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revision 1.436 by jmc, Wed Jan 26 00:20:49 2005 UTC revision 1.571 by jmc, Thu Oct 13 01:28:24 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  o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT";  o remove all the files from the cfc_offline test since they are now
8      incorporated into tutorial_cfc_offline which has been producing
9      identical results for a few days of testing
10    o add new parameter: sideDragFactor to enable half-slip-side BC
11      and change side-drag S/R to use viscosity from mom_calc_visc
12      (can switch back by setting sideDragFactor=0.); affects results at
13      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
14       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
15    o vorticity & strain are now computed without masking, to account for
16      no-slip-side BC in variable viscosity calculation ; mask is applied
17      anyway later on, before computing advection/coriolis terms.
18    o modify exp4 to test new obcs support reading from external files
19      and for passive tracers
20    o fix behavior of ptracers_monitor when monitor output is written to a
21      netcdf-file; still not independent of monitor.F (writes in the same
22      file).
23    o change default value of tRef (put a uniform, meaningful value for ocean
24      & atmos) and initialize sRef (was missing, as Martin mentioned).
25    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
26      to be proportional to enstrophy dissipation length.  Thus,
27       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
28      This is now consistent with Smagorinsky and with the manual.
29    
30    checkpoint57u_post
31    o OBCS and PTRACERS: add open boundary support for passive tracers
32      - either use homogenous (pseudo) v.Neumann conditions or prescribe
33        OB-values from file; this is not different from the way theta and salinity
34        are treated
35      - however, Orlanski-radiation conditions are not supported, and the model
36        will stop if you use pTracers and Orlanski at the same time.
37      - beefed up the rountine obcs_external_fields_load: now only those open
38        boundary values are overwritten with values from files for which there
39        are really files, otherwise the OB-fields remain untouched. This makes
40        it possible to use different OBs at different ends of the domain (as
41        with EXF)
42    o reduce number of exch calls in shap_filt (s2).
43    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
44      truncation level) 4/5 MLAdjust test results (11&12 digits match).
45    
46    checkpoint57t_post
47    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
48    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
49      same truncation, independent of the face number: affects affects several
50      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
51    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
52      note that biharmonic viscosity + no-slip was not tested in any experiment.
53    o fix bug in non-linear free-surf side-drag ; generate new output for
54      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
55    o make mnc honor the writeBinaryPrec flag for most kinds of output
56    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
57    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
58      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
59    o add brackets in multi-terms sum to get same truncation, independent of
60      the face number (manage to get exactly same value of gU,gV at the cs-edge)
61      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
62    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
63      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
64      a maximum grid-scale Reynolds number.  Also, changes all length calculations
65      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
66      Suggested values of viscosity parameters found in mom_calc_visc.
67      Many new viscosity diagnostics available.
68    
69    checkpoint57s_post
70    o Add clearing-house for viscosity calculations, mom_calc_visc and
71      correct numerous bugs in LeithD and Smagorinsky discretizations.  
72      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
73      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
74      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
75      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
76      The Strain-Tension form is now called with useStrainTensonVisc=.true.
77      ViscAhStrain and viscAhTension are now retired.
78    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
79    o In response to JMC's bug report, genmake2 now ignores any soft-links
80      that it finds in the *current* directory when searching for files.
81      Soft-links found in any other source directories will still work as
82      they did before.
83    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
84      a C routine to unlimit the stack size
85    o mnc-ify pkg/aim snapshot vars
86    o mnc-ify pkg/land as requested by Daniel
87    o various changes to mnc including:
88      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
89      - output can now be grouped so that all files within a group
90          change the ITER portion of their names in lock-step together
91      - can now read ("global") PER-FACE (in addition to PER-TILE) files
92          and works with both EXCH1 and EXCH2 (but needs more testing)
93      - writing works for all verification test cases w/ g77 on Linux
94    
95    checkpoint57r_post
96    o make MNC variable initialization happen earlier
97    o add diagnostics for (almost) each term of the momentum Eq.
98    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
99    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
100    o remove MINIMAL_TAVE_OUTPUT option ;
101      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
102    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
103      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
104    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
105    o add time-dependent SST, SSS control
106    o cost terms in ecco/ modularized (new cost_generic.F)
107    o cost_averages routines are modularized (new cost_averagesgeneric.F)
108    o new infrastructure for seaice model vs. obs misfits in seaice/
109      * driver from the_main_loop.F is seaice_cost_driver.F
110      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
111      * gradient check in Exp. 6a of natl_box_adjoint/
112    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
113      (see README file)
114    
115    checkpoint57q_post
116    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
117    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
118      - bug was reported by Jean-Michel and Ian Fenty
119    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
120      update exp. cpl_aim+ocn output.
121    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
122      Needed for high-res. runs with large global files
123      to be able to limit tapelev size
124    o Changed some tests for adjoint:
125      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
126      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
127      * global_ocean.90x40x15/ back to default 3-level checkpointing
128    o Modifications to enable scripted COMMON to MODULE conversion
129      * verification/OpenAD/code/ has necessary scripts and description;
130      * converts, compiles and runs successfully;
131    
132    checkpoint57p_post
133    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
134    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
135      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
136    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
137    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
138      (was already the case for dissipation with mom_vecinv,
139       and also the case for grad.PhiHyd when staggered-timeStep)
140      This will allow to put dissipation out-off the AB time-stepping.
141     Unfortunately, affects truncation error. Update output of exp. that "fails"
142      (cg2d matching number) and leave the others for later: front_relax(10),
143      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
144      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
145    
146    checkpoint57o_post
147    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
148      (2) its ready to be documented during the 20050801 DocFest
149    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
150      for ideal_2D_oce and lab_sea on linux_ia32_g77
151    o set to #undef CTRL_SET_OLD_MAXCVARS_30
152      in global1x1_tot/code_seaice_adj to access indices 32, 33
153      (worth another tag)
154    
155    checkpoint57n_post
156    o adding precip control xx_precip 32
157    o adding swflux control xx_swflux 33
158    o Replacing 10 forcing penalty cost routines by 1 generic.
159    o Implementing partitioning in time-mean and variable adjustment
160      for atmos. state.
161    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
162    o in natl_box_adjoint:
163      * updated exp 1 to 10
164        (but does not have time-mean vs. variable split results yet)
165    o updated global1x1/*_seaice_adj/
166      to incorporate latest changes
167    o enable useSingleCpuIO for mdsio vector routines
168      (applies in particular to tapelev I/O)
169    o removed inefficient K-loop in all active_file*control*.F
170    
171    checkpoint57m_post
172    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
173      and advect_cs (use EXCH-2 and standard cs-32 grid files).
174    o pkg/exch2: filling of face-corner halo regions is optional
175      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
176    
177    checkpoint57l_post
178     tag before updating tutorials (pre-release-2)
179    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
180       for output and interpolation of input fields onto model grid)
181    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
182       Affects results of exp. rotating_tank ; update output.txt.
183    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
184          and taking the square quantity and/or using a fraction-weight field.
185    o fix aim_diagnostics_init.F mate numbers.
186    o add mnc output capability to diagnostics/diagstat and update
187      our cvsignore files for the ACSII output generated
188    
189    checkpoint57k_post
190    o lab_sea now uses diagnostics package and provides a suite of
191      new EXF diagnostics output.
192    
193    checkpoint57j_post
194    o exf
195      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
196        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
197        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
198      * extended diagnostics output
199        - now includes all EXF variables
200        - hs, hl moved to common block
201        - separate S/R for diagnostics, called after ctrl vector is added
202        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
203        - EXFqnet contains true Qnet (i.e. includes qsw)
204      * updated verif. lab_sea, global_with_exf
205      * Rearranging hflux (exf_mapfields -> exf_getforcing)
206        to ensure that diagnostics sees a true EXFqnet
207    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
208    o diagnostics pkg: change pointers so that 1 diagnostic can be used
209      several times with different frequencies.
210    o mnc-ify the thsice package as requested by Daniel Enderton
211      - the monitor--MNC output needs work
212      - many attributes need to be added (most are currently blank)
213    o mnc-ify theaim_v23 package as requested by Daniel Enderton
214      - many attributes need to be added (most are currently blank)
215    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
216    o add Sadourny like discretization to the 4th.O vorticity advection scheme
217    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
218      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
219         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
220    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
221     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
222    
223    checkpoint57i_post
224    o Diagnostics package was changed: diagnostic allocation is now deactivated
225      by setting an empty file name in the namelist (used to be by setting 0 frequency)
226    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
227      add 1rst Order upwind vertical Shear.
228    o add a quick fix for A/B checkpointing in OFFLINE mode
229    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
230      end-run around the C/Fortran linking horror in eesup/src/timers.F
231    o added pkg/runclock: allows user to terminate run based on wall clock
232    o added non-hydrostatic scaling parameter: nh_am2
233    o pkg/my82: futile attempt to make results compiler-independent by adding
234      some "_d 0", etc. no effect.
235    o for mnc output, fill the 'T' coordinate var with myTime and create a
236      separate 'iter' variable for iteration count
237    o pkg/diagnostics:
238      add new capability: output of Global/Regional & per-level statistics ;
239      tested against monitor output (including land & thSIce) on various exp.
240    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
241    
242    checkpoint57h_done
243      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
244      data.diagnostics, data.gchem, data.ptracers) is done.
245    
246    o pkg/diagnostics: prepare for Global/Regional statistics.
247      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
248    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
249      and rename it: DIFFERENT_MULTIPLE
250    
251    checkpoint57h_post
252    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
253    o pkg/diagnostics: change output frequency, now in seconds (instead
254      of Nb of iterations). This requires to change data.diagnostics.
255    checkpoint57h_pre
256    
257    o in mnc, let the user create the output dir if both mnc_outdir_date
258      and mnc_outdir_num are false
259    o add fflags() to pkg/diagnostics which allows one to specify, on a
260      per-file basis, the file precision [default behavior is unchanged]
261    o added diagnostics to pkg/kpp, including computation of mixed layer
262      depth based on a temperature/density criterion
263    o updated verification/natl_box to test the new pkg/kpp diagnostics
264    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
265    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
266    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
267      not mnc -- this mistake was found by JMC and is now corrected
268    
269    checkpoint57g_post
270    o add Adams-Bashforth 3rd Order time stepping:
271      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
272      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
273    checkpoint57g_pre
274    
275    o make lambda[Theta,Salt]ClimRelax spatially varying
276      (default remains spatially uniform constant based on tau)
277    o added new control variables
278      * init. uVel, vVel, etanN
279      * lambda[Theta,Salt]ClimRelax
280    o separate masks used for ctrl_pack/unpack 'from write_grid' output
281      (suggested by G. Forget)
282    
283    checkpoint57f_post
284    o add parameter "baseTime" = model base time = time at iteration zero
285      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
286      account for baseTime shift
287    o move Coriolis arrays from PARAMS.h to GRID.h
288    checkpoint57f_pre
289    
290    o mnc-ifying the seaice package
291    o introduced an alternative length scale calculation for use in the limiting
292      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
293    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
294    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
295      as well as grad(vort3).  Made it compatible with both approximate form
296      for the cubed sphere and full form of these gradients.  Added flag
297      useFullLeith to select between approximate and full form.  
298    o add "d0" in getcon.F to reduce differences between compilers/platforms
299      update output.txt of exp. fizhi-gridalt-hs
300    o change port_rand funtion to allow to set the seed.
301    o fix obscure MNC bug involving conversion between reals and integers
302      - it caused no problems with certain (eg. gcc, ifc) compilers but the
303        new version is now more standards-compliant
304    o adjoint-related modifications
305      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
306      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
307      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
308    
309    checkpoint57e_post
310    o Adding eddy stress controls a la Ferreira et al.
311    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
312    
313    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
314      update output.txt of exp. fizhi-gridalt-hs
315    o add more "Z" dimensions and associated coordinate vars to MNC
316    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
317    o parameter calendarDumps: when set, approximate months (30-31 days) and years
318      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
319      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
320      months and years.  Requires pkg/cal.
321    o diagnostics: add pickup functionality
322      - off by default for backwards compatibility
323      - current version only uses MDSIO -- MNC will be added
324    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
325    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
326    
327    checkpoint57d_post
328    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
329    o modify verification/ideal_2D_oce so that it tests the creation of mnc
330      output from the diagnostics package
331    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
332    o make genmake2 more portable by using ".$FS" instead of ".f" for more
333      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
334    o add coordinate variables to the MNC output from the diagnostics package
335    o change MNC-flags default value: true when useMNC=TRUE
336    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
337      the ability (off by default) to read the grid information using MNC
338    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
339    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
340    o do snap-shot diagnostics at the middle of the time-interval (instead of
341      at the end).
342    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
343      new test for AIM with thSIce + slab-ocean
344    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
345    o move state variable diagnostics to the beginning of the time step ;
346      (note: still needs some work specially for snap-shot diagnostics)
347      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
348    
349    checkpoint57c_post
350    o Change testing option (-ieee) to get closer agreement between g77 & ifort
351    o generate new output.txt files on faulks with g77 & the new -ieee option
352    checkpoint57c_pre
353    
354    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
355    update output.txt of exp. global_ocean.90x40x15    update output.txt of exp. global_ocean.90x40x15
356  o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer  o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
357    results; update global_ocean_pressure & global_ocean.cs32x15 output.txt    results; update global_ocean_pressure & global_ocean.cs32x15 output.txt

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