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revision 1.238 by dimitri, Sat Jan 10 00:48:49 2004 UTC revision 1.355 by jmc, Fri Sep 24 17:10:22 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
7    o fix biharmonic diffusion on CS-grid.
8    o more obcs stuff
9      - added obcs_external_fields_load as an alternative to the EXF-pkg option
10        for reading boundary values. This routine is called from
11        obcs_prescribe_read
12      - updated obcs_check
13    
14    checkpoint55c_post
15    o obcs stuff
16      - new runtime flags useOBCSprescribe, useOBCSbalance
17      - re-arranged obcs_calc
18      - moved exf_getobcs to obcs_prescibe_read
19        obcs_prescibe_read is called after ORLANSKI stuff
20        and independent of it (executable can contain all).
21      - updated obcs_check
22      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
23        These may be necessary only if tangential velocities are
24        prescribed at OB, not sure, needs testing.
25    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
26      which simplifies the calls and passes the ifc check-bounds test
27    
28    checkpoint55b_post
29    o add a 2D scalar, Z location, exchange_2 routine.
30    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
31      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
32      affects advect_cs results (for the wrong reason): update output.txt
33    o use a more standard discretization for biharmonic viscosity ;
34     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
35      affects results of dome set-up: update output.txt
36    o fix gad_advection.F (CubedSphere part), back to version 1.23
37    o fix bug in mom_vi_del2uv.F (CubedSphere part).
38    
39    checkpoint55a_post
40    o merged code to
41      * prescribe/read time-dependent open boundaries
42        (works in conjunction with exf, cal)
43      * sponge layer code for open boundaries
44      * each boundary N/S/E/W now has its own CPP option
45        (healthy for the adjoint)
46    
47    checkpoint55
48    o up-to-date adjoint of previous breaks
49      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
50      - global_ocean_ebm: adjoint still needs fix (TLM ok)
51      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
52      - carbon: * remove tr1-related adjoint verification
53                * add ptracer as control variable
54    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
55      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
56    
57    checkpoint54f_post
58    o in verification/carbin/ remove experiment related to
59      ALLOW_PASSIVE_TRACER (array tr1 etc)
60      code_ad/ input_ad/ results_ad
61    
62    o add two new packages
63      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
64        + subject to optimization (memory)
65      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
66        + subject to reordering (many GOTOs in the original code)
67        + so far opps is called for every (i,j) point, and then operates in
68          the vertical; one may want to reorder the scheme in order operate in
69          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
70          fields)
71    o overhaul of IO so that we now have flags for MDSIO and/or MNC
72      - all verification tests compile and run with linux_ia32_g77
73      - defaults are compatible with current input files--nothing
74        should change if you were not previously using MNC
75      - MNC output has been added in numerous places (eg. timeave)
76        but there are still a few writes not yet do-able with MNC
77        (this is in progress)
78      - flags now allow for either/or/both use of MDSIO and MNC and
79        documentation will soon follow
80      - numerous small formatting cleanups for ProTeX
81    o add version info (via BUILD_INFO.h) to MNC and stdout
82    
83    checkpoint54e_post
84    o add two new packages
85      - pp81 (Packanowski and Philander, 1981), Richardson number and
86        stratification dependent mixing
87      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
88      - these scheme operate in a similar manner as KPP (without ghat, of
89        course), however there is only one diffusivity that is used for both
90        temperature and salinity (and passive tracers)ç
91    o add offline package
92    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
93      provided by Stephanie Dutkiewicz
94    o genmake2: add ability to search for C compilers and cleanup test output
95      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
96    
97    checkpoint54d_post
98    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
99    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
100      leading to additional shift by 5 days each year of integration
101       (i.e. leading to considerable offset over the years)
102    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
103    o start with no AB and no initial filtering (staggerTimeStep):
104      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
105    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
106      (external loading & cpl import/export stay in forward_step.F)
107    o update coupling interface to work with new staggerTimeStep
108    o change MDSIO ptracers_pickup.
109    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
110    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
111    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
112    
113    checkpoint54c_post
114    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
115      this affects (truncation error) output.txt of test-exp:
116       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
117    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
118    o change Qnet to always be the net heat flux, (+upward).
119      affects (truncation error) output of natl_box exp.: updated
120    o define the max number of passive tracers in PTRACERS_SIZE.h
121    o start to test mnc routinely in exp0
122    o add sea-ice loading (sIceLoad) as a new forcing field.
123    
124    checkpoint54b_post
125    o add testreport "-j JOBS" option for parallel builds (tested and pretty
126       impressive on Altix and Opteron systems)
127    o diagnostics can now write NetCDF files through the mnc package
128    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
129    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
130    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
131      affects (truncation error) output of lab_sea & natl_box exp.: updated
132    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
133    
134    checkpoint54a_post
135    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
136    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
137    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
138    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
139      + internal_wave (shift in writing cg2d_ini_res)
140    checkpoint54a_pre
141    
142    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
143      - modified verification/lab_sea and natl_box_adjoint accordingly
144    
145    checkpoint54
146    checkpoint53g_post
147    o prepare splitting of thermodynamics: store convect.counter in common block
148    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
149      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
150    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
151    o new parameter "nShapS": allow to treat differently S from T (nShapT)
152    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
153    o restore adjointability
154    
155    checkpoint53f_post
156    o modifications that affect AIM experiment results (update output.txt):
157      - no advection of S at top interface Nr (pkg/generic_advdiff)
158      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
159    o AIM pkg:
160      - include stability function into surf.Flux derivative relative to Tsurf
161      - calculate clear-sky radiation & surface temp. change (for diagnostics)
162    
163    checkpoint53e_post
164    o merged cylindrical coord configuration
165    o added rotating_tank experiment
166    checkpoint53e_pre
167    
168    checkpoint53d_post
169    o faulks upgraded: re-generate output.txt that have changed:
170       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
171    o Added Bryan and Lewis, 1979, vertical diffusivity profile
172    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
173    o added Sadourny discretization of Coriolis
174      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
175      - re-enabled use of omega3 (useAbsVorticity)
176    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
177      vector-invariant equations
178      - note: does *NOT* yet use same variable visc. for no-slip BC's.
179    o recoded the lateral boundary conditions for non-hydrostatic w, this time
180      hopefully without new bugs
181      - still to do: biharmonic friction for non-hydrostatic w
182    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
183    o regenerated output for global_ocean_ebm (using -ieee)
184    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
185      of mom_common/
186      - simple re-arrangement of instructions within computing loop
187    checkpoint53d_pre
188    
189    checkpoint53c_post
190    o new version of coupler for AIM+thSIce and Ocean models
191     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
192     - land: change Evaporation of snow
193     - aim with thSIce: fix bug in snow-precip.
194    o changes to calc_gw.F
195     - bug fix for w^2 term near the bottom boundary
196     - (hopefully) improve the lateral slip boundary condtions for use with
197        partial/looped cells
198      - because the bug fix changes two verification experiments anyway (exp5
199        and plume on slope), change the lateral boundary condition from half slip
200        to the value of no_slip_sides
201    o ebm package wasnt quite up to the parallel task. Fixed that.
202    o Adjoint of EBM package + verification
203      * TLM OK
204      * ADM not sufficient accuracy yet (needs further testing)
205    
206    checkpoint53b_post
207    o Commiting new energy balance model to repository
208      * package is pkg/ebm
209      * verif. is verification/global_ocean_ebm
210      * references are in ebm_driver.F
211    C      * X. Wang, P. Stone and J. Marotzke, 1999:
212    C        Global thermohaline circulation. Part I:
213    C        Sensitivity to atmospheric moisture transport.
214    C        J. Climate 12(1), 71-82
215    C      * X. Wang, P. Stone and J. Marotzke, 1999:
216    C        Global thermohaline circulation. Part II:
217    C        Sensitivity with interactive transport.
218    C        J. Climate 12(1), 83-91
219    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
220    C        Destabilization of the thermohaline circulation
221    C        by atmospheric eddy transports.
222    C        J. Climate 7(12), 1870-1882
223    o Will need long integration testing.
224    checkpoint53b_pre
225    
226    o created pkg/mom_common in preparation for variable viscosity code
227    o renamed and split ini_mnc_io
228    o pkg/land: only liquid water can diffuse or run-off
229    o AIM using land: soil wetness availability account for snow
230    o added printMapIncludesZeros to EEPARMS namelist
231    
232    checkpoint53a_post
233    o restore TAMC compatiility for exf_constants.h
234      (no usage of _d in .h)
235    o Additional storing in KPP in an attempt to fix
236      TAMC problem with adjoint of KPP code.
237      (no success...)
238      Identical code works fine with TAF.
239    o Fixed verification/natl_box_adjoint experiments.
240      Initial conditions for Experiments 4 and 5 are now
241      set to "SEAICE_initialHEFF=0", which is more reasonable,
242      and hence gives results closer to that of Experiment 2.
243      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
244    
245    checkpoint53
246    o stable checkpoint with up to date adjoint
247      TLM tests only run for 1st grdchk at the moment. Its unclear if
248      this is a code problem or a problem with resetting code for g_
249      variables that is being autogenerated wrong.
250      Otherwise:
251       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
252       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
253         are both still in chaos following their security messes.
254    
255    checkpoint52n_post
256    o various build (mostly genmake2) changes including:
257      - ability to build/run more easily within Cygwin and MacOS X
258      - more complicated Makefiles with a stronger dependence on Gnu Make
259    o pkg/seaice modifications
260      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
261        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
262        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
263      - changed proxy for geostrophic velocity and updated
264        verification/lab_sea/results/* accordingly
265      - removed ADI dynamic solver from pkg/seaice
266      - replaced all occurrences of 1/CSTICE or 1/CSUICE
267        they caused a segmentation fault under certain circumstances
268      - removed unused field WATR
269    o bug fix in exf-package:
270      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
271         now reflect that.
272    o small fixes in the cal-package:
273      - set reference date to first of January for the 'model'-calendar
274      - failing of cal_CheckDate in cal_FullDate now actually results in a
275        warning
276    o small modifications in exf-package to increase flexibility:
277      - change climtempfreeze from a constant to a runtime parameter that
278        is specified in data.exf_clim (default = -1.9)
279      - introduce runtime parameter windstressmax (default = 2.0) that is
280        specified in data.exf
281    o fix in pkg/thsice:
282      - update Evap (Tsf changes) to be consistent with Latent heat flux
283      - maintain snow precipitation unchanged (even if Tsf >=0).
284     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
285    
286    checkpoint52m_post
287    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
288      this does not change any of the results, because myIter=0 in swfrac always
289      lead to jwtype=2 (the default anyway), but the call makes little sense
290      as a default
291    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
292    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
293      atmospheric model (AIM) to use it ; add a "slab ocean" component.
294    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
295    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
296    o extending useSingleCpuIO option to work with new exch2 I/O format
297      - old-style, missing-tile I/O is still accessible by defining CPP
298        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
299    o monitor package can write to NetCDF files and/or STDOUT
300    o fix re-definition bug in MNC_GRID_INIT_ALL()
301    o doc/api_reference added
302      - a framework for building an API Reference Manual using all
303        the "protex" comments embedded in the code
304      - see pkg/generic_advdiff, pkg/mnc for examples
305    o MNC:
306      - make myThid the last argument for all subroutines
307      - new default for the grid files: NO halos
308      - add useMNC and other run-time flags
309      - separate per-file-group handling of the unlimited dimension
310      - early initialization of MNC w/ flags read at the eeboot stage
311        and lookup tables set in initialize_fixed
312      - write all MNC output to a freshly-created directory
313    o thermodynamics sea-ice (thsice) is now tested with testreport.
314    o test exp. advect_cs: use the standard cs32 grid ; update output.
315    o Added functionality to grdchk:
316      pick global i,j,k position (or nearest wet) where to perform check.
317    
318    checkpoint52l_post
319    o new land formulation:
320      a) use ground enthalpy as prognostic variable to ensure exact
321         energy conservation.
322      b) account for water temperature and for latent heat of freezing
323         in all processes (rain, run-off, ground storage)
324      c) compute surface and ground temperature implicitly.
325    o aim_v23 modification for new land model:
326      a) Treat separately land / ocean / sea-ice surface fluxes
327         to allow implicit computation of land & sea-ice surface temp.
328      b) add snow precipitation.
329    checkpoint52l_pre
330    
331    o fix problem (when 1 tile is empty) in min/max monitor.
332    o fix bug in timeAve (u,vZetatave in common block)
333    o no restoring terms under ice for pkg/seaice
334    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
335    o bug fix for pkg/seaice pickups
336    o change MNC call locations and add coordinate attributes
337    o mask vorticity at the corner ; affects global_ocean.cs output
338    o fix ini_curvilinear_grid ; test CS experiments with mpi
339    o aim.5l_cs: modify sea-ice fraction input file ; update output
340    o exf: Adding simple range check routine for exf fields after read
341    
342    checkpoint52k_post
343    o removed top-level directory "diags"
344      - we migrated these functions to pkg/timeave a long time ago
345    o fixed bug introduced in pkg/monitor
346    o accuracy ctrlprec = 32 insuffient for gradient checks using
347      averaged fields (I/O via cost_averages)
348      -> use ctrl.h in active_file*.F to control I/O precision.
349    o paramter list of CALL ADTHE_MAIN_LOOP
350    o added initial do_the_model_io to ecco
351    o set all ...Freq to zero after cost_final
352      taveFreq, dumpFreq, pChkptFreq
353    o MAIN and ECCO differentiability restored
354    
355    checkpoint52j_post
356    o fix nchklev in tamc.h for global_ocean...
357    o Bringing flow and store directives up-to-date
358    o Really weird thing!
359      call do_the_model_io from the_main_loop with parameters
360      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
361      TAF places a faulty re-call of initialise_varia
362      after cost_final call which should not be there!
363    checkpoint52j_pre
364    
365    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
366      error messages
367    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
368    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
369      debug output
370    o modfied mdsio_writefield.F to handle non-global files under exch2
371    o update AIM Cubed-Sphere exp (aim.5l_cs):
372      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
373    o update AIM Equatorial Channel exp:
374      use standard aim_v23 pkg and change the SST fields to be more realistic.
375    o globalFile now works with exch2
376    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
377      mon_vort3.F to make exch2 friendly with >1 tile per cube face
378    o limit timeave output for hi-res integrations
379    
380    checkpoint52i_post
381    o removed CPP_EEOPTIONS.h from verification/*/code
382    o updated the tiling for global_ocean_pressure
383    checkpoint52i_pre
384    
385    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
386      the old pkg/aim).
387    
388    checkpoint52h_pre
389    o shortened offending lines in exch2_send_rx?.template
390    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
391    o genmake2: add build & execute test for NetCDF code
392    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
393      old grid files, moved CPP_EEMACROS.h to pkg/exch2
394  o added useSingleCPUIO flag to monitor.F and mon_out.F  o added useSingleCPUIO flag to monitor.F and mon_out.F
395    o added temporary hack for sea-ice dynamics on the cube:
396      metric terms are ignored and it is assumed that
397      there is no sea-ice on cube faces 1, 2, 4, and 5.
398    
399  checkpoint52f_post  checkpoint52f_post
400  o added exch2 cube routines to pkg/exch2  o added exch2 cube routines to pkg/exch2

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