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revision 1.295 by heimbach, Fri May 14 21:04:01 2004 UTC revision 1.392 by mlosch, Tue Nov 23 20:22:12 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    o exf_check_range:
7      * default changed to .TRUE.
8      * will check values for niter0 if debLevA, every timestep if debLevB
9      * STOP in exf_check_range if 'out of range'
10      * range chosen generous to allow for potential extema
11      TBD: a version with stricter range
12           permitted range would be runtime parameters
13    o GMredi:
14      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
15      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
16      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
17    o GCHEM:
18      - move call to GCHEM_FORCING_SEP, so that it is now called before
19        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
20      - introduced a useGCHEM runtime flag and applied it everywhere.
21      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
22        this flag is now only visible within GCHEM-pkg routines.
23      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
24        be replaced by a 3D array that is computed before thermodynamics; for
25        this, the tracer ID iTracer had to be included into the parameter list
26        of ptracers_forcing
27      - set up forward_step for a call to gchem_forcing, that will replace
28        gchem_forcing_int in ptracers_forcing
29      - cleaning up
30    o small cleaning of exch2: remove files that are also in eesupp/src
31    
32    checkpoint56
33    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
34    o mnc: cleanup "full" files--fixes out-of-memory problem
35    o ECCO-GODAE
36      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
37      * fully merged and updated from SIO code
38        windstress sign change affects
39        - exf_inscal_[u/v]stress
40        - sign of xx_tau[u/v] adjustments
41        - signs in cost_scat
42      * ctrl_get_gen: avoid update of tau[u/v] for first few days
43      * natl_box_adjoint updated and compressed
44      * 2-level checkpoint switch added
45        (tested in EXP. 1 of natl_box_adjoint)
46      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
47    o SVD
48      * first complete, non-hacked version for SVD calculations
49      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
50        performed via direct access files admtlm_vector.it????
51        (via ctrl_[un]pack)
52      * optimcycle is used for ARPACK iteration counter
53        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
54      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
55        and add linear transforms where necessary
56      * controls are initial/final SST, SSS (can be extended; need to check
57        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
58    o mdsio: filename info to both stderr, stdout
59    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
60      from sign change
61    
62    checkpoint55j_post
63    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
64      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
65    o add consistent build directories and .cvsignore files to verification
66    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
67    o make all subroutines 30 or less characters in length for certain older
68      compilers to work (a thorough search only turns up two routines in
69      pkg/ptracers)
70    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
71      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
72    
73    checkpoint55i_post
74    o change arrays for total vertical diffusivity (2.D if explicit,
75      3.D if implicit) ; each ptracer uses its own background value.
76    o added mnc/NetCDF output capability to ocn_compon_interf
77      - added bits to verification/cpl_aim+ocn so that it can run on
78        ITRDA and other clusters without the mpirun "-wd" option
79    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
80      configuration
81    o give MNC the ability to create additional files rather than
82      exceeding a specified file size limit "MNC_MAX_FILESIZE"
83      - the default is just less than 2GB which is a practical limit
84        on many systems
85    o Compute the non-local term using either KPP vertical diffusivity (=default)
86       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
87    
88    checkpoint55h_post
89    o add verification test "vermix"
90    o remove all the *_ioinc flags and replace with the single global
91      outputTypesInclusive flag
92    o allow to set a vertical profile of vertical diffusivity for T & S
93    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
94    o useMNC moved from data.mnc to data.pkg
95    
96    checkpoint55g_post
97    o Renaming carbon AD experiments to comply with testreport conventions
98    o Updating adjoint of Held-Suarez hs94.1x64x5
99    o Fixing directives for non-ECCO forward_step, after ECCO directives
100      have been fixed to avoid recomp. of do_oceanic_phys
101      Works well for global_ocean.90x40x15,
102      but recomp. issue remains for carbon
103    o Updating adjoint output for natl_box_adjoint after
104      pkg/ecco has been modified (see taga c55d_post)
105    
106    checkpoint55f_post
107    o rename to timeave_init_fixed
108    
109    checkpoint55e_post
110    o some delicate re-shuffle of store directives to avoid one
111      extra call of do_oceanic_physics
112      affects ecco_the_main_loop.F, do_oceanic_physics.F
113      checkpoint_lev1_directives.h
114    o NB: this may break global_ocean adjoint temporarily,
115      but it is clear how to fix it. Will do later, need this now.
116    
117    checkpoint55d_post
118    o ECCO specific cost function terms (up-to-date with 1x1 runs)
119    o ecco_cost_weights is modified to 1x1 runs
120    o modifs to allow observations to be read in as
121      single file or yearly files
122    o enable to read exf forcing fields as either
123      single file or yearly files (flag useExfYearlyFields)
124    checkpoint55d_pre
125    
126    o switch between 2-level and 3-level checkpointing
127    o add ability of MNC to write local and "partial" (eg. 2D slices where
128      the full 3D field is never actually stored) arrays to NetCDF files
129      with the correct (that is, the complete multi-dimensional) set of
130      array indicies
131      - used in mom_vecinv() to write the diagFreq output
132      - tested (demonstrated) in verification/aim.5l_cs
133    o further mnc-ification
134      - add verification/lab_sea to the list with mnc setups
135      - fix undefined mnc v-names in cd_code
136      - add kpp to mnc output (both snapshot and timeave)
137    o non-hydrostatic code
138      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
139        in calc_gw.F
140      - defaults to viscAh
141      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
142        friction or Leith) in non-hydrostatic mode, as long as there is
143        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
144    o pkg/cost
145      extend simple cost functions to treat time mean quantities
146      (T,U,V) via cost_accumulate_state from cost_tile
147    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
148        be 2 times larger than the minimum size the advection scheme requires.
149        now get a perfect conservation of salt in advect_cs test-exp (updated)
150    o GGL90 (Gaspar's TKE mixed layer)
151      - add horizontal diffusion of TKE, requires exchanges in
152        do_fields_blocking_exchanges, horizontal diffusivity is zero by
153        default. In OPA there is no horizontal diffusion of TKE but the
154        mixing coefficients are computed from a horizontal average of TKE of
155        6 points or so. I think that diffusion has a little more physical
156        justification.
157      - clean up ggl90_calc in the hope of reducing memory usage (this hope
158        was in vain)
159      - mask tke-variable in ggl90_init
160    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
161    o fix biharmonic diffusion on CS-grid.
162    o more obcs stuff
163      - added obcs_external_fields_load as an alternative to the EXF-pkg option
164        for reading boundary values. This routine is called from
165        obcs_prescribe_read
166      - updated obcs_check
167      - changed sponge layer relaxation parameter units for days to seconds
168      - turned off sponge layer by default
169      - changed argument list of OBCS_CALC to myTime+deltaTclock
170      - fixed about 35 bugs in obcs_external_fields_load
171    
172    checkpoint55c_post
173    o obcs stuff
174      - new runtime flags useOBCSprescribe, useOBCSbalance
175      - re-arranged obcs_calc
176      - moved exf_getobcs to obcs_prescibe_read
177        obcs_prescibe_read is called after ORLANSKI stuff
178        and independent of it (executable can contain all).
179      - updated obcs_check
180      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
181        These may be necessary only if tangential velocities are
182        prescribed at OB, not sure, needs testing.
183    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
184      which simplifies the calls and passes the ifc check-bounds test
185    
186    checkpoint55b_post
187    o add a 2D scalar, Z location, exchange_2 routine.
188    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
189      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
190      affects advect_cs results (for the wrong reason): update output.txt
191    o use a more standard discretization for biharmonic viscosity ;
192     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
193      affects results of dome set-up: update output.txt
194    o fix gad_advection.F (CubedSphere part), back to version 1.23
195    o fix bug in mom_vi_del2uv.F (CubedSphere part).
196    
197    checkpoint55a_post
198    o merged code to
199      * prescribe/read time-dependent open boundaries
200        (works in conjunction with exf, cal)
201      * sponge layer code for open boundaries
202      * each boundary N/S/E/W now has its own CPP option
203        (healthy for the adjoint)
204    
205    checkpoint55
206    o up-to-date adjoint of previous breaks
207      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
208      - global_ocean_ebm: adjoint still needs fix (TLM ok)
209      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
210      - carbon: * remove tr1-related adjoint verification
211                * add ptracer as control variable
212    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
213      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
214    
215    checkpoint54f_post
216    o in verification/carbin/ remove experiment related to
217      ALLOW_PASSIVE_TRACER (array tr1 etc)
218      code_ad/ input_ad/ results_ad
219    
220    o add two new packages
221      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
222        + subject to optimization (memory)
223      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
224        + subject to reordering (many GOTOs in the original code)
225        + so far opps is called for every (i,j) point, and then operates in
226          the vertical; one may want to reorder the scheme in order operate in
227          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
228          fields)
229    o overhaul of IO so that we now have flags for MDSIO and/or MNC
230      - all verification tests compile and run with linux_ia32_g77
231      - defaults are compatible with current input files--nothing
232        should change if you were not previously using MNC
233      - MNC output has been added in numerous places (eg. timeave)
234        but there are still a few writes not yet do-able with MNC
235        (this is in progress)
236      - flags now allow for either/or/both use of MDSIO and MNC and
237        documentation will soon follow
238      - numerous small formatting cleanups for ProTeX
239    o add version info (via BUILD_INFO.h) to MNC and stdout
240    
241    checkpoint54e_post
242    o add two new packages
243      - pp81 (Packanowski and Philander, 1981), Richardson number and
244        stratification dependent mixing
245      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
246      - these scheme operate in a similar manner as KPP (without ghat, of
247        course), however there is only one diffusivity that is used for both
248        temperature and salinity (and passive tracers)ç
249    o add offline package
250    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
251      provided by Stephanie Dutkiewicz
252    o genmake2: add ability to search for C compilers and cleanup test output
253      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
254    
255    checkpoint54d_post
256    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
257    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
258      leading to additional shift by 5 days each year of integration
259       (i.e. leading to considerable offset over the years)
260    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
261    o start with no AB and no initial filtering (staggerTimeStep):
262      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
263    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
264      (external loading & cpl import/export stay in forward_step.F)
265    o update coupling interface to work with new staggerTimeStep
266    o change MDSIO ptracers_pickup.
267    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
268    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
269    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
270    
271    checkpoint54c_post
272    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
273      this affects (truncation error) output.txt of test-exp:
274       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
275    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
276    o change Qnet to always be the net heat flux, (+upward).
277      affects (truncation error) output of natl_box exp.: updated
278    o define the max number of passive tracers in PTRACERS_SIZE.h
279    o start to test mnc routinely in exp0
280    o add sea-ice loading (sIceLoad) as a new forcing field.
281    
282    checkpoint54b_post
283    o add testreport "-j JOBS" option for parallel builds (tested and pretty
284       impressive on Altix and Opteron systems)
285    o diagnostics can now write NetCDF files through the mnc package
286    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
287    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
288    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
289      affects (truncation error) output of lab_sea & natl_box exp.: updated
290    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
291    
292    checkpoint54a_post
293    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
294    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
295    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
296    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
297      + internal_wave (shift in writing cg2d_ini_res)
298    checkpoint54a_pre
299    
300    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
301      - modified verification/lab_sea and natl_box_adjoint accordingly
302    
303    checkpoint54
304    checkpoint53g_post
305    o prepare splitting of thermodynamics: store convect.counter in common block
306    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
307      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
308    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
309    o new parameter "nShapS": allow to treat differently S from T (nShapT)
310    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
311    o restore adjointability
312    
313    checkpoint53f_post
314    o modifications that affect AIM experiment results (update output.txt):
315      - no advection of S at top interface Nr (pkg/generic_advdiff)
316      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
317    o AIM pkg:
318      - include stability function into surf.Flux derivative relative to Tsurf
319      - calculate clear-sky radiation & surface temp. change (for diagnostics)
320    
321    checkpoint53e_post
322    o merged cylindrical coord configuration
323    o added rotating_tank experiment
324    checkpoint53e_pre
325    
326    checkpoint53d_post
327    o faulks upgraded: re-generate output.txt that have changed:
328       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
329    o Added Bryan and Lewis, 1979, vertical diffusivity profile
330    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
331    o added Sadourny discretization of Coriolis
332      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
333      - re-enabled use of omega3 (useAbsVorticity)
334    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
335      vector-invariant equations
336      - note: does *NOT* yet use same variable visc. for no-slip BC's.
337    o recoded the lateral boundary conditions for non-hydrostatic w, this time
338      hopefully without new bugs
339      - still to do: biharmonic friction for non-hydrostatic w
340    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
341    o regenerated output for global_ocean_ebm (using -ieee)
342    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
343      of mom_common/
344      - simple re-arrangement of instructions within computing loop
345    checkpoint53d_pre
346    
347    checkpoint53c_post
348    o new version of coupler for AIM+thSIce and Ocean models
349     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
350     - land: change Evaporation of snow
351     - aim with thSIce: fix bug in snow-precip.
352    o changes to calc_gw.F
353     - bug fix for w^2 term near the bottom boundary
354     - (hopefully) improve the lateral slip boundary condtions for use with
355        partial/looped cells
356      - because the bug fix changes two verification experiments anyway (exp5
357        and plume on slope), change the lateral boundary condition from half slip
358        to the value of no_slip_sides
359    o ebm package wasnt quite up to the parallel task. Fixed that.
360    o Adjoint of EBM package + verification
361      * TLM OK
362      * ADM not sufficient accuracy yet (needs further testing)
363    
364    checkpoint53b_post
365    o Commiting new energy balance model to repository
366      * package is pkg/ebm
367      * verif. is verification/global_ocean_ebm
368      * references are in ebm_driver.F
369    C      * X. Wang, P. Stone and J. Marotzke, 1999:
370    C        Global thermohaline circulation. Part I:
371    C        Sensitivity to atmospheric moisture transport.
372    C        J. Climate 12(1), 71-82
373    C      * X. Wang, P. Stone and J. Marotzke, 1999:
374    C        Global thermohaline circulation. Part II:
375    C        Sensitivity with interactive transport.
376    C        J. Climate 12(1), 83-91
377    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
378    C        Destabilization of the thermohaline circulation
379    C        by atmospheric eddy transports.
380    C        J. Climate 7(12), 1870-1882
381    o Will need long integration testing.
382  checkpoint53b_pre  checkpoint53b_pre
383    
384  o created pkg/mom_common in preparation for variable viscosity code  o created pkg/mom_common in preparation for variable viscosity code

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