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revision 1.480 by dimitri, Fri Apr 29 18:47:02 2005 UTC revision 1.591 by jmc, Tue Dec 13 23:29:25 2005 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o no AB-2 at the first iteration for Gw (consistant with Gu,Gv,Gt,Gs ...)
8      affect results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
9    o transfert surface NH pressure to eta field (if exactConserv).
10    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
11         and update lab_sea output.txt file.
12    o completing 3-dim. relaxation code: additional term
13         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
14      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
15      * At compile time, in "EXF_OPTIONS.h" set
16          #define  ALLOW_CLIMTEMP_RELAXATION
17          #define  ALLOW_CLIMSALT_RELAXATION
18      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
19          tauThetaClimRelax3Dim = 15552000.0,
20          tauSaltClimRelax3Dim  = 15552000.0,
21      * 3 cases:
22          1) Use a constant-in-time 3-dim. field
23          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
24          3) Real-time relax. to time-evolving prescribed field
25    
26    checkpoint57y_post
27    First step for a NLFS adjoint
28    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
29    o new init. routines for calc_r_star, calc_surf_dr
30    o still need to deal with ini_masks_etc
31    o testreport seemed happy
32    checkpoint57y_pre
33    
34    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
35    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
36    o add new offset feature to offline pkg (plus minor cleanup)
37    o cfc fixes for final year of integration
38    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
39      be in GCHEM_OPTIONS).
40    
41    checkpoint57x_post
42    o fix testreport Pb in multiple test experiment.
43    o cleanup our namelist syntax in verification:
44      - make it more F95 standards compliant (some work still needed)
45      - allows the vast majority of our tests to work with gfortran
46    o Non-Hydrostatic:
47     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
48     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
49    o Allow to apply AB on T,S rather than on AB(gT,gS):
50     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
51     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
52       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
53     - need a "clever" read_pickup to restart from the other AB formulation
54    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
55    o remove some unused variables (reduces number of compiler warnings)
56    o adjoint
57      * Disable useVariableViscosity for adjoint for time being
58        (there are a number of extensive recomputations)
59      * Initialize certain variables needed for adjoint
60    
61    checkpoint57w_post
62    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
63                 fix the singleCpuIO RS version of MDSWRITEFIELD
64       and add a WARNING if using globalFiles=T with multi-processors.
65    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
66      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
67    o tracer advection scheme:
68      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
69       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
70       was not very convenient).
71      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
72       (further tests needed for the implicit DST & Flux-Limiter schemes).
73    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
74      and sRef for convenience, handy, when you want to initialize
75      ptracers in a large domain with a constant non-zero value. Also,
76      untangle ptracers_init.F a little.
77    
78    checkpoint57v_post
79    o change dome exp. to use variable viscosity in side-drag terms.
80    o remove all the files from the cfc_offline test since they are now
81      incorporated into tutorial_cfc_offline which has been producing
82      identical results for a few days of testing
83    o add new parameter: sideDragFactor to enable half-slip-side BC
84      and change side-drag S/R to use viscosity from mom_calc_visc
85      (can switch back by setting sideDragFactor=0.); affects results at
86      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
87       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
88    o vorticity & strain are now computed without masking, to account for
89      no-slip-side BC in variable viscosity calculation ; mask is applied
90      anyway later on, before computing advection/coriolis terms.
91    o modify exp4 to test new obcs support for reading from external files
92      and for passive tracers
93    o fix behavior of ptracers_monitor when monitor output is written to a
94      netcdf-file; still not independent of monitor.F (writes in the same
95      file).
96    o change default value of tRef (put a uniform, meaningful value for ocean
97      & atmos) and initialize sRef (was missing, as Martin mentioned).
98    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
99      to be proportional to enstrophy dissipation length.  Thus,
100       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
101      This is now consistent with Smagorinsky and with the manual.
102    
103    checkpoint57u_post
104    o OBCS and PTRACERS: add open boundary support for passive tracers
105      - either use homogenous (pseudo) v.Neumann conditions or prescribe
106        OB-values from file; this is not different from the way theta and salinity
107        are treated
108      - however, Orlanski-radiation conditions are not supported, and the model
109        will stop if you use pTracers and Orlanski at the same time.
110      - beefed up the rountine obcs_external_fields_load: now only those open
111        boundary values are overwritten with values from files for which there
112        are really files, otherwise the OB-fields remain untouched. This makes
113        it possible to use different OBs at different ends of the domain (as
114        with EXF)
115    o reduce number of exch calls in shap_filt (s2).
116    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
117      truncation level) 4/5 MLAdjust test results (11&12 digits match).
118    
119    checkpoint57t_post
120    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
121    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
122      same truncation, independent of the face number: affects affects several
123      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
124    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
125      note that biharmonic viscosity + no-slip was not tested in any experiment.
126    o fix bug in non-linear free-surf side-drag ; generate new output for
127      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
128    o make mnc honor the writeBinaryPrec flag for most kinds of output
129    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
130    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
131      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
132    o add brackets in multi-terms sum to get same truncation, independent of
133      the face number (manage to get exactly same value of gU,gV at the cs-edge)
134      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
135    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
136      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
137      a maximum grid-scale Reynolds number.  Also, changes all length calculations
138      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
139      Suggested values of viscosity parameters found in mom_calc_visc.
140      Many new viscosity diagnostics available.
141    
142    checkpoint57s_post
143    o Add clearing-house for viscosity calculations, mom_calc_visc and
144      correct numerous bugs in LeithD and Smagorinsky discretizations.  
145      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
146      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
147      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
148      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
149      The Strain-Tension form is now called with useStrainTensonVisc=.true.
150      ViscAhStrain and viscAhTension are now retired.
151    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
152    o In response to JMC's bug report, genmake2 now ignores any soft-links
153      that it finds in the *current* directory when searching for files.
154      Soft-links found in any other source directories will still work as
155      they did before.
156    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
157      a C routine to unlimit the stack size
158    o mnc-ify pkg/aim snapshot vars
159    o mnc-ify pkg/land as requested by Daniel
160    o various changes to mnc including:
161      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
162      - output can now be grouped so that all files within a group
163          change the ITER portion of their names in lock-step together
164      - can now read ("global") PER-FACE (in addition to PER-TILE) files
165          and works with both EXCH1 and EXCH2 (but needs more testing)
166      - writing works for all verification test cases w/ g77 on Linux
167    
168    checkpoint57r_post
169    o make MNC variable initialization happen earlier
170    o add diagnostics for (almost) each term of the momentum Eq.
171    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
172    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
173    o remove MINIMAL_TAVE_OUTPUT option ;
174      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
175    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
176      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
177    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
178    o add time-dependent SST, SSS control
179    o cost terms in ecco/ modularized (new cost_generic.F)
180    o cost_averages routines are modularized (new cost_averagesgeneric.F)
181    o new infrastructure for seaice model vs. obs misfits in seaice/
182      * driver from the_main_loop.F is seaice_cost_driver.F
183      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
184      * gradient check in Exp. 6a of natl_box_adjoint/
185    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
186      (see README file)
187    
188    checkpoint57q_post
189    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
190    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
191      - bug was reported by Jean-Michel and Ian Fenty
192    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
193      update exp. cpl_aim+ocn output.
194    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
195      Needed for high-res. runs with large global files
196      to be able to limit tapelev size
197    o Changed some tests for adjoint:
198      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
199      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
200      * global_ocean.90x40x15/ back to default 3-level checkpointing
201    o Modifications to enable scripted COMMON to MODULE conversion
202      * verification/OpenAD/code/ has necessary scripts and description;
203      * converts, compiles and runs successfully;
204    
205    checkpoint57p_post
206    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
207    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
208      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
209    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
210    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
211      (was already the case for dissipation with mom_vecinv,
212       and also the case for grad.PhiHyd when staggered-timeStep)
213      This will allow to put dissipation out-off the AB time-stepping.
214     Unfortunately, affects truncation error. Update output of exp. that "fails"
215      (cg2d matching number) and leave the others for later: front_relax(10),
216      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
217      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
218    
219    checkpoint57o_post
220    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
221      (2) its ready to be documented during the 20050801 DocFest
222    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
223      for ideal_2D_oce and lab_sea on linux_ia32_g77
224    o set to #undef CTRL_SET_OLD_MAXCVARS_30
225      in global1x1_tot/code_seaice_adj to access indices 32, 33
226      (worth another tag)
227    
228    checkpoint57n_post
229    o adding precip control xx_precip 32
230    o adding swflux control xx_swflux 33
231    o Replacing 10 forcing penalty cost routines by 1 generic.
232    o Implementing partitioning in time-mean and variable adjustment
233      for atmos. state.
234    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
235    o in natl_box_adjoint:
236      * updated exp 1 to 10
237        (but does not have time-mean vs. variable split results yet)
238    o updated global1x1/*_seaice_adj/
239      to incorporate latest changes
240    o enable useSingleCpuIO for mdsio vector routines
241      (applies in particular to tapelev I/O)
242    o removed inefficient K-loop in all active_file*control*.F
243    
244    checkpoint57m_post
245    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
246      and advect_cs (use EXCH-2 and standard cs-32 grid files).
247    o pkg/exch2: filling of face-corner halo regions is optional
248      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
249    
250    checkpoint57l_post
251     tag before updating tutorials (pre-release-2)
252    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
253       for output and interpolation of input fields onto model grid)
254    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
255       Affects results of exp. rotating_tank ; update output.txt.
256    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
257          and taking the square quantity and/or using a fraction-weight field.
258    o fix aim_diagnostics_init.F mate numbers.
259    o add mnc output capability to diagnostics/diagstat and update
260      our cvsignore files for the ACSII output generated
261    
262    checkpoint57k_post
263    o lab_sea now uses diagnostics package and provides a suite of
264      new EXF diagnostics output.
265    
266    checkpoint57j_post
267    o exf
268      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
269        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
270        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
271      * extended diagnostics output
272        - now includes all EXF variables
273        - hs, hl moved to common block
274        - separate S/R for diagnostics, called after ctrl vector is added
275        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
276        - EXFqnet contains true Qnet (i.e. includes qsw)
277      * updated verif. lab_sea, global_with_exf
278      * Rearranging hflux (exf_mapfields -> exf_getforcing)
279        to ensure that diagnostics sees a true EXFqnet
280    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
281    o diagnostics pkg: change pointers so that 1 diagnostic can be used
282      several times with different frequencies.
283    o mnc-ify the thsice package as requested by Daniel Enderton
284      - the monitor--MNC output needs work
285      - many attributes need to be added (most are currently blank)
286    o mnc-ify theaim_v23 package as requested by Daniel Enderton
287      - many attributes need to be added (most are currently blank)
288    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
289    o add Sadourny like discretization to the 4th.O vorticity advection scheme
290    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
291      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
292         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
293    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
294     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
295    
296    checkpoint57i_post
297    o Diagnostics package was changed: diagnostic allocation is now deactivated
298      by setting an empty file name in the namelist (used to be by setting 0 frequency)
299    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
300      add 1rst Order upwind vertical Shear.
301    o add a quick fix for A/B checkpointing in OFFLINE mode
302    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
303      end-run around the C/Fortran linking horror in eesup/src/timers.F
304    o added pkg/runclock: allows user to terminate run based on wall clock
305    o added non-hydrostatic scaling parameter: nh_am2
306    o pkg/my82: futile attempt to make results compiler-independent by adding
307      some "_d 0", etc. no effect.
308    o for mnc output, fill the 'T' coordinate var with myTime and create a
309      separate 'iter' variable for iteration count
310    o pkg/diagnostics:
311      add new capability: output of Global/Regional & per-level statistics ;
312      tested against monitor output (including land & thSIce) on various exp.
313    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
314    
315    checkpoint57h_done
316      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
317      data.diagnostics, data.gchem, data.ptracers) is done.
318    
319    o pkg/diagnostics: prepare for Global/Regional statistics.
320      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
321    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
322      and rename it: DIFFERENT_MULTIPLE
323    
324    checkpoint57h_post
325    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
326    o pkg/diagnostics: change output frequency, now in seconds (instead
327      of Nb of iterations). This requires to change data.diagnostics.
328    checkpoint57h_pre
329    
330    o in mnc, let the user create the output dir if both mnc_outdir_date
331      and mnc_outdir_num are false
332    o add fflags() to pkg/diagnostics which allows one to specify, on a
333      per-file basis, the file precision [default behavior is unchanged]
334  o added diagnostics to pkg/kpp, including computation of mixed layer  o added diagnostics to pkg/kpp, including computation of mixed layer
335    depth based on a temperature/density criterion    depth based on a temperature/density criterion
336  o updated verification/natl_box to test the new pkg/kpp diagnostics  o updated verification/natl_box to test the new pkg/kpp diagnostics

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