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revision 1.280 by mlosch, Mon Apr 19 22:30:46 2004 UTC revision 1.376 by jmc, Thu Oct 28 01:22:02 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint55g_post
7    o change arrays for total vertical diffusivity (2.D if explicit,
8      3.D if implicit) ; each ptracer uses its own background value.
9    o added mnc/NetCDF output capability to ocn_compon_interf
10      - added bits to verification/cpl_aim+ocn so that it can run on
11        ITRDA and other clusters without the mpirun "-wd" option
12    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
13      configuration
14    o give MNC the ability to create additional files rather than
15      exceeding a specified file size limit "MNC_MAX_FILESIZE"
16      - the default is just less than 2GB which is a practical limit
17        on many systems
18    o Compute the non-local term using either KPP vertical diffusivity (=default)
19       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
20    
21    checkpoint55h_post
22    o add verification test "vermix"
23    o remove all the *_ioinc flags and replace with the single global
24      outputTypesInclusive flag
25    o allow to set a vertical profile of vertical diffusivity for T & S
26    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
27    o useMNC moved from data.mnc to data.pkg
28    
29    checkpoint55g_post
30    o Renaming carbon AD experiments to comply with testreport conventions
31    o Updating adjoint of Held-Suarez hs94.1x64x5
32    o Fixing directives for non-ECCO forward_step, after ECCO directives
33      have been fixed to avoid recomp. of do_oceanic_phys
34      Works well for global_ocean.90x40x15,
35      but recomp. issue remains for carbon
36    o Updating adjoint output for natl_box_adjoint after
37      pkg/ecco has been modified (see taga c55d_post)
38    
39    checkpoint55f_post
40    o rename to timeave_init_fixed
41    
42    checkpoint55e_post
43    o some delicate re-shuffle of store directives to avoid one
44      extra call of do_oceanic_physics
45      affects ecco_the_main_loop.F, do_oceanic_physics.F
46      checkpoint_lev1_directives.h
47    o NB: this may break global_ocean adjoint temporarily,
48      but it is clear how to fix it. Will do later, need this now.
49    
50    checkpoint55d_post
51    o ECCO specific cost function terms (up-to-date with 1x1 runs)
52    o ecco_cost_weights is modified to 1x1 runs
53    o modifs to allow observations to be read in as
54      single file or yearly files
55    o enable to read exf forcing fields as either
56      single file or yearly files (flag useExfYearlyFields)
57    checkpoint55d_pre
58    
59    o switch between 2-level and 3-level checkpointing
60    o add ability of MNC to write local and "partial" (eg. 2D slices where
61      the full 3D field is never actually stored) arrays to NetCDF files
62      with the correct (that is, the complete multi-dimensional) set of
63      array indicies
64      - used in mom_vecinv() to write the diagFreq output
65      - tested (demonstrated) in verification/aim.5l_cs
66    o further mnc-ification
67      - add verification/lab_sea to the list with mnc setups
68      - fix undefined mnc v-names in cd_code
69      - add kpp to mnc output (both snapshot and timeave)
70    o non-hydrostatic code
71      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
72        in calc_gw.F
73      - defaults to viscAh
74      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
75        friction or Leith) in non-hydrostatic mode, as long as there is
76        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
77    o pkg/cost
78      extend simple cost functions to treat time mean quantities
79      (T,U,V) via cost_accumulate_state from cost_tile
80    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
81        be 2 times larger than the minimum size the advection scheme requires.
82        now get a perfect conservation of salt in advect_cs test-exp (updated)
83    o GGL90 (Gaspar's TKE mixed layer)
84      - add horizontal diffusion of TKE, requires exchanges in
85        do_fields_blocking_exchanges, horizontal diffusivity is zero by
86        default. In OPA there is no horizontal diffusion of TKE but the
87        mixing coefficients are computed from a horizontal average of TKE of
88        6 points or so. I think that diffusion has a little more physical
89        justification.
90      - clean up ggl90_calc in the hope of reducing memory usage (this hope
91        was in vain)
92      - mask tke-variable in ggl90_init
93    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
94    o fix biharmonic diffusion on CS-grid.
95    o more obcs stuff
96      - added obcs_external_fields_load as an alternative to the EXF-pkg option
97        for reading boundary values. This routine is called from
98        obcs_prescribe_read
99      - updated obcs_check
100      - changed sponge layer relaxation parameter units for days to seconds
101      - turned off sponge layer by default
102      - changed argument list of OBCS_CALC to myTime+deltaTclock
103      - fixed about 35 bugs in obcs_external_fields_load
104    
105    checkpoint55c_post
106    o obcs stuff
107      - new runtime flags useOBCSprescribe, useOBCSbalance
108      - re-arranged obcs_calc
109      - moved exf_getobcs to obcs_prescibe_read
110        obcs_prescibe_read is called after ORLANSKI stuff
111        and independent of it (executable can contain all).
112      - updated obcs_check
113      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
114        These may be necessary only if tangential velocities are
115        prescribed at OB, not sure, needs testing.
116    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
117      which simplifies the calls and passes the ifc check-bounds test
118    
119    checkpoint55b_post
120    o add a 2D scalar, Z location, exchange_2 routine.
121    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
122      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
123      affects advect_cs results (for the wrong reason): update output.txt
124    o use a more standard discretization for biharmonic viscosity ;
125     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
126      affects results of dome set-up: update output.txt
127    o fix gad_advection.F (CubedSphere part), back to version 1.23
128    o fix bug in mom_vi_del2uv.F (CubedSphere part).
129    
130    checkpoint55a_post
131    o merged code to
132      * prescribe/read time-dependent open boundaries
133        (works in conjunction with exf, cal)
134      * sponge layer code for open boundaries
135      * each boundary N/S/E/W now has its own CPP option
136        (healthy for the adjoint)
137    
138    checkpoint55
139    o up-to-date adjoint of previous breaks
140      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
141      - global_ocean_ebm: adjoint still needs fix (TLM ok)
142      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
143      - carbon: * remove tr1-related adjoint verification
144                * add ptracer as control variable
145    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
146      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
147    
148    checkpoint54f_post
149    o in verification/carbin/ remove experiment related to
150      ALLOW_PASSIVE_TRACER (array tr1 etc)
151      code_ad/ input_ad/ results_ad
152    
153    o add two new packages
154      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
155        + subject to optimization (memory)
156      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
157        + subject to reordering (many GOTOs in the original code)
158        + so far opps is called for every (i,j) point, and then operates in
159          the vertical; one may want to reorder the scheme in order operate in
160          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
161          fields)
162    o overhaul of IO so that we now have flags for MDSIO and/or MNC
163      - all verification tests compile and run with linux_ia32_g77
164      - defaults are compatible with current input files--nothing
165        should change if you were not previously using MNC
166      - MNC output has been added in numerous places (eg. timeave)
167        but there are still a few writes not yet do-able with MNC
168        (this is in progress)
169      - flags now allow for either/or/both use of MDSIO and MNC and
170        documentation will soon follow
171      - numerous small formatting cleanups for ProTeX
172    o add version info (via BUILD_INFO.h) to MNC and stdout
173    
174    checkpoint54e_post
175    o add two new packages
176      - pp81 (Packanowski and Philander, 1981), Richardson number and
177        stratification dependent mixing
178      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
179      - these scheme operate in a similar manner as KPP (without ghat, of
180        course), however there is only one diffusivity that is used for both
181        temperature and salinity (and passive tracers)ç
182    o add offline package
183    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
184      provided by Stephanie Dutkiewicz
185    o genmake2: add ability to search for C compilers and cleanup test output
186      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
187    
188    checkpoint54d_post
189    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
190    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
191      leading to additional shift by 5 days each year of integration
192       (i.e. leading to considerable offset over the years)
193    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
194    o start with no AB and no initial filtering (staggerTimeStep):
195      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
196    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
197      (external loading & cpl import/export stay in forward_step.F)
198    o update coupling interface to work with new staggerTimeStep
199    o change MDSIO ptracers_pickup.
200    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
201    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
202    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
203    
204    checkpoint54c_post
205    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
206      this affects (truncation error) output.txt of test-exp:
207       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
208    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
209    o change Qnet to always be the net heat flux, (+upward).
210      affects (truncation error) output of natl_box exp.: updated
211    o define the max number of passive tracers in PTRACERS_SIZE.h
212    o start to test mnc routinely in exp0
213    o add sea-ice loading (sIceLoad) as a new forcing field.
214    
215    checkpoint54b_post
216    o add testreport "-j JOBS" option for parallel builds (tested and pretty
217       impressive on Altix and Opteron systems)
218    o diagnostics can now write NetCDF files through the mnc package
219    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
220    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
221    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
222      affects (truncation error) output of lab_sea & natl_box exp.: updated
223    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
224    
225    checkpoint54a_post
226    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
227    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
228    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
229    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
230      + internal_wave (shift in writing cg2d_ini_res)
231    checkpoint54a_pre
232    
233    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
234      - modified verification/lab_sea and natl_box_adjoint accordingly
235    
236    checkpoint54
237    checkpoint53g_post
238    o prepare splitting of thermodynamics: store convect.counter in common block
239    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
240      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
241    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
242    o new parameter "nShapS": allow to treat differently S from T (nShapT)
243    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
244    o restore adjointability
245    
246    checkpoint53f_post
247    o modifications that affect AIM experiment results (update output.txt):
248      - no advection of S at top interface Nr (pkg/generic_advdiff)
249      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
250    o AIM pkg:
251      - include stability function into surf.Flux derivative relative to Tsurf
252      - calculate clear-sky radiation & surface temp. change (for diagnostics)
253    
254    checkpoint53e_post
255    o merged cylindrical coord configuration
256    o added rotating_tank experiment
257    checkpoint53e_pre
258    
259    checkpoint53d_post
260    o faulks upgraded: re-generate output.txt that have changed:
261       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
262    o Added Bryan and Lewis, 1979, vertical diffusivity profile
263    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
264    o added Sadourny discretization of Coriolis
265      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
266      - re-enabled use of omega3 (useAbsVorticity)
267    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
268      vector-invariant equations
269      - note: does *NOT* yet use same variable visc. for no-slip BC's.
270    o recoded the lateral boundary conditions for non-hydrostatic w, this time
271      hopefully without new bugs
272      - still to do: biharmonic friction for non-hydrostatic w
273    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
274    o regenerated output for global_ocean_ebm (using -ieee)
275    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
276      of mom_common/
277      - simple re-arrangement of instructions within computing loop
278    checkpoint53d_pre
279    
280    checkpoint53c_post
281    o new version of coupler for AIM+thSIce and Ocean models
282     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
283     - land: change Evaporation of snow
284     - aim with thSIce: fix bug in snow-precip.
285    o changes to calc_gw.F
286     - bug fix for w^2 term near the bottom boundary
287     - (hopefully) improve the lateral slip boundary condtions for use with
288        partial/looped cells
289      - because the bug fix changes two verification experiments anyway (exp5
290        and plume on slope), change the lateral boundary condition from half slip
291        to the value of no_slip_sides
292    o ebm package wasnt quite up to the parallel task. Fixed that.
293    o Adjoint of EBM package + verification
294      * TLM OK
295      * ADM not sufficient accuracy yet (needs further testing)
296    
297    checkpoint53b_post
298    o Commiting new energy balance model to repository
299      * package is pkg/ebm
300      * verif. is verification/global_ocean_ebm
301      * references are in ebm_driver.F
302    C      * X. Wang, P. Stone and J. Marotzke, 1999:
303    C        Global thermohaline circulation. Part I:
304    C        Sensitivity to atmospheric moisture transport.
305    C        J. Climate 12(1), 71-82
306    C      * X. Wang, P. Stone and J. Marotzke, 1999:
307    C        Global thermohaline circulation. Part II:
308    C        Sensitivity with interactive transport.
309    C        J. Climate 12(1), 83-91
310    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
311    C        Destabilization of the thermohaline circulation
312    C        by atmospheric eddy transports.
313    C        J. Climate 7(12), 1870-1882
314    o Will need long integration testing.
315    checkpoint53b_pre
316    
317    o created pkg/mom_common in preparation for variable viscosity code
318    o renamed and split ini_mnc_io
319    o pkg/land: only liquid water can diffuse or run-off
320    o AIM using land: soil wetness availability account for snow
321    o added printMapIncludesZeros to EEPARMS namelist
322    
323    checkpoint53a_post
324    o restore TAMC compatiility for exf_constants.h
325      (no usage of _d in .h)
326    o Additional storing in KPP in an attempt to fix
327      TAMC problem with adjoint of KPP code.
328      (no success...)
329      Identical code works fine with TAF.
330    o Fixed verification/natl_box_adjoint experiments.
331      Initial conditions for Experiments 4 and 5 are now
332      set to "SEAICE_initialHEFF=0", which is more reasonable,
333      and hence gives results closer to that of Experiment 2.
334      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
335    
336    checkpoint53
337    o stable checkpoint with up to date adjoint
338      TLM tests only run for 1st grdchk at the moment. Its unclear if
339      this is a code problem or a problem with resetting code for g_
340      variables that is being autogenerated wrong.
341      Otherwise:
342       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
343       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
344         are both still in chaos following their security messes.
345    
346    checkpoint52n_post
347    o various build (mostly genmake2) changes including:
348      - ability to build/run more easily within Cygwin and MacOS X
349      - more complicated Makefiles with a stronger dependence on Gnu Make
350    o pkg/seaice modifications
351      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
352        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
353        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
354      - changed proxy for geostrophic velocity and updated
355        verification/lab_sea/results/* accordingly
356      - removed ADI dynamic solver from pkg/seaice
357      - replaced all occurrences of 1/CSTICE or 1/CSUICE
358        they caused a segmentation fault under certain circumstances
359      - removed unused field WATR
360    o bug fix in exf-package:
361      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
362         now reflect that.
363    o small fixes in the cal-package:
364      - set reference date to first of January for the 'model'-calendar
365      - failing of cal_CheckDate in cal_FullDate now actually results in a
366        warning
367  o small modifications in exf-package to increase flexibility:  o small modifications in exf-package to increase flexibility:
368    - change climtempfreeze from a constant to a runtime parameter that    - change climtempfreeze from a constant to a runtime parameter that
369      is specified in data.exf_clim (default = -1.9)      is specified in data.exf_clim (default = -1.9)

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