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revision 1.211 by jmc, Sun Nov 23 00:44:11 2003 UTC revision 1.333 by edhill, Wed Jul 21 16:34:46 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 genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
7    
8    checkpoint54c_post
9    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
10      this affects (truncation error) output.txt of test-exp:
11       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
12    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
13    o change Qnet to always be the net heat flux, (+upward).
14      affects (truncation error) output of natl_box exp.: updated
15    o define the max number of passive tracers in PTRACERS_SIZE.h
16    o start to test mnc routinely in exp0
17    o add sea-ice loading (sIceLoad) as a new forcing field.
18    
19    checkpoint54b_post
20    o add testreport "-j JOBS" option for parallel builds (tested and pretty
21       impressive on Altix and Opteron systems)
22    o diagnostics can now write NetCDF files through the mnc package
23    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
24    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
25    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
26      affects (truncation error) output of lab_sea & natl_box exp.: updated
27    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
28    
29    checkpoint54a_post
30    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
31    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
32    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
33    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
34      + internal_wave (shift in writing cg2d_ini_res)
35    checkpoint54a_pre
36    
37    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
38      - modified verification/lab_sea and natl_box_adjoint accordingly
39    
40    checkpoint54
41    checkpoint53g_post
42    o prepare splitting of thermodynamics: store convect.counter in common block
43    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
44      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
45    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
46    o new parameter "nShapS": allow to treat differently S from T (nShapT)
47    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
48    o restore adjointability
49    
50    checkpoint53f_post
51    o modifications that affect AIM experiment results (update output.txt):
52      - no advection of S at top interface Nr (pkg/generic_advdiff)
53      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
54    o AIM pkg:
55      - include stability function into surf.Flux derivative relative to Tsurf
56      - calculate clear-sky radiation & surface temp. change (for diagnostics)
57    
58    checkpoint53e_post
59    o merged cylindrical coord configuration
60    o added rotating_tank experiment
61    checkpoint53e_pre
62    
63    checkpoint53d_post
64    o faulks upgraded: re-generate output.txt that have changed:
65       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
66    o Added Bryan and Lewis, 1979, vertical diffusivity profile
67    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
68    o added Sadourny discretization of Coriolis
69      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
70      - re-enabled use of omega3 (useAbsVorticity)
71    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
72      vector-invariant equations
73      - note: does *NOT* yet use same variable visc. for no-slip BC's.
74    o recoded the lateral boundary conditions for non-hydrostatic w, this time
75      hopefully without new bugs
76      - still to do: biharmonic friction for non-hydrostatic w
77    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
78    o regenerated output for global_ocean_ebm (using -ieee)
79    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
80      of mom_common/
81      - simple re-arrangement of instructions within computing loop
82    checkpoint53d_pre
83    
84    checkpoint53c_post
85    o new version of coupler for AIM+thSIce and Ocean models
86     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
87     - land: change Evaporation of snow
88     - aim with thSIce: fix bug in snow-precip.
89    o changes to calc_gw.F
90     - bug fix for w^2 term near the bottom boundary
91     - (hopefully) improve the lateral slip boundary condtions for use with
92        partial/looped cells
93      - because the bug fix changes two verification experiments anyway (exp5
94        and plume on slope), change the lateral boundary condition from half slip
95        to the value of no_slip_sides
96    o ebm package wasnt quite up to the parallel task. Fixed that.
97    o Adjoint of EBM package + verification
98      * TLM OK
99      * ADM not sufficient accuracy yet (needs further testing)
100    
101    checkpoint53b_post
102    o Commiting new energy balance model to repository
103      * package is pkg/ebm
104      * verif. is verification/global_ocean_ebm
105      * references are in ebm_driver.F
106    C      * X. Wang, P. Stone and J. Marotzke, 1999:
107    C        Global thermohaline circulation. Part I:
108    C        Sensitivity to atmospheric moisture transport.
109    C        J. Climate 12(1), 71-82
110    C      * X. Wang, P. Stone and J. Marotzke, 1999:
111    C        Global thermohaline circulation. Part II:
112    C        Sensitivity with interactive transport.
113    C        J. Climate 12(1), 83-91
114    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
115    C        Destabilization of the thermohaline circulation
116    C        by atmospheric eddy transports.
117    C        J. Climate 7(12), 1870-1882
118    o Will need long integration testing.
119    checkpoint53b_pre
120    
121    o created pkg/mom_common in preparation for variable viscosity code
122    o renamed and split ini_mnc_io
123    o pkg/land: only liquid water can diffuse or run-off
124    o AIM using land: soil wetness availability account for snow
125    o added printMapIncludesZeros to EEPARMS namelist
126    
127    checkpoint53a_post
128    o restore TAMC compatiility for exf_constants.h
129      (no usage of _d in .h)
130    o Additional storing in KPP in an attempt to fix
131      TAMC problem with adjoint of KPP code.
132      (no success...)
133      Identical code works fine with TAF.
134    o Fixed verification/natl_box_adjoint experiments.
135      Initial conditions for Experiments 4 and 5 are now
136      set to "SEAICE_initialHEFF=0", which is more reasonable,
137      and hence gives results closer to that of Experiment 2.
138      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
139    
140    checkpoint53
141    o stable checkpoint with up to date adjoint
142      TLM tests only run for 1st grdchk at the moment. Its unclear if
143      this is a code problem or a problem with resetting code for g_
144      variables that is being autogenerated wrong.
145      Otherwise:
146       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
147       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
148         are both still in chaos following their security messes.
149    
150    checkpoint52n_post
151    o various build (mostly genmake2) changes including:
152      - ability to build/run more easily within Cygwin and MacOS X
153      - more complicated Makefiles with a stronger dependence on Gnu Make
154    o pkg/seaice modifications
155      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
156        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
157        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
158      - changed proxy for geostrophic velocity and updated
159        verification/lab_sea/results/* accordingly
160      - removed ADI dynamic solver from pkg/seaice
161      - replaced all occurrences of 1/CSTICE or 1/CSUICE
162        they caused a segmentation fault under certain circumstances
163      - removed unused field WATR
164    o bug fix in exf-package:
165      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
166         now reflect that.
167    o small fixes in the cal-package:
168      - set reference date to first of January for the 'model'-calendar
169      - failing of cal_CheckDate in cal_FullDate now actually results in a
170        warning
171    o small modifications in exf-package to increase flexibility:
172      - change climtempfreeze from a constant to a runtime parameter that
173        is specified in data.exf_clim (default = -1.9)
174      - introduce runtime parameter windstressmax (default = 2.0) that is
175        specified in data.exf
176    o fix in pkg/thsice:
177      - update Evap (Tsf changes) to be consistent with Latent heat flux
178      - maintain snow precipitation unchanged (even if Tsf >=0).
179     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
180    
181    checkpoint52m_post
182    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
183      this does not change any of the results, because myIter=0 in swfrac always
184      lead to jwtype=2 (the default anyway), but the call makes little sense
185      as a default
186    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
187    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
188      atmospheric model (AIM) to use it ; add a "slab ocean" component.
189    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
190    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
191    o extending useSingleCpuIO option to work with new exch2 I/O format
192      - old-style, missing-tile I/O is still accessible by defining CPP
193        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
194    o monitor package can write to NetCDF files and/or STDOUT
195    o fix re-definition bug in MNC_GRID_INIT_ALL()
196    o doc/api_reference added
197      - a framework for building an API Reference Manual using all
198        the "protex" comments embedded in the code
199      - see pkg/generic_advdiff, pkg/mnc for examples
200    o MNC:
201      - make myThid the last argument for all subroutines
202      - new default for the grid files: NO halos
203      - add useMNC and other run-time flags
204      - separate per-file-group handling of the unlimited dimension
205      - early initialization of MNC w/ flags read at the eeboot stage
206        and lookup tables set in initialize_fixed
207      - write all MNC output to a freshly-created directory
208    o thermodynamics sea-ice (thsice) is now tested with testreport.
209    o test exp. advect_cs: use the standard cs32 grid ; update output.
210    o Added functionality to grdchk:
211      pick global i,j,k position (or nearest wet) where to perform check.
212    
213    checkpoint52l_post
214    o new land formulation:
215      a) use ground enthalpy as prognostic variable to ensure exact
216         energy conservation.
217      b) account for water temperature and for latent heat of freezing
218         in all processes (rain, run-off, ground storage)
219      c) compute surface and ground temperature implicitly.
220    o aim_v23 modification for new land model:
221      a) Treat separately land / ocean / sea-ice surface fluxes
222         to allow implicit computation of land & sea-ice surface temp.
223      b) add snow precipitation.
224    checkpoint52l_pre
225    
226    o fix problem (when 1 tile is empty) in min/max monitor.
227    o fix bug in timeAve (u,vZetatave in common block)
228    o no restoring terms under ice for pkg/seaice
229    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
230    o bug fix for pkg/seaice pickups
231    o change MNC call locations and add coordinate attributes
232    o mask vorticity at the corner ; affects global_ocean.cs output
233    o fix ini_curvilinear_grid ; test CS experiments with mpi
234    o aim.5l_cs: modify sea-ice fraction input file ; update output
235    o exf: Adding simple range check routine for exf fields after read
236    
237    checkpoint52k_post
238    o removed top-level directory "diags"
239      - we migrated these functions to pkg/timeave a long time ago
240    o fixed bug introduced in pkg/monitor
241    o accuracy ctrlprec = 32 insuffient for gradient checks using
242      averaged fields (I/O via cost_averages)
243      -> use ctrl.h in active_file*.F to control I/O precision.
244    o paramter list of CALL ADTHE_MAIN_LOOP
245    o added initial do_the_model_io to ecco
246    o set all ...Freq to zero after cost_final
247      taveFreq, dumpFreq, pChkptFreq
248    o MAIN and ECCO differentiability restored
249    
250    checkpoint52j_post
251    o fix nchklev in tamc.h for global_ocean...
252    o Bringing flow and store directives up-to-date
253    o Really weird thing!
254      call do_the_model_io from the_main_loop with parameters
255      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
256      TAF places a faulty re-call of initialise_varia
257      after cost_final call which should not be there!
258    checkpoint52j_pre
259    
260    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
261      error messages
262    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
263    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
264      debug output
265    o modfied mdsio_writefield.F to handle non-global files under exch2
266    o update AIM Cubed-Sphere exp (aim.5l_cs):
267      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
268    o update AIM Equatorial Channel exp:
269      use standard aim_v23 pkg and change the SST fields to be more realistic.
270    o globalFile now works with exch2
271    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
272      mon_vort3.F to make exch2 friendly with >1 tile per cube face
273    o limit timeave output for hi-res integrations
274    
275    checkpoint52i_post
276    o removed CPP_EEOPTIONS.h from verification/*/code
277    o updated the tiling for global_ocean_pressure
278    checkpoint52i_pre
279    
280    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
281      the old pkg/aim).
282    
283    checkpoint52h_pre
284    o shortened offending lines in exch2_send_rx?.template
285    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
286    o genmake2: add build & execute test for NetCDF code
287    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
288      old grid files, moved CPP_EEMACROS.h to pkg/exch2
289    o added useSingleCPUIO flag to monitor.F and mon_out.F
290    o added temporary hack for sea-ice dynamics on the cube:
291      metric terms are ignored and it is assumed that
292      there is no sea-ice on cube faces 1, 2, 4, and 5.
293    
294    checkpoint52f_post
295    o added exch2 cube routines to pkg/exch2
296    o modified hs94.cs-32x32x5 to use it
297    o added new grid files to hs94.cs-32x32x5
298    checkpoint52f_pre
299    
300    checkpoint52e_post
301    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
302      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
303    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
304      to work with implicit vertical advection and AB ;
305    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
306    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
307     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
308    checkpoint52e_pre
309    
310    o fix bug in impldiff when Nr=1 or Nr=2.
311    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
312    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
313    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
314      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
315    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
316    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
317    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
318    
319    checkpoint52d_post
320    o re-tiled many expts to allow comparison in multi-processor mode
321      - updated output accordingly
322      - changed hs94.128x64x5 to use intial T from file rather than use the
323        random number generator
324    o add infrastructure in model routines for fizhi and gridalt packages
325    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
326    o changes to permit hi-res, cubed-sphere, configuration
327      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
328      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
329      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
330        of surface winds for the cube
331      (A verification experiment, based on global_ocean.cs32x15, but with
332       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
333       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
334       complete with example surface forcing files and matlab scripts to look
335       at the output and compare it with that of global_ocean.cs32x15.)
336    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
337       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
338       to conform to the common rule.
339    o check-in the first version of the coupler + interfaces for multi-components
340       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
341       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
342       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
343       - ocean and atmos. share the same horizontal grid (no interpolation).
344       - exchanges between component and coupler is done in forward_step
345    o new verification experiment, cpl_aim+ocn:
346       coupled ocean - AIM atmosphere on cs32 grid.
347    
348    checkpoint52d_pre
349    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
350    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
351    
352    checkpoint52c_post
353    o Fixing OPTIONS files for use of exf:
354      - ALLOW_ECCO not needed
355      - ECCO_CPPOPTIONS.h should not be included from
356        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
357        as has been the case in the past
358      - All cal/exf related options are currently set in
359        single header file. Should remain so until we
360        agree on a consistent new policy.
361    o Removed all CPP options for cal package.
362      cal has no more CPP options.
363    o modified STOREs in GAD_ADVECTION
364    o corrected key comp. for passkey
365    
366    checkpoint52b_post
367    o new version: "thsice" of thermodynamic sea-ice pkg:
368     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
369     - modify fluxes but do not change theta directly;
370     - light cleaning of bulk_force pkg (still needed with thsice).
371     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
372       + output_thsice.txt to test thsice & bulk_force pkgs.
373    o put back grid & coriolis monitor output.
374  checkpoint52b_pre  checkpoint52b_pre
375    
376  o call "do_the_model_io" at the beginning (=> dump initial state)  o call "do_the_model_io" at the beginning (=> dump initial state)

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