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revision 1.390 by jmc, Sun Nov 21 22:22:31 2004 UTC revision 1.517 by heimbach, Thu Jul 28 13:43:14 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    checkpoint57m_post
8    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
9      and advect_cs (use EXCH-2 and standard cs-32 grid files).
10    o pkg/exch2: filling of face-corner halo regions is optional
11      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
12    
13    checkpoint57l_post
14     tag before updating tutorials (pre-release-2)
15    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
16       for output and interpolation of input fields onto model grid)
17    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
18       Affects results of exp. rotating_tank ; update output.txt.
19    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
20          and taking the square quantity and/or using a fraction-weight field.
21    o fix aim_diagnostics_init.F mate numbers.
22    o add mnc output capability to diagnostics/diagstat and update
23      our cvsignore files for the ACSII output generated
24    
25    checkpoint57k_post
26    o lab_sea now uses diagnostics package and provides a suite of
27      new EXF diagnostics output.
28    
29    checkpoint57j_post
30    o exf
31      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
32        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
33        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
34      * extended diagnostics output
35        - now includes all EXF variables
36        - hs, hl moved to common block
37        - separate S/R for diagnostics, called after ctrl vector is added
38        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
39        - EXFqnet contains true Qnet (i.e. includes qsw)
40      * updated verif. lab_sea, global_with_exf
41      * Rearranging hflux (exf_mapfields -> exf_getforcing)
42        to ensure that diagnostics sees a true EXFqnet
43    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
44    o diagnostics pkg: change pointers so that 1 diagnostic can be used
45      several times with different frequencies.
46    o mnc-ify the thsice package as requested by Daniel Enderton
47      - the monitor--MNC output needs work
48      - many attributes need to be added (most are currently blank)
49    o mnc-ify theaim_v23 package as requested by Daniel Enderton
50      - many attributes need to be added (most are currently blank)
51    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
52    o add Sadourny like discretization to the 4th.O vorticity advection scheme
53    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
54      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
55         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
56    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
57     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
58    
59    checkpoint57i_post
60    o Diagnostics package was changed: diagnostic allocation is now deactivated
61      by setting an empty file name in the namelist (used to be by setting 0 frequency)
62    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
63      add 1rst Order upwind vertical Shear.
64    o add a quick fix for A/B checkpointing in OFFLINE mode
65    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
66      end-run around the C/Fortran linking horror in eesup/src/timers.F
67    o added pkg/runclock: allows user to terminate run based on wall clock
68    o added non-hydrostatic scaling parameter: nh_am2
69    o pkg/my82: futile attempt to make results compiler-independent by adding
70      some "_d 0", etc. no effect.
71    o for mnc output, fill the 'T' coordinate var with myTime and create a
72      separate 'iter' variable for iteration count
73    o pkg/diagnostics:
74      add new capability: output of Global/Regional & per-level statistics ;
75      tested against monitor output (including land & thSIce) on various exp.
76    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
77    
78    checkpoint57h_done
79      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
80      data.diagnostics, data.gchem, data.ptracers) is done.
81    
82    o pkg/diagnostics: prepare for Global/Regional statistics.
83      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
84    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
85      and rename it: DIFFERENT_MULTIPLE
86    
87    checkpoint57h_post
88    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
89    o pkg/diagnostics: change output frequency, now in seconds (instead
90      of Nb of iterations). This requires to change data.diagnostics.
91    checkpoint57h_pre
92    
93    o in mnc, let the user create the output dir if both mnc_outdir_date
94      and mnc_outdir_num are false
95    o add fflags() to pkg/diagnostics which allows one to specify, on a
96      per-file basis, the file precision [default behavior is unchanged]
97    o added diagnostics to pkg/kpp, including computation of mixed layer
98      depth based on a temperature/density criterion
99    o updated verification/natl_box to test the new pkg/kpp diagnostics
100    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
101    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
102    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
103      not mnc -- this mistake was found by JMC and is now corrected
104    
105    checkpoint57g_post
106    o add Adams-Bashforth 3rd Order time stepping:
107      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
108      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
109    checkpoint57g_pre
110    
111    o make lambda[Theta,Salt]ClimRelax spatially varying
112      (default remains spatially uniform constant based on tau)
113    o added new control variables
114      * init. uVel, vVel, etanN
115      * lambda[Theta,Salt]ClimRelax
116    o separate masks used for ctrl_pack/unpack 'from write_grid' output
117      (suggested by G. Forget)
118    
119    checkpoint57f_post
120    o add parameter "baseTime" = model base time = time at iteration zero
121      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
122      account for baseTime shift
123    o move Coriolis arrays from PARAMS.h to GRID.h
124    checkpoint57f_pre
125    
126    o mnc-ifying the seaice package
127    o introduced an alternative length scale calculation for use in the limiting
128      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
129    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
130    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
131      as well as grad(vort3).  Made it compatible with both approximate form
132      for the cubed sphere and full form of these gradients.  Added flag
133      useFullLeith to select between approximate and full form.  
134    o add "d0" in getcon.F to reduce differences between compilers/platforms
135      update output.txt of exp. fizhi-gridalt-hs
136    o change port_rand funtion to allow to set the seed.
137    o fix obscure MNC bug involving conversion between reals and integers
138      - it caused no problems with certain (eg. gcc, ifc) compilers but the
139        new version is now more standards-compliant
140    o adjoint-related modifications
141      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
142      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
143      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
144    
145    checkpoint57e_post
146    o Adding eddy stress controls a la Ferreira et al.
147    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
148    
149    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
150      update output.txt of exp. fizhi-gridalt-hs
151    o add more "Z" dimensions and associated coordinate vars to MNC
152    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
153    o parameter calendarDumps: when set, approximate months (30-31 days) and years
154      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
155      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
156      months and years.  Requires pkg/cal.
157    o diagnostics: add pickup functionality
158      - off by default for backwards compatibility
159      - current version only uses MDSIO -- MNC will be added
160    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
161    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
162    
163    checkpoint57d_post
164    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
165    o modify verification/ideal_2D_oce so that it tests the creation of mnc
166      output from the diagnostics package
167    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
168    o make genmake2 more portable by using ".$FS" instead of ".f" for more
169      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
170    o add coordinate variables to the MNC output from the diagnostics package
171    o change MNC-flags default value: true when useMNC=TRUE
172    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
173      the ability (off by default) to read the grid information using MNC
174    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
175    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
176    o do snap-shot diagnostics at the middle of the time-interval (instead of
177      at the end).
178    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
179      new test for AIM with thSIce + slab-ocean
180    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
181    o move state variable diagnostics to the beginning of the time step ;
182      (note: still needs some work specially for snap-shot diagnostics)
183      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
184    
185    checkpoint57c_post
186    o Change testing option (-ieee) to get closer agreement between g77 & ifort
187    o generate new output.txt files on faulks with g77 & the new -ieee option
188    checkpoint57c_pre
189    
190    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
191      update output.txt of exp. global_ocean.90x40x15
192    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
193      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
194    o add saltFlux(+File) forcing capability with periodicExternalForcing
195    o allow to use pkg diagnostics for GM-Redi & ThSIce output
196    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
197    o improvements for the MNC output from DIAGNOSTICS:
198      - correct handling of the unlimitied dimension
199      - all dims now have associated coordinate variables
200      - variables located at U, V, and Corner ("Z") points are now written
201        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
202        *all* data points are output
203    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
204    o added pkg/seaice/seaice_monitor.F
205    o mdsio_readfield.F can now read files visible only to master MPI process.
206    o pkg/seaice: some test code for ice-modified ocean stress
207    o exf_getffields interpolation defaults to bilinear for all scalar forcing
208      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
209      spurious negative numbers for precipitation and humidity.  Will cause
210      some small numerical differences for integrations using pkg/exf/exf_interp.F.
211    o pkg/ctrl/
212      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
213        May be enabled via doPackDiag
214      *  introduce z-scaling of
215         + gradient (doZscalePack) and
216         + control (doZscaleUnpack)
217    o pkg/mdsio/
218      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
219      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
220    
221    checkpoint57b_post
222    o simplify options in diagnostics_fill arguments (remove weird combinations)
223    o fix MNC coordinate variables so that they now contain per-face index
224      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
225      general, EXCH2 grids are only aligned to a "local" coordinate system
226    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
227    o Implement instantaneous output within pkg diagnostics:
228      setting a negative frequency in data.diagnostics produces
229     "snap-shot" output (as opposed to time-average if freq > 0)
230    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
231      NOTE: change ptracer diagnostics name: use 2 characters to work with
232            more than 9 tracers. Add also diagnostics of advect & diffus flux.
233    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
234      becomes the coordinate variable for the 'T' dimension
235    o add CF-style coordinate variables to MNC
236      - just a first cut:  numbers are meaningless on the cubesphere and
237        missing along the T axis but otherwise it works!
238    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
239    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
240    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
241      this is based directly on what the model compute, so that the content of
242      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
243    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
244    o clean up build options files for SunOS, in particular
245      - remove -traditional from xmakedepend
246      - change -xarch=v9 to -xarch=native for f77
247      - restore use of make (not gmake)
248      - add CC=gcc if using g77
249    o changes per discussion of AM, JMC, & EH3 today:
250      - move redundant "grid" variables out of "state" -- in preparation of
251        creating proper CF-style coordinate variables and in recognition
252        that any/all grid variables can be easily copied (eg. w/NCO) from
253        the grid files into any of the other NetCDF files
254      - *always* output grid variables with MDSIO (this will eventually be
255        changed)
256      - output MNC grid file if useMNC is true
257    o every instance of _END_MASTER() has been found and replaced with
258      _END_MASTER( myThid ) in order to satisfy certain picky Sun
259      preprocessors
260    o re-arrange diagnostics pkg initialisation:
261     - allow each package to extend the available diagnostics list
262     - add some checking and fix small problems (multi-threaded, ...)
263     - new S/R diagnostics_fill (replace fill_diagnostics):
264       look through the short list of active diag. (instead of the long list)
265       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
266    
267    checkpoint57a_post
268    o this set of changes restores TAMC compatibility
269      tested for global_ocean.90x40x15 adjoint on trough
270      (what a pain)
271    
272    checkpoint57a_pre
273    o some modifs in tools/build_options for sunos
274    o call ctrl_pack for ctrl at end for optimcycle=0
275    
276    checkpoint57
277    o add horizontal bi-harmonic viscosity for vertical velocity
278      - new parameter viscA4W (defaults to viscA4)
279      - affects only non-hydrostatic code
280      - to be done: no-slip lateral boundary conditions
281    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
282    o implement Implicit Vertical advection for pTracers
283    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
284      (implemented also for implicit vertical diffusion & advection)
285    o OBCS: extend application of tracer open boundary conditions
286      to a strip beyond the boundary of width Olx/Oly
287    o add call monitor to TAF set of required calls (flow directives)
288      and include in natl_box_adjoint
289    o untangle a few ifdefs related to cost, ctrl, autodiff
290      untangel a few ALLOW_ECCO_OPTIMIZATION
291    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
292      (theta2, salt2 in ecco_cost_weights)
293    
294    checkpoint56c_post
295    o OBCS as control variables
296      - update ctrl_ad_diff.list, obcs_ad_diff.list
297      - remove balance of obcs controls from default
298      - fix index bug nobcs in ctrl_init
299      - fix dummy fields filen in ctrl_pack
300      - add dummy weights for obcs
301    o lsopt: comment out fort.94 output
302    o optim:
303      - remove unnecessary header files
304      - adjusted namelists
305      - add xerbla.F to Makefile
306    o exf:
307      - multiple modifications of exf_check_range
308      - unit change in exf_init_runoff from [m/year] to [m/s]
309    o mdsio:
310      - i/o-vector change debugLevel from debLevA to debLevB
311    
312    checkpoint56b_post
313    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
314      is called from DO_THE_MODEL_IO
315      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
316      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
317      - clean up PTRACERS_WRITE_TIMEAVE a little
318    o add another verification experiment that tests both the cfc-pkg and
319      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
320      reactive tendencies treated inline with regular timestepping
321    o testreport previously did a lousy job of comparing small numbers, so
322      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
323      implemented in the little c-progam tmp_cmpnum.c which is embedded in
324      testreport.
325    o ptracers_monitor: bug fix for MPI
326    
327    checkpoint56a_post
328    o GCHEM: finish reorganizating the package
329      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
330        (introduces another 3D-array for each passive tracer, but only if
331        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
332        gchemTendency is not needed because the timestep is done separately)
333      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
334      - GCHEM is now---more or less cleanly---separate from PTRACERS
335      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
336        so clear to me how that should be done in a general way.
337    o CFC: improve formatting of output in CFC_ATMOS
338    o PTRACERS:
339      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
340        that ALL experiments with ptracers enable can be checked. This makes
341        GCHEM_MONITOR obsolete.
342      - include a runtime parameter PTRACERS_monitorFreq that defaults to
343        monitorFreq
344      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
345    o add PTRACERS (PTR0[1-5]) to testreport output
346    o exf_check_range:
347      * default changed to .TRUE.
348      * will check values for niter0 if debLevA, every timestep if debLevB
349      * STOP in exf_check_range if 'out of range'
350      * range chosen generous to allow for potential extema
351      TBD: a version with stricter range
352           permitted range would be runtime parameters
353  o GMredi:  o GMredi:
354    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
355    - 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 358  o GCHEM:
358    - 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
359      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
360    - introduced a useGCHEM runtime flag and applied it everywhere.    - introduced a useGCHEM runtime flag and applied it everywhere.
361      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
362        this flag is now only visible within GCHEM-pkg routines.
363      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
364        be replaced by a 3D array that is computed before thermodynamics; for
365        this, the tracer ID iTracer had to be included into the parameter list
366        of ptracers_forcing
367      - set up forward_step to call gchem_forcing, that will replace
368        gchem_forcing_int in ptracers_forcing
369      - cleaning up
370  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
371    
372  checkpoint56  checkpoint56

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