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revision 1.297 by mlosch, Wed May 19 08:43:38 2004 UTC revision 1.396 by mlosch, Mon Nov 29 22:50:47 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 add another verification experiment that tests both the cfc-pkg and
7      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
8      reactive tendencies treated inline with regular timestepping
9    o testreport previously did a lousy job of comparing small numbers, so
10      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
11      implemented in the little c-progam tmp_cmpnum.c which is embedded in
12      testreport.
13    o ptracers_monitor: bug fix for MPI
14    
15    checkpoint56a_post
16    o GCHEM: finish reorganizating the package
17      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
18        (introduces another 3D-array for each passive tracer, but only if
19        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
20        gchemTendency is not needed because the timestep is done separately)
21      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
22      - GCHEM is now---more or less cleanly---separate from PTRACERS
23      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
24        so clear to me how that should be done in a general way.
25    o CFC: improve formatting of output in CFC_ATMOS
26    o PTRACERS:
27      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
28        that ALL experiments with ptracers enable can be checked. This makes
29        GCHEM_MONITOR obsolete.
30      - include a runtime parameter PTRACERS_monitorFreq that defaults to
31        monitorFreq
32      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
33    o add PTRACERS (PTR0[1-5]) to testreport output
34    o exf_check_range:
35      * default changed to .TRUE.
36      * will check values for niter0 if debLevA, every timestep if debLevB
37      * STOP in exf_check_range if 'out of range'
38      * range chosen generous to allow for potential extema
39      TBD: a version with stricter range
40           permitted range would be runtime parameters
41    o GMredi:
42      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
43      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
44      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
45    o GCHEM:
46      - move call to GCHEM_FORCING_SEP, so that it is now called before
47        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
48      - introduced a useGCHEM runtime flag and applied it everywhere.
49      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
50        this flag is now only visible within GCHEM-pkg routines.
51      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
52        be replaced by a 3D array that is computed before thermodynamics; for
53        this, the tracer ID iTracer had to be included into the parameter list
54        of ptracers_forcing
55      - set up forward_step to call gchem_forcing, that will replace
56        gchem_forcing_int in ptracers_forcing
57      - cleaning up
58    o small cleaning of exch2: remove files that are also in eesupp/src
59    
60    checkpoint56
61    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
62    o mnc: cleanup "full" files--fixes out-of-memory problem
63    o ECCO-GODAE
64      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
65      * fully merged and updated from SIO code
66        windstress sign change affects
67        - exf_inscal_[u/v]stress
68        - sign of xx_tau[u/v] adjustments
69        - signs in cost_scat
70      * ctrl_get_gen: avoid update of tau[u/v] for first few days
71      * natl_box_adjoint updated and compressed
72      * 2-level checkpoint switch added
73        (tested in EXP. 1 of natl_box_adjoint)
74      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
75    o SVD
76      * first complete, non-hacked version for SVD calculations
77      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
78        performed via direct access files admtlm_vector.it????
79        (via ctrl_[un]pack)
80      * optimcycle is used for ARPACK iteration counter
81        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
82      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
83        and add linear transforms where necessary
84      * controls are initial/final SST, SSS (can be extended; need to check
85        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
86    o mdsio: filename info to both stderr, stdout
87    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
88      from sign change
89    
90    checkpoint55j_post
91    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
92      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
93    o add consistent build directories and .cvsignore files to verification
94    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
95    o make all subroutines 30 or less characters in length for certain older
96      compilers to work (a thorough search only turns up two routines in
97      pkg/ptracers)
98    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
99      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
100    
101    checkpoint55i_post
102    o change arrays for total vertical diffusivity (2.D if explicit,
103      3.D if implicit) ; each ptracer uses its own background value.
104    o added mnc/NetCDF output capability to ocn_compon_interf
105      - added bits to verification/cpl_aim+ocn so that it can run on
106        ITRDA and other clusters without the mpirun "-wd" option
107    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
108      configuration
109    o give MNC the ability to create additional files rather than
110      exceeding a specified file size limit "MNC_MAX_FILESIZE"
111      - the default is just less than 2GB which is a practical limit
112        on many systems
113    o Compute the non-local term using either KPP vertical diffusivity (=default)
114       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
115    
116    checkpoint55h_post
117    o add verification test "vermix"
118    o remove all the *_ioinc flags and replace with the single global
119      outputTypesInclusive flag
120    o allow to set a vertical profile of vertical diffusivity for T & S
121    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
122    o useMNC moved from data.mnc to data.pkg
123    
124    checkpoint55g_post
125    o Renaming carbon AD experiments to comply with testreport conventions
126    o Updating adjoint of Held-Suarez hs94.1x64x5
127    o Fixing directives for non-ECCO forward_step, after ECCO directives
128      have been fixed to avoid recomp. of do_oceanic_phys
129      Works well for global_ocean.90x40x15,
130      but recomp. issue remains for carbon
131    o Updating adjoint output for natl_box_adjoint after
132      pkg/ecco has been modified (see taga c55d_post)
133    
134    checkpoint55f_post
135    o rename to timeave_init_fixed
136    
137    checkpoint55e_post
138    o some delicate re-shuffle of store directives to avoid one
139      extra call of do_oceanic_physics
140      affects ecco_the_main_loop.F, do_oceanic_physics.F
141      checkpoint_lev1_directives.h
142    o NB: this may break global_ocean adjoint temporarily,
143      but it is clear how to fix it. Will do later, need this now.
144    
145    checkpoint55d_post
146    o ECCO specific cost function terms (up-to-date with 1x1 runs)
147    o ecco_cost_weights is modified to 1x1 runs
148    o modifs to allow observations to be read in as
149      single file or yearly files
150    o enable to read exf forcing fields as either
151      single file or yearly files (flag useExfYearlyFields)
152    checkpoint55d_pre
153    
154    o switch between 2-level and 3-level checkpointing
155    o add ability of MNC to write local and "partial" (eg. 2D slices where
156      the full 3D field is never actually stored) arrays to NetCDF files
157      with the correct (that is, the complete multi-dimensional) set of
158      array indicies
159      - used in mom_vecinv() to write the diagFreq output
160      - tested (demonstrated) in verification/aim.5l_cs
161    o further mnc-ification
162      - add verification/lab_sea to the list with mnc setups
163      - fix undefined mnc v-names in cd_code
164      - add kpp to mnc output (both snapshot and timeave)
165    o non-hydrostatic code
166      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
167        in calc_gw.F
168      - defaults to viscAh
169      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
170        friction or Leith) in non-hydrostatic mode, as long as there is
171        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
172    o pkg/cost
173      extend simple cost functions to treat time mean quantities
174      (T,U,V) via cost_accumulate_state from cost_tile
175    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
176        be 2 times larger than the minimum size the advection scheme requires.
177        now get a perfect conservation of salt in advect_cs test-exp (updated)
178    o GGL90 (Gaspar's TKE mixed layer)
179      - add horizontal diffusion of TKE, requires exchanges in
180        do_fields_blocking_exchanges, horizontal diffusivity is zero by
181        default. In OPA there is no horizontal diffusion of TKE but the
182        mixing coefficients are computed from a horizontal average of TKE of
183        6 points or so. I think that diffusion has a little more physical
184        justification.
185      - clean up ggl90_calc in the hope of reducing memory usage (this hope
186        was in vain)
187      - mask tke-variable in ggl90_init
188    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
189    o fix biharmonic diffusion on CS-grid.
190    o more obcs stuff
191      - added obcs_external_fields_load as an alternative to the EXF-pkg option
192        for reading boundary values. This routine is called from
193        obcs_prescribe_read
194      - updated obcs_check
195      - changed sponge layer relaxation parameter units for days to seconds
196      - turned off sponge layer by default
197      - changed argument list of OBCS_CALC to myTime+deltaTclock
198      - fixed about 35 bugs in obcs_external_fields_load
199    
200    checkpoint55c_post
201    o obcs stuff
202      - new runtime flags useOBCSprescribe, useOBCSbalance
203      - re-arranged obcs_calc
204      - moved exf_getobcs to obcs_prescibe_read
205        obcs_prescibe_read is called after ORLANSKI stuff
206        and independent of it (executable can contain all).
207      - updated obcs_check
208      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
209        These may be necessary only if tangential velocities are
210        prescribed at OB, not sure, needs testing.
211    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
212      which simplifies the calls and passes the ifc check-bounds test
213    
214    checkpoint55b_post
215    o add a 2D scalar, Z location, exchange_2 routine.
216    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
217      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
218      affects advect_cs results (for the wrong reason): update output.txt
219    o use a more standard discretization for biharmonic viscosity ;
220     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
221      affects results of dome set-up: update output.txt
222    o fix gad_advection.F (CubedSphere part), back to version 1.23
223    o fix bug in mom_vi_del2uv.F (CubedSphere part).
224    
225    checkpoint55a_post
226    o merged code to
227      * prescribe/read time-dependent open boundaries
228        (works in conjunction with exf, cal)
229      * sponge layer code for open boundaries
230      * each boundary N/S/E/W now has its own CPP option
231        (healthy for the adjoint)
232    
233    checkpoint55
234    o up-to-date adjoint of previous breaks
235      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
236      - global_ocean_ebm: adjoint still needs fix (TLM ok)
237      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
238      - carbon: * remove tr1-related adjoint verification
239                * add ptracer as control variable
240    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
241      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
242    
243    checkpoint54f_post
244    o in verification/carbin/ remove experiment related to
245      ALLOW_PASSIVE_TRACER (array tr1 etc)
246      code_ad/ input_ad/ results_ad
247    
248    o add two new packages
249      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
250        + subject to optimization (memory)
251      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
252        + subject to reordering (many GOTOs in the original code)
253        + so far opps is called for every (i,j) point, and then operates in
254          the vertical; one may want to reorder the scheme in order operate in
255          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
256          fields)
257    o overhaul of IO so that we now have flags for MDSIO and/or MNC
258      - all verification tests compile and run with linux_ia32_g77
259      - defaults are compatible with current input files--nothing
260        should change if you were not previously using MNC
261      - MNC output has been added in numerous places (eg. timeave)
262        but there are still a few writes not yet do-able with MNC
263        (this is in progress)
264      - flags now allow for either/or/both use of MDSIO and MNC and
265        documentation will soon follow
266      - numerous small formatting cleanups for ProTeX
267    o add version info (via BUILD_INFO.h) to MNC and stdout
268    
269    checkpoint54e_post
270    o add two new packages
271      - pp81 (Packanowski and Philander, 1981), Richardson number and
272        stratification dependent mixing
273      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
274      - these scheme operate in a similar manner as KPP (without ghat, of
275        course), however there is only one diffusivity that is used for both
276        temperature and salinity (and passive tracers)ç
277    o add offline package
278    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
279      provided by Stephanie Dutkiewicz
280    o genmake2: add ability to search for C compilers and cleanup test output
281      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
282    
283    checkpoint54d_post
284    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
285    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
286      leading to additional shift by 5 days each year of integration
287       (i.e. leading to considerable offset over the years)
288    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
289    o start with no AB and no initial filtering (staggerTimeStep):
290      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
291    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
292      (external loading & cpl import/export stay in forward_step.F)
293    o update coupling interface to work with new staggerTimeStep
294    o change MDSIO ptracers_pickup.
295    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
296    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
297    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
298    
299    checkpoint54c_post
300    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
301      this affects (truncation error) output.txt of test-exp:
302       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
303    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
304    o change Qnet to always be the net heat flux, (+upward).
305      affects (truncation error) output of natl_box exp.: updated
306    o define the max number of passive tracers in PTRACERS_SIZE.h
307    o start to test mnc routinely in exp0
308    o add sea-ice loading (sIceLoad) as a new forcing field.
309    
310    checkpoint54b_post
311    o add testreport "-j JOBS" option for parallel builds (tested and pretty
312       impressive on Altix and Opteron systems)
313    o diagnostics can now write NetCDF files through the mnc package
314    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
315    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
316    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
317      affects (truncation error) output of lab_sea & natl_box exp.: updated
318    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
319    
320    checkpoint54a_post
321    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
322    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
323    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
324    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
325      + internal_wave (shift in writing cg2d_ini_res)
326    checkpoint54a_pre
327    
328    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
329      - modified verification/lab_sea and natl_box_adjoint accordingly
330    
331    checkpoint54
332    checkpoint53g_post
333    o prepare splitting of thermodynamics: store convect.counter in common block
334    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
335      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
336    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
337    o new parameter "nShapS": allow to treat differently S from T (nShapT)
338    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
339    o restore adjointability
340    
341    checkpoint53f_post
342    o modifications that affect AIM experiment results (update output.txt):
343      - no advection of S at top interface Nr (pkg/generic_advdiff)
344      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
345    o AIM pkg:
346      - include stability function into surf.Flux derivative relative to Tsurf
347      - calculate clear-sky radiation & surface temp. change (for diagnostics)
348    
349    checkpoint53e_post
350    o merged cylindrical coord configuration
351    o added rotating_tank experiment
352    checkpoint53e_pre
353    
354    checkpoint53d_post
355    o faulks upgraded: re-generate output.txt that have changed:
356       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
357    o Added Bryan and Lewis, 1979, vertical diffusivity profile
358    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
359    o added Sadourny discretization of Coriolis
360      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
361      - re-enabled use of omega3 (useAbsVorticity)
362    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
363      vector-invariant equations
364      - note: does *NOT* yet use same variable visc. for no-slip BC's.
365    o recoded the lateral boundary conditions for non-hydrostatic w, this time
366      hopefully without new bugs
367      - still to do: biharmonic friction for non-hydrostatic w
368    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
369    o regenerated output for global_ocean_ebm (using -ieee)
370    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
371      of mom_common/
372      - simple re-arrangement of instructions within computing loop
373    checkpoint53d_pre
374    
375    checkpoint53c_post
376    o new version of coupler for AIM+thSIce and Ocean models
377     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
378     - land: change Evaporation of snow
379     - aim with thSIce: fix bug in snow-precip.
380  o changes to calc_gw.F  o changes to calc_gw.F
381   - bug fix for w^2 term near the bottom boundary   - bug fix for w^2 term near the bottom boundary
382   - (hopefully) improve the lateral slip boundary condtions for use with   - (hopefully) improve the lateral slip boundary condtions for use with
# Line 10  o changes to calc_gw.F Line 384  o changes to calc_gw.F
384    - because the bug fix changes two verification experiments anyway (exp5    - because the bug fix changes two verification experiments anyway (exp5
385      and plume on slope), change the lateral boundary condition from half slip      and plume on slope), change the lateral boundary condition from half slip
386      to the value of no_slip_sides      to the value of no_slip_sides
387    o ebm package wasnt quite up to the parallel task. Fixed that.
388    o Adjoint of EBM package + verification
389      * TLM OK
390      * ADM not sufficient accuracy yet (needs further testing)
391    
392  checkpoint53b_post  checkpoint53b_post
393  o Commiting new energy balance model to repository  o Commiting new energy balance model to repository

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