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revision 1.311 by afe, Thu Jun 24 20:27:32 2004 UTC revision 1.405 by dimitri, Mon Dec 6 06:08:24 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 switch back to "sflux = sflux - runoff" in exf_getforcing.F
7    o implement Implicit Vertical advection for pTracers
8    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
9      (implemented also for implicit vertical diffusion & advection)
10    o OBCS: extend application of tracer open boundary conditions
11      to a strip beyond the boundary of width Olx/Oly
12    o add call monitor to TAF set of required calls (flow directives)
13      and include in natl_box_adjoint
14    o untangle a few ifdefs related to cost, ctrl, autodiff
15      untangel a few ALLOW_ECCO_OPTIMIZATION
16    
17    checkpoint56c_post
18    o OBCS as control variables
19      - update ctrl_ad_diff.list, obcs_ad_diff.list
20      - remove balance of obcs controls from default
21      - fix index bug nobcs in ctrl_init
22      - fix dummy fields filen in ctrl_pack
23      - add dummy weights for obcs
24    o lsopt: comment out fort.94 output
25    o optim:
26      - remove unnecessary header files
27      - adjusted namelists
28      - add xerbla.F to Makefile
29    o exf:
30      - multiple modifications of exf_check_range
31      - unit change in exf_init_runoff from [m/year] to [m/s]
32    o mdsio:
33      - i/o-vector change debugLevel from debLevA to debLevB
34    
35    checkpoint56b_post
36    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
37      is called from DO_THE_MODEL_IO
38      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
39      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
40      - clean up PTRACERS_WRITE_TIMEAVE a little
41    o add another verification experiment that tests both the cfc-pkg and
42      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
43      reactive tendencies treated inline with regular timestepping
44    o testreport previously did a lousy job of comparing small numbers, so
45      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
46      implemented in the little c-progam tmp_cmpnum.c which is embedded in
47      testreport.
48    o ptracers_monitor: bug fix for MPI
49    
50    checkpoint56a_post
51    o GCHEM: finish reorganizating the package
52      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
53        (introduces another 3D-array for each passive tracer, but only if
54        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
55        gchemTendency is not needed because the timestep is done separately)
56      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
57      - GCHEM is now---more or less cleanly---separate from PTRACERS
58      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
59        so clear to me how that should be done in a general way.
60    o CFC: improve formatting of output in CFC_ATMOS
61    o PTRACERS:
62      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
63        that ALL experiments with ptracers enable can be checked. This makes
64        GCHEM_MONITOR obsolete.
65      - include a runtime parameter PTRACERS_monitorFreq that defaults to
66        monitorFreq
67      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
68    o add PTRACERS (PTR0[1-5]) to testreport output
69    o exf_check_range:
70      * default changed to .TRUE.
71      * will check values for niter0 if debLevA, every timestep if debLevB
72      * STOP in exf_check_range if 'out of range'
73      * range chosen generous to allow for potential extema
74      TBD: a version with stricter range
75           permitted range would be runtime parameters
76    o GMredi:
77      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
78      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
79      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
80    o GCHEM:
81      - move call to GCHEM_FORCING_SEP, so that it is now called before
82        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
83      - introduced a useGCHEM runtime flag and applied it everywhere.
84      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
85        this flag is now only visible within GCHEM-pkg routines.
86      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
87        be replaced by a 3D array that is computed before thermodynamics; for
88        this, the tracer ID iTracer had to be included into the parameter list
89        of ptracers_forcing
90      - set up forward_step to call gchem_forcing, that will replace
91        gchem_forcing_int in ptracers_forcing
92      - cleaning up
93    o small cleaning of exch2: remove files that are also in eesupp/src
94    
95    checkpoint56
96    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
97    o mnc: cleanup "full" files--fixes out-of-memory problem
98    o ECCO-GODAE
99      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
100      * fully merged and updated from SIO code
101        windstress sign change affects
102        - exf_inscal_[u/v]stress
103        - sign of xx_tau[u/v] adjustments
104        - signs in cost_scat
105      * ctrl_get_gen: avoid update of tau[u/v] for first few days
106      * natl_box_adjoint updated and compressed
107      * 2-level checkpoint switch added
108        (tested in EXP. 1 of natl_box_adjoint)
109      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
110    o SVD
111      * first complete, non-hacked version for SVD calculations
112      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
113        performed via direct access files admtlm_vector.it????
114        (via ctrl_[un]pack)
115      * optimcycle is used for ARPACK iteration counter
116        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
117      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
118        and add linear transforms where necessary
119      * controls are initial/final SST, SSS (can be extended; need to check
120        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
121    o mdsio: filename info to both stderr, stdout
122    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
123      from sign change
124    
125    checkpoint55j_post
126    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
127      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
128    o add consistent build directories and .cvsignore files to verification
129    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
130    o make all subroutines 30 or less characters in length for certain older
131      compilers to work (a thorough search only turns up two routines in
132      pkg/ptracers)
133    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
134      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
135    
136    checkpoint55i_post
137    o change arrays for total vertical diffusivity (2.D if explicit,
138      3.D if implicit) ; each ptracer uses its own background value.
139    o added mnc/NetCDF output capability to ocn_compon_interf
140      - added bits to verification/cpl_aim+ocn so that it can run on
141        ITRDA and other clusters without the mpirun "-wd" option
142    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
143      configuration
144    o give MNC the ability to create additional files rather than
145      exceeding a specified file size limit "MNC_MAX_FILESIZE"
146      - the default is just less than 2GB which is a practical limit
147        on many systems
148    o Compute the non-local term using either KPP vertical diffusivity (=default)
149       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
150    
151    checkpoint55h_post
152    o add verification test "vermix"
153    o remove all the *_ioinc flags and replace with the single global
154      outputTypesInclusive flag
155    o allow to set a vertical profile of vertical diffusivity for T & S
156    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
157    o useMNC moved from data.mnc to data.pkg
158    
159    checkpoint55g_post
160    o Renaming carbon AD experiments to comply with testreport conventions
161    o Updating adjoint of Held-Suarez hs94.1x64x5
162    o Fixing directives for non-ECCO forward_step, after ECCO directives
163      have been fixed to avoid recomp. of do_oceanic_phys
164      Works well for global_ocean.90x40x15,
165      but recomp. issue remains for carbon
166    o Updating adjoint output for natl_box_adjoint after
167      pkg/ecco has been modified (see taga c55d_post)
168    
169    checkpoint55f_post
170    o rename to timeave_init_fixed
171    
172    checkpoint55e_post
173    o some delicate re-shuffle of store directives to avoid one
174      extra call of do_oceanic_physics
175      affects ecco_the_main_loop.F, do_oceanic_physics.F
176      checkpoint_lev1_directives.h
177    o NB: this may break global_ocean adjoint temporarily,
178      but it is clear how to fix it. Will do later, need this now.
179    
180    checkpoint55d_post
181    o ECCO specific cost function terms (up-to-date with 1x1 runs)
182    o ecco_cost_weights is modified to 1x1 runs
183    o modifs to allow observations to be read in as
184      single file or yearly files
185    o enable to read exf forcing fields as either
186      single file or yearly files (flag useExfYearlyFields)
187    checkpoint55d_pre
188    
189    o switch between 2-level and 3-level checkpointing
190    o add ability of MNC to write local and "partial" (eg. 2D slices where
191      the full 3D field is never actually stored) arrays to NetCDF files
192      with the correct (that is, the complete multi-dimensional) set of
193      array indicies
194      - used in mom_vecinv() to write the diagFreq output
195      - tested (demonstrated) in verification/aim.5l_cs
196    o further mnc-ification
197      - add verification/lab_sea to the list with mnc setups
198      - fix undefined mnc v-names in cd_code
199      - add kpp to mnc output (both snapshot and timeave)
200    o non-hydrostatic code
201      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
202        in calc_gw.F
203      - defaults to viscAh
204      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
205        friction or Leith) in non-hydrostatic mode, as long as there is
206        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
207    o pkg/cost
208      extend simple cost functions to treat time mean quantities
209      (T,U,V) via cost_accumulate_state from cost_tile
210    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
211        be 2 times larger than the minimum size the advection scheme requires.
212        now get a perfect conservation of salt in advect_cs test-exp (updated)
213    o GGL90 (Gaspar's TKE mixed layer)
214      - add horizontal diffusion of TKE, requires exchanges in
215        do_fields_blocking_exchanges, horizontal diffusivity is zero by
216        default. In OPA there is no horizontal diffusion of TKE but the
217        mixing coefficients are computed from a horizontal average of TKE of
218        6 points or so. I think that diffusion has a little more physical
219        justification.
220      - clean up ggl90_calc in the hope of reducing memory usage (this hope
221        was in vain)
222      - mask tke-variable in ggl90_init
223    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
224    o fix biharmonic diffusion on CS-grid.
225    o more obcs stuff
226      - added obcs_external_fields_load as an alternative to the EXF-pkg option
227        for reading boundary values. This routine is called from
228        obcs_prescribe_read
229      - updated obcs_check
230      - changed sponge layer relaxation parameter units for days to seconds
231      - turned off sponge layer by default
232      - changed argument list of OBCS_CALC to myTime+deltaTclock
233      - fixed about 35 bugs in obcs_external_fields_load
234    
235    checkpoint55c_post
236    o obcs stuff
237      - new runtime flags useOBCSprescribe, useOBCSbalance
238      - re-arranged obcs_calc
239      - moved exf_getobcs to obcs_prescibe_read
240        obcs_prescibe_read is called after ORLANSKI stuff
241        and independent of it (executable can contain all).
242      - updated obcs_check
243      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
244        These may be necessary only if tangential velocities are
245        prescribed at OB, not sure, needs testing.
246    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
247      which simplifies the calls and passes the ifc check-bounds test
248    
249    checkpoint55b_post
250    o add a 2D scalar, Z location, exchange_2 routine.
251    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
252      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
253      affects advect_cs results (for the wrong reason): update output.txt
254    o use a more standard discretization for biharmonic viscosity ;
255     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
256      affects results of dome set-up: update output.txt
257    o fix gad_advection.F (CubedSphere part), back to version 1.23
258    o fix bug in mom_vi_del2uv.F (CubedSphere part).
259    
260    checkpoint55a_post
261    o merged code to
262      * prescribe/read time-dependent open boundaries
263        (works in conjunction with exf, cal)
264      * sponge layer code for open boundaries
265      * each boundary N/S/E/W now has its own CPP option
266        (healthy for the adjoint)
267    
268    checkpoint55
269    o up-to-date adjoint of previous breaks
270      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
271      - global_ocean_ebm: adjoint still needs fix (TLM ok)
272      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
273      - carbon: * remove tr1-related adjoint verification
274                * add ptracer as control variable
275    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
276      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
277    
278    checkpoint54f_post
279    o in verification/carbin/ remove experiment related to
280      ALLOW_PASSIVE_TRACER (array tr1 etc)
281      code_ad/ input_ad/ results_ad
282    
283    o add two new packages
284      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
285        + subject to optimization (memory)
286      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
287        + subject to reordering (many GOTOs in the original code)
288        + so far opps is called for every (i,j) point, and then operates in
289          the vertical; one may want to reorder the scheme in order operate in
290          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
291          fields)
292    o overhaul of IO so that we now have flags for MDSIO and/or MNC
293      - all verification tests compile and run with linux_ia32_g77
294      - defaults are compatible with current input files--nothing
295        should change if you were not previously using MNC
296      - MNC output has been added in numerous places (eg. timeave)
297        but there are still a few writes not yet do-able with MNC
298        (this is in progress)
299      - flags now allow for either/or/both use of MDSIO and MNC and
300        documentation will soon follow
301      - numerous small formatting cleanups for ProTeX
302    o add version info (via BUILD_INFO.h) to MNC and stdout
303    
304    checkpoint54e_post
305    o add two new packages
306      - pp81 (Packanowski and Philander, 1981), Richardson number and
307        stratification dependent mixing
308      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
309      - these scheme operate in a similar manner as KPP (without ghat, of
310        course), however there is only one diffusivity that is used for both
311        temperature and salinity (and passive tracers)ç
312    o add offline package
313    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
314      provided by Stephanie Dutkiewicz
315    o genmake2: add ability to search for C compilers and cleanup test output
316      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
317    
318    checkpoint54d_post
319    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
320    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
321      leading to additional shift by 5 days each year of integration
322       (i.e. leading to considerable offset over the years)
323    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
324    o start with no AB and no initial filtering (staggerTimeStep):
325      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
326    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
327      (external loading & cpl import/export stay in forward_step.F)
328    o update coupling interface to work with new staggerTimeStep
329    o change MDSIO ptracers_pickup.
330    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
331    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
332    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
333    
334    checkpoint54c_post
335    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
336      this affects (truncation error) output.txt of test-exp:
337       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
338    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
339    o change Qnet to always be the net heat flux, (+upward).
340      affects (truncation error) output of natl_box exp.: updated
341    o define the max number of passive tracers in PTRACERS_SIZE.h
342    o start to test mnc routinely in exp0
343    o add sea-ice loading (sIceLoad) as a new forcing field.
344    
345    checkpoint54b_post
346    o add testreport "-j JOBS" option for parallel builds (tested and pretty
347       impressive on Altix and Opteron systems)
348    o diagnostics can now write NetCDF files through the mnc package
349    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
350    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
351    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
352      affects (truncation error) output of lab_sea & natl_box exp.: updated
353    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
354    
355    checkpoint54a_post
356    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
357    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
358    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
359    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
360      + internal_wave (shift in writing cg2d_ini_res)
361    checkpoint54a_pre
362    
363    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
364      - modified verification/lab_sea and natl_box_adjoint accordingly
365    
366    checkpoint54
367    checkpoint53g_post
368    o prepare splitting of thermodynamics: store convect.counter in common block
369    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
370      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
371    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
372    o new parameter "nShapS": allow to treat differently S from T (nShapT)
373    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
374    o restore adjointability
375    
376    checkpoint53f_post
377    o modifications that affect AIM experiment results (update output.txt):
378      - no advection of S at top interface Nr (pkg/generic_advdiff)
379      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
380    o AIM pkg:
381      - include stability function into surf.Flux derivative relative to Tsurf
382      - calculate clear-sky radiation & surface temp. change (for diagnostics)
383    
384  checkpoint53e_post  checkpoint53e_post
385  o merged cylindrical coord configuration  o merged cylindrical coord configuration
386  o added rotating_tank experiment  o added rotating_tank experiment

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