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revision 1.465 by baylor, Thu Mar 24 14:51:34 2005 UTC revision 1.587 by heimbach, Thu Dec 8 15:34:24 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_pre
8    
9    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
10    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
11    o add new offset feature to offline pkg (plus minor cleanup)
12    o cfc fixes for final year of integration
13    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
14      be in GCHEM_OPTIONS).
15    
16    checkpoint57x_post
17    o fix testreport Pb in multiple test experiment.
18    o cleanup our namelist syntax in verification:
19      - make it more F95 standards compliant (some work still needed)
20      - allows the vast majority of our tests to work with gfortran
21    o Non-Hydrostatic:
22     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
23     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
24    o Allow to apply AB on T,S rather than on AB(gT,gS):
25     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
26     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
27       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
28     - need a "clever" read_pickup to restart from the other AB formulation
29    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
30    o remove some unused variables (reduces number of compiler warnings)
31    o adjoint
32      * Disable useVariableViscosity for adjoint for time being
33        (there are a number of extensive recomputations)
34      * Initialize certain variables needed for adjoint
35    
36    checkpoint57w_post
37    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
38                 fix the singleCpuIO RS version of MDSWRITEFIELD
39       and add a WARNING if using globalFiles=T with multi-processors.
40    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
41      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
42    o tracer advection scheme:
43      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
44       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
45       was not very convenient).
46      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
47       (further tests needed for the implicit DST & Flux-Limiter schemes).
48    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
49      and sRef for convenience, handy, when you want to initialize
50      ptracers in a large domain with a constant non-zero value. Also,
51      untangle ptracers_init.F a little.
52    
53    checkpoint57v_post
54    o change dome exp. to use variable viscosity in side-drag terms.
55    o remove all the files from the cfc_offline test since they are now
56      incorporated into tutorial_cfc_offline which has been producing
57      identical results for a few days of testing
58    o add new parameter: sideDragFactor to enable half-slip-side BC
59      and change side-drag S/R to use viscosity from mom_calc_visc
60      (can switch back by setting sideDragFactor=0.); affects results at
61      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
62       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
63    o vorticity & strain are now computed without masking, to account for
64      no-slip-side BC in variable viscosity calculation ; mask is applied
65      anyway later on, before computing advection/coriolis terms.
66    o modify exp4 to test new obcs support for reading from external files
67      and for passive tracers
68    o fix behavior of ptracers_monitor when monitor output is written to a
69      netcdf-file; still not independent of monitor.F (writes in the same
70      file).
71    o change default value of tRef (put a uniform, meaningful value for ocean
72      & atmos) and initialize sRef (was missing, as Martin mentioned).
73    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
74      to be proportional to enstrophy dissipation length.  Thus,
75       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
76      This is now consistent with Smagorinsky and with the manual.
77    
78    checkpoint57u_post
79    o OBCS and PTRACERS: add open boundary support for passive tracers
80      - either use homogenous (pseudo) v.Neumann conditions or prescribe
81        OB-values from file; this is not different from the way theta and salinity
82        are treated
83      - however, Orlanski-radiation conditions are not supported, and the model
84        will stop if you use pTracers and Orlanski at the same time.
85      - beefed up the rountine obcs_external_fields_load: now only those open
86        boundary values are overwritten with values from files for which there
87        are really files, otherwise the OB-fields remain untouched. This makes
88        it possible to use different OBs at different ends of the domain (as
89        with EXF)
90    o reduce number of exch calls in shap_filt (s2).
91    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
92      truncation level) 4/5 MLAdjust test results (11&12 digits match).
93    
94    checkpoint57t_post
95    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
96    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
97      same truncation, independent of the face number: affects affects several
98      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
99    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
100      note that biharmonic viscosity + no-slip was not tested in any experiment.
101    o fix bug in non-linear free-surf side-drag ; generate new output for
102      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
103    o make mnc honor the writeBinaryPrec flag for most kinds of output
104    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
105    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
106      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
107    o add brackets in multi-terms sum to get same truncation, independent of
108      the face number (manage to get exactly same value of gU,gV at the cs-edge)
109      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
110    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
111      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
112      a maximum grid-scale Reynolds number.  Also, changes all length calculations
113      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
114      Suggested values of viscosity parameters found in mom_calc_visc.
115      Many new viscosity diagnostics available.
116    
117    checkpoint57s_post
118    o Add clearing-house for viscosity calculations, mom_calc_visc and
119      correct numerous bugs in LeithD and Smagorinsky discretizations.  
120      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
121      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
122      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
123      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
124      The Strain-Tension form is now called with useStrainTensonVisc=.true.
125      ViscAhStrain and viscAhTension are now retired.
126    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
127    o In response to JMC's bug report, genmake2 now ignores any soft-links
128      that it finds in the *current* directory when searching for files.
129      Soft-links found in any other source directories will still work as
130      they did before.
131    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
132      a C routine to unlimit the stack size
133    o mnc-ify pkg/aim snapshot vars
134    o mnc-ify pkg/land as requested by Daniel
135    o various changes to mnc including:
136      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
137      - output can now be grouped so that all files within a group
138          change the ITER portion of their names in lock-step together
139      - can now read ("global") PER-FACE (in addition to PER-TILE) files
140          and works with both EXCH1 and EXCH2 (but needs more testing)
141      - writing works for all verification test cases w/ g77 on Linux
142    
143    checkpoint57r_post
144    o make MNC variable initialization happen earlier
145    o add diagnostics for (almost) each term of the momentum Eq.
146    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
147    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
148    o remove MINIMAL_TAVE_OUTPUT option ;
149      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
150    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
151      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
152    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
153    o add time-dependent SST, SSS control
154    o cost terms in ecco/ modularized (new cost_generic.F)
155    o cost_averages routines are modularized (new cost_averagesgeneric.F)
156    o new infrastructure for seaice model vs. obs misfits in seaice/
157      * driver from the_main_loop.F is seaice_cost_driver.F
158      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
159      * gradient check in Exp. 6a of natl_box_adjoint/
160    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
161      (see README file)
162    
163    checkpoint57q_post
164    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
165    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
166      - bug was reported by Jean-Michel and Ian Fenty
167    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
168      update exp. cpl_aim+ocn output.
169    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
170      Needed for high-res. runs with large global files
171      to be able to limit tapelev size
172    o Changed some tests for adjoint:
173      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
174      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
175      * global_ocean.90x40x15/ back to default 3-level checkpointing
176    o Modifications to enable scripted COMMON to MODULE conversion
177      * verification/OpenAD/code/ has necessary scripts and description;
178      * converts, compiles and runs successfully;
179    
180    checkpoint57p_post
181    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
182    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
183      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
184    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
185    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
186      (was already the case for dissipation with mom_vecinv,
187       and also the case for grad.PhiHyd when staggered-timeStep)
188      This will allow to put dissipation out-off the AB time-stepping.
189     Unfortunately, affects truncation error. Update output of exp. that "fails"
190      (cg2d matching number) and leave the others for later: front_relax(10),
191      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
192      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
193    
194    checkpoint57o_post
195    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
196      (2) its ready to be documented during the 20050801 DocFest
197    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
198      for ideal_2D_oce and lab_sea on linux_ia32_g77
199    o set to #undef CTRL_SET_OLD_MAXCVARS_30
200      in global1x1_tot/code_seaice_adj to access indices 32, 33
201      (worth another tag)
202    
203    checkpoint57n_post
204    o adding precip control xx_precip 32
205    o adding swflux control xx_swflux 33
206    o Replacing 10 forcing penalty cost routines by 1 generic.
207    o Implementing partitioning in time-mean and variable adjustment
208      for atmos. state.
209    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
210    o in natl_box_adjoint:
211      * updated exp 1 to 10
212        (but does not have time-mean vs. variable split results yet)
213    o updated global1x1/*_seaice_adj/
214      to incorporate latest changes
215    o enable useSingleCpuIO for mdsio vector routines
216      (applies in particular to tapelev I/O)
217    o removed inefficient K-loop in all active_file*control*.F
218    
219    checkpoint57m_post
220    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
221      and advect_cs (use EXCH-2 and standard cs-32 grid files).
222    o pkg/exch2: filling of face-corner halo regions is optional
223      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
224    
225    checkpoint57l_post
226     tag before updating tutorials (pre-release-2)
227    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
228       for output and interpolation of input fields onto model grid)
229    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
230       Affects results of exp. rotating_tank ; update output.txt.
231    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
232          and taking the square quantity and/or using a fraction-weight field.
233    o fix aim_diagnostics_init.F mate numbers.
234    o add mnc output capability to diagnostics/diagstat and update
235      our cvsignore files for the ACSII output generated
236    
237    checkpoint57k_post
238    o lab_sea now uses diagnostics package and provides a suite of
239      new EXF diagnostics output.
240    
241    checkpoint57j_post
242    o exf
243      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
244        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
245        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
246      * extended diagnostics output
247        - now includes all EXF variables
248        - hs, hl moved to common block
249        - separate S/R for diagnostics, called after ctrl vector is added
250        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
251        - EXFqnet contains true Qnet (i.e. includes qsw)
252      * updated verif. lab_sea, global_with_exf
253      * Rearranging hflux (exf_mapfields -> exf_getforcing)
254        to ensure that diagnostics sees a true EXFqnet
255    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
256    o diagnostics pkg: change pointers so that 1 diagnostic can be used
257      several times with different frequencies.
258    o mnc-ify the thsice package as requested by Daniel Enderton
259      - the monitor--MNC output needs work
260      - many attributes need to be added (most are currently blank)
261    o mnc-ify theaim_v23 package as requested by Daniel Enderton
262      - many attributes need to be added (most are currently blank)
263    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
264    o add Sadourny like discretization to the 4th.O vorticity advection scheme
265    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
266      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
267         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
268    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
269     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
270    
271    checkpoint57i_post
272    o Diagnostics package was changed: diagnostic allocation is now deactivated
273      by setting an empty file name in the namelist (used to be by setting 0 frequency)
274    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
275      add 1rst Order upwind vertical Shear.
276    o add a quick fix for A/B checkpointing in OFFLINE mode
277    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
278      end-run around the C/Fortran linking horror in eesup/src/timers.F
279    o added pkg/runclock: allows user to terminate run based on wall clock
280    o added non-hydrostatic scaling parameter: nh_am2
281    o pkg/my82: futile attempt to make results compiler-independent by adding
282      some "_d 0", etc. no effect.
283    o for mnc output, fill the 'T' coordinate var with myTime and create a
284      separate 'iter' variable for iteration count
285    o pkg/diagnostics:
286      add new capability: output of Global/Regional & per-level statistics ;
287      tested against monitor output (including land & thSIce) on various exp.
288    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
289    
290    checkpoint57h_done
291      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
292      data.diagnostics, data.gchem, data.ptracers) is done.
293    
294    o pkg/diagnostics: prepare for Global/Regional statistics.
295      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
296    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
297      and rename it: DIFFERENT_MULTIPLE
298    
299    checkpoint57h_post
300    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
301    o pkg/diagnostics: change output frequency, now in seconds (instead
302      of Nb of iterations). This requires to change data.diagnostics.
303    checkpoint57h_pre
304    
305    o in mnc, let the user create the output dir if both mnc_outdir_date
306      and mnc_outdir_num are false
307    o add fflags() to pkg/diagnostics which allows one to specify, on a
308      per-file basis, the file precision [default behavior is unchanged]
309    o added diagnostics to pkg/kpp, including computation of mixed layer
310      depth based on a temperature/density criterion
311    o updated verification/natl_box to test the new pkg/kpp diagnostics
312    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
313    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
314    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
315      not mnc -- this mistake was found by JMC and is now corrected
316    
317    checkpoint57g_post
318    o add Adams-Bashforth 3rd Order time stepping:
319      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
320      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
321    checkpoint57g_pre
322    
323    o make lambda[Theta,Salt]ClimRelax spatially varying
324      (default remains spatially uniform constant based on tau)
325    o added new control variables
326      * init. uVel, vVel, etanN
327      * lambda[Theta,Salt]ClimRelax
328    o separate masks used for ctrl_pack/unpack 'from write_grid' output
329      (suggested by G. Forget)
330    
331    checkpoint57f_post
332    o add parameter "baseTime" = model base time = time at iteration zero
333      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
334      account for baseTime shift
335    o move Coriolis arrays from PARAMS.h to GRID.h
336    checkpoint57f_pre
337    
338    o mnc-ifying the seaice package
339    o introduced an alternative length scale calculation for use in the limiting
340      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
341    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
342  o added modified Leith scheme with viscosity proportional to grad(Hdiv)  o added modified Leith scheme with viscosity proportional to grad(Hdiv)
343    as well as grad(vort3).  Made it compatible with both approximate form    as well as grad(vort3).  Made it compatible with both approximate form
344    for the cubed sphere and full form of these gradients.  Added flag    for the cubed sphere and full form of these gradients.  Added flag
# Line 13  o change port_rand funtion to allow to s Line 349  o change port_rand funtion to allow to s
349  o fix obscure MNC bug involving conversion between reals and integers  o fix obscure MNC bug involving conversion between reals and integers
350    - it caused no problems with certain (eg. gcc, ifc) compilers but the    - it caused no problems with certain (eg. gcc, ifc) compilers but the
351      new version is now more standards-compliant      new version is now more standards-compliant
352    o adjoint-related modifications
353      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
354      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
355      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
356    
357  checkpoint57e_post  checkpoint57e_post
358  o Adding eddy stress controls a la Ferreira et al.  o Adding eddy stress controls a la Ferreira et al.
359  checkpoint57e_pre  checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
360    
361  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
362    update output.txt of exp. fizhi-gridalt-hs    update output.txt of exp. fizhi-gridalt-hs

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