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revision 1.249 by dimitri, Sun Jan 25 00:31:52 2004 UTC revision 1.351 by edhill, Wed Sep 22 21:19:44 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 make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
7      which simplifies the calls and passes the ifc check-bounds test
8    
9    checkpoint55b_post
10    o add a 2D scalar, Z location, exchange_2 routine.
11    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
12      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
13      affects advect_cs results (for the wrong reason): update output.txt
14    o use a more standard discretization for biharmonic viscosity ;
15     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
16      affects results of dome set-up: update output.txt
17    o fix gad_advection.F (CubedSphere part), back to version 1.23
18    o fix bug in mom_vi_del2uv.F (CubedSphere part).
19    
20    checkpoint55a_post
21    o merged code to
22      * prescribe/read time-dependent open boundaries
23        (works in conjunction with exf, cal)
24      * sponge layer code for open boundaries
25      * each boundary N/S/E/W now has its own CPP option
26        (healthy for the adjoint)
27    
28    checkpoint55
29    o up-to-date adjoint of previous breaks
30      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
31      - global_ocean_ebm: adjoint still needs fix (TLM ok)
32      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
33      - carbon: * remove tr1-related adjoint verification
34                * add ptracer as control variable
35    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
36      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
37    
38    checkpoint54f_post
39    o in verification/carbin/ remove experiment related to
40      ALLOW_PASSIVE_TRACER (array tr1 etc)
41      code_ad/ input_ad/ results_ad
42    
43    o add two new packages
44      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
45        + subject to optimization (memory)
46      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
47        + subject to reordering (many GOTOs in the original code)
48        + so far opps is called for every (i,j) point, and then operates in
49          the vertical; one may want to reorder the scheme in order operate in
50          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
51          fields)
52    o overhaul of IO so that we now have flags for MDSIO and/or MNC
53      - all verification tests compile and run with linux_ia32_g77
54      - defaults are compatible with current input files--nothing
55        should change if you were not previously using MNC
56      - MNC output has been added in numerous places (eg. timeave)
57        but there are still a few writes not yet do-able with MNC
58        (this is in progress)
59      - flags now allow for either/or/both use of MDSIO and MNC and
60        documentation will soon follow
61      - numerous small formatting cleanups for ProTeX
62    o add version info (via BUILD_INFO.h) to MNC and stdout
63    
64    checkpoint54e_post
65    o add two new packages
66      - pp81 (Packanowski and Philander, 1981), Richardson number and
67        stratification dependent mixing
68      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
69      - these scheme operate in a similar manner as KPP (without ghat, of
70        course), however there is only one diffusivity that is used for both
71        temperature and salinity (and passive tracers)ç
72    o add offline package
73    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
74      provided by Stephanie Dutkiewicz
75    o genmake2: add ability to search for C compilers and cleanup test output
76      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
77    
78    checkpoint54d_post
79    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
80    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
81      leading to additional shift by 5 days each year of integration
82       (i.e. leading to considerable offset over the years)
83    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
84    o start with no AB and no initial filtering (staggerTimeStep):
85      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
86    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
87      (external loading & cpl import/export stay in forward_step.F)
88    o update coupling interface to work with new staggerTimeStep
89    o change MDSIO ptracers_pickup.
90    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
91    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
92    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
93    
94    checkpoint54c_post
95    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
96      this affects (truncation error) output.txt of test-exp:
97       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
98    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
99    o change Qnet to always be the net heat flux, (+upward).
100      affects (truncation error) output of natl_box exp.: updated
101    o define the max number of passive tracers in PTRACERS_SIZE.h
102    o start to test mnc routinely in exp0
103    o add sea-ice loading (sIceLoad) as a new forcing field.
104    
105    checkpoint54b_post
106    o add testreport "-j JOBS" option for parallel builds (tested and pretty
107       impressive on Altix and Opteron systems)
108    o diagnostics can now write NetCDF files through the mnc package
109    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
110    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
111    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
112      affects (truncation error) output of lab_sea & natl_box exp.: updated
113    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
114    
115    checkpoint54a_post
116    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
117    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
118    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
119    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
120      + internal_wave (shift in writing cg2d_ini_res)
121    checkpoint54a_pre
122    
123    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
124      - modified verification/lab_sea and natl_box_adjoint accordingly
125    
126    checkpoint54
127    checkpoint53g_post
128    o prepare splitting of thermodynamics: store convect.counter in common block
129    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
130      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
131    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
132    o new parameter "nShapS": allow to treat differently S from T (nShapT)
133    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
134    o restore adjointability
135    
136    checkpoint53f_post
137    o modifications that affect AIM experiment results (update output.txt):
138      - no advection of S at top interface Nr (pkg/generic_advdiff)
139      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
140    o AIM pkg:
141      - include stability function into surf.Flux derivative relative to Tsurf
142      - calculate clear-sky radiation & surface temp. change (for diagnostics)
143    
144    checkpoint53e_post
145    o merged cylindrical coord configuration
146    o added rotating_tank experiment
147    checkpoint53e_pre
148    
149    checkpoint53d_post
150    o faulks upgraded: re-generate output.txt that have changed:
151       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
152    o Added Bryan and Lewis, 1979, vertical diffusivity profile
153    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
154    o added Sadourny discretization of Coriolis
155      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
156      - re-enabled use of omega3 (useAbsVorticity)
157    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
158      vector-invariant equations
159      - note: does *NOT* yet use same variable visc. for no-slip BC's.
160    o recoded the lateral boundary conditions for non-hydrostatic w, this time
161      hopefully without new bugs
162      - still to do: biharmonic friction for non-hydrostatic w
163    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
164    o regenerated output for global_ocean_ebm (using -ieee)
165    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
166      of mom_common/
167      - simple re-arrangement of instructions within computing loop
168    checkpoint53d_pre
169    
170    checkpoint53c_post
171    o new version of coupler for AIM+thSIce and Ocean models
172     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
173     - land: change Evaporation of snow
174     - aim with thSIce: fix bug in snow-precip.
175    o changes to calc_gw.F
176     - bug fix for w^2 term near the bottom boundary
177     - (hopefully) improve the lateral slip boundary condtions for use with
178        partial/looped cells
179      - because the bug fix changes two verification experiments anyway (exp5
180        and plume on slope), change the lateral boundary condition from half slip
181        to the value of no_slip_sides
182    o ebm package wasnt quite up to the parallel task. Fixed that.
183    o Adjoint of EBM package + verification
184      * TLM OK
185      * ADM not sufficient accuracy yet (needs further testing)
186    
187    checkpoint53b_post
188    o Commiting new energy balance model to repository
189      * package is pkg/ebm
190      * verif. is verification/global_ocean_ebm
191      * references are in ebm_driver.F
192    C      * X. Wang, P. Stone and J. Marotzke, 1999:
193    C        Global thermohaline circulation. Part I:
194    C        Sensitivity to atmospheric moisture transport.
195    C        J. Climate 12(1), 71-82
196    C      * X. Wang, P. Stone and J. Marotzke, 1999:
197    C        Global thermohaline circulation. Part II:
198    C        Sensitivity with interactive transport.
199    C        J. Climate 12(1), 83-91
200    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
201    C        Destabilization of the thermohaline circulation
202    C        by atmospheric eddy transports.
203    C        J. Climate 7(12), 1870-1882
204    o Will need long integration testing.
205    checkpoint53b_pre
206    
207    o created pkg/mom_common in preparation for variable viscosity code
208    o renamed and split ini_mnc_io
209    o pkg/land: only liquid water can diffuse or run-off
210    o AIM using land: soil wetness availability account for snow
211    o added printMapIncludesZeros to EEPARMS namelist
212    
213    checkpoint53a_post
214    o restore TAMC compatiility for exf_constants.h
215      (no usage of _d in .h)
216    o Additional storing in KPP in an attempt to fix
217      TAMC problem with adjoint of KPP code.
218      (no success...)
219      Identical code works fine with TAF.
220    o Fixed verification/natl_box_adjoint experiments.
221      Initial conditions for Experiments 4 and 5 are now
222      set to "SEAICE_initialHEFF=0", which is more reasonable,
223      and hence gives results closer to that of Experiment 2.
224      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
225    
226    checkpoint53
227    o stable checkpoint with up to date adjoint
228      TLM tests only run for 1st grdchk at the moment. Its unclear if
229      this is a code problem or a problem with resetting code for g_
230      variables that is being autogenerated wrong.
231      Otherwise:
232       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
233       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
234         are both still in chaos following their security messes.
235    
236    checkpoint52n_post
237    o various build (mostly genmake2) changes including:
238      - ability to build/run more easily within Cygwin and MacOS X
239      - more complicated Makefiles with a stronger dependence on Gnu Make
240    o pkg/seaice modifications
241      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
242        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
243        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
244      - changed proxy for geostrophic velocity and updated
245        verification/lab_sea/results/* accordingly
246      - removed ADI dynamic solver from pkg/seaice
247      - replaced all occurrences of 1/CSTICE or 1/CSUICE
248        they caused a segmentation fault under certain circumstances
249      - removed unused field WATR
250    o bug fix in exf-package:
251      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
252         now reflect that.
253    o small fixes in the cal-package:
254      - set reference date to first of January for the 'model'-calendar
255      - failing of cal_CheckDate in cal_FullDate now actually results in a
256        warning
257    o small modifications in exf-package to increase flexibility:
258      - change climtempfreeze from a constant to a runtime parameter that
259        is specified in data.exf_clim (default = -1.9)
260      - introduce runtime parameter windstressmax (default = 2.0) that is
261        specified in data.exf
262    o fix in pkg/thsice:
263      - update Evap (Tsf changes) to be consistent with Latent heat flux
264      - maintain snow precipitation unchanged (even if Tsf >=0).
265     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
266    
267    checkpoint52m_post
268    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
269      this does not change any of the results, because myIter=0 in swfrac always
270      lead to jwtype=2 (the default anyway), but the call makes little sense
271      as a default
272    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
273    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
274      atmospheric model (AIM) to use it ; add a "slab ocean" component.
275    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
276    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
277    o extending useSingleCpuIO option to work with new exch2 I/O format
278      - old-style, missing-tile I/O is still accessible by defining CPP
279        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
280    o monitor package can write to NetCDF files and/or STDOUT
281    o fix re-definition bug in MNC_GRID_INIT_ALL()
282    o doc/api_reference added
283      - a framework for building an API Reference Manual using all
284        the "protex" comments embedded in the code
285      - see pkg/generic_advdiff, pkg/mnc for examples
286    o MNC:
287      - make myThid the last argument for all subroutines
288      - new default for the grid files: NO halos
289      - add useMNC and other run-time flags
290      - separate per-file-group handling of the unlimited dimension
291      - early initialization of MNC w/ flags read at the eeboot stage
292        and lookup tables set in initialize_fixed
293      - write all MNC output to a freshly-created directory
294    o thermodynamics sea-ice (thsice) is now tested with testreport.
295    o test exp. advect_cs: use the standard cs32 grid ; update output.
296    o Added functionality to grdchk:
297      pick global i,j,k position (or nearest wet) where to perform check.
298    
299    checkpoint52l_post
300    o new land formulation:
301      a) use ground enthalpy as prognostic variable to ensure exact
302         energy conservation.
303      b) account for water temperature and for latent heat of freezing
304         in all processes (rain, run-off, ground storage)
305      c) compute surface and ground temperature implicitly.
306    o aim_v23 modification for new land model:
307      a) Treat separately land / ocean / sea-ice surface fluxes
308         to allow implicit computation of land & sea-ice surface temp.
309      b) add snow precipitation.
310    checkpoint52l_pre
311    
312    o fix problem (when 1 tile is empty) in min/max monitor.
313    o fix bug in timeAve (u,vZetatave in common block)
314    o no restoring terms under ice for pkg/seaice
315    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
316    o bug fix for pkg/seaice pickups
317    o change MNC call locations and add coordinate attributes
318    o mask vorticity at the corner ; affects global_ocean.cs output
319    o fix ini_curvilinear_grid ; test CS experiments with mpi
320    o aim.5l_cs: modify sea-ice fraction input file ; update output
321    o exf: Adding simple range check routine for exf fields after read
322    
323    checkpoint52k_post
324    o removed top-level directory "diags"
325      - we migrated these functions to pkg/timeave a long time ago
326    o fixed bug introduced in pkg/monitor
327    o accuracy ctrlprec = 32 insuffient for gradient checks using
328      averaged fields (I/O via cost_averages)
329      -> use ctrl.h in active_file*.F to control I/O precision.
330    o paramter list of CALL ADTHE_MAIN_LOOP
331    o added initial do_the_model_io to ecco
332    o set all ...Freq to zero after cost_final
333      taveFreq, dumpFreq, pChkptFreq
334    o MAIN and ECCO differentiability restored
335    
336    checkpoint52j_post
337    o fix nchklev in tamc.h for global_ocean...
338    o Bringing flow and store directives up-to-date
339    o Really weird thing!
340      call do_the_model_io from the_main_loop with parameters
341      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
342      TAF places a faulty re-call of initialise_varia
343      after cost_final call which should not be there!
344    checkpoint52j_pre
345    
346    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
347      error messages
348    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
349    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
350      debug output
351    o modfied mdsio_writefield.F to handle non-global files under exch2
352    o update AIM Cubed-Sphere exp (aim.5l_cs):
353      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
354    o update AIM Equatorial Channel exp:
355      use standard aim_v23 pkg and change the SST fields to be more realistic.
356  o globalFile now works with exch2  o globalFile now works with exch2
357  o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and  o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
358    mon_vort3.F to make exch2 friendly with >1 tile per cube    mon_vort3.F to make exch2 friendly with >1 tile per cube face
   face  
359  o limit timeave output for hi-res integrations  o limit timeave output for hi-res integrations
360    
361  checkpoint52i_post  checkpoint52i_post

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