.h
112    checkpoint57f_pre
113    
114    o mnc-ifying the seaice package
115    o introduced an alternative length scale calculation for use in the limiting
116      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
117    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
118    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
119      as well as grad(vort3).  Made it compatible with both approximate form
120      for the cubed sphere and full form of these gradients.  Added flag
121      useFullLeith to select between approximate and full form.  
122    o add "d0" in getcon.F to reduce differences between compilers/platforms
123      update output.txt of exp. fizhi-gridalt-hs
124    o change port_rand funtion to allow to set the seed.
125    o fix obscure MNC bug involving conversion between reals and integers
126      - it caused no problems with certain (eg. gcc, ifc) compilers but the
127        new version is now more standards-compliant
128    o adjoint-related modifications
129      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
130      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
131      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
132    
133    checkpoint57e_post
134    o Adding eddy stress controls a la Ferreira et al.
135    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
136    
137    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
138      update output.txt of exp. fizhi-gridalt-hs
139    o add more "Z" dimensions and associated coordinate vars to MNC
140    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
141    o parameter calendarDumps: when set, approximate months (30-31 days) and years
142      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
143      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
144      months and years.  Requires pkg/cal.
145    o diagnostics: add pickup functionality
146      - off by default for backwards compatibility
147      - current version only uses MDSIO -- MNC will be added
148    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
149    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
150    
151    checkpoint57d_post
152    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
153    o modify verification/ideal_2D_oce so that it tests the creation of mnc
154      output from the diagnostics package
155    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
156    o make genmake2 more portable by using ".$FS" instead of ".f" for more
157      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
158    o add coordinate variables to the MNC output from the diagnostics package
159    o change MNC-flags default value: true when useMNC=TRUE
160    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
161      the ability (off by default) to read the grid information using MNC
162    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
163    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
164    o do snap-shot diagnostics at the middle of the time-interval (instead of
165      at the end).
166    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
167      new test for AIM with thSIce + slab-ocean
168    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
169    o move state variable diagnostics to the beginning of the time step ;
170      (note: still needs some work specially for snap-shot diagnostics)
171      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
172    
173    checkpoint57c_post
174    o Change testing option (-ieee) to get closer agreement between g77 & ifort
175    o generate new output.txt files on faulks with g77 & the new -ieee option
176    checkpoint57c_pre
177    
178    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
179      update output.txt of exp. global_ocean.90x40x15
180    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
181      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
182    o add saltFlux(+File) forcing capability with periodicExternalForcing
183    o allow to use pkg diagnostics for GM-Redi & ThSIce output
184    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
185    o improvements for the MNC output from DIAGNOSTICS:
186      - correct handling of the unlimitied dimension
187      - all dims now have associated coordinate variables
188      - variables located at U, V, and Corner ("Z") points are now written
189        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
190        *all* data points are output
191    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
192    o added pkg/seaice/seaice_monitor.F
193    o mdsio_readfield.F can now read files visible only to master MPI process.
194    o pkg/seaice: some test code for ice-modified ocean stress
195    o exf_getffields interpolation defaults to bilinear for all scalar forcing
196      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
197      spurious negative numbers for precipitation and humidity.  Will cause
198      some small numerical differences for integrations using pkg/exf/exf_interp.F.
199    o pkg/ctrl/
200      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
201        May be enabled via doPackDiag
202      *  introduce z-scaling of
203         + gradient (doZscalePack) and
204         + control (doZscaleUnpack)
205    o pkg/mdsio/
206      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
207      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
208    
209    checkpoint57b_post
210    o simplify options in diagnostics_fill arguments (remove weird combinations)
211    o fix MNC coordinate variables so that they now contain per-face index
212      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
213      general, EXCH2 grids are only aligned to a "local" coordinate system
214    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
215    o Implement instantaneous output within pkg diagnostics:
216      setting a negative frequency in data.diagnostics produces
217     "snap-shot" output (as opposed to time-average if freq > 0)
218    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
219      NOTE: change ptracer diagnostics name: use 2 characters to work with
220            more than 9 tracers. Add also diagnostics of advect & diffus flux.
221    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
222      becomes the coordinate variable for the 'T' dimension
223    o add CF-style coordinate variables to MNC
224      - just a first cut:  numbers are meaningless on the cubesphere and
225        missing along the T axis but otherwise it works!
226    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
227    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
228    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
229      this is based directly on what the model compute, so that the content of
230      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
231    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
232    o clean up build options files for SunOS, in particular
233      - remove -traditional from xmakedepend
234      - change -xarch=v9 to -xarch=native for f77
235      - restore use of make (not gmake)
236      - add CC=gcc if using g77
237    o changes per discussion of AM, JMC, & EH3 today:
238      - move redundant "grid" variables out of "state" -- in preparation of
239        creating proper CF-style coordinate variables and in recognition
240        that any/all grid variables can be easily copied (eg. w/NCO) from
241        the grid files into any of the other NetCDF files
242      - *always* output grid variables with MDSIO (this will eventually be
243        changed)
244      - output MNC grid file if useMNC is true
245    o every instance of _END_MASTER() has been found and replaced with
246      _END_MASTER( myThid ) in order to satisfy certain picky Sun
247      preprocessors
248    o re-arrange diagnostics pkg initialisation:
249     - allow each package to extend the available diagnostics list
250     - add some checking and fix small problems (multi-threaded, ...)
251     - new S/R diagnostics_fill (replace fill_diagnostics):
252       look through the short list of active diag. (instead of the long list)
253       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
254    
255    checkpoint57a_post
256    o this set of changes restores TAMC compatibility
257      tested for global_ocean.90x40x15 adjoint on trough
258      (what a pain)
259    
260    checkpoint57a_pre
261    o some modifs in tools/build_options for sunos
262    o call ctrl_pack for ctrl at end for optimcycle=0
263    
264    checkpoint57
265    o add horizontal bi-harmonic viscosity for vertical velocity
266      - new parameter viscA4W (defaults to viscA4)
267      - affects only non-hydrostatic code
268      - to be done: no-slip lateral boundary conditions
269    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
270    o implement Implicit Vertical advection for pTracers
271    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
272      (implemented also for implicit vertical diffusion & advection)
273    o OBCS: extend application of tracer open boundary conditions
274      to a strip beyond the boundary of width Olx/Oly
275    o add call monitor to TAF set of required calls (flow directives)
276      and include in natl_box_adjoint
277    o untangle a few ifdefs related to cost, ctrl, autodiff
278      untangel a few ALLOW_ECCO_OPTIMIZATION
279    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
280      (theta2, salt2 in ecco_cost_weights)
281    
282    checkpoint56c_post
283    o OBCS as control variables
284      - update ctrl_ad_diff.list, obcs_ad_diff.list
285      - remove balance of obcs controls from default
286      - fix index bug nobcs in ctrl_init
287      - fix dummy fields filen in ctrl_pack
288      - add dummy weights for obcs
289    o lsopt: comment out fort.94 output
290    o optim:
291      - remove unnecessary header files
292      - adjusted namelists
293      - add xerbla.F to Makefile
294    o exf:
295      - multiple modifications of exf_check_range
296      - unit change in exf_init_runoff from [m/year] to [m/s]
297    o mdsio:
298      - i/o-vector change debugLevel from debLevA to debLevB
299    
300    checkpoint56b_post
301    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
302      is called from DO_THE_MODEL_IO
303      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
304      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
305      - clean up PTRACERS_WRITE_TIMEAVE a little
306    o add another verification experiment that tests both the cfc-pkg and
307      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
308      reactive tendencies treated inline with regular timestepping
309    o testreport previously did a lousy job of comparing small numbers, so
310      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
311      implemented in the little c-progam tmp_cmpnum.c which is embedded in
312      testreport.
313    o ptracers_monitor: bug fix for MPI
314    
315    checkpoint56a_post
316    o GCHEM: finish reorganizating the package
317      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
318        (introduces another 3D-array for each passive tracer, but only if
319        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
320        gchemTendency is not needed because the timestep is done separately)
321      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
322      - GCHEM is now---more or less cleanly---separate from PTRACERS
323      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
324        so clear to me how that should be done in a general way.
325    o CFC: improve formatting of output in CFC_ATMOS
326    o PTRACERS:
327      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
328        that ALL experiments with ptracers enable can be checked. This makes
329        GCHEM_MONITOR obsolete.
330      - include a runtime parameter PTRACERS_monitorFreq that defaults to
331        monitorFreq
332      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
333    o add PTRACERS (PTR0[1-5]) to testreport output
334    o exf_check_range:
335      * default changed to .TRUE.
336      * will check values for niter0 if debLevA, every timestep if debLevB
337      * STOP in exf_check_range if 'out of range'
338      * range chosen generous to allow for potential extema
339      TBD: a version with stricter range
340           permitted range would be runtime parameters
341  o GMredi:  o GMredi:
342    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
343    - 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 346  o GCHEM:
346    - 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
347      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
348    - introduced a useGCHEM runtime flag and applied it everywhere.    - introduced a useGCHEM runtime flag and applied it everywhere.
349      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
350        this flag is now only visible within GCHEM-pkg routines.
351      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
352        be replaced by a 3D array that is computed before thermodynamics; for
353        this, the tracer ID iTracer had to be included into the parameter list
354        of ptracers_forcing
355      - set up forward_step to call gchem_forcing, that will replace
356        gchem_forcing_int in ptracers_forcing
357      - cleaning up
358  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
359    
360  checkpoint56  checkpoint56

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