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revision 1.455 by edhill, Sun Feb 20 04:31:54 2005 UTC revision 1.582 by edhill, Fri Nov 25 06:07:19 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 cleanup our namelist syntax in verification:
8      - make it more F95 standards compliant (some work still needed)
9      - allows the vast majority of our tests to work with gfortran
10    o Non-Hydrostatic:
11     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
12     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
13    o Allow to apply AB on T,S rather than on AB(gT,gS):
14     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
15     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
16       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
17     - need a "clever" read_pickup to restart from the other AB formulation
18    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
19    o remove some unused variables (reduces number of compiler warnings)
20    o adjoint
21      * Disable useVariableViscosity for adjoint for time being
22        (there are a number of extensive recomputations)
23      * Initialize certain variables needed for adjoint
24    
25    checkpoint57w_post
26    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
27                 fix the singleCpuIO RS version of MDSWRITEFIELD
28       and add a WARNING if using globalFiles=T with multi-processors.
29    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
30      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
31    o tracer advection scheme:
32      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
33       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
34       was not very convenient).
35      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
36       (further tests needed for the implicit DST & Flux-Limiter schemes).
37    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
38      and sRef for convenience, handy, when you want to initialize
39      ptracers in a large domain with a constant non-zero value. Also,
40      untangle ptracers_init.F a little.
41    
42    checkpoint57v_post
43    o change dome exp. to use variable viscosity in side-drag terms.
44    o remove all the files from the cfc_offline test since they are now
45      incorporated into tutorial_cfc_offline which has been producing
46      identical results for a few days of testing
47    o add new parameter: sideDragFactor to enable half-slip-side BC
48      and change side-drag S/R to use viscosity from mom_calc_visc
49      (can switch back by setting sideDragFactor=0.); affects results at
50      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
51       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
52    o vorticity & strain are now computed without masking, to account for
53      no-slip-side BC in variable viscosity calculation ; mask is applied
54      anyway later on, before computing advection/coriolis terms.
55    o modify exp4 to test new obcs support for reading from external files
56      and for passive tracers
57    o fix behavior of ptracers_monitor when monitor output is written to a
58      netcdf-file; still not independent of monitor.F (writes in the same
59      file).
60    o change default value of tRef (put a uniform, meaningful value for ocean
61      & atmos) and initialize sRef (was missing, as Martin mentioned).
62    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
63      to be proportional to enstrophy dissipation length.  Thus,
64       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
65      This is now consistent with Smagorinsky and with the manual.
66    
67    checkpoint57u_post
68    o OBCS and PTRACERS: add open boundary support for passive tracers
69      - either use homogenous (pseudo) v.Neumann conditions or prescribe
70        OB-values from file; this is not different from the way theta and salinity
71        are treated
72      - however, Orlanski-radiation conditions are not supported, and the model
73        will stop if you use pTracers and Orlanski at the same time.
74      - beefed up the rountine obcs_external_fields_load: now only those open
75        boundary values are overwritten with values from files for which there
76        are really files, otherwise the OB-fields remain untouched. This makes
77        it possible to use different OBs at different ends of the domain (as
78        with EXF)
79    o reduce number of exch calls in shap_filt (s2).
80    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
81      truncation level) 4/5 MLAdjust test results (11&12 digits match).
82    
83    checkpoint57t_post
84    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
85    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
86      same truncation, independent of the face number: affects affects several
87      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
88    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
89      note that biharmonic viscosity + no-slip was not tested in any experiment.
90    o fix bug in non-linear free-surf side-drag ; generate new output for
91      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
92    o make mnc honor the writeBinaryPrec flag for most kinds of output
93    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
94    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
95      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
96    o add brackets in multi-terms sum to get same truncation, independent of
97      the face number (manage to get exactly same value of gU,gV at the cs-edge)
98      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
99    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
100      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
101      a maximum grid-scale Reynolds number.  Also, changes all length calculations
102      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
103      Suggested values of viscosity parameters found in mom_calc_visc.
104      Many new viscosity diagnostics available.
105    
106    checkpoint57s_post
107    o Add clearing-house for viscosity calculations, mom_calc_visc and
108      correct numerous bugs in LeithD and Smagorinsky discretizations.  
109      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
110      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
111      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
112      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
113      The Strain-Tension form is now called with useStrainTensonVisc=.true.
114      ViscAhStrain and viscAhTension are now retired.
115    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
116    o In response to JMC's bug report, genmake2 now ignores any soft-links
117      that it finds in the *current* directory when searching for files.
118      Soft-links found in any other source directories will still work as
119      they did before.
120    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
121      a C routine to unlimit the stack size
122    o mnc-ify pkg/aim snapshot vars
123    o mnc-ify pkg/land as requested by Daniel
124    o various changes to mnc including:
125      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
126      - output can now be grouped so that all files within a group
127          change the ITER portion of their names in lock-step together
128      - can now read ("global") PER-FACE (in addition to PER-TILE) files
129          and works with both EXCH1 and EXCH2 (but needs more testing)
130      - writing works for all verification test cases w/ g77 on Linux
131    
132    checkpoint57r_post
133    o make MNC variable initialization happen earlier
134    o add diagnostics for (almost) each term of the momentum Eq.
135    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
136    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
137    o remove MINIMAL_TAVE_OUTPUT option ;
138      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
139    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
140      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
141    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
142    o add time-dependent SST, SSS control
143    o cost terms in ecco/ modularized (new cost_generic.F)
144    o cost_averages routines are modularized (new cost_averagesgeneric.F)
145    o new infrastructure for seaice model vs. obs misfits in seaice/
146      * driver from the_main_loop.F is seaice_cost_driver.F
147      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
148      * gradient check in Exp. 6a of natl_box_adjoint/
149    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
150      (see README file)
151    
152    checkpoint57q_post
153    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
154    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
155      - bug was reported by Jean-Michel and Ian Fenty
156    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
157      update exp. cpl_aim+ocn output.
158    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
159      Needed for high-res. runs with large global files
160      to be able to limit tapelev size
161    o Changed some tests for adjoint:
162      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
163      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
164      * global_ocean.90x40x15/ back to default 3-level checkpointing
165    o Modifications to enable scripted COMMON to MODULE conversion
166      * verification/OpenAD/code/ has necessary scripts and description;
167      * converts, compiles and runs successfully;
168    
169    checkpoint57p_post
170    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
171    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
172      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
173    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
174    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
175      (was already the case for dissipation with mom_vecinv,
176       and also the case for grad.PhiHyd when staggered-timeStep)
177      This will allow to put dissipation out-off the AB time-stepping.
178     Unfortunately, affects truncation error. Update output of exp. that "fails"
179      (cg2d matching number) and leave the others for later: front_relax(10),
180      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
181      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
182    
183    checkpoint57o_post
184    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
185      (2) its ready to be documented during the 20050801 DocFest
186    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
187      for ideal_2D_oce and lab_sea on linux_ia32_g77
188    o set to #undef CTRL_SET_OLD_MAXCVARS_30
189      in global1x1_tot/code_seaice_adj to access indices 32, 33
190      (worth another tag)
191    
192    checkpoint57n_post
193    o adding precip control xx_precip 32
194    o adding swflux control xx_swflux 33
195    o Replacing 10 forcing penalty cost routines by 1 generic.
196    o Implementing partitioning in time-mean and variable adjustment
197      for atmos. state.
198    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
199    o in natl_box_adjoint:
200      * updated exp 1 to 10
201        (but does not have time-mean vs. variable split results yet)
202    o updated global1x1/*_seaice_adj/
203      to incorporate latest changes
204    o enable useSingleCpuIO for mdsio vector routines
205      (applies in particular to tapelev I/O)
206    o removed inefficient K-loop in all active_file*control*.F
207    
208    checkpoint57m_post
209    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
210      and advect_cs (use EXCH-2 and standard cs-32 grid files).
211    o pkg/exch2: filling of face-corner halo regions is optional
212      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
213    
214    checkpoint57l_post
215     tag before updating tutorials (pre-release-2)
216    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
217       for output and interpolation of input fields onto model grid)
218    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
219       Affects results of exp. rotating_tank ; update output.txt.
220    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
221          and taking the square quantity and/or using a fraction-weight field.
222    o fix aim_diagnostics_init.F mate numbers.
223    o add mnc output capability to diagnostics/diagstat and update
224      our cvsignore files for the ACSII output generated
225    
226    checkpoint57k_post
227    o lab_sea now uses diagnostics package and provides a suite of
228      new EXF diagnostics output.
229    
230    checkpoint57j_post
231    o exf
232      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
233        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
234        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
235      * extended diagnostics output
236        - now includes all EXF variables
237        - hs, hl moved to common block
238        - separate S/R for diagnostics, called after ctrl vector is added
239        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
240        - EXFqnet contains true Qnet (i.e. includes qsw)
241      * updated verif. lab_sea, global_with_exf
242      * Rearranging hflux (exf_mapfields -> exf_getforcing)
243        to ensure that diagnostics sees a true EXFqnet
244    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
245    o diagnostics pkg: change pointers so that 1 diagnostic can be used
246      several times with different frequencies.
247    o mnc-ify the thsice package as requested by Daniel Enderton
248      - the monitor--MNC output needs work
249      - many attributes need to be added (most are currently blank)
250    o mnc-ify theaim_v23 package as requested by Daniel Enderton
251      - many attributes need to be added (most are currently blank)
252    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
253    o add Sadourny like discretization to the 4th.O vorticity advection scheme
254    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
255      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
256         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
257    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
258     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
259    
260    checkpoint57i_post
261    o Diagnostics package was changed: diagnostic allocation is now deactivated
262      by setting an empty file name in the namelist (used to be by setting 0 frequency)
263    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
264      add 1rst Order upwind vertical Shear.
265    o add a quick fix for A/B checkpointing in OFFLINE mode
266    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
267      end-run around the C/Fortran linking horror in eesup/src/timers.F
268    o added pkg/runclock: allows user to terminate run based on wall clock
269    o added non-hydrostatic scaling parameter: nh_am2
270    o pkg/my82: futile attempt to make results compiler-independent by adding
271      some "_d 0", etc. no effect.
272    o for mnc output, fill the 'T' coordinate var with myTime and create a
273      separate 'iter' variable for iteration count
274    o pkg/diagnostics:
275      add new capability: output of Global/Regional & per-level statistics ;
276      tested against monitor output (including land & thSIce) on various exp.
277    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
278    
279    checkpoint57h_done
280      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
281      data.diagnostics, data.gchem, data.ptracers) is done.
282    
283    o pkg/diagnostics: prepare for Global/Regional statistics.
284      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
285    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
286      and rename it: DIFFERENT_MULTIPLE
287    
288    checkpoint57h_post
289    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
290    o pkg/diagnostics: change output frequency, now in seconds (instead
291      of Nb of iterations). This requires to change data.diagnostics.
292    checkpoint57h_pre
293    
294    o in mnc, let the user create the output dir if both mnc_outdir_date
295      and mnc_outdir_num are false
296    o add fflags() to pkg/diagnostics which allows one to specify, on a
297      per-file basis, the file precision [default behavior is unchanged]
298    o added diagnostics to pkg/kpp, including computation of mixed layer
299      depth based on a temperature/density criterion
300    o updated verification/natl_box to test the new pkg/kpp diagnostics
301    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
302    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
303    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
304      not mnc -- this mistake was found by JMC and is now corrected
305    
306    checkpoint57g_post
307    o add Adams-Bashforth 3rd Order time stepping:
308      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
309      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
310    checkpoint57g_pre
311    
312    o make lambda[Theta,Salt]ClimRelax spatially varying
313      (default remains spatially uniform constant based on tau)
314    o added new control variables
315      * init. uVel, vVel, etanN
316      * lambda[Theta,Salt]ClimRelax
317    o separate masks used for ctrl_pack/unpack 'from write_grid' output
318      (suggested by G. Forget)
319    
320    checkpoint57f_post
321    o add parameter "baseTime" = model base time = time at iteration zero
322      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
323      account for baseTime shift
324    o move Coriolis arrays from PARAMS.h to GRID.h
325    checkpoint57f_pre
326    
327    o mnc-ifying the seaice package
328    o introduced an alternative length scale calculation for use in the limiting
329      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
330    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
331    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
332      as well as grad(vort3).  Made it compatible with both approximate form
333      for the cubed sphere and full form of these gradients.  Added flag
334      useFullLeith to select between approximate and full form.  
335    o add "d0" in getcon.F to reduce differences between compilers/platforms
336      update output.txt of exp. fizhi-gridalt-hs
337    o change port_rand funtion to allow to set the seed.
338    o fix obscure MNC bug involving conversion between reals and integers
339      - it caused no problems with certain (eg. gcc, ifc) compilers but the
340        new version is now more standards-compliant
341    o adjoint-related modifications
342      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
343      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
344      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
345    
346    checkpoint57e_post
347    o Adding eddy stress controls a la Ferreira et al.
348    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
349    
350    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
351      update output.txt of exp. fizhi-gridalt-hs
352    o add more "Z" dimensions and associated coordinate vars to MNC
353    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
354    o parameter calendarDumps: when set, approximate months (30-31 days) and years
355      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
356      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
357      months and years.  Requires pkg/cal.
358  o diagnostics: add pickup functionality  o diagnostics: add pickup functionality
359    - off by default for backwards compatibility    - off by default for backwards compatibility
360    - current version only uses MDSIO -- MNC will be added    - current version only uses MDSIO -- MNC will be added

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