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revision 1.469 by heimbach, Sun Apr 3 16:11:00 2005 UTC revision 1.588 by heimbach, Thu Dec 8 15:47:40 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    checkpoint57y_post
8    First step for a NLFS adjoint
9    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
10    o new init. routines for calc_r_star, calc_surf_dr
11    o still need to deal with ini_masks_etc
12    o testreport seemed happy
13    checkpoint57y_pre
14    
15    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
16    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
17    o add new offset feature to offline pkg (plus minor cleanup)
18    o cfc fixes for final year of integration
19    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
20      be in GCHEM_OPTIONS).
21    
22    checkpoint57x_post
23    o fix testreport Pb in multiple test experiment.
24    o cleanup our namelist syntax in verification:
25      - make it more F95 standards compliant (some work still needed)
26      - allows the vast majority of our tests to work with gfortran
27    o Non-Hydrostatic:
28     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
29     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
30    o Allow to apply AB on T,S rather than on AB(gT,gS):
31     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
32     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
33       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
34     - need a "clever" read_pickup to restart from the other AB formulation
35    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
36    o remove some unused variables (reduces number of compiler warnings)
37    o adjoint
38      * Disable useVariableViscosity for adjoint for time being
39        (there are a number of extensive recomputations)
40      * Initialize certain variables needed for adjoint
41    
42    checkpoint57w_post
43    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
44                 fix the singleCpuIO RS version of MDSWRITEFIELD
45       and add a WARNING if using globalFiles=T with multi-processors.
46    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
47      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
48    o tracer advection scheme:
49      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
50       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
51       was not very convenient).
52      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
53       (further tests needed for the implicit DST & Flux-Limiter schemes).
54    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
55      and sRef for convenience, handy, when you want to initialize
56      ptracers in a large domain with a constant non-zero value. Also,
57      untangle ptracers_init.F a little.
58    
59    checkpoint57v_post
60    o change dome exp. to use variable viscosity in side-drag terms.
61    o remove all the files from the cfc_offline test since they are now
62      incorporated into tutorial_cfc_offline which has been producing
63      identical results for a few days of testing
64    o add new parameter: sideDragFactor to enable half-slip-side BC
65      and change side-drag S/R to use viscosity from mom_calc_visc
66      (can switch back by setting sideDragFactor=0.); affects results at
67      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
68       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
69    o vorticity & strain are now computed without masking, to account for
70      no-slip-side BC in variable viscosity calculation ; mask is applied
71      anyway later on, before computing advection/coriolis terms.
72    o modify exp4 to test new obcs support for reading from external files
73      and for passive tracers
74    o fix behavior of ptracers_monitor when monitor output is written to a
75      netcdf-file; still not independent of monitor.F (writes in the same
76      file).
77    o change default value of tRef (put a uniform, meaningful value for ocean
78      & atmos) and initialize sRef (was missing, as Martin mentioned).
79    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
80      to be proportional to enstrophy dissipation length.  Thus,
81       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
82      This is now consistent with Smagorinsky and with the manual.
83    
84    checkpoint57u_post
85    o OBCS and PTRACERS: add open boundary support for passive tracers
86      - either use homogenous (pseudo) v.Neumann conditions or prescribe
87        OB-values from file; this is not different from the way theta and salinity
88        are treated
89      - however, Orlanski-radiation conditions are not supported, and the model
90        will stop if you use pTracers and Orlanski at the same time.
91      - beefed up the rountine obcs_external_fields_load: now only those open
92        boundary values are overwritten with values from files for which there
93        are really files, otherwise the OB-fields remain untouched. This makes
94        it possible to use different OBs at different ends of the domain (as
95        with EXF)
96    o reduce number of exch calls in shap_filt (s2).
97    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
98      truncation level) 4/5 MLAdjust test results (11&12 digits match).
99    
100    checkpoint57t_post
101    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
102    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
103      same truncation, independent of the face number: affects affects several
104      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
105    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
106      note that biharmonic viscosity + no-slip was not tested in any experiment.
107    o fix bug in non-linear free-surf side-drag ; generate new output for
108      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
109    o make mnc honor the writeBinaryPrec flag for most kinds of output
110    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
111    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
112      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
113    o add brackets in multi-terms sum to get same truncation, independent of
114      the face number (manage to get exactly same value of gU,gV at the cs-edge)
115      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
116    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
117      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
118      a maximum grid-scale Reynolds number.  Also, changes all length calculations
119      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
120      Suggested values of viscosity parameters found in mom_calc_visc.
121      Many new viscosity diagnostics available.
122    
123    checkpoint57s_post
124    o Add clearing-house for viscosity calculations, mom_calc_visc and
125      correct numerous bugs in LeithD and Smagorinsky discretizations.  
126      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
127      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
128      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
129      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
130      The Strain-Tension form is now called with useStrainTensonVisc=.true.
131      ViscAhStrain and viscAhTension are now retired.
132    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
133    o In response to JMC's bug report, genmake2 now ignores any soft-links
134      that it finds in the *current* directory when searching for files.
135      Soft-links found in any other source directories will still work as
136      they did before.
137    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
138      a C routine to unlimit the stack size
139    o mnc-ify pkg/aim snapshot vars
140    o mnc-ify pkg/land as requested by Daniel
141    o various changes to mnc including:
142      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
143      - output can now be grouped so that all files within a group
144          change the ITER portion of their names in lock-step together
145      - can now read ("global") PER-FACE (in addition to PER-TILE) files
146          and works with both EXCH1 and EXCH2 (but needs more testing)
147      - writing works for all verification test cases w/ g77 on Linux
148    
149    checkpoint57r_post
150    o make MNC variable initialization happen earlier
151    o add diagnostics for (almost) each term of the momentum Eq.
152    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
153    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
154    o remove MINIMAL_TAVE_OUTPUT option ;
155      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
156    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
157      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
158    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
159    o add time-dependent SST, SSS control
160    o cost terms in ecco/ modularized (new cost_generic.F)
161    o cost_averages routines are modularized (new cost_averagesgeneric.F)
162    o new infrastructure for seaice model vs. obs misfits in seaice/
163      * driver from the_main_loop.F is seaice_cost_driver.F
164      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
165      * gradient check in Exp. 6a of natl_box_adjoint/
166    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
167      (see README file)
168    
169    checkpoint57q_post
170    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
171    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
172      - bug was reported by Jean-Michel and Ian Fenty
173    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
174      update exp. cpl_aim+ocn output.
175    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
176      Needed for high-res. runs with large global files
177      to be able to limit tapelev size
178    o Changed some tests for adjoint:
179      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
180      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
181      * global_ocean.90x40x15/ back to default 3-level checkpointing
182    o Modifications to enable scripted COMMON to MODULE conversion
183      * verification/OpenAD/code/ has necessary scripts and description;
184      * converts, compiles and runs successfully;
185    
186    checkpoint57p_post
187    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
188    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
189      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
190    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
191    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
192      (was already the case for dissipation with mom_vecinv,
193       and also the case for grad.PhiHyd when staggered-timeStep)
194      This will allow to put dissipation out-off the AB time-stepping.
195     Unfortunately, affects truncation error. Update output of exp. that "fails"
196      (cg2d matching number) and leave the others for later: front_relax(10),
197      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
198      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
199    
200    checkpoint57o_post
201    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
202      (2) its ready to be documented during the 20050801 DocFest
203    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
204      for ideal_2D_oce and lab_sea on linux_ia32_g77
205    o set to #undef CTRL_SET_OLD_MAXCVARS_30
206      in global1x1_tot/code_seaice_adj to access indices 32, 33
207      (worth another tag)
208    
209    checkpoint57n_post
210    o adding precip control xx_precip 32
211    o adding swflux control xx_swflux 33
212    o Replacing 10 forcing penalty cost routines by 1 generic.
213    o Implementing partitioning in time-mean and variable adjustment
214      for atmos. state.
215    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
216    o in natl_box_adjoint:
217      * updated exp 1 to 10
218        (but does not have time-mean vs. variable split results yet)
219    o updated global1x1/*_seaice_adj/
220      to incorporate latest changes
221    o enable useSingleCpuIO for mdsio vector routines
222      (applies in particular to tapelev I/O)
223    o removed inefficient K-loop in all active_file*control*.F
224    
225    checkpoint57m_post
226    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
227      and advect_cs (use EXCH-2 and standard cs-32 grid files).
228    o pkg/exch2: filling of face-corner halo regions is optional
229      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
230    
231    checkpoint57l_post
232     tag before updating tutorials (pre-release-2)
233    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
234       for output and interpolation of input fields onto model grid)
235    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
236       Affects results of exp. rotating_tank ; update output.txt.
237    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
238          and taking the square quantity and/or using a fraction-weight field.
239    o fix aim_diagnostics_init.F mate numbers.
240    o add mnc output capability to diagnostics/diagstat and update
241      our cvsignore files for the ACSII output generated
242    
243    checkpoint57k_post
244    o lab_sea now uses diagnostics package and provides a suite of
245      new EXF diagnostics output.
246    
247    checkpoint57j_post
248    o exf
249      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
250        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
251        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
252      * extended diagnostics output
253        - now includes all EXF variables
254        - hs, hl moved to common block
255        - separate S/R for diagnostics, called after ctrl vector is added
256        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
257        - EXFqnet contains true Qnet (i.e. includes qsw)
258      * updated verif. lab_sea, global_with_exf
259      * Rearranging hflux (exf_mapfields -> exf_getforcing)
260        to ensure that diagnostics sees a true EXFqnet
261    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
262    o diagnostics pkg: change pointers so that 1 diagnostic can be used
263      several times with different frequencies.
264    o mnc-ify the thsice package as requested by Daniel Enderton
265      - the monitor--MNC output needs work
266      - many attributes need to be added (most are currently blank)
267    o mnc-ify theaim_v23 package as requested by Daniel Enderton
268      - many attributes need to be added (most are currently blank)
269    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
270    o add Sadourny like discretization to the 4th.O vorticity advection scheme
271    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
272      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
273         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
274    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
275     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
276    
277    checkpoint57i_post
278    o Diagnostics package was changed: diagnostic allocation is now deactivated
279      by setting an empty file name in the namelist (used to be by setting 0 frequency)
280    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
281      add 1rst Order upwind vertical Shear.
282    o add a quick fix for A/B checkpointing in OFFLINE mode
283    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
284      end-run around the C/Fortran linking horror in eesup/src/timers.F
285    o added pkg/runclock: allows user to terminate run based on wall clock
286    o added non-hydrostatic scaling parameter: nh_am2
287    o pkg/my82: futile attempt to make results compiler-independent by adding
288      some "_d 0", etc. no effect.
289    o for mnc output, fill the 'T' coordinate var with myTime and create a
290      separate 'iter' variable for iteration count
291    o pkg/diagnostics:
292      add new capability: output of Global/Regional & per-level statistics ;
293      tested against monitor output (including land & thSIce) on various exp.
294    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
295    
296    checkpoint57h_done
297      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
298      data.diagnostics, data.gchem, data.ptracers) is done.
299    
300    o pkg/diagnostics: prepare for Global/Regional statistics.
301      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
302    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
303      and rename it: DIFFERENT_MULTIPLE
304    
305    checkpoint57h_post
306    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
307    o pkg/diagnostics: change output frequency, now in seconds (instead
308      of Nb of iterations). This requires to change data.diagnostics.
309    checkpoint57h_pre
310    
311    o in mnc, let the user create the output dir if both mnc_outdir_date
312      and mnc_outdir_num are false
313    o add fflags() to pkg/diagnostics which allows one to specify, on a
314      per-file basis, the file precision [default behavior is unchanged]
315    o added diagnostics to pkg/kpp, including computation of mixed layer
316      depth based on a temperature/density criterion
317    o updated verification/natl_box to test the new pkg/kpp diagnostics
318    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
319    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
320    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
321      not mnc -- this mistake was found by JMC and is now corrected
322    
323    checkpoint57g_post
324    o add Adams-Bashforth 3rd Order time stepping:
325      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
326      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
327    checkpoint57g_pre
328    
329    o make lambda[Theta,Salt]ClimRelax spatially varying
330      (default remains spatially uniform constant based on tau)
331    o added new control variables
332      * init. uVel, vVel, etanN
333      * lambda[Theta,Salt]ClimRelax
334    o separate masks used for ctrl_pack/unpack 'from write_grid' output
335      (suggested by G. Forget)
336    
337    checkpoint57f_post
338    o add parameter "baseTime" = model base time = time at iteration zero
339      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
340      account for baseTime shift
341    o move Coriolis arrays from PARAMS.h to GRID.h
342    checkpoint57f_pre
343    
344  o mnc-ifying the seaice package  o mnc-ifying the seaice package
345  o introduced an alternative length scale calculation for use in the limiting  o introduced an alternative length scale calculation for use in the limiting
346    maximum viscosity (off by default, see mom_vi_hdissip.F for details)    maximum viscosity (off by default, see mom_vi_hdissip.F for details)
# Line 24  o adjoint-related modifications Line 362  o adjoint-related modifications
362    
363  checkpoint57e_post  checkpoint57e_post
364  o Adding eddy stress controls a la Ferreira et al.  o Adding eddy stress controls a la Ferreira et al.
365  checkpoint57e_pre  checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
366    
367  o fizhi pkg: fix AtoC and CtoA when called with same input & output array  o fizhi pkg: fix AtoC and CtoA when called with same input & output array
368    update output.txt of exp. fizhi-gridalt-hs    update output.txt of exp. fizhi-gridalt-hs

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