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revision 1.237 by afe, Fri Jan 9 21:29:24 2004 UTC revision 1.360 by heimbach, Mon Sep 27 18:01:22 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6  checkpoint52f_pre  o pkg/cost
7      extend simple cost functions to treat time mean quantities
8      (T,U,V) via cost_accumulate_state from cost_tile
9    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
10        be 2 times larger than the minimum size the advection scheme requires.
11        now get a perfect conservation of salt in advect_cs test-exp (updated)
12    o GGL90 (Gaspar's TKE mixed layer)
13      - add horizontal diffusion of TKE, requires exchanges in
14        do_fields_blocking_exchanges, horizontal diffusivity is zero by
15        default. In OPA there is no horizontal diffusion of TKE but the
16        mixing coefficients are computed from a horizontal average of TKE of
17        6 points or so. I think that diffusion has a little more physical
18        justification.
19      - clean up ggl90_calc in the hope of reducing memory usage (this hope
20        was in vain)
21      - mask tke-variable in ggl90_init
22    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
23    o fix biharmonic diffusion on CS-grid.
24    o more obcs stuff
25      - added obcs_external_fields_load as an alternative to the EXF-pkg option
26        for reading boundary values. This routine is called from
27        obcs_prescribe_read
28      - updated obcs_check
29      - changed sponge layer relaxation parameter units for days to seconds
30      - turned off sponge layer by default
31      - changed argument list of OBCS_CALC to myTime+deltaTclock
32    
33    checkpoint55c_post
34    o obcs stuff
35      - new runtime flags useOBCSprescribe, useOBCSbalance
36      - re-arranged obcs_calc
37      - moved exf_getobcs to obcs_prescibe_read
38        obcs_prescibe_read is called after ORLANSKI stuff
39        and independent of it (executable can contain all).
40      - updated obcs_check
41      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
42        These may be necessary only if tangential velocities are
43        prescribed at OB, not sure, needs testing.
44    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
45      which simplifies the calls and passes the ifc check-bounds test
46    
47    checkpoint55b_post
48    o add a 2D scalar, Z location, exchange_2 routine.
49    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
50      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
51      affects advect_cs results (for the wrong reason): update output.txt
52    o use a more standard discretization for biharmonic viscosity ;
53     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
54      affects results of dome set-up: update output.txt
55    o fix gad_advection.F (CubedSphere part), back to version 1.23
56    o fix bug in mom_vi_del2uv.F (CubedSphere part).
57    
58    checkpoint55a_post
59    o merged code to
60      * prescribe/read time-dependent open boundaries
61        (works in conjunction with exf, cal)
62      * sponge layer code for open boundaries
63      * each boundary N/S/E/W now has its own CPP option
64        (healthy for the adjoint)
65    
66    checkpoint55
67    o up-to-date adjoint of previous breaks
68      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
69      - global_ocean_ebm: adjoint still needs fix (TLM ok)
70      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
71      - carbon: * remove tr1-related adjoint verification
72                * add ptracer as control variable
73    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
74      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
75    
76    checkpoint54f_post
77    o in verification/carbin/ remove experiment related to
78      ALLOW_PASSIVE_TRACER (array tr1 etc)
79      code_ad/ input_ad/ results_ad
80    
81    o add two new packages
82      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
83        + subject to optimization (memory)
84      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
85        + subject to reordering (many GOTOs in the original code)
86        + so far opps is called for every (i,j) point, and then operates in
87          the vertical; one may want to reorder the scheme in order operate in
88          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
89          fields)
90    o overhaul of IO so that we now have flags for MDSIO and/or MNC
91      - all verification tests compile and run with linux_ia32_g77
92      - defaults are compatible with current input files--nothing
93        should change if you were not previously using MNC
94      - MNC output has been added in numerous places (eg. timeave)
95        but there are still a few writes not yet do-able with MNC
96        (this is in progress)
97      - flags now allow for either/or/both use of MDSIO and MNC and
98        documentation will soon follow
99      - numerous small formatting cleanups for ProTeX
100    o add version info (via BUILD_INFO.h) to MNC and stdout
101    
102    checkpoint54e_post
103    o add two new packages
104      - pp81 (Packanowski and Philander, 1981), Richardson number and
105        stratification dependent mixing
106      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
107      - these scheme operate in a similar manner as KPP (without ghat, of
108        course), however there is only one diffusivity that is used for both
109        temperature and salinity (and passive tracers)ç
110    o add offline package
111    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
112      provided by Stephanie Dutkiewicz
113    o genmake2: add ability to search for C compilers and cleanup test output
114      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
115    
116    checkpoint54d_post
117    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
118    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
119      leading to additional shift by 5 days each year of integration
120       (i.e. leading to considerable offset over the years)
121    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
122    o start with no AB and no initial filtering (staggerTimeStep):
123      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
124    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
125      (external loading & cpl import/export stay in forward_step.F)
126    o update coupling interface to work with new staggerTimeStep
127    o change MDSIO ptracers_pickup.
128    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
129    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
130    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
131    
132    checkpoint54c_post
133    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
134      this affects (truncation error) output.txt of test-exp:
135       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
136    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
137    o change Qnet to always be the net heat flux, (+upward).
138      affects (truncation error) output of natl_box exp.: updated
139    o define the max number of passive tracers in PTRACERS_SIZE.h
140    o start to test mnc routinely in exp0
141    o add sea-ice loading (sIceLoad) as a new forcing field.
142    
143    checkpoint54b_post
144    o add testreport "-j JOBS" option for parallel builds (tested and pretty
145       impressive on Altix and Opteron systems)
146    o diagnostics can now write NetCDF files through the mnc package
147    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
148    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
149    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
150      affects (truncation error) output of lab_sea & natl_box exp.: updated
151    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
152    
153    checkpoint54a_post
154    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
155    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
156    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
157    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
158      + internal_wave (shift in writing cg2d_ini_res)
159    checkpoint54a_pre
160    
161    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
162      - modified verification/lab_sea and natl_box_adjoint accordingly
163    
164    checkpoint54
165    checkpoint53g_post
166    o prepare splitting of thermodynamics: store convect.counter in common block
167    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
168      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
169    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
170    o new parameter "nShapS": allow to treat differently S from T (nShapT)
171    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
172    o restore adjointability
173    
174    checkpoint53f_post
175    o modifications that affect AIM experiment results (update output.txt):
176      - no advection of S at top interface Nr (pkg/generic_advdiff)
177      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
178    o AIM pkg:
179      - include stability function into surf.Flux derivative relative to Tsurf
180      - calculate clear-sky radiation & surface temp. change (for diagnostics)
181    
182    checkpoint53e_post
183    o merged cylindrical coord configuration
184    o added rotating_tank experiment
185    checkpoint53e_pre
186    
187    checkpoint53d_post
188    o faulks upgraded: re-generate output.txt that have changed:
189       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
190    o Added Bryan and Lewis, 1979, vertical diffusivity profile
191    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
192    o added Sadourny discretization of Coriolis
193      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
194      - re-enabled use of omega3 (useAbsVorticity)
195    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
196      vector-invariant equations
197      - note: does *NOT* yet use same variable visc. for no-slip BC's.
198    o recoded the lateral boundary conditions for non-hydrostatic w, this time
199      hopefully without new bugs
200      - still to do: biharmonic friction for non-hydrostatic w
201    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
202    o regenerated output for global_ocean_ebm (using -ieee)
203    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
204      of mom_common/
205      - simple re-arrangement of instructions within computing loop
206    checkpoint53d_pre
207    
208    checkpoint53c_post
209    o new version of coupler for AIM+thSIce and Ocean models
210     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
211     - land: change Evaporation of snow
212     - aim with thSIce: fix bug in snow-precip.
213    o changes to calc_gw.F
214     - bug fix for w^2 term near the bottom boundary
215     - (hopefully) improve the lateral slip boundary condtions for use with
216        partial/looped cells
217      - because the bug fix changes two verification experiments anyway (exp5
218        and plume on slope), change the lateral boundary condition from half slip
219        to the value of no_slip_sides
220    o ebm package wasnt quite up to the parallel task. Fixed that.
221    o Adjoint of EBM package + verification
222      * TLM OK
223      * ADM not sufficient accuracy yet (needs further testing)
224    
225    checkpoint53b_post
226    o Commiting new energy balance model to repository
227      * package is pkg/ebm
228      * verif. is verification/global_ocean_ebm
229      * references are in ebm_driver.F
230    C      * X. Wang, P. Stone and J. Marotzke, 1999:
231    C        Global thermohaline circulation. Part I:
232    C        Sensitivity to atmospheric moisture transport.
233    C        J. Climate 12(1), 71-82
234    C      * X. Wang, P. Stone and J. Marotzke, 1999:
235    C        Global thermohaline circulation. Part II:
236    C        Sensitivity with interactive transport.
237    C        J. Climate 12(1), 83-91
238    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
239    C        Destabilization of the thermohaline circulation
240    C        by atmospheric eddy transports.
241    C        J. Climate 7(12), 1870-1882
242    o Will need long integration testing.
243    checkpoint53b_pre
244    
245    o created pkg/mom_common in preparation for variable viscosity code
246    o renamed and split ini_mnc_io
247    o pkg/land: only liquid water can diffuse or run-off
248    o AIM using land: soil wetness availability account for snow
249    o added printMapIncludesZeros to EEPARMS namelist
250    
251    checkpoint53a_post
252    o restore TAMC compatiility for exf_constants.h
253      (no usage of _d in .h)
254    o Additional storing in KPP in an attempt to fix
255      TAMC problem with adjoint of KPP code.
256      (no success...)
257      Identical code works fine with TAF.
258    o Fixed verification/natl_box_adjoint experiments.
259      Initial conditions for Experiments 4 and 5 are now
260      set to "SEAICE_initialHEFF=0", which is more reasonable,
261      and hence gives results closer to that of Experiment 2.
262      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
263    
264    checkpoint53
265    o stable checkpoint with up to date adjoint
266      TLM tests only run for 1st grdchk at the moment. Its unclear if
267      this is a code problem or a problem with resetting code for g_
268      variables that is being autogenerated wrong.
269      Otherwise:
270       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
271       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
272         are both still in chaos following their security messes.
273    
274    checkpoint52n_post
275    o various build (mostly genmake2) changes including:
276      - ability to build/run more easily within Cygwin and MacOS X
277      - more complicated Makefiles with a stronger dependence on Gnu Make
278    o pkg/seaice modifications
279      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
280        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
281        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
282      - changed proxy for geostrophic velocity and updated
283        verification/lab_sea/results/* accordingly
284      - removed ADI dynamic solver from pkg/seaice
285      - replaced all occurrences of 1/CSTICE or 1/CSUICE
286        they caused a segmentation fault under certain circumstances
287      - removed unused field WATR
288    o bug fix in exf-package:
289      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
290         now reflect that.
291    o small fixes in the cal-package:
292      - set reference date to first of January for the 'model'-calendar
293      - failing of cal_CheckDate in cal_FullDate now actually results in a
294        warning
295    o small modifications in exf-package to increase flexibility:
296      - change climtempfreeze from a constant to a runtime parameter that
297        is specified in data.exf_clim (default = -1.9)
298      - introduce runtime parameter windstressmax (default = 2.0) that is
299        specified in data.exf
300    o fix in pkg/thsice:
301      - update Evap (Tsf changes) to be consistent with Latent heat flux
302      - maintain snow precipitation unchanged (even if Tsf >=0).
303     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
304    
305    checkpoint52m_post
306    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
307      this does not change any of the results, because myIter=0 in swfrac always
308      lead to jwtype=2 (the default anyway), but the call makes little sense
309      as a default
310    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
311    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
312      atmospheric model (AIM) to use it ; add a "slab ocean" component.
313    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
314    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
315    o extending useSingleCpuIO option to work with new exch2 I/O format
316      - old-style, missing-tile I/O is still accessible by defining CPP
317        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
318    o monitor package can write to NetCDF files and/or STDOUT
319    o fix re-definition bug in MNC_GRID_INIT_ALL()
320    o doc/api_reference added
321      - a framework for building an API Reference Manual using all
322        the "protex" comments embedded in the code
323      - see pkg/generic_advdiff, pkg/mnc for examples
324    o MNC:
325      - make myThid the last argument for all subroutines
326      - new default for the grid files: NO halos
327      - add useMNC and other run-time flags
328      - separate per-file-group handling of the unlimited dimension
329      - early initialization of MNC w/ flags read at the eeboot stage
330        and lookup tables set in initialize_fixed
331      - write all MNC output to a freshly-created directory
332    o thermodynamics sea-ice (thsice) is now tested with testreport.
333    o test exp. advect_cs: use the standard cs32 grid ; update output.
334    o Added functionality to grdchk:
335      pick global i,j,k position (or nearest wet) where to perform check.
336    
337    checkpoint52l_post
338    o new land formulation:
339      a) use ground enthalpy as prognostic variable to ensure exact
340         energy conservation.
341      b) account for water temperature and for latent heat of freezing
342         in all processes (rain, run-off, ground storage)
343      c) compute surface and ground temperature implicitly.
344    o aim_v23 modification for new land model:
345      a) Treat separately land / ocean / sea-ice surface fluxes
346         to allow implicit computation of land & sea-ice surface temp.
347      b) add snow precipitation.
348    checkpoint52l_pre
349    
350    o fix problem (when 1 tile is empty) in min/max monitor.
351    o fix bug in timeAve (u,vZetatave in common block)
352    o no restoring terms under ice for pkg/seaice
353    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
354    o bug fix for pkg/seaice pickups
355    o change MNC call locations and add coordinate attributes
356    o mask vorticity at the corner ; affects global_ocean.cs output
357    o fix ini_curvilinear_grid ; test CS experiments with mpi
358    o aim.5l_cs: modify sea-ice fraction input file ; update output
359    o exf: Adding simple range check routine for exf fields after read
360    
361    checkpoint52k_post
362    o removed top-level directory "diags"
363      - we migrated these functions to pkg/timeave a long time ago
364    o fixed bug introduced in pkg/monitor
365    o accuracy ctrlprec = 32 insuffient for gradient checks using
366      averaged fields (I/O via cost_averages)
367      -> use ctrl.h in active_file*.F to control I/O precision.
368    o paramter list of CALL ADTHE_MAIN_LOOP
369    o added initial do_the_model_io to ecco
370    o set all ...Freq to zero after cost_final
371      taveFreq, dumpFreq, pChkptFreq
372    o MAIN and ECCO differentiability restored
373    
374    checkpoint52j_post
375    o fix nchklev in tamc.h for global_ocean...
376    o Bringing flow and store directives up-to-date
377    o Really weird thing!
378      call do_the_model_io from the_main_loop with parameters
379      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
380      TAF places a faulty re-call of initialise_varia
381      after cost_final call which should not be there!
382    checkpoint52j_pre
383    
384    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
385      error messages
386    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
387    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
388      debug output
389    o modfied mdsio_writefield.F to handle non-global files under exch2
390    o update AIM Cubed-Sphere exp (aim.5l_cs):
391      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
392    o update AIM Equatorial Channel exp:
393      use standard aim_v23 pkg and change the SST fields to be more realistic.
394    o globalFile now works with exch2
395    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
396      mon_vort3.F to make exch2 friendly with >1 tile per cube face
397    o limit timeave output for hi-res integrations
398    
399    checkpoint52i_post
400    o removed CPP_EEOPTIONS.h from verification/*/code
401    o updated the tiling for global_ocean_pressure
402    checkpoint52i_pre
403    
404    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
405      the old pkg/aim).
406    
407    checkpoint52h_pre
408    o shortened offending lines in exch2_send_rx?.template
409    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
410    o genmake2: add build & execute test for NetCDF code
411    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
412      old grid files, moved CPP_EEMACROS.h to pkg/exch2
413    o added useSingleCPUIO flag to monitor.F and mon_out.F
414    o added temporary hack for sea-ice dynamics on the cube:
415      metric terms are ignored and it is assumed that
416      there is no sea-ice on cube faces 1, 2, 4, and 5.
417    
418    checkpoint52f_post
419  o added exch2 cube routines to pkg/exch2  o added exch2 cube routines to pkg/exch2
420  o modified hs94.cs-32x32x5 to use it  o modified hs94.cs-32x32x5 to use it
421  o added new grid files to hs94.cs-32x32x5  o added new grid files to hs94.cs-32x32x5
422  checkpoint52f_post  checkpoint52f_pre
423    
424  checkpoint52e_post  checkpoint52e_post
425  o first attempt to solve vertical advection (momemtum & T,S) Implicitly  o first attempt to solve vertical advection (momemtum & T,S) Implicitly

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