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revision 1.214 by heimbach, Tue Nov 25 19:06:08 2003 UTC revision 1.332 by jmc, Sun Jul 18 14:20:17 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint54c_post
7    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
8      this affects (truncation error) output.txt of test-exp:
9       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
10    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
11    o change Qnet to always be the net heat flux, (+upward).
12      affects (truncation error) output of natl_box exp.: updated
13    o define the max number of passive tracers in PTRACERS_SIZE.h
14    o start to test mnc routinely in exp0
15    o add sea-ice loading (sIceLoad) as a new forcing field.
16    
17    checkpoint54b_post
18    o add testreport "-j JOBS" option for parallel builds (tested and pretty
19       impressive on Altix and Opteron systems)
20    o diagnostics can now write NetCDF files through the mnc package
21    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
22    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
23    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
24      affects (truncation error) output of lab_sea & natl_box exp.: updated
25    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
26    
27    checkpoint54a_post
28    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
29    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
30    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
31    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
32      + internal_wave (shift in writing cg2d_ini_res)
33    checkpoint54a_pre
34    
35    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
36      - modified verification/lab_sea and natl_box_adjoint accordingly
37    
38    checkpoint54
39    checkpoint53g_post
40    o prepare splitting of thermodynamics: store convect.counter in common block
41    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
42      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
43    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
44    o new parameter "nShapS": allow to treat differently S from T (nShapT)
45    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
46    o restore adjointability
47    
48    checkpoint53f_post
49    o modifications that affect AIM experiment results (update output.txt):
50      - no advection of S at top interface Nr (pkg/generic_advdiff)
51      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
52    o AIM pkg:
53      - include stability function into surf.Flux derivative relative to Tsurf
54      - calculate clear-sky radiation & surface temp. change (for diagnostics)
55    
56    checkpoint53e_post
57    o merged cylindrical coord configuration
58    o added rotating_tank experiment
59    checkpoint53e_pre
60    
61    checkpoint53d_post
62    o faulks upgraded: re-generate output.txt that have changed:
63       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
64    o Added Bryan and Lewis, 1979, vertical diffusivity profile
65    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
66    o added Sadourny discretization of Coriolis
67      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
68      - re-enabled use of omega3 (useAbsVorticity)
69    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
70      vector-invariant equations
71      - note: does *NOT* yet use same variable visc. for no-slip BC's.
72    o recoded the lateral boundary conditions for non-hydrostatic w, this time
73      hopefully without new bugs
74      - still to do: biharmonic friction for non-hydrostatic w
75    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
76    o regenerated output for global_ocean_ebm (using -ieee)
77    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
78      of mom_common/
79      - simple re-arrangement of instructions within computing loop
80    checkpoint53d_pre
81    
82    checkpoint53c_post
83    o new version of coupler for AIM+thSIce and Ocean models
84     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
85     - land: change Evaporation of snow
86     - aim with thSIce: fix bug in snow-precip.
87    o changes to calc_gw.F
88     - bug fix for w^2 term near the bottom boundary
89     - (hopefully) improve the lateral slip boundary condtions for use with
90        partial/looped cells
91      - because the bug fix changes two verification experiments anyway (exp5
92        and plume on slope), change the lateral boundary condition from half slip
93        to the value of no_slip_sides
94    o ebm package wasnt quite up to the parallel task. Fixed that.
95    o Adjoint of EBM package + verification
96      * TLM OK
97      * ADM not sufficient accuracy yet (needs further testing)
98    
99    checkpoint53b_post
100    o Commiting new energy balance model to repository
101      * package is pkg/ebm
102      * verif. is verification/global_ocean_ebm
103      * references are in ebm_driver.F
104    C      * X. Wang, P. Stone and J. Marotzke, 1999:
105    C        Global thermohaline circulation. Part I:
106    C        Sensitivity to atmospheric moisture transport.
107    C        J. Climate 12(1), 71-82
108    C      * X. Wang, P. Stone and J. Marotzke, 1999:
109    C        Global thermohaline circulation. Part II:
110    C        Sensitivity with interactive transport.
111    C        J. Climate 12(1), 83-91
112    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
113    C        Destabilization of the thermohaline circulation
114    C        by atmospheric eddy transports.
115    C        J. Climate 7(12), 1870-1882
116    o Will need long integration testing.
117    checkpoint53b_pre
118    
119    o created pkg/mom_common in preparation for variable viscosity code
120    o renamed and split ini_mnc_io
121    o pkg/land: only liquid water can diffuse or run-off
122    o AIM using land: soil wetness availability account for snow
123    o added printMapIncludesZeros to EEPARMS namelist
124    
125    checkpoint53a_post
126    o restore TAMC compatiility for exf_constants.h
127      (no usage of _d in .h)
128    o Additional storing in KPP in an attempt to fix
129      TAMC problem with adjoint of KPP code.
130      (no success...)
131      Identical code works fine with TAF.
132    o Fixed verification/natl_box_adjoint experiments.
133      Initial conditions for Experiments 4 and 5 are now
134      set to "SEAICE_initialHEFF=0", which is more reasonable,
135      and hence gives results closer to that of Experiment 2.
136      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
137    
138    checkpoint53
139    o stable checkpoint with up to date adjoint
140      TLM tests only run for 1st grdchk at the moment. Its unclear if
141      this is a code problem or a problem with resetting code for g_
142      variables that is being autogenerated wrong.
143      Otherwise:
144       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
145       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
146         are both still in chaos following their security messes.
147    
148    checkpoint52n_post
149    o various build (mostly genmake2) changes including:
150      - ability to build/run more easily within Cygwin and MacOS X
151      - more complicated Makefiles with a stronger dependence on Gnu Make
152    o pkg/seaice modifications
153      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
154        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
155        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
156      - changed proxy for geostrophic velocity and updated
157        verification/lab_sea/results/* accordingly
158      - removed ADI dynamic solver from pkg/seaice
159      - replaced all occurrences of 1/CSTICE or 1/CSUICE
160        they caused a segmentation fault under certain circumstances
161      - removed unused field WATR
162    o bug fix in exf-package:
163      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
164         now reflect that.
165    o small fixes in the cal-package:
166      - set reference date to first of January for the 'model'-calendar
167      - failing of cal_CheckDate in cal_FullDate now actually results in a
168        warning
169    o small modifications in exf-package to increase flexibility:
170      - change climtempfreeze from a constant to a runtime parameter that
171        is specified in data.exf_clim (default = -1.9)
172      - introduce runtime parameter windstressmax (default = 2.0) that is
173        specified in data.exf
174    o fix in pkg/thsice:
175      - update Evap (Tsf changes) to be consistent with Latent heat flux
176      - maintain snow precipitation unchanged (even if Tsf >=0).
177     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
178    
179    checkpoint52m_post
180    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
181      this does not change any of the results, because myIter=0 in swfrac always
182      lead to jwtype=2 (the default anyway), but the call makes little sense
183      as a default
184    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
185    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
186      atmospheric model (AIM) to use it ; add a "slab ocean" component.
187    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
188    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
189    o extending useSingleCpuIO option to work with new exch2 I/O format
190      - old-style, missing-tile I/O is still accessible by defining CPP
191        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
192    o monitor package can write to NetCDF files and/or STDOUT
193    o fix re-definition bug in MNC_GRID_INIT_ALL()
194    o doc/api_reference added
195      - a framework for building an API Reference Manual using all
196        the "protex" comments embedded in the code
197      - see pkg/generic_advdiff, pkg/mnc for examples
198    o MNC:
199      - make myThid the last argument for all subroutines
200      - new default for the grid files: NO halos
201      - add useMNC and other run-time flags
202      - separate per-file-group handling of the unlimited dimension
203      - early initialization of MNC w/ flags read at the eeboot stage
204        and lookup tables set in initialize_fixed
205      - write all MNC output to a freshly-created directory
206    o thermodynamics sea-ice (thsice) is now tested with testreport.
207    o test exp. advect_cs: use the standard cs32 grid ; update output.
208    o Added functionality to grdchk:
209      pick global i,j,k position (or nearest wet) where to perform check.
210    
211    checkpoint52l_post
212    o new land formulation:
213      a) use ground enthalpy as prognostic variable to ensure exact
214         energy conservation.
215      b) account for water temperature and for latent heat of freezing
216         in all processes (rain, run-off, ground storage)
217      c) compute surface and ground temperature implicitly.
218    o aim_v23 modification for new land model:
219      a) Treat separately land / ocean / sea-ice surface fluxes
220         to allow implicit computation of land & sea-ice surface temp.
221      b) add snow precipitation.
222    checkpoint52l_pre
223    
224    o fix problem (when 1 tile is empty) in min/max monitor.
225    o fix bug in timeAve (u,vZetatave in common block)
226    o no restoring terms under ice for pkg/seaice
227    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
228    o bug fix for pkg/seaice pickups
229    o change MNC call locations and add coordinate attributes
230    o mask vorticity at the corner ; affects global_ocean.cs output
231    o fix ini_curvilinear_grid ; test CS experiments with mpi
232    o aim.5l_cs: modify sea-ice fraction input file ; update output
233    o exf: Adding simple range check routine for exf fields after read
234    
235    checkpoint52k_post
236    o removed top-level directory "diags"
237      - we migrated these functions to pkg/timeave a long time ago
238    o fixed bug introduced in pkg/monitor
239    o accuracy ctrlprec = 32 insuffient for gradient checks using
240      averaged fields (I/O via cost_averages)
241      -> use ctrl.h in active_file*.F to control I/O precision.
242    o paramter list of CALL ADTHE_MAIN_LOOP
243    o added initial do_the_model_io to ecco
244    o set all ...Freq to zero after cost_final
245      taveFreq, dumpFreq, pChkptFreq
246    o MAIN and ECCO differentiability restored
247    
248    checkpoint52j_post
249    o fix nchklev in tamc.h for global_ocean...
250    o Bringing flow and store directives up-to-date
251    o Really weird thing!
252      call do_the_model_io from the_main_loop with parameters
253      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
254      TAF places a faulty re-call of initialise_varia
255      after cost_final call which should not be there!
256    checkpoint52j_pre
257    
258    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
259      error messages
260    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
261    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
262      debug output
263    o modfied mdsio_writefield.F to handle non-global files under exch2
264    o update AIM Cubed-Sphere exp (aim.5l_cs):
265      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
266    o update AIM Equatorial Channel exp:
267      use standard aim_v23 pkg and change the SST fields to be more realistic.
268    o globalFile now works with exch2
269    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
270      mon_vort3.F to make exch2 friendly with >1 tile per cube face
271    o limit timeave output for hi-res integrations
272    
273    checkpoint52i_post
274    o removed CPP_EEOPTIONS.h from verification/*/code
275    o updated the tiling for global_ocean_pressure
276    checkpoint52i_pre
277    
278    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
279      the old pkg/aim).
280    
281    checkpoint52h_pre
282    o shortened offending lines in exch2_send_rx?.template
283    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
284    o genmake2: add build & execute test for NetCDF code
285    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
286      old grid files, moved CPP_EEMACROS.h to pkg/exch2
287    o added useSingleCPUIO flag to monitor.F and mon_out.F
288    o added temporary hack for sea-ice dynamics on the cube:
289      metric terms are ignored and it is assumed that
290      there is no sea-ice on cube faces 1, 2, 4, and 5.
291    
292    checkpoint52f_post
293    o added exch2 cube routines to pkg/exch2
294    o modified hs94.cs-32x32x5 to use it
295    o added new grid files to hs94.cs-32x32x5
296    checkpoint52f_pre
297    
298    checkpoint52e_post
299    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
300      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
301    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
302      to work with implicit vertical advection and AB ;
303    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
304    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
305     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
306    checkpoint52e_pre
307    
308    o fix bug in impldiff when Nr=1 or Nr=2.
309    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
310    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
311    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
312      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
313    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
314    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
315    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
316    
317    checkpoint52d_post
318    o re-tiled many expts to allow comparison in multi-processor mode
319      - updated output accordingly
320      - changed hs94.128x64x5 to use intial T from file rather than use the
321        random number generator
322    o add infrastructure in model routines for fizhi and gridalt packages
323    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
324    o changes to permit hi-res, cubed-sphere, configuration
325      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
326      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
327      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
328        of surface winds for the cube
329      (A verification experiment, based on global_ocean.cs32x15, but with
330       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
331       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
332       complete with example surface forcing files and matlab scripts to look
333       at the output and compare it with that of global_ocean.cs32x15.)
334    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
335       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
336       to conform to the common rule.
337    o check-in the first version of the coupler + interfaces for multi-components
338       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
339       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
340       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
341       - ocean and atmos. share the same horizontal grid (no interpolation).
342       - exchanges between component and coupler is done in forward_step
343    o new verification experiment, cpl_aim+ocn:
344       coupled ocean - AIM atmosphere on cs32 grid.
345    
346    checkpoint52d_pre
347    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
348    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
349    
350    checkpoint52c_post
351  o Fixing OPTIONS files for use of exf:  o Fixing OPTIONS files for use of exf:
352    - ALLOW_ECCO not needed    - ALLOW_ECCO not needed
353    - ECCO_CPPOPTIONS.h should not be included from    - ECCO_CPPOPTIONS.h should not be included from
# Line 13  o Fixing OPTIONS files for use of exf: Line 358  o Fixing OPTIONS files for use of exf:
358      agree on a consistent new policy.      agree on a consistent new policy.
359  o Removed all CPP options for cal package.  o Removed all CPP options for cal package.
360    cal has no more CPP options.    cal has no more CPP options.
361    o modified STOREs in GAD_ADVECTION
362    o corrected key comp. for passkey
363    
364  checkpoint52b_post  checkpoint52b_post
365  o new version: "thsice" of thermodynamic sea-ice pkg:  o new version: "thsice" of thermodynamic sea-ice pkg:

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