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revision 1.236 by afe, Fri Jan 9 20:46:09 2004 UTC revision 1.349 by jmc, Tue Sep 21 23:20:17 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6  checkpoint52e_pre  o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
7      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
8      affects advect_cs results (for the wrong reason): update output.txt
9    o use a more standard discretization for biharmonic viscosity ;
10     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
11      affects results of dome set-up: update output.txt
12    o fix gad_advection.F (CubedSphere part), back to version 1.23
13    o fix bug in mom_vi_del2uv.F (CubedSphere part).
14    
15    checkpoint55a_post
16    o merged code to
17      * prescribe/read time-dependent open boundaries
18        (works in conjunction with exf, cal)
19      * sponge layer code for open boundaries
20      * each boundary N/S/E/W now has its own CPP option
21        (healthy for the adjoint)
22    
23    checkpoint55
24    o up-to-date adjoint of previous breaks
25      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
26      - global_ocean_ebm: adjoint still needs fix (TLM ok)
27      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
28      - carbon: * remove tr1-related adjoint verification
29                * add ptracer as control variable
30    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
31      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
32    
33    checkpoint54f_post
34    o in verification/carbin/ remove experiment related to
35      ALLOW_PASSIVE_TRACER (array tr1 etc)
36      code_ad/ input_ad/ results_ad
37    
38    o add two new packages
39      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
40        + subject to optimization (memory)
41      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
42        + subject to reordering (many GOTOs in the original code)
43        + so far opps is called for every (i,j) point, and then operates in
44          the vertical; one may want to reorder the scheme in order operate in
45          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
46          fields)
47    o overhaul of IO so that we now have flags for MDSIO and/or MNC
48      - all verification tests compile and run with linux_ia32_g77
49      - defaults are compatible with current input files--nothing
50        should change if you were not previously using MNC
51      - MNC output has been added in numerous places (eg. timeave)
52        but there are still a few writes not yet do-able with MNC
53        (this is in progress)
54      - flags now allow for either/or/both use of MDSIO and MNC and
55        documentation will soon follow
56      - numerous small formatting cleanups for ProTeX
57    o add version info (via BUILD_INFO.h) to MNC and stdout
58    
59    checkpoint54e_post
60    o add two new packages
61      - pp81 (Packanowski and Philander, 1981), Richardson number and
62        stratification dependent mixing
63      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
64      - these scheme operate in a similar manner as KPP (without ghat, of
65        course), however there is only one diffusivity that is used for both
66        temperature and salinity (and passive tracers)ç
67    o add offline package
68    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
69      provided by Stephanie Dutkiewicz
70    o genmake2: add ability to search for C compilers and cleanup test output
71      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
72    
73    checkpoint54d_post
74    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
75    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
76      leading to additional shift by 5 days each year of integration
77       (i.e. leading to considerable offset over the years)
78    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
79    o start with no AB and no initial filtering (staggerTimeStep):
80      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
81    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
82      (external loading & cpl import/export stay in forward_step.F)
83    o update coupling interface to work with new staggerTimeStep
84    o change MDSIO ptracers_pickup.
85    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
86    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
87    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
88    
89    checkpoint54c_post
90    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
91      this affects (truncation error) output.txt of test-exp:
92       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
93    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
94    o change Qnet to always be the net heat flux, (+upward).
95      affects (truncation error) output of natl_box exp.: updated
96    o define the max number of passive tracers in PTRACERS_SIZE.h
97    o start to test mnc routinely in exp0
98    o add sea-ice loading (sIceLoad) as a new forcing field.
99    
100    checkpoint54b_post
101    o add testreport "-j JOBS" option for parallel builds (tested and pretty
102       impressive on Altix and Opteron systems)
103    o diagnostics can now write NetCDF files through the mnc package
104    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
105    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
106    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
107      affects (truncation error) output of lab_sea & natl_box exp.: updated
108    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
109    
110    checkpoint54a_post
111    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
112    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
113    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
114    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
115      + internal_wave (shift in writing cg2d_ini_res)
116    checkpoint54a_pre
117    
118    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
119      - modified verification/lab_sea and natl_box_adjoint accordingly
120    
121    checkpoint54
122    checkpoint53g_post
123    o prepare splitting of thermodynamics: store convect.counter in common block
124    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
125      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
126    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
127    o new parameter "nShapS": allow to treat differently S from T (nShapT)
128    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
129    o restore adjointability
130    
131    checkpoint53f_post
132    o modifications that affect AIM experiment results (update output.txt):
133      - no advection of S at top interface Nr (pkg/generic_advdiff)
134      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
135    o AIM pkg:
136      - include stability function into surf.Flux derivative relative to Tsurf
137      - calculate clear-sky radiation & surface temp. change (for diagnostics)
138    
139    checkpoint53e_post
140    o merged cylindrical coord configuration
141    o added rotating_tank experiment
142    checkpoint53e_pre
143    
144    checkpoint53d_post
145    o faulks upgraded: re-generate output.txt that have changed:
146       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
147    o Added Bryan and Lewis, 1979, vertical diffusivity profile
148    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
149    o added Sadourny discretization of Coriolis
150      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
151      - re-enabled use of omega3 (useAbsVorticity)
152    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
153      vector-invariant equations
154      - note: does *NOT* yet use same variable visc. for no-slip BC's.
155    o recoded the lateral boundary conditions for non-hydrostatic w, this time
156      hopefully without new bugs
157      - still to do: biharmonic friction for non-hydrostatic w
158    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
159    o regenerated output for global_ocean_ebm (using -ieee)
160    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
161      of mom_common/
162      - simple re-arrangement of instructions within computing loop
163    checkpoint53d_pre
164    
165    checkpoint53c_post
166    o new version of coupler for AIM+thSIce and Ocean models
167     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
168     - land: change Evaporation of snow
169     - aim with thSIce: fix bug in snow-precip.
170    o changes to calc_gw.F
171     - bug fix for w^2 term near the bottom boundary
172     - (hopefully) improve the lateral slip boundary condtions for use with
173        partial/looped cells
174      - because the bug fix changes two verification experiments anyway (exp5
175        and plume on slope), change the lateral boundary condition from half slip
176        to the value of no_slip_sides
177    o ebm package wasnt quite up to the parallel task. Fixed that.
178    o Adjoint of EBM package + verification
179      * TLM OK
180      * ADM not sufficient accuracy yet (needs further testing)
181    
182    checkpoint53b_post
183    o Commiting new energy balance model to repository
184      * package is pkg/ebm
185      * verif. is verification/global_ocean_ebm
186      * references are in ebm_driver.F
187    C      * X. Wang, P. Stone and J. Marotzke, 1999:
188    C        Global thermohaline circulation. Part I:
189    C        Sensitivity to atmospheric moisture transport.
190    C        J. Climate 12(1), 71-82
191    C      * X. Wang, P. Stone and J. Marotzke, 1999:
192    C        Global thermohaline circulation. Part II:
193    C        Sensitivity with interactive transport.
194    C        J. Climate 12(1), 83-91
195    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
196    C        Destabilization of the thermohaline circulation
197    C        by atmospheric eddy transports.
198    C        J. Climate 7(12), 1870-1882
199    o Will need long integration testing.
200    checkpoint53b_pre
201    
202    o created pkg/mom_common in preparation for variable viscosity code
203    o renamed and split ini_mnc_io
204    o pkg/land: only liquid water can diffuse or run-off
205    o AIM using land: soil wetness availability account for snow
206    o added printMapIncludesZeros to EEPARMS namelist
207    
208    checkpoint53a_post
209    o restore TAMC compatiility for exf_constants.h
210      (no usage of _d in .h)
211    o Additional storing in KPP in an attempt to fix
212      TAMC problem with adjoint of KPP code.
213      (no success...)
214      Identical code works fine with TAF.
215    o Fixed verification/natl_box_adjoint experiments.
216      Initial conditions for Experiments 4 and 5 are now
217      set to "SEAICE_initialHEFF=0", which is more reasonable,
218      and hence gives results closer to that of Experiment 2.
219      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
220    
221    checkpoint53
222    o stable checkpoint with up to date adjoint
223      TLM tests only run for 1st grdchk at the moment. Its unclear if
224      this is a code problem or a problem with resetting code for g_
225      variables that is being autogenerated wrong.
226      Otherwise:
227       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
228       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
229         are both still in chaos following their security messes.
230    
231    checkpoint52n_post
232    o various build (mostly genmake2) changes including:
233      - ability to build/run more easily within Cygwin and MacOS X
234      - more complicated Makefiles with a stronger dependence on Gnu Make
235    o pkg/seaice modifications
236      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
237        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
238        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
239      - changed proxy for geostrophic velocity and updated
240        verification/lab_sea/results/* accordingly
241      - removed ADI dynamic solver from pkg/seaice
242      - replaced all occurrences of 1/CSTICE or 1/CSUICE
243        they caused a segmentation fault under certain circumstances
244      - removed unused field WATR
245    o bug fix in exf-package:
246      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
247         now reflect that.
248    o small fixes in the cal-package:
249      - set reference date to first of January for the 'model'-calendar
250      - failing of cal_CheckDate in cal_FullDate now actually results in a
251        warning
252    o small modifications in exf-package to increase flexibility:
253      - change climtempfreeze from a constant to a runtime parameter that
254        is specified in data.exf_clim (default = -1.9)
255      - introduce runtime parameter windstressmax (default = 2.0) that is
256        specified in data.exf
257    o fix in pkg/thsice:
258      - update Evap (Tsf changes) to be consistent with Latent heat flux
259      - maintain snow precipitation unchanged (even if Tsf >=0).
260     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
261    
262    checkpoint52m_post
263    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
264      this does not change any of the results, because myIter=0 in swfrac always
265      lead to jwtype=2 (the default anyway), but the call makes little sense
266      as a default
267    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
268    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
269      atmospheric model (AIM) to use it ; add a "slab ocean" component.
270    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
271    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
272    o extending useSingleCpuIO option to work with new exch2 I/O format
273      - old-style, missing-tile I/O is still accessible by defining CPP
274        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
275    o monitor package can write to NetCDF files and/or STDOUT
276    o fix re-definition bug in MNC_GRID_INIT_ALL()
277    o doc/api_reference added
278      - a framework for building an API Reference Manual using all
279        the "protex" comments embedded in the code
280      - see pkg/generic_advdiff, pkg/mnc for examples
281    o MNC:
282      - make myThid the last argument for all subroutines
283      - new default for the grid files: NO halos
284      - add useMNC and other run-time flags
285      - separate per-file-group handling of the unlimited dimension
286      - early initialization of MNC w/ flags read at the eeboot stage
287        and lookup tables set in initialize_fixed
288      - write all MNC output to a freshly-created directory
289    o thermodynamics sea-ice (thsice) is now tested with testreport.
290    o test exp. advect_cs: use the standard cs32 grid ; update output.
291    o Added functionality to grdchk:
292      pick global i,j,k position (or nearest wet) where to perform check.
293    
294    checkpoint52l_post
295    o new land formulation:
296      a) use ground enthalpy as prognostic variable to ensure exact
297         energy conservation.
298      b) account for water temperature and for latent heat of freezing
299         in all processes (rain, run-off, ground storage)
300      c) compute surface and ground temperature implicitly.
301    o aim_v23 modification for new land model:
302      a) Treat separately land / ocean / sea-ice surface fluxes
303         to allow implicit computation of land & sea-ice surface temp.
304      b) add snow precipitation.
305    checkpoint52l_pre
306    
307    o fix problem (when 1 tile is empty) in min/max monitor.
308    o fix bug in timeAve (u,vZetatave in common block)
309    o no restoring terms under ice for pkg/seaice
310    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
311    o bug fix for pkg/seaice pickups
312    o change MNC call locations and add coordinate attributes
313    o mask vorticity at the corner ; affects global_ocean.cs output
314    o fix ini_curvilinear_grid ; test CS experiments with mpi
315    o aim.5l_cs: modify sea-ice fraction input file ; update output
316    o exf: Adding simple range check routine for exf fields after read
317    
318    checkpoint52k_post
319    o removed top-level directory "diags"
320      - we migrated these functions to pkg/timeave a long time ago
321    o fixed bug introduced in pkg/monitor
322    o accuracy ctrlprec = 32 insuffient for gradient checks using
323      averaged fields (I/O via cost_averages)
324      -> use ctrl.h in active_file*.F to control I/O precision.
325    o paramter list of CALL ADTHE_MAIN_LOOP
326    o added initial do_the_model_io to ecco
327    o set all ...Freq to zero after cost_final
328      taveFreq, dumpFreq, pChkptFreq
329    o MAIN and ECCO differentiability restored
330    
331    checkpoint52j_post
332    o fix nchklev in tamc.h for global_ocean...
333    o Bringing flow and store directives up-to-date
334    o Really weird thing!
335      call do_the_model_io from the_main_loop with parameters
336      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
337      TAF places a faulty re-call of initialise_varia
338      after cost_final call which should not be there!
339    checkpoint52j_pre
340    
341    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
342      error messages
343    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
344    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
345      debug output
346    o modfied mdsio_writefield.F to handle non-global files under exch2
347    o update AIM Cubed-Sphere exp (aim.5l_cs):
348      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
349    o update AIM Equatorial Channel exp:
350      use standard aim_v23 pkg and change the SST fields to be more realistic.
351    o globalFile now works with exch2
352    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
353      mon_vort3.F to make exch2 friendly with >1 tile per cube face
354    o limit timeave output for hi-res integrations
355    
356    checkpoint52i_post
357    o removed CPP_EEOPTIONS.h from verification/*/code
358    o updated the tiling for global_ocean_pressure
359    checkpoint52i_pre
360    
361    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
362      the old pkg/aim).
363    
364    checkpoint52h_pre
365    o shortened offending lines in exch2_send_rx?.template
366    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
367    o genmake2: add build & execute test for NetCDF code
368    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
369      old grid files, moved CPP_EEMACROS.h to pkg/exch2
370    o added useSingleCPUIO flag to monitor.F and mon_out.F
371    o added temporary hack for sea-ice dynamics on the cube:
372      metric terms are ignored and it is assumed that
373      there is no sea-ice on cube faces 1, 2, 4, and 5.
374    
375    checkpoint52f_post
376  o added exch2 cube routines to pkg/exch2  o added exch2 cube routines to pkg/exch2
377  o modified hs94.cs-32x32x5 to use it  o modified hs94.cs-32x32x5 to use it
378  o added new grid files to hs94.cs-32x32x5  o added new grid files to hs94.cs-32x32x5
379  checkpoint52e_post  checkpoint52f_pre
380    
381  checkpoint52e_post  checkpoint52e_post
382  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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