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revision 1.226 by jmc, Tue Dec 16 15:16:39 2003 UTC revision 1.345 by heimbach, Thu Sep 16 22:25:23 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint54f_post
7    o in verification/carbin/ remove experiment related to
8      ALLOW_PASSIVE_TRACER (array tr1 etc)
9      code_ad/ input_ad/ results_ad
10    
11    o add two new packages
12      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
13        + subject to optimization (memory)
14      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
15        + subject to reordering (many GOTOs in the original code)
16        + so far opps is called for every (i,j) point, and then operates in
17          the vertical; one may want to reorder the scheme in order operate in
18          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
19          fields)
20    o overhaul of IO so that we now have flags for MDSIO and/or MNC
21      - all verification tests compile and run with linux_ia32_g77
22      - defaults are compatible with current input files--nothing
23        should change if you were not previously using MNC
24      - MNC output has been added in numerous places (eg. timeave)
25        but there are still a few writes not yet do-able with MNC
26        (this is in progress)
27      - flags now allow for either/or/both use of MDSIO and MNC and
28        documentation will soon follow
29      - numerous small formatting cleanups for ProTeX
30    o add version info (via BUILD_INFO.h) to MNC and stdout
31    
32    checkpoint54e_post
33    o add two new packages
34      - pp81 (Packanowski and Philander, 1981), Richardson number and
35        stratification dependent mixing
36      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
37      - these scheme operate in a similar manner as KPP (without ghat, of
38        course), however there is only one diffusivity that is used for both
39        temperature and salinity (and passive tracers)ç
40    o add offline package
41    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
42      provided by Stephanie Dutkiewicz
43    o genmake2: add ability to search for C compilers and cleanup test output
44      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
45    
46    checkpoint54d_post
47    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
48    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
49      leading to additional shift by 5 days each year of integration
50       (i.e. leading to considerable offset over the years)
51    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
52    o start with no AB and no initial filtering (staggerTimeStep):
53      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
54    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
55      (external loading & cpl import/export stay in forward_step.F)
56    o update coupling interface to work with new staggerTimeStep
57    o change MDSIO ptracers_pickup.
58    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
59    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
60    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
61    
62    checkpoint54c_post
63    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
64      this affects (truncation error) output.txt of test-exp:
65       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
66    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
67    o change Qnet to always be the net heat flux, (+upward).
68      affects (truncation error) output of natl_box exp.: updated
69    o define the max number of passive tracers in PTRACERS_SIZE.h
70    o start to test mnc routinely in exp0
71    o add sea-ice loading (sIceLoad) as a new forcing field.
72    
73    checkpoint54b_post
74    o add testreport "-j JOBS" option for parallel builds (tested and pretty
75       impressive on Altix and Opteron systems)
76    o diagnostics can now write NetCDF files through the mnc package
77    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
78    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
79    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
80      affects (truncation error) output of lab_sea & natl_box exp.: updated
81    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
82    
83    checkpoint54a_post
84    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
85    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
86    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
87    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
88      + internal_wave (shift in writing cg2d_ini_res)
89    checkpoint54a_pre
90    
91    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
92      - modified verification/lab_sea and natl_box_adjoint accordingly
93    
94    checkpoint54
95    checkpoint53g_post
96    o prepare splitting of thermodynamics: store convect.counter in common block
97    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
98      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
99    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
100    o new parameter "nShapS": allow to treat differently S from T (nShapT)
101    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
102    o restore adjointability
103    
104    checkpoint53f_post
105    o modifications that affect AIM experiment results (update output.txt):
106      - no advection of S at top interface Nr (pkg/generic_advdiff)
107      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
108    o AIM pkg:
109      - include stability function into surf.Flux derivative relative to Tsurf
110      - calculate clear-sky radiation & surface temp. change (for diagnostics)
111    
112    checkpoint53e_post
113    o merged cylindrical coord configuration
114    o added rotating_tank experiment
115    checkpoint53e_pre
116    
117    checkpoint53d_post
118    o faulks upgraded: re-generate output.txt that have changed:
119       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
120    o Added Bryan and Lewis, 1979, vertical diffusivity profile
121    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
122    o added Sadourny discretization of Coriolis
123      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
124      - re-enabled use of omega3 (useAbsVorticity)
125    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
126      vector-invariant equations
127      - note: does *NOT* yet use same variable visc. for no-slip BC's.
128    o recoded the lateral boundary conditions for non-hydrostatic w, this time
129      hopefully without new bugs
130      - still to do: biharmonic friction for non-hydrostatic w
131    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
132    o regenerated output for global_ocean_ebm (using -ieee)
133    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
134      of mom_common/
135      - simple re-arrangement of instructions within computing loop
136    checkpoint53d_pre
137    
138    checkpoint53c_post
139    o new version of coupler for AIM+thSIce and Ocean models
140     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
141     - land: change Evaporation of snow
142     - aim with thSIce: fix bug in snow-precip.
143    o changes to calc_gw.F
144     - bug fix for w^2 term near the bottom boundary
145     - (hopefully) improve the lateral slip boundary condtions for use with
146        partial/looped cells
147      - because the bug fix changes two verification experiments anyway (exp5
148        and plume on slope), change the lateral boundary condition from half slip
149        to the value of no_slip_sides
150    o ebm package wasnt quite up to the parallel task. Fixed that.
151    o Adjoint of EBM package + verification
152      * TLM OK
153      * ADM not sufficient accuracy yet (needs further testing)
154    
155    checkpoint53b_post
156    o Commiting new energy balance model to repository
157      * package is pkg/ebm
158      * verif. is verification/global_ocean_ebm
159      * references are in ebm_driver.F
160    C      * X. Wang, P. Stone and J. Marotzke, 1999:
161    C        Global thermohaline circulation. Part I:
162    C        Sensitivity to atmospheric moisture transport.
163    C        J. Climate 12(1), 71-82
164    C      * X. Wang, P. Stone and J. Marotzke, 1999:
165    C        Global thermohaline circulation. Part II:
166    C        Sensitivity with interactive transport.
167    C        J. Climate 12(1), 83-91
168    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
169    C        Destabilization of the thermohaline circulation
170    C        by atmospheric eddy transports.
171    C        J. Climate 7(12), 1870-1882
172    o Will need long integration testing.
173    checkpoint53b_pre
174    
175    o created pkg/mom_common in preparation for variable viscosity code
176    o renamed and split ini_mnc_io
177    o pkg/land: only liquid water can diffuse or run-off
178    o AIM using land: soil wetness availability account for snow
179    o added printMapIncludesZeros to EEPARMS namelist
180    
181    checkpoint53a_post
182    o restore TAMC compatiility for exf_constants.h
183      (no usage of _d in .h)
184    o Additional storing in KPP in an attempt to fix
185      TAMC problem with adjoint of KPP code.
186      (no success...)
187      Identical code works fine with TAF.
188    o Fixed verification/natl_box_adjoint experiments.
189      Initial conditions for Experiments 4 and 5 are now
190      set to "SEAICE_initialHEFF=0", which is more reasonable,
191      and hence gives results closer to that of Experiment 2.
192      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
193    
194    checkpoint53
195    o stable checkpoint with up to date adjoint
196      TLM tests only run for 1st grdchk at the moment. Its unclear if
197      this is a code problem or a problem with resetting code for g_
198      variables that is being autogenerated wrong.
199      Otherwise:
200       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
201       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
202         are both still in chaos following their security messes.
203    
204    checkpoint52n_post
205    o various build (mostly genmake2) changes including:
206      - ability to build/run more easily within Cygwin and MacOS X
207      - more complicated Makefiles with a stronger dependence on Gnu Make
208    o pkg/seaice modifications
209      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
210        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
211        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
212      - changed proxy for geostrophic velocity and updated
213        verification/lab_sea/results/* accordingly
214      - removed ADI dynamic solver from pkg/seaice
215      - replaced all occurrences of 1/CSTICE or 1/CSUICE
216        they caused a segmentation fault under certain circumstances
217      - removed unused field WATR
218    o bug fix in exf-package:
219      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
220         now reflect that.
221    o small fixes in the cal-package:
222      - set reference date to first of January for the 'model'-calendar
223      - failing of cal_CheckDate in cal_FullDate now actually results in a
224        warning
225    o small modifications in exf-package to increase flexibility:
226      - change climtempfreeze from a constant to a runtime parameter that
227        is specified in data.exf_clim (default = -1.9)
228      - introduce runtime parameter windstressmax (default = 2.0) that is
229        specified in data.exf
230    o fix in pkg/thsice:
231      - update Evap (Tsf changes) to be consistent with Latent heat flux
232      - maintain snow precipitation unchanged (even if Tsf >=0).
233     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
234    
235    checkpoint52m_post
236    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
237      this does not change any of the results, because myIter=0 in swfrac always
238      lead to jwtype=2 (the default anyway), but the call makes little sense
239      as a default
240    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
241    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
242      atmospheric model (AIM) to use it ; add a "slab ocean" component.
243    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
244    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
245    o extending useSingleCpuIO option to work with new exch2 I/O format
246      - old-style, missing-tile I/O is still accessible by defining CPP
247        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
248    o monitor package can write to NetCDF files and/or STDOUT
249    o fix re-definition bug in MNC_GRID_INIT_ALL()
250    o doc/api_reference added
251      - a framework for building an API Reference Manual using all
252        the "protex" comments embedded in the code
253      - see pkg/generic_advdiff, pkg/mnc for examples
254    o MNC:
255      - make myThid the last argument for all subroutines
256      - new default for the grid files: NO halos
257      - add useMNC and other run-time flags
258      - separate per-file-group handling of the unlimited dimension
259      - early initialization of MNC w/ flags read at the eeboot stage
260        and lookup tables set in initialize_fixed
261      - write all MNC output to a freshly-created directory
262    o thermodynamics sea-ice (thsice) is now tested with testreport.
263    o test exp. advect_cs: use the standard cs32 grid ; update output.
264    o Added functionality to grdchk:
265      pick global i,j,k position (or nearest wet) where to perform check.
266    
267    checkpoint52l_post
268    o new land formulation:
269      a) use ground enthalpy as prognostic variable to ensure exact
270         energy conservation.
271      b) account for water temperature and for latent heat of freezing
272         in all processes (rain, run-off, ground storage)
273      c) compute surface and ground temperature implicitly.
274    o aim_v23 modification for new land model:
275      a) Treat separately land / ocean / sea-ice surface fluxes
276         to allow implicit computation of land & sea-ice surface temp.
277      b) add snow precipitation.
278    checkpoint52l_pre
279    
280    o fix problem (when 1 tile is empty) in min/max monitor.
281    o fix bug in timeAve (u,vZetatave in common block)
282    o no restoring terms under ice for pkg/seaice
283    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
284    o bug fix for pkg/seaice pickups
285    o change MNC call locations and add coordinate attributes
286    o mask vorticity at the corner ; affects global_ocean.cs output
287    o fix ini_curvilinear_grid ; test CS experiments with mpi
288    o aim.5l_cs: modify sea-ice fraction input file ; update output
289    o exf: Adding simple range check routine for exf fields after read
290    
291    checkpoint52k_post
292    o removed top-level directory "diags"
293      - we migrated these functions to pkg/timeave a long time ago
294    o fixed bug introduced in pkg/monitor
295    o accuracy ctrlprec = 32 insuffient for gradient checks using
296      averaged fields (I/O via cost_averages)
297      -> use ctrl.h in active_file*.F to control I/O precision.
298    o paramter list of CALL ADTHE_MAIN_LOOP
299    o added initial do_the_model_io to ecco
300    o set all ...Freq to zero after cost_final
301      taveFreq, dumpFreq, pChkptFreq
302    o MAIN and ECCO differentiability restored
303    
304    checkpoint52j_post
305    o fix nchklev in tamc.h for global_ocean...
306    o Bringing flow and store directives up-to-date
307    o Really weird thing!
308      call do_the_model_io from the_main_loop with parameters
309      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
310      TAF places a faulty re-call of initialise_varia
311      after cost_final call which should not be there!
312    checkpoint52j_pre
313    
314    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
315      error messages
316    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
317    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
318      debug output
319    o modfied mdsio_writefield.F to handle non-global files under exch2
320    o update AIM Cubed-Sphere exp (aim.5l_cs):
321      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
322    o update AIM Equatorial Channel exp:
323      use standard aim_v23 pkg and change the SST fields to be more realistic.
324    o globalFile now works with exch2
325    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
326      mon_vort3.F to make exch2 friendly with >1 tile per cube face
327    o limit timeave output for hi-res integrations
328    
329    checkpoint52i_post
330    o removed CPP_EEOPTIONS.h from verification/*/code
331    o updated the tiling for global_ocean_pressure
332    checkpoint52i_pre
333    
334    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
335      the old pkg/aim).
336    
337    checkpoint52h_pre
338    o shortened offending lines in exch2_send_rx?.template
339    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
340    o genmake2: add build & execute test for NetCDF code
341    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
342      old grid files, moved CPP_EEMACROS.h to pkg/exch2
343    o added useSingleCPUIO flag to monitor.F and mon_out.F
344    o added temporary hack for sea-ice dynamics on the cube:
345      metric terms are ignored and it is assumed that
346      there is no sea-ice on cube faces 1, 2, 4, and 5.
347    
348    checkpoint52f_post
349    o added exch2 cube routines to pkg/exch2
350    o modified hs94.cs-32x32x5 to use it
351    o added new grid files to hs94.cs-32x32x5
352    checkpoint52f_pre
353    
354    checkpoint52e_post
355    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
356      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
357    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
358      to work with implicit vertical advection and AB ;
359    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
360    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
361     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
362    checkpoint52e_pre
363    
364    o fix bug in impldiff when Nr=1 or Nr=2.
365    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
366    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
367    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
368      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
369    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
370    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
371    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
372    
373  checkpoint52d_post  checkpoint52d_post
374    o re-tiled many expts to allow comparison in multi-processor mode
375      - updated output accordingly
376      - changed hs94.128x64x5 to use intial T from file rather than use the
377        random number generator
378    o add infrastructure in model routines for fizhi and gridalt packages
379  o change global_ocean.cs32x15 because of Pb with GM on CS-grid.  o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
380  o changes to permit hi-res, cubed-sphere, configuration  o changes to permit hi-res, cubed-sphere, configuration
381    - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F    - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F

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