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revision 1.237 by afe, Fri Jan 9 21:29:24 2004 UTC revision 1.353 by heimbach, Thu Sep 23 17:48:23 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6  checkpoint52f_pre  checkpoint55c_post
7    o obcs stuff
8      - new runtime flags useOBCSprescribe, useOBCSbalance
9      - re-arranged obcs_calc
10      - moved exf_getobcs to obcs_prescibe_read
11        obcs_prescibe_read is called after ORLANSKI stuff
12        and independent of it (executable can contain all).
13      - updated obcs_check
14      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
15        These may be necessary only if tangential velocities are
16        prescribed at OB, not sure, needs testing.
17    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
18      which simplifies the calls and passes the ifc check-bounds test
19    
20    checkpoint55b_post
21    o add a 2D scalar, Z location, exchange_2 routine.
22    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
23      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
24      affects advect_cs results (for the wrong reason): update output.txt
25    o use a more standard discretization for biharmonic viscosity ;
26     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
27      affects results of dome set-up: update output.txt
28    o fix gad_advection.F (CubedSphere part), back to version 1.23
29    o fix bug in mom_vi_del2uv.F (CubedSphere part).
30    
31    checkpoint55a_post
32    o merged code to
33      * prescribe/read time-dependent open boundaries
34        (works in conjunction with exf, cal)
35      * sponge layer code for open boundaries
36      * each boundary N/S/E/W now has its own CPP option
37        (healthy for the adjoint)
38    
39    checkpoint55
40    o up-to-date adjoint of previous breaks
41      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
42      - global_ocean_ebm: adjoint still needs fix (TLM ok)
43      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
44      - carbon: * remove tr1-related adjoint verification
45                * add ptracer as control variable
46    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
47      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
48    
49    checkpoint54f_post
50    o in verification/carbin/ remove experiment related to
51      ALLOW_PASSIVE_TRACER (array tr1 etc)
52      code_ad/ input_ad/ results_ad
53    
54    o add two new packages
55      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
56        + subject to optimization (memory)
57      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
58        + subject to reordering (many GOTOs in the original code)
59        + so far opps is called for every (i,j) point, and then operates in
60          the vertical; one may want to reorder the scheme in order operate in
61          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
62          fields)
63    o overhaul of IO so that we now have flags for MDSIO and/or MNC
64      - all verification tests compile and run with linux_ia32_g77
65      - defaults are compatible with current input files--nothing
66        should change if you were not previously using MNC
67      - MNC output has been added in numerous places (eg. timeave)
68        but there are still a few writes not yet do-able with MNC
69        (this is in progress)
70      - flags now allow for either/or/both use of MDSIO and MNC and
71        documentation will soon follow
72      - numerous small formatting cleanups for ProTeX
73    o add version info (via BUILD_INFO.h) to MNC and stdout
74    
75    checkpoint54e_post
76    o add two new packages
77      - pp81 (Packanowski and Philander, 1981), Richardson number and
78        stratification dependent mixing
79      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
80      - these scheme operate in a similar manner as KPP (without ghat, of
81        course), however there is only one diffusivity that is used for both
82        temperature and salinity (and passive tracers)ç
83    o add offline package
84    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
85      provided by Stephanie Dutkiewicz
86    o genmake2: add ability to search for C compilers and cleanup test output
87      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
88    
89    checkpoint54d_post
90    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
91    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
92      leading to additional shift by 5 days each year of integration
93       (i.e. leading to considerable offset over the years)
94    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
95    o start with no AB and no initial filtering (staggerTimeStep):
96      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
97    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
98      (external loading & cpl import/export stay in forward_step.F)
99    o update coupling interface to work with new staggerTimeStep
100    o change MDSIO ptracers_pickup.
101    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
102    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
103    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
104    
105    checkpoint54c_post
106    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
107      this affects (truncation error) output.txt of test-exp:
108       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
109    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
110    o change Qnet to always be the net heat flux, (+upward).
111      affects (truncation error) output of natl_box exp.: updated
112    o define the max number of passive tracers in PTRACERS_SIZE.h
113    o start to test mnc routinely in exp0
114    o add sea-ice loading (sIceLoad) as a new forcing field.
115    
116    checkpoint54b_post
117    o add testreport "-j JOBS" option for parallel builds (tested and pretty
118       impressive on Altix and Opteron systems)
119    o diagnostics can now write NetCDF files through the mnc package
120    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
121    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
122    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
123      affects (truncation error) output of lab_sea & natl_box exp.: updated
124    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
125    
126    checkpoint54a_post
127    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
128    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
129    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
130    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
131      + internal_wave (shift in writing cg2d_ini_res)
132    checkpoint54a_pre
133    
134    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
135      - modified verification/lab_sea and natl_box_adjoint accordingly
136    
137    checkpoint54
138    checkpoint53g_post
139    o prepare splitting of thermodynamics: store convect.counter in common block
140    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
141      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
142    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
143    o new parameter "nShapS": allow to treat differently S from T (nShapT)
144    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
145    o restore adjointability
146    
147    checkpoint53f_post
148    o modifications that affect AIM experiment results (update output.txt):
149      - no advection of S at top interface Nr (pkg/generic_advdiff)
150      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
151    o AIM pkg:
152      - include stability function into surf.Flux derivative relative to Tsurf
153      - calculate clear-sky radiation & surface temp. change (for diagnostics)
154    
155    checkpoint53e_post
156    o merged cylindrical coord configuration
157    o added rotating_tank experiment
158    checkpoint53e_pre
159    
160    checkpoint53d_post
161    o faulks upgraded: re-generate output.txt that have changed:
162       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
163    o Added Bryan and Lewis, 1979, vertical diffusivity profile
164    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
165    o added Sadourny discretization of Coriolis
166      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
167      - re-enabled use of omega3 (useAbsVorticity)
168    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
169      vector-invariant equations
170      - note: does *NOT* yet use same variable visc. for no-slip BC's.
171    o recoded the lateral boundary conditions for non-hydrostatic w, this time
172      hopefully without new bugs
173      - still to do: biharmonic friction for non-hydrostatic w
174    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
175    o regenerated output for global_ocean_ebm (using -ieee)
176    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
177      of mom_common/
178      - simple re-arrangement of instructions within computing loop
179    checkpoint53d_pre
180    
181    checkpoint53c_post
182    o new version of coupler for AIM+thSIce and Ocean models
183     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
184     - land: change Evaporation of snow
185     - aim with thSIce: fix bug in snow-precip.
186    o changes to calc_gw.F
187     - bug fix for w^2 term near the bottom boundary
188     - (hopefully) improve the lateral slip boundary condtions for use with
189        partial/looped cells
190      - because the bug fix changes two verification experiments anyway (exp5
191        and plume on slope), change the lateral boundary condition from half slip
192        to the value of no_slip_sides
193    o ebm package wasnt quite up to the parallel task. Fixed that.
194    o Adjoint of EBM package + verification
195      * TLM OK
196      * ADM not sufficient accuracy yet (needs further testing)
197    
198    checkpoint53b_post
199    o Commiting new energy balance model to repository
200      * package is pkg/ebm
201      * verif. is verification/global_ocean_ebm
202      * references are in ebm_driver.F
203    C      * X. Wang, P. Stone and J. Marotzke, 1999:
204    C        Global thermohaline circulation. Part I:
205    C        Sensitivity to atmospheric moisture transport.
206    C        J. Climate 12(1), 71-82
207    C      * X. Wang, P. Stone and J. Marotzke, 1999:
208    C        Global thermohaline circulation. Part II:
209    C        Sensitivity with interactive transport.
210    C        J. Climate 12(1), 83-91
211    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
212    C        Destabilization of the thermohaline circulation
213    C        by atmospheric eddy transports.
214    C        J. Climate 7(12), 1870-1882
215    o Will need long integration testing.
216    checkpoint53b_pre
217    
218    o created pkg/mom_common in preparation for variable viscosity code
219    o renamed and split ini_mnc_io
220    o pkg/land: only liquid water can diffuse or run-off
221    o AIM using land: soil wetness availability account for snow
222    o added printMapIncludesZeros to EEPARMS namelist
223    
224    checkpoint53a_post
225    o restore TAMC compatiility for exf_constants.h
226      (no usage of _d in .h)
227    o Additional storing in KPP in an attempt to fix
228      TAMC problem with adjoint of KPP code.
229      (no success...)
230      Identical code works fine with TAF.
231    o Fixed verification/natl_box_adjoint experiments.
232      Initial conditions for Experiments 4 and 5 are now
233      set to "SEAICE_initialHEFF=0", which is more reasonable,
234      and hence gives results closer to that of Experiment 2.
235      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
236    
237    checkpoint53
238    o stable checkpoint with up to date adjoint
239      TLM tests only run for 1st grdchk at the moment. Its unclear if
240      this is a code problem or a problem with resetting code for g_
241      variables that is being autogenerated wrong.
242      Otherwise:
243       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
244       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
245         are both still in chaos following their security messes.
246    
247    checkpoint52n_post
248    o various build (mostly genmake2) changes including:
249      - ability to build/run more easily within Cygwin and MacOS X
250      - more complicated Makefiles with a stronger dependence on Gnu Make
251    o pkg/seaice modifications
252      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
253        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
254        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
255      - changed proxy for geostrophic velocity and updated
256        verification/lab_sea/results/* accordingly
257      - removed ADI dynamic solver from pkg/seaice
258      - replaced all occurrences of 1/CSTICE or 1/CSUICE
259        they caused a segmentation fault under certain circumstances
260      - removed unused field WATR
261    o bug fix in exf-package:
262      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
263         now reflect that.
264    o small fixes in the cal-package:
265      - set reference date to first of January for the 'model'-calendar
266      - failing of cal_CheckDate in cal_FullDate now actually results in a
267        warning
268    o small modifications in exf-package to increase flexibility:
269      - change climtempfreeze from a constant to a runtime parameter that
270        is specified in data.exf_clim (default = -1.9)
271      - introduce runtime parameter windstressmax (default = 2.0) that is
272        specified in data.exf
273    o fix in pkg/thsice:
274      - update Evap (Tsf changes) to be consistent with Latent heat flux
275      - maintain snow precipitation unchanged (even if Tsf >=0).
276     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
277    
278    checkpoint52m_post
279    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
280      this does not change any of the results, because myIter=0 in swfrac always
281      lead to jwtype=2 (the default anyway), but the call makes little sense
282      as a default
283    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
284    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
285      atmospheric model (AIM) to use it ; add a "slab ocean" component.
286    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
287    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
288    o extending useSingleCpuIO option to work with new exch2 I/O format
289      - old-style, missing-tile I/O is still accessible by defining CPP
290        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
291    o monitor package can write to NetCDF files and/or STDOUT
292    o fix re-definition bug in MNC_GRID_INIT_ALL()
293    o doc/api_reference added
294      - a framework for building an API Reference Manual using all
295        the "protex" comments embedded in the code
296      - see pkg/generic_advdiff, pkg/mnc for examples
297    o MNC:
298      - make myThid the last argument for all subroutines
299      - new default for the grid files: NO halos
300      - add useMNC and other run-time flags
301      - separate per-file-group handling of the unlimited dimension
302      - early initialization of MNC w/ flags read at the eeboot stage
303        and lookup tables set in initialize_fixed
304      - write all MNC output to a freshly-created directory
305    o thermodynamics sea-ice (thsice) is now tested with testreport.
306    o test exp. advect_cs: use the standard cs32 grid ; update output.
307    o Added functionality to grdchk:
308      pick global i,j,k position (or nearest wet) where to perform check.
309    
310    checkpoint52l_post
311    o new land formulation:
312      a) use ground enthalpy as prognostic variable to ensure exact
313         energy conservation.
314      b) account for water temperature and for latent heat of freezing
315         in all processes (rain, run-off, ground storage)
316      c) compute surface and ground temperature implicitly.
317    o aim_v23 modification for new land model:
318      a) Treat separately land / ocean / sea-ice surface fluxes
319         to allow implicit computation of land & sea-ice surface temp.
320      b) add snow precipitation.
321    checkpoint52l_pre
322    
323    o fix problem (when 1 tile is empty) in min/max monitor.
324    o fix bug in timeAve (u,vZetatave in common block)
325    o no restoring terms under ice for pkg/seaice
326    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
327    o bug fix for pkg/seaice pickups
328    o change MNC call locations and add coordinate attributes
329    o mask vorticity at the corner ; affects global_ocean.cs output
330    o fix ini_curvilinear_grid ; test CS experiments with mpi
331    o aim.5l_cs: modify sea-ice fraction input file ; update output
332    o exf: Adding simple range check routine for exf fields after read
333    
334    checkpoint52k_post
335    o removed top-level directory "diags"
336      - we migrated these functions to pkg/timeave a long time ago
337    o fixed bug introduced in pkg/monitor
338    o accuracy ctrlprec = 32 insuffient for gradient checks using
339      averaged fields (I/O via cost_averages)
340      -> use ctrl.h in active_file*.F to control I/O precision.
341    o paramter list of CALL ADTHE_MAIN_LOOP
342    o added initial do_the_model_io to ecco
343    o set all ...Freq to zero after cost_final
344      taveFreq, dumpFreq, pChkptFreq
345    o MAIN and ECCO differentiability restored
346    
347    checkpoint52j_post
348    o fix nchklev in tamc.h for global_ocean...
349    o Bringing flow and store directives up-to-date
350    o Really weird thing!
351      call do_the_model_io from the_main_loop with parameters
352      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
353      TAF places a faulty re-call of initialise_varia
354      after cost_final call which should not be there!
355    checkpoint52j_pre
356    
357    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
358      error messages
359    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
360    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
361      debug output
362    o modfied mdsio_writefield.F to handle non-global files under exch2
363    o update AIM Cubed-Sphere exp (aim.5l_cs):
364      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
365    o update AIM Equatorial Channel exp:
366      use standard aim_v23 pkg and change the SST fields to be more realistic.
367    o globalFile now works with exch2
368    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
369      mon_vort3.F to make exch2 friendly with >1 tile per cube face
370    o limit timeave output for hi-res integrations
371    
372    checkpoint52i_post
373    o removed CPP_EEOPTIONS.h from verification/*/code
374    o updated the tiling for global_ocean_pressure
375    checkpoint52i_pre
376    
377    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
378      the old pkg/aim).
379    
380    checkpoint52h_pre
381    o shortened offending lines in exch2_send_rx?.template
382    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
383    o genmake2: add build & execute test for NetCDF code
384    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
385      old grid files, moved CPP_EEMACROS.h to pkg/exch2
386    o added useSingleCPUIO flag to monitor.F and mon_out.F
387    o added temporary hack for sea-ice dynamics on the cube:
388      metric terms are ignored and it is assumed that
389      there is no sea-ice on cube faces 1, 2, 4, and 5.
390    
391    checkpoint52f_post
392  o added exch2 cube routines to pkg/exch2  o added exch2 cube routines to pkg/exch2
393  o modified hs94.cs-32x32x5 to use it  o modified hs94.cs-32x32x5 to use it
394  o added new grid files to hs94.cs-32x32x5  o added new grid files to hs94.cs-32x32x5
395  checkpoint52f_post  checkpoint52f_pre
396    
397  checkpoint52e_post  checkpoint52e_post
398  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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