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revision 1.250 by jmc, Mon Jan 26 18:06:42 2004 UTC revision 1.359 by heimbach, Mon Sep 27 14:56:42 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 multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
7        be 2 times larger than the minimum size the advection scheme requires.
8        now get a perfect conservation of salt in advect_cs test-exp (updated)
9    o GGL90 (Gaspar's TKE mixed layer)
10      - add horizontal diffusion of TKE, requires exchanges in
11        do_fields_blocking_exchanges, horizontal diffusivity is zero by
12        default. In OPA there is no horizontal diffusion of TKE but the
13        mixing coefficients are computed from a horizontal average of TKE of
14        6 points or so. I think that diffusion has a little more physical
15        justification.
16      - clean up ggl90_calc in the hope of reducing memory usage (this hope
17        was in vain)
18      - mask tke-variable in ggl90_init
19    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
20    o fix biharmonic diffusion on CS-grid.
21    o more obcs stuff
22      - added obcs_external_fields_load as an alternative to the EXF-pkg option
23        for reading boundary values. This routine is called from
24        obcs_prescribe_read
25      - updated obcs_check
26      - changed sponge layer relaxation parameter units for days to seconds
27      - turned off sponge layer by default
28      - changed argument list of OBCS_CALC to myTime+deltaTclock
29    
30    checkpoint55c_post
31    o obcs stuff
32      - new runtime flags useOBCSprescribe, useOBCSbalance
33      - re-arranged obcs_calc
34      - moved exf_getobcs to obcs_prescibe_read
35        obcs_prescibe_read is called after ORLANSKI stuff
36        and independent of it (executable can contain all).
37      - updated obcs_check
38      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
39        These may be necessary only if tangential velocities are
40        prescribed at OB, not sure, needs testing.
41    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
42      which simplifies the calls and passes the ifc check-bounds test
43    
44    checkpoint55b_post
45    o add a 2D scalar, Z location, exchange_2 routine.
46    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
47      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
48      affects advect_cs results (for the wrong reason): update output.txt
49    o use a more standard discretization for biharmonic viscosity ;
50     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
51      affects results of dome set-up: update output.txt
52    o fix gad_advection.F (CubedSphere part), back to version 1.23
53    o fix bug in mom_vi_del2uv.F (CubedSphere part).
54    
55    checkpoint55a_post
56    o merged code to
57      * prescribe/read time-dependent open boundaries
58        (works in conjunction with exf, cal)
59      * sponge layer code for open boundaries
60      * each boundary N/S/E/W now has its own CPP option
61        (healthy for the adjoint)
62    
63    checkpoint55
64    o up-to-date adjoint of previous breaks
65      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
66      - global_ocean_ebm: adjoint still needs fix (TLM ok)
67      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
68      - carbon: * remove tr1-related adjoint verification
69                * add ptracer as control variable
70    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
71      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
72    
73    checkpoint54f_post
74    o in verification/carbin/ remove experiment related to
75      ALLOW_PASSIVE_TRACER (array tr1 etc)
76      code_ad/ input_ad/ results_ad
77    
78    o add two new packages
79      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
80        + subject to optimization (memory)
81      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
82        + subject to reordering (many GOTOs in the original code)
83        + so far opps is called for every (i,j) point, and then operates in
84          the vertical; one may want to reorder the scheme in order operate in
85          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
86          fields)
87    o overhaul of IO so that we now have flags for MDSIO and/or MNC
88      - all verification tests compile and run with linux_ia32_g77
89      - defaults are compatible with current input files--nothing
90        should change if you were not previously using MNC
91      - MNC output has been added in numerous places (eg. timeave)
92        but there are still a few writes not yet do-able with MNC
93        (this is in progress)
94      - flags now allow for either/or/both use of MDSIO and MNC and
95        documentation will soon follow
96      - numerous small formatting cleanups for ProTeX
97    o add version info (via BUILD_INFO.h) to MNC and stdout
98    
99    checkpoint54e_post
100    o add two new packages
101      - pp81 (Packanowski and Philander, 1981), Richardson number and
102        stratification dependent mixing
103      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
104      - these scheme operate in a similar manner as KPP (without ghat, of
105        course), however there is only one diffusivity that is used for both
106        temperature and salinity (and passive tracers)ç
107    o add offline package
108    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
109      provided by Stephanie Dutkiewicz
110    o genmake2: add ability to search for C compilers and cleanup test output
111      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
112    
113    checkpoint54d_post
114    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
115    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
116      leading to additional shift by 5 days each year of integration
117       (i.e. leading to considerable offset over the years)
118    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
119    o start with no AB and no initial filtering (staggerTimeStep):
120      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
121    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
122      (external loading & cpl import/export stay in forward_step.F)
123    o update coupling interface to work with new staggerTimeStep
124    o change MDSIO ptracers_pickup.
125    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
126    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
127    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
128    
129    checkpoint54c_post
130    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
131      this affects (truncation error) output.txt of test-exp:
132       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
133    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
134    o change Qnet to always be the net heat flux, (+upward).
135      affects (truncation error) output of natl_box exp.: updated
136    o define the max number of passive tracers in PTRACERS_SIZE.h
137    o start to test mnc routinely in exp0
138    o add sea-ice loading (sIceLoad) as a new forcing field.
139    
140    checkpoint54b_post
141    o add testreport "-j JOBS" option for parallel builds (tested and pretty
142       impressive on Altix and Opteron systems)
143    o diagnostics can now write NetCDF files through the mnc package
144    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
145    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
146    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
147      affects (truncation error) output of lab_sea & natl_box exp.: updated
148    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
149    
150    checkpoint54a_post
151    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
152    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
153    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
154    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
155      + internal_wave (shift in writing cg2d_ini_res)
156    checkpoint54a_pre
157    
158    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
159      - modified verification/lab_sea and natl_box_adjoint accordingly
160    
161    checkpoint54
162    checkpoint53g_post
163    o prepare splitting of thermodynamics: store convect.counter in common block
164    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
165      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
166    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
167    o new parameter "nShapS": allow to treat differently S from T (nShapT)
168    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
169    o restore adjointability
170    
171    checkpoint53f_post
172    o modifications that affect AIM experiment results (update output.txt):
173      - no advection of S at top interface Nr (pkg/generic_advdiff)
174      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
175    o AIM pkg:
176      - include stability function into surf.Flux derivative relative to Tsurf
177      - calculate clear-sky radiation & surface temp. change (for diagnostics)
178    
179    checkpoint53e_post
180    o merged cylindrical coord configuration
181    o added rotating_tank experiment
182    checkpoint53e_pre
183    
184    checkpoint53d_post
185    o faulks upgraded: re-generate output.txt that have changed:
186       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
187    o Added Bryan and Lewis, 1979, vertical diffusivity profile
188    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
189    o added Sadourny discretization of Coriolis
190      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
191      - re-enabled use of omega3 (useAbsVorticity)
192    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
193      vector-invariant equations
194      - note: does *NOT* yet use same variable visc. for no-slip BC's.
195    o recoded the lateral boundary conditions for non-hydrostatic w, this time
196      hopefully without new bugs
197      - still to do: biharmonic friction for non-hydrostatic w
198    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
199    o regenerated output for global_ocean_ebm (using -ieee)
200    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
201      of mom_common/
202      - simple re-arrangement of instructions within computing loop
203    checkpoint53d_pre
204    
205    checkpoint53c_post
206    o new version of coupler for AIM+thSIce and Ocean models
207     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
208     - land: change Evaporation of snow
209     - aim with thSIce: fix bug in snow-precip.
210    o changes to calc_gw.F
211     - bug fix for w^2 term near the bottom boundary
212     - (hopefully) improve the lateral slip boundary condtions for use with
213        partial/looped cells
214      - because the bug fix changes two verification experiments anyway (exp5
215        and plume on slope), change the lateral boundary condition from half slip
216        to the value of no_slip_sides
217    o ebm package wasnt quite up to the parallel task. Fixed that.
218    o Adjoint of EBM package + verification
219      * TLM OK
220      * ADM not sufficient accuracy yet (needs further testing)
221    
222    checkpoint53b_post
223    o Commiting new energy balance model to repository
224      * package is pkg/ebm
225      * verif. is verification/global_ocean_ebm
226      * references are in ebm_driver.F
227    C      * X. Wang, P. Stone and J. Marotzke, 1999:
228    C        Global thermohaline circulation. Part I:
229    C        Sensitivity to atmospheric moisture transport.
230    C        J. Climate 12(1), 71-82
231    C      * X. Wang, P. Stone and J. Marotzke, 1999:
232    C        Global thermohaline circulation. Part II:
233    C        Sensitivity with interactive transport.
234    C        J. Climate 12(1), 83-91
235    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
236    C        Destabilization of the thermohaline circulation
237    C        by atmospheric eddy transports.
238    C        J. Climate 7(12), 1870-1882
239    o Will need long integration testing.
240    checkpoint53b_pre
241    
242    o created pkg/mom_common in preparation for variable viscosity code
243    o renamed and split ini_mnc_io
244    o pkg/land: only liquid water can diffuse or run-off
245    o AIM using land: soil wetness availability account for snow
246    o added printMapIncludesZeros to EEPARMS namelist
247    
248    checkpoint53a_post
249    o restore TAMC compatiility for exf_constants.h
250      (no usage of _d in .h)
251    o Additional storing in KPP in an attempt to fix
252      TAMC problem with adjoint of KPP code.
253      (no success...)
254      Identical code works fine with TAF.
255    o Fixed verification/natl_box_adjoint experiments.
256      Initial conditions for Experiments 4 and 5 are now
257      set to "SEAICE_initialHEFF=0", which is more reasonable,
258      and hence gives results closer to that of Experiment 2.
259      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
260    
261    checkpoint53
262    o stable checkpoint with up to date adjoint
263      TLM tests only run for 1st grdchk at the moment. Its unclear if
264      this is a code problem or a problem with resetting code for g_
265      variables that is being autogenerated wrong.
266      Otherwise:
267       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
268       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
269         are both still in chaos following their security messes.
270    
271    checkpoint52n_post
272    o various build (mostly genmake2) changes including:
273      - ability to build/run more easily within Cygwin and MacOS X
274      - more complicated Makefiles with a stronger dependence on Gnu Make
275    o pkg/seaice modifications
276      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
277        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
278        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
279      - changed proxy for geostrophic velocity and updated
280        verification/lab_sea/results/* accordingly
281      - removed ADI dynamic solver from pkg/seaice
282      - replaced all occurrences of 1/CSTICE or 1/CSUICE
283        they caused a segmentation fault under certain circumstances
284      - removed unused field WATR
285    o bug fix in exf-package:
286      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
287         now reflect that.
288    o small fixes in the cal-package:
289      - set reference date to first of January for the 'model'-calendar
290      - failing of cal_CheckDate in cal_FullDate now actually results in a
291        warning
292    o small modifications in exf-package to increase flexibility:
293      - change climtempfreeze from a constant to a runtime parameter that
294        is specified in data.exf_clim (default = -1.9)
295      - introduce runtime parameter windstressmax (default = 2.0) that is
296        specified in data.exf
297    o fix in pkg/thsice:
298      - update Evap (Tsf changes) to be consistent with Latent heat flux
299      - maintain snow precipitation unchanged (even if Tsf >=0).
300     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
301    
302    checkpoint52m_post
303    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
304      this does not change any of the results, because myIter=0 in swfrac always
305      lead to jwtype=2 (the default anyway), but the call makes little sense
306      as a default
307    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
308    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
309      atmospheric model (AIM) to use it ; add a "slab ocean" component.
310    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
311    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
312    o extending useSingleCpuIO option to work with new exch2 I/O format
313      - old-style, missing-tile I/O is still accessible by defining CPP
314        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
315    o monitor package can write to NetCDF files and/or STDOUT
316    o fix re-definition bug in MNC_GRID_INIT_ALL()
317    o doc/api_reference added
318      - a framework for building an API Reference Manual using all
319        the "protex" comments embedded in the code
320      - see pkg/generic_advdiff, pkg/mnc for examples
321    o MNC:
322      - make myThid the last argument for all subroutines
323      - new default for the grid files: NO halos
324      - add useMNC and other run-time flags
325      - separate per-file-group handling of the unlimited dimension
326      - early initialization of MNC w/ flags read at the eeboot stage
327        and lookup tables set in initialize_fixed
328      - write all MNC output to a freshly-created directory
329    o thermodynamics sea-ice (thsice) is now tested with testreport.
330    o test exp. advect_cs: use the standard cs32 grid ; update output.
331    o Added functionality to grdchk:
332      pick global i,j,k position (or nearest wet) where to perform check.
333    
334    checkpoint52l_post
335    o new land formulation:
336      a) use ground enthalpy as prognostic variable to ensure exact
337         energy conservation.
338      b) account for water temperature and for latent heat of freezing
339         in all processes (rain, run-off, ground storage)
340      c) compute surface and ground temperature implicitly.
341    o aim_v23 modification for new land model:
342      a) Treat separately land / ocean / sea-ice surface fluxes
343         to allow implicit computation of land & sea-ice surface temp.
344      b) add snow precipitation.
345    checkpoint52l_pre
346    
347    o fix problem (when 1 tile is empty) in min/max monitor.
348    o fix bug in timeAve (u,vZetatave in common block)
349    o no restoring terms under ice for pkg/seaice
350    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
351    o bug fix for pkg/seaice pickups
352    o change MNC call locations and add coordinate attributes
353    o mask vorticity at the corner ; affects global_ocean.cs output
354    o fix ini_curvilinear_grid ; test CS experiments with mpi
355    o aim.5l_cs: modify sea-ice fraction input file ; update output
356    o exf: Adding simple range check routine for exf fields after read
357    
358    checkpoint52k_post
359    o removed top-level directory "diags"
360      - we migrated these functions to pkg/timeave a long time ago
361    o fixed bug introduced in pkg/monitor
362    o accuracy ctrlprec = 32 insuffient for gradient checks using
363      averaged fields (I/O via cost_averages)
364      -> use ctrl.h in active_file*.F to control I/O precision.
365    o paramter list of CALL ADTHE_MAIN_LOOP
366    o added initial do_the_model_io to ecco
367    o set all ...Freq to zero after cost_final
368      taveFreq, dumpFreq, pChkptFreq
369    o MAIN and ECCO differentiability restored
370    
371    checkpoint52j_post
372    o fix nchklev in tamc.h for global_ocean...
373    o Bringing flow and store directives up-to-date
374    o Really weird thing!
375      call do_the_model_io from the_main_loop with parameters
376      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
377      TAF places a faulty re-call of initialise_varia
378      after cost_final call which should not be there!
379    checkpoint52j_pre
380    
381    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
382      error messages
383    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
384    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
385      debug output
386    o modfied mdsio_writefield.F to handle non-global files under exch2
387  o update AIM Cubed-Sphere exp (aim.5l_cs):  o update AIM Cubed-Sphere exp (aim.5l_cs):
388    use land, p*, and Franco.M forcing fields with fractional land-sea mask.    use land, p*, and Franco.M forcing fields with fractional land-sea mask.
389  o update AIM Equatorial Channel exp:  o update AIM Equatorial Channel exp:
390    use standard aim_v23 pkg and change the SST fields to be more realistic.    use standard aim_v23 pkg and change the SST fields to be more realistic.
391  o globalFile now works with exch2  o globalFile now works with exch2
392  o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and  o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
393    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  
394  o limit timeave output for hi-res integrations  o limit timeave output for hi-res integrations
395    
396  checkpoint52i_post  checkpoint52i_post

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