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revision 1.268 by jmc, Fri Mar 12 20:57:21 2004 UTC revision 1.384 by edhill, Sun Nov 14 03:36:51 2004 UTC
# Line 2  $Header$ Line 2  $Header$
2    
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    o mnc: cleanup "full" files--fixes out-of-memory problem
7    
8    checkpoint55j_post
9    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
10      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
11    o add consistent build directories and .cvsignore files to verification
12    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
13    o make all subroutines 30 or less characters in length for certain older
14      compilers to work (a thorough search only turns up two routines in
15      pkg/ptracers)
16    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
17      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
18    
19    checkpoint55i_post
20    o change arrays for total vertical diffusivity (2.D if explicit,
21      3.D if implicit) ; each ptracer uses its own background value.
22    o added mnc/NetCDF output capability to ocn_compon_interf
23      - added bits to verification/cpl_aim+ocn so that it can run on
24        ITRDA and other clusters without the mpirun "-wd" option
25    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
26      configuration
27    o give MNC the ability to create additional files rather than
28      exceeding a specified file size limit "MNC_MAX_FILESIZE"
29      - the default is just less than 2GB which is a practical limit
30        on many systems
31    o Compute the non-local term using either KPP vertical diffusivity (=default)
32       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
33    
34    checkpoint55h_post
35    o add verification test "vermix"
36    o remove all the *_ioinc flags and replace with the single global
37      outputTypesInclusive flag
38    o allow to set a vertical profile of vertical diffusivity for T & S
39    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
40    o useMNC moved from data.mnc to data.pkg
41    
42    checkpoint55g_post
43    o Renaming carbon AD experiments to comply with testreport conventions
44    o Updating adjoint of Held-Suarez hs94.1x64x5
45    o Fixing directives for non-ECCO forward_step, after ECCO directives
46      have been fixed to avoid recomp. of do_oceanic_phys
47      Works well for global_ocean.90x40x15,
48      but recomp. issue remains for carbon
49    o Updating adjoint output for natl_box_adjoint after
50      pkg/ecco has been modified (see taga c55d_post)
51    
52    checkpoint55f_post
53    o rename to timeave_init_fixed
54    
55    checkpoint55e_post
56    o some delicate re-shuffle of store directives to avoid one
57      extra call of do_oceanic_physics
58      affects ecco_the_main_loop.F, do_oceanic_physics.F
59      checkpoint_lev1_directives.h
60    o NB: this may break global_ocean adjoint temporarily,
61      but it is clear how to fix it. Will do later, need this now.
62    
63    checkpoint55d_post
64    o ECCO specific cost function terms (up-to-date with 1x1 runs)
65    o ecco_cost_weights is modified to 1x1 runs
66    o modifs to allow observations to be read in as
67      single file or yearly files
68    o enable to read exf forcing fields as either
69      single file or yearly files (flag useExfYearlyFields)
70    checkpoint55d_pre
71    
72    o switch between 2-level and 3-level checkpointing
73    o add ability of MNC to write local and "partial" (eg. 2D slices where
74      the full 3D field is never actually stored) arrays to NetCDF files
75      with the correct (that is, the complete multi-dimensional) set of
76      array indicies
77      - used in mom_vecinv() to write the diagFreq output
78      - tested (demonstrated) in verification/aim.5l_cs
79    o further mnc-ification
80      - add verification/lab_sea to the list with mnc setups
81      - fix undefined mnc v-names in cd_code
82      - add kpp to mnc output (both snapshot and timeave)
83    o non-hydrostatic code
84      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
85        in calc_gw.F
86      - defaults to viscAh
87      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
88        friction or Leith) in non-hydrostatic mode, as long as there is
89        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
90    o pkg/cost
91      extend simple cost functions to treat time mean quantities
92      (T,U,V) via cost_accumulate_state from cost_tile
93    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
94        be 2 times larger than the minimum size the advection scheme requires.
95        now get a perfect conservation of salt in advect_cs test-exp (updated)
96    o GGL90 (Gaspar's TKE mixed layer)
97      - add horizontal diffusion of TKE, requires exchanges in
98        do_fields_blocking_exchanges, horizontal diffusivity is zero by
99        default. In OPA there is no horizontal diffusion of TKE but the
100        mixing coefficients are computed from a horizontal average of TKE of
101        6 points or so. I think that diffusion has a little more physical
102        justification.
103      - clean up ggl90_calc in the hope of reducing memory usage (this hope
104        was in vain)
105      - mask tke-variable in ggl90_init
106    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
107    o fix biharmonic diffusion on CS-grid.
108    o more obcs stuff
109      - added obcs_external_fields_load as an alternative to the EXF-pkg option
110        for reading boundary values. This routine is called from
111        obcs_prescribe_read
112      - updated obcs_check
113      - changed sponge layer relaxation parameter units for days to seconds
114      - turned off sponge layer by default
115      - changed argument list of OBCS_CALC to myTime+deltaTclock
116      - fixed about 35 bugs in obcs_external_fields_load
117    
118    checkpoint55c_post
119    o obcs stuff
120      - new runtime flags useOBCSprescribe, useOBCSbalance
121      - re-arranged obcs_calc
122      - moved exf_getobcs to obcs_prescibe_read
123        obcs_prescibe_read is called after ORLANSKI stuff
124        and independent of it (executable can contain all).
125      - updated obcs_check
126      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
127        These may be necessary only if tangential velocities are
128        prescribed at OB, not sure, needs testing.
129    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
130      which simplifies the calls and passes the ifc check-bounds test
131    
132    checkpoint55b_post
133    o add a 2D scalar, Z location, exchange_2 routine.
134    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
135      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
136      affects advect_cs results (for the wrong reason): update output.txt
137    o use a more standard discretization for biharmonic viscosity ;
138     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
139      affects results of dome set-up: update output.txt
140    o fix gad_advection.F (CubedSphere part), back to version 1.23
141    o fix bug in mom_vi_del2uv.F (CubedSphere part).
142    
143    checkpoint55a_post
144    o merged code to
145      * prescribe/read time-dependent open boundaries
146        (works in conjunction with exf, cal)
147      * sponge layer code for open boundaries
148      * each boundary N/S/E/W now has its own CPP option
149        (healthy for the adjoint)
150    
151    checkpoint55
152    o up-to-date adjoint of previous breaks
153      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
154      - global_ocean_ebm: adjoint still needs fix (TLM ok)
155      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
156      - carbon: * remove tr1-related adjoint verification
157                * add ptracer as control variable
158    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
159      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
160    
161    checkpoint54f_post
162    o in verification/carbin/ remove experiment related to
163      ALLOW_PASSIVE_TRACER (array tr1 etc)
164      code_ad/ input_ad/ results_ad
165    
166    o add two new packages
167      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
168        + subject to optimization (memory)
169      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
170        + subject to reordering (many GOTOs in the original code)
171        + so far opps is called for every (i,j) point, and then operates in
172          the vertical; one may want to reorder the scheme in order operate in
173          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
174          fields)
175    o overhaul of IO so that we now have flags for MDSIO and/or MNC
176      - all verification tests compile and run with linux_ia32_g77
177      - defaults are compatible with current input files--nothing
178        should change if you were not previously using MNC
179      - MNC output has been added in numerous places (eg. timeave)
180        but there are still a few writes not yet do-able with MNC
181        (this is in progress)
182      - flags now allow for either/or/both use of MDSIO and MNC and
183        documentation will soon follow
184      - numerous small formatting cleanups for ProTeX
185    o add version info (via BUILD_INFO.h) to MNC and stdout
186    
187    checkpoint54e_post
188    o add two new packages
189      - pp81 (Packanowski and Philander, 1981), Richardson number and
190        stratification dependent mixing
191      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
192      - these scheme operate in a similar manner as KPP (without ghat, of
193        course), however there is only one diffusivity that is used for both
194        temperature and salinity (and passive tracers)ç
195    o add offline package
196    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
197      provided by Stephanie Dutkiewicz
198    o genmake2: add ability to search for C compilers and cleanup test output
199      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
200    
201    checkpoint54d_post
202    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
203    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
204      leading to additional shift by 5 days each year of integration
205       (i.e. leading to considerable offset over the years)
206    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
207    o start with no AB and no initial filtering (staggerTimeStep):
208      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
209    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
210      (external loading & cpl import/export stay in forward_step.F)
211    o update coupling interface to work with new staggerTimeStep
212    o change MDSIO ptracers_pickup.
213    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
214    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
215    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
216    
217    checkpoint54c_post
218    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
219      this affects (truncation error) output.txt of test-exp:
220       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
221    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
222    o change Qnet to always be the net heat flux, (+upward).
223      affects (truncation error) output of natl_box exp.: updated
224    o define the max number of passive tracers in PTRACERS_SIZE.h
225    o start to test mnc routinely in exp0
226    o add sea-ice loading (sIceLoad) as a new forcing field.
227    
228    checkpoint54b_post
229    o add testreport "-j JOBS" option for parallel builds (tested and pretty
230       impressive on Altix and Opteron systems)
231    o diagnostics can now write NetCDF files through the mnc package
232    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
233    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
234    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
235      affects (truncation error) output of lab_sea & natl_box exp.: updated
236    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
237    
238    checkpoint54a_post
239    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
240    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
241    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
242    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
243      + internal_wave (shift in writing cg2d_ini_res)
244    checkpoint54a_pre
245    
246    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
247      - modified verification/lab_sea and natl_box_adjoint accordingly
248    
249    checkpoint54
250    checkpoint53g_post
251    o prepare splitting of thermodynamics: store convect.counter in common block
252    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
253      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
254    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
255    o new parameter "nShapS": allow to treat differently S from T (nShapT)
256    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
257    o restore adjointability
258    
259    checkpoint53f_post
260    o modifications that affect AIM experiment results (update output.txt):
261      - no advection of S at top interface Nr (pkg/generic_advdiff)
262      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
263    o AIM pkg:
264      - include stability function into surf.Flux derivative relative to Tsurf
265      - calculate clear-sky radiation & surface temp. change (for diagnostics)
266    
267    checkpoint53e_post
268    o merged cylindrical coord configuration
269    o added rotating_tank experiment
270    checkpoint53e_pre
271    
272    checkpoint53d_post
273    o faulks upgraded: re-generate output.txt that have changed:
274       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
275    o Added Bryan and Lewis, 1979, vertical diffusivity profile
276    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
277    o added Sadourny discretization of Coriolis
278      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
279      - re-enabled use of omega3 (useAbsVorticity)
280    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
281      vector-invariant equations
282      - note: does *NOT* yet use same variable visc. for no-slip BC's.
283    o recoded the lateral boundary conditions for non-hydrostatic w, this time
284      hopefully without new bugs
285      - still to do: biharmonic friction for non-hydrostatic w
286    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
287    o regenerated output for global_ocean_ebm (using -ieee)
288    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
289      of mom_common/
290      - simple re-arrangement of instructions within computing loop
291    checkpoint53d_pre
292    
293    checkpoint53c_post
294    o new version of coupler for AIM+thSIce and Ocean models
295     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
296     - land: change Evaporation of snow
297     - aim with thSIce: fix bug in snow-precip.
298    o changes to calc_gw.F
299     - bug fix for w^2 term near the bottom boundary
300     - (hopefully) improve the lateral slip boundary condtions for use with
301        partial/looped cells
302      - because the bug fix changes two verification experiments anyway (exp5
303        and plume on slope), change the lateral boundary condition from half slip
304        to the value of no_slip_sides
305    o ebm package wasnt quite up to the parallel task. Fixed that.
306    o Adjoint of EBM package + verification
307      * TLM OK
308      * ADM not sufficient accuracy yet (needs further testing)
309    
310    checkpoint53b_post
311    o Commiting new energy balance model to repository
312      * package is pkg/ebm
313      * verif. is verification/global_ocean_ebm
314      * references are in ebm_driver.F
315    C      * X. Wang, P. Stone and J. Marotzke, 1999:
316    C        Global thermohaline circulation. Part I:
317    C        Sensitivity to atmospheric moisture transport.
318    C        J. Climate 12(1), 71-82
319    C      * X. Wang, P. Stone and J. Marotzke, 1999:
320    C        Global thermohaline circulation. Part II:
321    C        Sensitivity with interactive transport.
322    C        J. Climate 12(1), 83-91
323    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
324    C        Destabilization of the thermohaline circulation
325    C        by atmospheric eddy transports.
326    C        J. Climate 7(12), 1870-1882
327    o Will need long integration testing.
328    checkpoint53b_pre
329    
330    o created pkg/mom_common in preparation for variable viscosity code
331    o renamed and split ini_mnc_io
332    o pkg/land: only liquid water can diffuse or run-off
333    o AIM using land: soil wetness availability account for snow
334    o added printMapIncludesZeros to EEPARMS namelist
335    
336    checkpoint53a_post
337    o restore TAMC compatiility for exf_constants.h
338      (no usage of _d in .h)
339    o Additional storing in KPP in an attempt to fix
340      TAMC problem with adjoint of KPP code.
341      (no success...)
342      Identical code works fine with TAF.
343    o Fixed verification/natl_box_adjoint experiments.
344      Initial conditions for Experiments 4 and 5 are now
345      set to "SEAICE_initialHEFF=0", which is more reasonable,
346      and hence gives results closer to that of Experiment 2.
347      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
348    
349    checkpoint53
350    o stable checkpoint with up to date adjoint
351      TLM tests only run for 1st grdchk at the moment. Its unclear if
352      this is a code problem or a problem with resetting code for g_
353      variables that is being autogenerated wrong.
354      Otherwise:
355       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
356       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
357         are both still in chaos following their security messes.
358    
359    checkpoint52n_post
360    o various build (mostly genmake2) changes including:
361      - ability to build/run more easily within Cygwin and MacOS X
362      - more complicated Makefiles with a stronger dependence on Gnu Make
363    o pkg/seaice modifications
364      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
365        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
366        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
367      - changed proxy for geostrophic velocity and updated
368        verification/lab_sea/results/* accordingly
369      - removed ADI dynamic solver from pkg/seaice
370      - replaced all occurrences of 1/CSTICE or 1/CSUICE
371        they caused a segmentation fault under certain circumstances
372      - removed unused field WATR
373    o bug fix in exf-package:
374      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
375         now reflect that.
376    o small fixes in the cal-package:
377      - set reference date to first of January for the 'model'-calendar
378      - failing of cal_CheckDate in cal_FullDate now actually results in a
379        warning
380    o small modifications in exf-package to increase flexibility:
381      - change climtempfreeze from a constant to a runtime parameter that
382        is specified in data.exf_clim (default = -1.9)
383      - introduce runtime parameter windstressmax (default = 2.0) that is
384        specified in data.exf
385    o fix in pkg/thsice:
386      - update Evap (Tsf changes) to be consistent with Latent heat flux
387      - maintain snow precipitation unchanged (even if Tsf >=0).
388     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
389    
390    checkpoint52m_post
391    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
392      this does not change any of the results, because myIter=0 in swfrac always
393      lead to jwtype=2 (the default anyway), but the call makes little sense
394      as a default
395    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
396    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
397      atmospheric model (AIM) to use it ; add a "slab ocean" component.
398    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
399    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
400    o extending useSingleCpuIO option to work with new exch2 I/O format
401      - old-style, missing-tile I/O is still accessible by defining CPP
402        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
403    o monitor package can write to NetCDF files and/or STDOUT
404    o fix re-definition bug in MNC_GRID_INIT_ALL()
405    o doc/api_reference added
406      - a framework for building an API Reference Manual using all
407        the "protex" comments embedded in the code
408      - see pkg/generic_advdiff, pkg/mnc for examples
409    o MNC:
410      - make myThid the last argument for all subroutines
411      - new default for the grid files: NO halos
412      - add useMNC and other run-time flags
413      - separate per-file-group handling of the unlimited dimension
414      - early initialization of MNC w/ flags read at the eeboot stage
415        and lookup tables set in initialize_fixed
416      - write all MNC output to a freshly-created directory
417  o thermodynamics sea-ice (thsice) is now tested with testreport.  o thermodynamics sea-ice (thsice) is now tested with testreport.
418  o test exp. advect_cs: use the standard cs32 grid ; update output.  o test exp. advect_cs: use the standard cs32 grid ; update output.
419    o Added functionality to grdchk:
420      pick global i,j,k position (or nearest wet) where to perform check.
421    
422  checkpoint52l_post  checkpoint52l_post
423  o new land formulation:  o new land formulation:

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