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revision 1.257 by heimbach, Mon Feb 23 19:19:15 2004 UTC revision 1.367 by edhill, Wed Oct 13 21:49:05 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint55f_post
7    o rename to timeave_init_fixed
8    
9    checkpoint55e_post
10    o some delicate re-shuffle of store directives to avoid one
11      extra call of do_oceanic_physics
12      affects ecco_the_main_loop.F, do_oceanic_physics.F
13      checkpoint_lev1_directives.h
14    o NB: this may break global_ocean adjoint temporarily,
15      but it is clear how to fix it. Will do later, need this now.
16    
17    checkpoint55d_post
18    o ECCO specific cost function terms (up-to-date with 1x1 runs)
19    o ecco_cost_weights is modified to 1x1 runs
20    o modifs to allow observations to be read in as
21      single file or yearly files
22    o enable to read exf forcing fields as either
23      single file or yearly files (flag useExfYearlyFields)
24    checkpoint55d_pre
25    
26    o switch between 2-level and 3-level checkpointing
27    o add ability of MNC to write local and "partial" (eg. 2D slices where
28      the full 3D field is never actually stored) arrays to NetCDF files
29      with the correct (that is, the complete multi-dimensional) set of
30      array indicies
31      - used in mom_vecinv() to write the diagFreq output
32      - tested (demonstrated) in verification/aim.5l_cs
33    o further mnc-ification
34      - add verification/lab_sea to the list with mnc setups
35      - fix undefined mnc v-names in cd_code
36      - add kpp to mnc output (both snapshot and timeave)
37    o non-hydrostatic code
38      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
39        in calc_gw.F
40      - defaults to viscAh
41      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
42        friction or Leith) in non-hydrostatic mode, as long as there is
43        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
44    o pkg/cost
45      extend simple cost functions to treat time mean quantities
46      (T,U,V) via cost_accumulate_state from cost_tile
47    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
48        be 2 times larger than the minimum size the advection scheme requires.
49        now get a perfect conservation of salt in advect_cs test-exp (updated)
50    o GGL90 (Gaspar's TKE mixed layer)
51      - add horizontal diffusion of TKE, requires exchanges in
52        do_fields_blocking_exchanges, horizontal diffusivity is zero by
53        default. In OPA there is no horizontal diffusion of TKE but the
54        mixing coefficients are computed from a horizontal average of TKE of
55        6 points or so. I think that diffusion has a little more physical
56        justification.
57      - clean up ggl90_calc in the hope of reducing memory usage (this hope
58        was in vain)
59      - mask tke-variable in ggl90_init
60    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
61    o fix biharmonic diffusion on CS-grid.
62    o more obcs stuff
63      - added obcs_external_fields_load as an alternative to the EXF-pkg option
64        for reading boundary values. This routine is called from
65        obcs_prescribe_read
66      - updated obcs_check
67      - changed sponge layer relaxation parameter units for days to seconds
68      - turned off sponge layer by default
69      - changed argument list of OBCS_CALC to myTime+deltaTclock
70      - fixed about 35 bugs in obcs_external_fields_load
71    
72    checkpoint55c_post
73    o obcs stuff
74      - new runtime flags useOBCSprescribe, useOBCSbalance
75      - re-arranged obcs_calc
76      - moved exf_getobcs to obcs_prescibe_read
77        obcs_prescibe_read is called after ORLANSKI stuff
78        and independent of it (executable can contain all).
79      - updated obcs_check
80      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
81        These may be necessary only if tangential velocities are
82        prescribed at OB, not sure, needs testing.
83    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
84      which simplifies the calls and passes the ifc check-bounds test
85    
86    checkpoint55b_post
87    o add a 2D scalar, Z location, exchange_2 routine.
88    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
89      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
90      affects advect_cs results (for the wrong reason): update output.txt
91    o use a more standard discretization for biharmonic viscosity ;
92     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
93      affects results of dome set-up: update output.txt
94    o fix gad_advection.F (CubedSphere part), back to version 1.23
95    o fix bug in mom_vi_del2uv.F (CubedSphere part).
96    
97    checkpoint55a_post
98    o merged code to
99      * prescribe/read time-dependent open boundaries
100        (works in conjunction with exf, cal)
101      * sponge layer code for open boundaries
102      * each boundary N/S/E/W now has its own CPP option
103        (healthy for the adjoint)
104    
105    checkpoint55
106    o up-to-date adjoint of previous breaks
107      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
108      - global_ocean_ebm: adjoint still needs fix (TLM ok)
109      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
110      - carbon: * remove tr1-related adjoint verification
111                * add ptracer as control variable
112    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
113      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
114    
115    checkpoint54f_post
116    o in verification/carbin/ remove experiment related to
117      ALLOW_PASSIVE_TRACER (array tr1 etc)
118      code_ad/ input_ad/ results_ad
119    
120    o add two new packages
121      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
122        + subject to optimization (memory)
123      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
124        + subject to reordering (many GOTOs in the original code)
125        + so far opps is called for every (i,j) point, and then operates in
126          the vertical; one may want to reorder the scheme in order operate in
127          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
128          fields)
129    o overhaul of IO so that we now have flags for MDSIO and/or MNC
130      - all verification tests compile and run with linux_ia32_g77
131      - defaults are compatible with current input files--nothing
132        should change if you were not previously using MNC
133      - MNC output has been added in numerous places (eg. timeave)
134        but there are still a few writes not yet do-able with MNC
135        (this is in progress)
136      - flags now allow for either/or/both use of MDSIO and MNC and
137        documentation will soon follow
138      - numerous small formatting cleanups for ProTeX
139    o add version info (via BUILD_INFO.h) to MNC and stdout
140    
141    checkpoint54e_post
142    o add two new packages
143      - pp81 (Packanowski and Philander, 1981), Richardson number and
144        stratification dependent mixing
145      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
146      - these scheme operate in a similar manner as KPP (without ghat, of
147        course), however there is only one diffusivity that is used for both
148        temperature and salinity (and passive tracers)ç
149    o add offline package
150    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
151      provided by Stephanie Dutkiewicz
152    o genmake2: add ability to search for C compilers and cleanup test output
153      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
154    
155    checkpoint54d_post
156    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
157    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
158      leading to additional shift by 5 days each year of integration
159       (i.e. leading to considerable offset over the years)
160    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
161    o start with no AB and no initial filtering (staggerTimeStep):
162      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
163    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
164      (external loading & cpl import/export stay in forward_step.F)
165    o update coupling interface to work with new staggerTimeStep
166    o change MDSIO ptracers_pickup.
167    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
168    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
169    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
170    
171    checkpoint54c_post
172    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
173      this affects (truncation error) output.txt of test-exp:
174       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
175    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
176    o change Qnet to always be the net heat flux, (+upward).
177      affects (truncation error) output of natl_box exp.: updated
178    o define the max number of passive tracers in PTRACERS_SIZE.h
179    o start to test mnc routinely in exp0
180    o add sea-ice loading (sIceLoad) as a new forcing field.
181    
182    checkpoint54b_post
183    o add testreport "-j JOBS" option for parallel builds (tested and pretty
184       impressive on Altix and Opteron systems)
185    o diagnostics can now write NetCDF files through the mnc package
186    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
187    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
188    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
189      affects (truncation error) output of lab_sea & natl_box exp.: updated
190    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
191    
192    checkpoint54a_post
193    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
194    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
195    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
196    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
197      + internal_wave (shift in writing cg2d_ini_res)
198    checkpoint54a_pre
199    
200    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
201      - modified verification/lab_sea and natl_box_adjoint accordingly
202    
203    checkpoint54
204    checkpoint53g_post
205    o prepare splitting of thermodynamics: store convect.counter in common block
206    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
207      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
208    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
209    o new parameter "nShapS": allow to treat differently S from T (nShapT)
210    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
211    o restore adjointability
212    
213    checkpoint53f_post
214    o modifications that affect AIM experiment results (update output.txt):
215      - no advection of S at top interface Nr (pkg/generic_advdiff)
216      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
217    o AIM pkg:
218      - include stability function into surf.Flux derivative relative to Tsurf
219      - calculate clear-sky radiation & surface temp. change (for diagnostics)
220    
221    checkpoint53e_post
222    o merged cylindrical coord configuration
223    o added rotating_tank experiment
224    checkpoint53e_pre
225    
226    checkpoint53d_post
227    o faulks upgraded: re-generate output.txt that have changed:
228       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
229    o Added Bryan and Lewis, 1979, vertical diffusivity profile
230    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
231    o added Sadourny discretization of Coriolis
232      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
233      - re-enabled use of omega3 (useAbsVorticity)
234    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
235      vector-invariant equations
236      - note: does *NOT* yet use same variable visc. for no-slip BC's.
237    o recoded the lateral boundary conditions for non-hydrostatic w, this time
238      hopefully without new bugs
239      - still to do: biharmonic friction for non-hydrostatic w
240    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
241    o regenerated output for global_ocean_ebm (using -ieee)
242    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
243      of mom_common/
244      - simple re-arrangement of instructions within computing loop
245    checkpoint53d_pre
246    
247    checkpoint53c_post
248    o new version of coupler for AIM+thSIce and Ocean models
249     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
250     - land: change Evaporation of snow
251     - aim with thSIce: fix bug in snow-precip.
252    o changes to calc_gw.F
253     - bug fix for w^2 term near the bottom boundary
254     - (hopefully) improve the lateral slip boundary condtions for use with
255        partial/looped cells
256      - because the bug fix changes two verification experiments anyway (exp5
257        and plume on slope), change the lateral boundary condition from half slip
258        to the value of no_slip_sides
259    o ebm package wasnt quite up to the parallel task. Fixed that.
260    o Adjoint of EBM package + verification
261      * TLM OK
262      * ADM not sufficient accuracy yet (needs further testing)
263    
264    checkpoint53b_post
265    o Commiting new energy balance model to repository
266      * package is pkg/ebm
267      * verif. is verification/global_ocean_ebm
268      * references are in ebm_driver.F
269    C      * X. Wang, P. Stone and J. Marotzke, 1999:
270    C        Global thermohaline circulation. Part I:
271    C        Sensitivity to atmospheric moisture transport.
272    C        J. Climate 12(1), 71-82
273    C      * X. Wang, P. Stone and J. Marotzke, 1999:
274    C        Global thermohaline circulation. Part II:
275    C        Sensitivity with interactive transport.
276    C        J. Climate 12(1), 83-91
277    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
278    C        Destabilization of the thermohaline circulation
279    C        by atmospheric eddy transports.
280    C        J. Climate 7(12), 1870-1882
281    o Will need long integration testing.
282    checkpoint53b_pre
283    
284    o created pkg/mom_common in preparation for variable viscosity code
285    o renamed and split ini_mnc_io
286    o pkg/land: only liquid water can diffuse or run-off
287    o AIM using land: soil wetness availability account for snow
288    o added printMapIncludesZeros to EEPARMS namelist
289    
290    checkpoint53a_post
291    o restore TAMC compatiility for exf_constants.h
292      (no usage of _d in .h)
293    o Additional storing in KPP in an attempt to fix
294      TAMC problem with adjoint of KPP code.
295      (no success...)
296      Identical code works fine with TAF.
297    o Fixed verification/natl_box_adjoint experiments.
298      Initial conditions for Experiments 4 and 5 are now
299      set to "SEAICE_initialHEFF=0", which is more reasonable,
300      and hence gives results closer to that of Experiment 2.
301      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
302    
303    checkpoint53
304    o stable checkpoint with up to date adjoint
305      TLM tests only run for 1st grdchk at the moment. Its unclear if
306      this is a code problem or a problem with resetting code for g_
307      variables that is being autogenerated wrong.
308      Otherwise:
309       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
310       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
311         are both still in chaos following their security messes.
312    
313    checkpoint52n_post
314    o various build (mostly genmake2) changes including:
315      - ability to build/run more easily within Cygwin and MacOS X
316      - more complicated Makefiles with a stronger dependence on Gnu Make
317    o pkg/seaice modifications
318      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
319        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
320        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
321      - changed proxy for geostrophic velocity and updated
322        verification/lab_sea/results/* accordingly
323      - removed ADI dynamic solver from pkg/seaice
324      - replaced all occurrences of 1/CSTICE or 1/CSUICE
325        they caused a segmentation fault under certain circumstances
326      - removed unused field WATR
327    o bug fix in exf-package:
328      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
329         now reflect that.
330    o small fixes in the cal-package:
331      - set reference date to first of January for the 'model'-calendar
332      - failing of cal_CheckDate in cal_FullDate now actually results in a
333        warning
334    o small modifications in exf-package to increase flexibility:
335      - change climtempfreeze from a constant to a runtime parameter that
336        is specified in data.exf_clim (default = -1.9)
337      - introduce runtime parameter windstressmax (default = 2.0) that is
338        specified in data.exf
339    o fix in pkg/thsice:
340      - update Evap (Tsf changes) to be consistent with Latent heat flux
341      - maintain snow precipitation unchanged (even if Tsf >=0).
342     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
343    
344    checkpoint52m_post
345    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
346      this does not change any of the results, because myIter=0 in swfrac always
347      lead to jwtype=2 (the default anyway), but the call makes little sense
348      as a default
349    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
350    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
351      atmospheric model (AIM) to use it ; add a "slab ocean" component.
352    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
353    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
354    o extending useSingleCpuIO option to work with new exch2 I/O format
355      - old-style, missing-tile I/O is still accessible by defining CPP
356        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
357    o monitor package can write to NetCDF files and/or STDOUT
358    o fix re-definition bug in MNC_GRID_INIT_ALL()
359    o doc/api_reference added
360      - a framework for building an API Reference Manual using all
361        the "protex" comments embedded in the code
362      - see pkg/generic_advdiff, pkg/mnc for examples
363    o MNC:
364      - make myThid the last argument for all subroutines
365      - new default for the grid files: NO halos
366      - add useMNC and other run-time flags
367      - separate per-file-group handling of the unlimited dimension
368      - early initialization of MNC w/ flags read at the eeboot stage
369        and lookup tables set in initialize_fixed
370      - write all MNC output to a freshly-created directory
371    o thermodynamics sea-ice (thsice) is now tested with testreport.
372    o test exp. advect_cs: use the standard cs32 grid ; update output.
373    o Added functionality to grdchk:
374      pick global i,j,k position (or nearest wet) where to perform check.
375    
376    checkpoint52l_post
377    o new land formulation:
378      a) use ground enthalpy as prognostic variable to ensure exact
379         energy conservation.
380      b) account for water temperature and for latent heat of freezing
381         in all processes (rain, run-off, ground storage)
382      c) compute surface and ground temperature implicitly.
383    o aim_v23 modification for new land model:
384      a) Treat separately land / ocean / sea-ice surface fluxes
385         to allow implicit computation of land & sea-ice surface temp.
386      b) add snow precipitation.
387    checkpoint52l_pre
388    
389    o fix problem (when 1 tile is empty) in min/max monitor.
390    o fix bug in timeAve (u,vZetatave in common block)
391    o no restoring terms under ice for pkg/seaice
392    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
393    o bug fix for pkg/seaice pickups
394    o change MNC call locations and add coordinate attributes
395    o mask vorticity at the corner ; affects global_ocean.cs output
396    o fix ini_curvilinear_grid ; test CS experiments with mpi
397    o aim.5l_cs: modify sea-ice fraction input file ; update output
398    o exf: Adding simple range check routine for exf fields after read
399    
400  checkpoint52k_post  checkpoint52k_post
401  o removed top-level directory "diags"  o removed top-level directory "diags"
402    - we migrated these functions to pkg/timeave a long time ago    - we migrated these functions to pkg/timeave a long time ago
# Line 14  o paramter list of CALL ADTHE_MAIN_LOOP Line 408  o paramter list of CALL ADTHE_MAIN_LOOP
408  o added initial do_the_model_io to ecco  o added initial do_the_model_io to ecco
409  o set all ...Freq to zero after cost_final  o set all ...Freq to zero after cost_final
410    taveFreq, dumpFreq, pChkptFreq    taveFreq, dumpFreq, pChkptFreq
411    o MAIN and ECCO differentiability restored
412    
413  checkpoint52j_post  checkpoint52j_post
414  o fix nchklev in tamc.h for global_ocean...  o fix nchklev in tamc.h for global_ocean...

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