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revision 1.474 by jmc, Fri Apr 8 18:31:46 2005 UTC revision 1.561 by jmc, Fri Oct 7 00:36:29 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 reduce number of exch calls in shap_filt (s2).
8    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
9      truncation level) 4/5 MLAdjust test results (11&12 digits match).
10    
11    checkpoint57t_post
12    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
13    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
14      same truncation, independent of the face number: affects affects several
15      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
16    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
17      note that biharmonic viscosity + no-slip was not tested in any experiment.
18    o fix bug in non-linear free-surf side-drag ; generate new output for
19      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
20    o make mnc honor the writeBinaryPrec flag for most kinds of output
21    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
22    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
23      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
24    o add brackets in multi-terms sum to get same truncation, independent of
25      the face number (manage to get exactly same value of gU,gV at the cs-edge)
26      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
27    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
28      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
29      a maximum grid-scale Reynolds number.  Also, changes all length calculations
30      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
31      Suggested values of viscosity parameters found in mom_calc_visc.
32      Many new viscosity diagnostics available.
33    
34    checkpoint57s_post
35    o Add clearing-house for viscosity calculations, mom_calc_visc and
36      correct numerous bugs in LeithD and Smagorinsky discretizations.  
37      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
38      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
39      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
40      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
41      The Strain-Tension form is now called with useStrainTensonVisc=.true.
42      ViscAhStrain and viscAhTension are now retired.
43    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
44    o In response to JMC's bug report, genmake2 now ignores any soft-links
45      that it finds in the *current* directory when searching for files.
46      Soft-links found in any other source directories will still work as
47      they did before.
48    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
49      a C routine to unlimit the stack size
50    o mnc-ify pkg/aim snapshot vars
51    o mnc-ify pkg/land as requested by Daniel
52    o various changes to mnc including:
53      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
54      - output can now be grouped so that all files within a group
55          change the ITER portion of their names in lock-step together
56      - can now read ("global") PER-FACE (in addition to PER-TILE) files
57          and works with both EXCH1 and EXCH2 (but needs more testing)
58      - writing works for all verification test cases w/ g77 on Linux
59    
60    checkpoint57r_post
61    o make MNC variable initialization happen earlier
62    o add diagnostics for (almost) each term of the momentum Eq.
63    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
64    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
65    o remove MINIMAL_TAVE_OUTPUT option ;
66      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
67    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
68      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
69    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
70    o add time-dependent SST, SSS control
71    o cost terms in ecco/ modularized (new cost_generic.F)
72    o cost_averages routines are modularized (new cost_averagesgeneric.F)
73    o new infrastructure for seaice model vs. obs misfits in seaice/
74      * driver from the_main_loop.F is seaice_cost_driver.F
75      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
76      * gradient check in Exp. 6a of natl_box_adjoint/
77    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
78      (see README file)
79    
80    checkpoint57q_post
81    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
82    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
83      - bug was reported by Jean-Michel and Ian Fenty
84    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
85      update exp. cpl_aim+ocn output.
86    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
87      Needed for high-res. runs with large global files
88      to be able to limit tapelev size
89    o Changed some tests for adjoint:
90      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
91      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
92      * global_ocean.90x40x15/ back to default 3-level checkpointing
93    o Modifications to enable scripted COMMON to MODULE conversion
94      * verification/OpenAD/code/ has necessary scripts and description;
95      * converts, compiles and runs successfully;
96    
97    checkpoint57p_post
98    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
99    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
100      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
101    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
102    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
103      (was already the case for dissipation with mom_vecinv,
104       and also the case for grad.PhiHyd when staggered-timeStep)
105      This will allow to put dissipation out-off the AB time-stepping.
106     Unfortunately, affects truncation error. Update output of exp. that "fails"
107      (cg2d matching number) and leave the others for later: front_relax(10),
108      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
109      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
110    
111    checkpoint57o_post
112    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
113      (2) its ready to be documented during the 20050801 DocFest
114    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
115      for ideal_2D_oce and lab_sea on linux_ia32_g77
116    o set to #undef CTRL_SET_OLD_MAXCVARS_30
117      in global1x1_tot/code_seaice_adj to access indices 32, 33
118      (worth another tag)
119    
120    checkpoint57n_post
121    o adding precip control xx_precip 32
122    o adding swflux control xx_swflux 33
123    o Replacing 10 forcing penalty cost routines by 1 generic.
124    o Implementing partitioning in time-mean and variable adjustment
125      for atmos. state.
126    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
127    o in natl_box_adjoint:
128      * updated exp 1 to 10
129        (but does not have time-mean vs. variable split results yet)
130    o updated global1x1/*_seaice_adj/
131      to incorporate latest changes
132    o enable useSingleCpuIO for mdsio vector routines
133      (applies in particular to tapelev I/O)
134    o removed inefficient K-loop in all active_file*control*.F
135    
136    checkpoint57m_post
137    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
138      and advect_cs (use EXCH-2 and standard cs-32 grid files).
139    o pkg/exch2: filling of face-corner halo regions is optional
140      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
141    
142    checkpoint57l_post
143     tag before updating tutorials (pre-release-2)
144    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
145       for output and interpolation of input fields onto model grid)
146    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
147       Affects results of exp. rotating_tank ; update output.txt.
148    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
149          and taking the square quantity and/or using a fraction-weight field.
150    o fix aim_diagnostics_init.F mate numbers.
151    o add mnc output capability to diagnostics/diagstat and update
152      our cvsignore files for the ACSII output generated
153    
154    checkpoint57k_post
155    o lab_sea now uses diagnostics package and provides a suite of
156      new EXF diagnostics output.
157    
158    checkpoint57j_post
159    o exf
160      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
161        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
162        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
163      * extended diagnostics output
164        - now includes all EXF variables
165        - hs, hl moved to common block
166        - separate S/R for diagnostics, called after ctrl vector is added
167        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
168        - EXFqnet contains true Qnet (i.e. includes qsw)
169      * updated verif. lab_sea, global_with_exf
170      * Rearranging hflux (exf_mapfields -> exf_getforcing)
171        to ensure that diagnostics sees a true EXFqnet
172    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
173    o diagnostics pkg: change pointers so that 1 diagnostic can be used
174      several times with different frequencies.
175    o mnc-ify the thsice package as requested by Daniel Enderton
176      - the monitor--MNC output needs work
177      - many attributes need to be added (most are currently blank)
178    o mnc-ify theaim_v23 package as requested by Daniel Enderton
179      - many attributes need to be added (most are currently blank)
180    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
181    o add Sadourny like discretization to the 4th.O vorticity advection scheme
182    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
183      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
184         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
185    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
186     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
187    
188    checkpoint57i_post
189    o Diagnostics package was changed: diagnostic allocation is now deactivated
190      by setting an empty file name in the namelist (used to be by setting 0 frequency)
191    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
192      add 1rst Order upwind vertical Shear.
193    o add a quick fix for A/B checkpointing in OFFLINE mode
194    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
195      end-run around the C/Fortran linking horror in eesup/src/timers.F
196    o added pkg/runclock: allows user to terminate run based on wall clock
197    o added non-hydrostatic scaling parameter: nh_am2
198    o pkg/my82: futile attempt to make results compiler-independent by adding
199      some "_d 0", etc. no effect.
200    o for mnc output, fill the 'T' coordinate var with myTime and create a
201      separate 'iter' variable for iteration count
202    o pkg/diagnostics:
203      add new capability: output of Global/Regional & per-level statistics ;
204      tested against monitor output (including land & thSIce) on various exp.
205    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
206    
207    checkpoint57h_done
208      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
209      data.diagnostics, data.gchem, data.ptracers) is done.
210    
211    o pkg/diagnostics: prepare for Global/Regional statistics.
212      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
213    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
214      and rename it: DIFFERENT_MULTIPLE
215    
216    checkpoint57h_post
217    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
218    o pkg/diagnostics: change output frequency, now in seconds (instead
219      of Nb of iterations). This requires to change data.diagnostics.
220    checkpoint57h_pre
221    
222    o in mnc, let the user create the output dir if both mnc_outdir_date
223      and mnc_outdir_num are false
224    o add fflags() to pkg/diagnostics which allows one to specify, on a
225      per-file basis, the file precision [default behavior is unchanged]
226    o added diagnostics to pkg/kpp, including computation of mixed layer
227      depth based on a temperature/density criterion
228    o updated verification/natl_box to test the new pkg/kpp diagnostics
229    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
230    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
231    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
232      not mnc -- this mistake was found by JMC and is now corrected
233    
234    checkpoint57g_post
235    o add Adams-Bashforth 3rd Order time stepping:
236      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
237      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
238    checkpoint57g_pre
239    
240  o make lambda[Theta,Salt]ClimRelax spatially varying  o make lambda[Theta,Salt]ClimRelax spatially varying
241    (default remains spatially uniform constant based on tau)    (default remains spatially uniform constant based on tau)
242  o added new control variables  o added new control variables

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