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revision 1.241 by dimitri, Thu Jan 15 03:38:22 2004 UTC revision 1.357 by mlosch, Mon Sep 27 09:01:16 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 GGL90 (Gaspar's TKE mixed layer)
7      - add horizontal diffusion of TKE, requires exchanges in
8        do_fields_blocking_exchanges, horizontal diffusivity is zero by
9        default. In OPA there is no horizontal diffusion of TKE but the
10        mixing coefficients are computed from a horizontal average of TKE of
11        6 points or so. I think that diffusion has a little more physical
12        justification.
13      - clean up ggl90_calc in the hope of reducing memory usage (this hope
14        was in vain)
15      - mask tke-variable in ggl90_init
16    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
17    o fix biharmonic diffusion on CS-grid.
18    o more obcs stuff
19      - added obcs_external_fields_load as an alternative to the EXF-pkg option
20        for reading boundary values. This routine is called from
21        obcs_prescribe_read
22      - updated obcs_check
23      - changed sponge layer relaxation parameter units for days to seconds
24      - turned off sponge layer by default
25    
26    checkpoint55c_post
27    o obcs stuff
28      - new runtime flags useOBCSprescribe, useOBCSbalance
29      - re-arranged obcs_calc
30      - moved exf_getobcs to obcs_prescibe_read
31        obcs_prescibe_read is called after ORLANSKI stuff
32        and independent of it (executable can contain all).
33      - updated obcs_check
34      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
35        These may be necessary only if tangential velocities are
36        prescribed at OB, not sure, needs testing.
37    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
38      which simplifies the calls and passes the ifc check-bounds test
39    
40    checkpoint55b_post
41    o add a 2D scalar, Z location, exchange_2 routine.
42    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
43      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
44      affects advect_cs results (for the wrong reason): update output.txt
45    o use a more standard discretization for biharmonic viscosity ;
46     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
47      affects results of dome set-up: update output.txt
48    o fix gad_advection.F (CubedSphere part), back to version 1.23
49    o fix bug in mom_vi_del2uv.F (CubedSphere part).
50    
51    checkpoint55a_post
52    o merged code to
53      * prescribe/read time-dependent open boundaries
54        (works in conjunction with exf, cal)
55      * sponge layer code for open boundaries
56      * each boundary N/S/E/W now has its own CPP option
57        (healthy for the adjoint)
58    
59    checkpoint55
60    o up-to-date adjoint of previous breaks
61      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
62      - global_ocean_ebm: adjoint still needs fix (TLM ok)
63      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
64      - carbon: * remove tr1-related adjoint verification
65                * add ptracer as control variable
66    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
67      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
68    
69    checkpoint54f_post
70    o in verification/carbin/ remove experiment related to
71      ALLOW_PASSIVE_TRACER (array tr1 etc)
72      code_ad/ input_ad/ results_ad
73    
74    o add two new packages
75      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
76        + subject to optimization (memory)
77      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
78        + subject to reordering (many GOTOs in the original code)
79        + so far opps is called for every (i,j) point, and then operates in
80          the vertical; one may want to reorder the scheme in order operate in
81          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
82          fields)
83    o overhaul of IO so that we now have flags for MDSIO and/or MNC
84      - all verification tests compile and run with linux_ia32_g77
85      - defaults are compatible with current input files--nothing
86        should change if you were not previously using MNC
87      - MNC output has been added in numerous places (eg. timeave)
88        but there are still a few writes not yet do-able with MNC
89        (this is in progress)
90      - flags now allow for either/or/both use of MDSIO and MNC and
91        documentation will soon follow
92      - numerous small formatting cleanups for ProTeX
93    o add version info (via BUILD_INFO.h) to MNC and stdout
94    
95    checkpoint54e_post
96    o add two new packages
97      - pp81 (Packanowski and Philander, 1981), Richardson number and
98        stratification dependent mixing
99      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
100      - these scheme operate in a similar manner as KPP (without ghat, of
101        course), however there is only one diffusivity that is used for both
102        temperature and salinity (and passive tracers)ç
103    o add offline package
104    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
105      provided by Stephanie Dutkiewicz
106    o genmake2: add ability to search for C compilers and cleanup test output
107      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
108    
109    checkpoint54d_post
110    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
111    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
112      leading to additional shift by 5 days each year of integration
113       (i.e. leading to considerable offset over the years)
114    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
115    o start with no AB and no initial filtering (staggerTimeStep):
116      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
117    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
118      (external loading & cpl import/export stay in forward_step.F)
119    o update coupling interface to work with new staggerTimeStep
120    o change MDSIO ptracers_pickup.
121    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
122    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
123    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
124    
125    checkpoint54c_post
126    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
127      this affects (truncation error) output.txt of test-exp:
128       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
129    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
130    o change Qnet to always be the net heat flux, (+upward).
131      affects (truncation error) output of natl_box exp.: updated
132    o define the max number of passive tracers in PTRACERS_SIZE.h
133    o start to test mnc routinely in exp0
134    o add sea-ice loading (sIceLoad) as a new forcing field.
135    
136    checkpoint54b_post
137    o add testreport "-j JOBS" option for parallel builds (tested and pretty
138       impressive on Altix and Opteron systems)
139    o diagnostics can now write NetCDF files through the mnc package
140    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
141    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
142    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
143      affects (truncation error) output of lab_sea & natl_box exp.: updated
144    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
145    
146    checkpoint54a_post
147    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
148    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
149    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
150    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
151      + internal_wave (shift in writing cg2d_ini_res)
152    checkpoint54a_pre
153    
154    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
155      - modified verification/lab_sea and natl_box_adjoint accordingly
156    
157    checkpoint54
158    checkpoint53g_post
159    o prepare splitting of thermodynamics: store convect.counter in common block
160    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
161      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
162    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
163    o new parameter "nShapS": allow to treat differently S from T (nShapT)
164    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
165    o restore adjointability
166    
167    checkpoint53f_post
168    o modifications that affect AIM experiment results (update output.txt):
169      - no advection of S at top interface Nr (pkg/generic_advdiff)
170      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
171    o AIM pkg:
172      - include stability function into surf.Flux derivative relative to Tsurf
173      - calculate clear-sky radiation & surface temp. change (for diagnostics)
174    
175    checkpoint53e_post
176    o merged cylindrical coord configuration
177    o added rotating_tank experiment
178    checkpoint53e_pre
179    
180    checkpoint53d_post
181    o faulks upgraded: re-generate output.txt that have changed:
182       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
183    o Added Bryan and Lewis, 1979, vertical diffusivity profile
184    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
185    o added Sadourny discretization of Coriolis
186      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
187      - re-enabled use of omega3 (useAbsVorticity)
188    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
189      vector-invariant equations
190      - note: does *NOT* yet use same variable visc. for no-slip BC's.
191    o recoded the lateral boundary conditions for non-hydrostatic w, this time
192      hopefully without new bugs
193      - still to do: biharmonic friction for non-hydrostatic w
194    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
195    o regenerated output for global_ocean_ebm (using -ieee)
196    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
197      of mom_common/
198      - simple re-arrangement of instructions within computing loop
199    checkpoint53d_pre
200    
201    checkpoint53c_post
202    o new version of coupler for AIM+thSIce and Ocean models
203     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
204     - land: change Evaporation of snow
205     - aim with thSIce: fix bug in snow-precip.
206    o changes to calc_gw.F
207     - bug fix for w^2 term near the bottom boundary
208     - (hopefully) improve the lateral slip boundary condtions for use with
209        partial/looped cells
210      - because the bug fix changes two verification experiments anyway (exp5
211        and plume on slope), change the lateral boundary condition from half slip
212        to the value of no_slip_sides
213    o ebm package wasnt quite up to the parallel task. Fixed that.
214    o Adjoint of EBM package + verification
215      * TLM OK
216      * ADM not sufficient accuracy yet (needs further testing)
217    
218    checkpoint53b_post
219    o Commiting new energy balance model to repository
220      * package is pkg/ebm
221      * verif. is verification/global_ocean_ebm
222      * references are in ebm_driver.F
223    C      * X. Wang, P. Stone and J. Marotzke, 1999:
224    C        Global thermohaline circulation. Part I:
225    C        Sensitivity to atmospheric moisture transport.
226    C        J. Climate 12(1), 71-82
227    C      * X. Wang, P. Stone and J. Marotzke, 1999:
228    C        Global thermohaline circulation. Part II:
229    C        Sensitivity with interactive transport.
230    C        J. Climate 12(1), 83-91
231    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
232    C        Destabilization of the thermohaline circulation
233    C        by atmospheric eddy transports.
234    C        J. Climate 7(12), 1870-1882
235    o Will need long integration testing.
236    checkpoint53b_pre
237    
238    o created pkg/mom_common in preparation for variable viscosity code
239    o renamed and split ini_mnc_io
240    o pkg/land: only liquid water can diffuse or run-off
241    o AIM using land: soil wetness availability account for snow
242    o added printMapIncludesZeros to EEPARMS namelist
243    
244    checkpoint53a_post
245    o restore TAMC compatiility for exf_constants.h
246      (no usage of _d in .h)
247    o Additional storing in KPP in an attempt to fix
248      TAMC problem with adjoint of KPP code.
249      (no success...)
250      Identical code works fine with TAF.
251    o Fixed verification/natl_box_adjoint experiments.
252      Initial conditions for Experiments 4 and 5 are now
253      set to "SEAICE_initialHEFF=0", which is more reasonable,
254      and hence gives results closer to that of Experiment 2.
255      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
256    
257    checkpoint53
258    o stable checkpoint with up to date adjoint
259      TLM tests only run for 1st grdchk at the moment. Its unclear if
260      this is a code problem or a problem with resetting code for g_
261      variables that is being autogenerated wrong.
262      Otherwise:
263       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
264       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
265         are both still in chaos following their security messes.
266    
267    checkpoint52n_post
268    o various build (mostly genmake2) changes including:
269      - ability to build/run more easily within Cygwin and MacOS X
270      - more complicated Makefiles with a stronger dependence on Gnu Make
271    o pkg/seaice modifications
272      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
273        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
274        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
275      - changed proxy for geostrophic velocity and updated
276        verification/lab_sea/results/* accordingly
277      - removed ADI dynamic solver from pkg/seaice
278      - replaced all occurrences of 1/CSTICE or 1/CSUICE
279        they caused a segmentation fault under certain circumstances
280      - removed unused field WATR
281    o bug fix in exf-package:
282      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
283         now reflect that.
284    o small fixes in the cal-package:
285      - set reference date to first of January for the 'model'-calendar
286      - failing of cal_CheckDate in cal_FullDate now actually results in a
287        warning
288    o small modifications in exf-package to increase flexibility:
289      - change climtempfreeze from a constant to a runtime parameter that
290        is specified in data.exf_clim (default = -1.9)
291      - introduce runtime parameter windstressmax (default = 2.0) that is
292        specified in data.exf
293    o fix in pkg/thsice:
294      - update Evap (Tsf changes) to be consistent with Latent heat flux
295      - maintain snow precipitation unchanged (even if Tsf >=0).
296     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
297    
298    checkpoint52m_post
299    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
300      this does not change any of the results, because myIter=0 in swfrac always
301      lead to jwtype=2 (the default anyway), but the call makes little sense
302      as a default
303    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
304    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
305      atmospheric model (AIM) to use it ; add a "slab ocean" component.
306    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
307    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
308    o extending useSingleCpuIO option to work with new exch2 I/O format
309      - old-style, missing-tile I/O is still accessible by defining CPP
310        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
311    o monitor package can write to NetCDF files and/or STDOUT
312    o fix re-definition bug in MNC_GRID_INIT_ALL()
313    o doc/api_reference added
314      - a framework for building an API Reference Manual using all
315        the "protex" comments embedded in the code
316      - see pkg/generic_advdiff, pkg/mnc for examples
317    o MNC:
318      - make myThid the last argument for all subroutines
319      - new default for the grid files: NO halos
320      - add useMNC and other run-time flags
321      - separate per-file-group handling of the unlimited dimension
322      - early initialization of MNC w/ flags read at the eeboot stage
323        and lookup tables set in initialize_fixed
324      - write all MNC output to a freshly-created directory
325    o thermodynamics sea-ice (thsice) is now tested with testreport.
326    o test exp. advect_cs: use the standard cs32 grid ; update output.
327    o Added functionality to grdchk:
328      pick global i,j,k position (or nearest wet) where to perform check.
329    
330    checkpoint52l_post
331    o new land formulation:
332      a) use ground enthalpy as prognostic variable to ensure exact
333         energy conservation.
334      b) account for water temperature and for latent heat of freezing
335         in all processes (rain, run-off, ground storage)
336      c) compute surface and ground temperature implicitly.
337    o aim_v23 modification for new land model:
338      a) Treat separately land / ocean / sea-ice surface fluxes
339         to allow implicit computation of land & sea-ice surface temp.
340      b) add snow precipitation.
341    checkpoint52l_pre
342    
343    o fix problem (when 1 tile is empty) in min/max monitor.
344    o fix bug in timeAve (u,vZetatave in common block)
345    o no restoring terms under ice for pkg/seaice
346    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
347    o bug fix for pkg/seaice pickups
348    o change MNC call locations and add coordinate attributes
349    o mask vorticity at the corner ; affects global_ocean.cs output
350    o fix ini_curvilinear_grid ; test CS experiments with mpi
351    o aim.5l_cs: modify sea-ice fraction input file ; update output
352    o exf: Adding simple range check routine for exf fields after read
353    
354    checkpoint52k_post
355    o removed top-level directory "diags"
356      - we migrated these functions to pkg/timeave a long time ago
357    o fixed bug introduced in pkg/monitor
358    o accuracy ctrlprec = 32 insuffient for gradient checks using
359      averaged fields (I/O via cost_averages)
360      -> use ctrl.h in active_file*.F to control I/O precision.
361    o paramter list of CALL ADTHE_MAIN_LOOP
362    o added initial do_the_model_io to ecco
363    o set all ...Freq to zero after cost_final
364      taveFreq, dumpFreq, pChkptFreq
365    o MAIN and ECCO differentiability restored
366    
367    checkpoint52j_post
368    o fix nchklev in tamc.h for global_ocean...
369    o Bringing flow and store directives up-to-date
370    o Really weird thing!
371      call do_the_model_io from the_main_loop with parameters
372      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
373      TAF places a faulty re-call of initialise_varia
374      after cost_final call which should not be there!
375    checkpoint52j_pre
376    
377    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
378      error messages
379    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
380    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
381      debug output
382    o modfied mdsio_writefield.F to handle non-global files under exch2
383    o update AIM Cubed-Sphere exp (aim.5l_cs):
384      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
385    o update AIM Equatorial Channel exp:
386      use standard aim_v23 pkg and change the SST fields to be more realistic.
387    o globalFile now works with exch2
388    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
389      mon_vort3.F to make exch2 friendly with >1 tile per cube face
390    o limit timeave output for hi-res integrations
391    
392    checkpoint52i_post
393    o removed CPP_EEOPTIONS.h from verification/*/code
394    o updated the tiling for global_ocean_pressure
395    checkpoint52i_pre
396    
397    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
398      the old pkg/aim).
399    
400    checkpoint52h_pre
401    o shortened offending lines in exch2_send_rx?.template
402    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
403  o genmake2: add build & execute test for NetCDF code  o genmake2: add build & execute test for NetCDF code
404  o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed  o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
405    old grid files, moved CPP_EEMACROS.h to pkg/exch2    old grid files, moved CPP_EEMACROS.h to pkg/exch2

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