/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.685 by baylor, Thu Jun 22 19:39:21 2006 UTC revision 1.935 by dimitri, Thu Jan 10 23:32:15 2008 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice/seaice_growth.F: use a different time constant for freezing
8      ice due to supercooled sea water, hardwired to SEAICE_deltaTtherm/0.1
9    o gad_som : fix flux output (& diagnostics) to have same units as other
10      advection scheme fluxes (was previously multiplied by deltaT).
11    o added verification/seaice_obcs both to test seaice open boundaries
12      and to provide an example matlab scrpt for generating them
13    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
14    o pkg/salt_plume: clean up salt_plume_frac.F to
15      remove redundancy in PlumeMethod 1 and 4
16    o pkg/kpp: added saltplume diagnostics
17    o pkg/obcs and pkg/seaice:
18      - do not set uice and vice to zero when OB*icefile are unspecified
19      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
20      - moved seaice tracer obcs after call to seaice_growth
21    o pkg/salt_plume: added various options for salt plume depth
22      criterion and for vertical distribution of the salt
23    
24    checkpoint59l
25    o pkg/ptracers: new version of ptracers pickup:
26      read meta file and write only fields which are needed to restart.
27      ( same logic as main pickup file ; also using pickupStrictlyMatch )
28    o pkg/seaice:
29      - add timescale for melting due to warm mixed layer as a means of
30        setting SEAICE_availHeatFrac more conveniently
31      - add a CPP-flag/runtime parameter check for flooding algorithm
32      - reformulated availHeat in seaice_growth.F to be independent of AREA
33    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
34      unit changes
35    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
36    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
37      SX vector computer.
38    o pkg/seaice:
39      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
40        seaice forcing fields can now be read only through pkg/exf
41      - removed some unused halos
42    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
43    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
44      or U/VICE from U/VWIND before computing U/VSTRESS
45    
46    checkpoint59k
47    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
48      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
49    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
50      all experiments pass when compile with un-initialised var. checking option.
51    o added pkg/salt_plume
52    o script to test restart (for now, in MITgcm_contrib/jmc_script)
53    o pkg/seaice: new read/write pickup version.
54      read meta file and write only fields which are needed to restart.
55      ( same logic as main pickup file ; also using pickupStrictlyMatch )
56    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
57    o lab_sea.hb87: modify the domain & update output.hb87.txt :
58      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
59      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
60      process. Fixed here by closing the domain at the Northern boundary.
61    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
62    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
63      a set of consecutive levels in/from a 3-D array.
64    o pkg/ptracers:
65      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
66      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
67    
68    checkpoint59j
69    o in pkgs: dic, obcs, offline, rbcs:
70      standard way to compute coeff. for time interpolation between 2 time reccords
71      which retains full precision (& make results less dependent on compiler).
72      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
73    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
74      packages instead of reading ice cover and wind speed separately
75    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
76     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
77      to allow to compile customized code before the update)
78    o cleaning-up:
79      - fix CPP instruction syntax in pkg/obcs
80      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
81        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
82      - fix some threads issue in IO parts.
83    o pkg/dic:
84      - add tons of "_d 0" (--> much better testreports !)
85       and then update outputs of tutorial_global_oce_biogeo
86    o pkg/mom_fluxform:
87      add a special version of momentum advection intended to conserve momentum
88      next to a bathymetry step or a coastline edge. (default = off = #undef)
89    o new read/write pickup version:
90      - for now, only implemented for main (mdsio) pickup file.
91      - write out only what is needed to restart; merge pickup_nh , pickup_ph
92        and main pickup together.
93      - read meta file; read only what is needed to restart; stop if a field
94        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
95        if it make sense (even if the restart is not perfect).
96      - if no meta file, assume that pickup to read corresponds exactly to
97        a pickup that would currently be written.
98      - read pickup written in the old format (until checkpoint59i) if it
99        recognizes an old meta file (no field-list).
100      - add a meta file in exp. which starts from a pickup: 2 cases:
101        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
102         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
103        b) a meta file describing the content of the associated pickup file
104         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
105    o pkg/mdsio & pkg/rw:
106      - new routine to read a meta file ; new set of routine to read
107        Multiple-fields file (with meta file).
108    o added open boundary conditions capability for seaice
109        HSNOW, HSALT, UICE, and VICE
110    
111    checkpoint59i
112    o adjoint:
113      * fix multiDimAdvection adjoint
114        (partial recomputation problem by TAF for fVerT(:,:,kDown)
115        and comlev1 size definition (maxpass vs. max. number of tracers)
116      * verification/global_ocean.90x45x15 adjoint now tests
117        NLFS and multiDimAdvection using DST3 (=30)
118      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
119    o pkg/kpp: add "_d 0" to real constant (if missing);
120      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
121      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
122    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
123      for internal parameters related to restart process (formerly from PARAMS.h)
124      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
125    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
126      as argument. (only atm2d & obcs write_pickup have not yet been updated)
127    o pkg/monitor:
128      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
129      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
130      - account for deep Atmosphere factor and density factor (anelastic)
131    o added open boundary conditions capability for seaice HEFF and AREA
132    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
133      thermodynamics
134      - requires a little reorganization, which affects the testreport results
135        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
136        so that now the conservative form is tested
137      - add a few comments
138    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
139    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
140    o add new diagnostics to seaice: advective, diffusive fluxes (only for
141      multidim-advection, for scheme 2 they are not filled) and transports,
142      thermodynamic growth rates
143    o change units of EmPmR (inside the code, + within coupling interface)
144      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
145      Affects results @ truncation level (cg2d match) and update output of
146       experiments: lab_sea(6), global_ocean.90x40x15(10),
147      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
148      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
149      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
150      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
151    
152    checkpoint59h
153    o pkg/exf:
154      - improve vectorization by moving if-statement out of loops in
155        exf_mapfields, exf_radiation
156      - exf_bulkformulae.F: introduce 2D fields and vectorize code
157    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
158    o testreport:
159      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
160        monitor & update offline_exf_seaice exp. output.
161      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
162    o pkg/seaice:
163      - bug fix in the evp solver: boundary conditions were affected be
164        masking of zMax/zMin (changes results)
165      - minor bug fix in boundary conditions in seaice_calc_strainrates
166        (changes results for no_slip)
167      - seaice_lsr.F: make interpolation of eta dependent on boundaries
168      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
169      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
170        stress formulation and no-slip boundary conditions
171    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
172      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
173    o pkg/seaice: a first HSALT time stepping equation has been checked in
174    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
175      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
176      without requiring DO-IF statements
177    o pkg/thsice:
178      use continuous power-law function for partition of energy between lateral
179      melting/freezing and thinning/thickening ; old code using step function
180      still available with #undef THSICE_FRACEN_POWERLAW
181      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
182    o testreport: change AD testing : check against results/output_adm.txt
183      using same scripts as for forward test.
184    
185    checkpoint59g
186    o adjoint testing: in preparation for changing testreport:
187      - output format: cost and grad written on separated lines
188      - ad output results in directory "results" (instead of "results_ad")
189    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
190    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
191    o pkg/ecco: allow user defined cost function contributions
192    o testreport:
193      Allow to choose (per experiment) the list of tested output variables
194       and the main variable (used to issue a pass/FAIL ) ;
195      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
196      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
197      Also modify printing of summary:
198       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
199       b) echo the list of tested variables in the individual summary.txt of
200          each experiment.
201    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
202      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
203      (but still depend on the tile decompostion of the domain).
204    o pkg/seaice: change a discretization detail to make the B-grid code
205      "more symmetric". This change is likely to remove all "ridges/leads" that
206      where quasi-aligned with the grid in B-grid solutions. It may also be
207      the solution to the stress coupling issues with the B-grid.
208    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
209      remove .cvsignore from input dir. (since testreport no longer run here).
210    o pkg/thsice:
211     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
212     - fix reshaping of sea-ice just after advection:
213       melt all the ice only if ice-volume is too small.
214     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
215       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
216     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
217    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
218      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
219    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
220      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
221      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
222      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
223      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
224      -> update output.txt
225    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
226     this affects truncation error: -> update output.txt of exp:
227      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
228      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
229    
230    checkpoint59f
231    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
232    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
233      a bounded range (in forward mode)
234    o pkg/ecco, ctrl, autodiff and mom_common:
235     internal parameter controls, completements of implementations
236    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
237    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
238      (not seem any difference in testing results).
239    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
240       at face corners.
241    o pkg/generic_advdiff:
242     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
243      loop range indices for computing vertical advection tendency
244      and do the calculation in the interior only (no overlap) ;
245      for now, only implemented for SOM advection (to save CPU time).
246     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
247    o exch2 adjoint
248      First set of changes:
249      - add exch2 hand-written adjoint templates
250      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
251        This will require cleanup in pkg/autodiff/*.F
252        (changed routines currently kept separate in verif. code/)
253      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
254        that used to hide exch2 or cubed-sphere specific code
255        (commented via 'cph-exch2')
256    o pkg/seaice
257      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
258    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
259       output of global_ocean.cs32x15.thsice .
260    
261    checkpoint59e
262    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
263      for B-grid vector (not yet tested) and C-grid vector (<- only used
264      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
265    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
266      (#ifdef ALLOW_SALT_PLUME)
267    o gather_2d/scatter_2d: removed halo regions
268    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
269      scheme and the corresponding test case (under front_relax dir). For now,
270      only available with Skew-flux form and not yet tested in realistic set-up.
271      adjoint: store directives updated, but gradient checks deteriorated,
272      so maybe GM/Redi adjoint is now broken.
273    o seaice adjoint
274      * add AREA, HEFF, HSNOW as control variable
275        (should not change lab_sea results)
276      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
277    o pkg/seaice:
278      * added computation of saltFlux in seaice_growth;
279        For time being, sea ice salinity is assumed constant
280        contribution of snow flooding to freshening of sea ice is neglected.
281        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
282        defaults to 0.0 in order to maintain backward compatibility.
283        Typical values for SEAICE_salinity are 4 to 10 g/kg.
284      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
285      * added SEAICE_availHeatFrac, which specifies fraction of surface level
286        heat content used to melt or grow ice
287      * commented out cap of HICE: it helps keep ice thinner
288      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
289      * applied OBCS T/S mask to HEFFM sea ice mask
290    
291    checkpoint59d
292    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
293     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
294     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
295    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
296     and change default value of parameter "GM_Small_Number";
297     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
298       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
299       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
300    o pkg/ecco: cost function when applying pkg/smooth to controls
301    o pkg/ctrl: add forcingPrecond run time parameter
302    o pkg/seaice:
303     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
304     - fix bug in metric terms of u-equation in LSR solver (implicit part),
305       changes verification/lab_sea
306     - rearrange implicit part of u-equation in LSR solver to make it easier to
307       read, understand, and debug. This causes changes at the truncation level.
308     - fix (serious) bug in the boundary conditions (sign error in the implicit
309       part) of the LSR solver. Changes all LSR results.
310     - fixed problem with HSNOW initialization to avoid thick snow when AREA
311       is initilized with small values - does not change lab_sea results.
312     - added HsnowFile initialization capability
313    o pkg/smooth: addition to model/src and pkg/ctrl so allow
314     initialization of pkg/smooth and application to control vector
315    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
316    o dependencies: pkg/profiles requires pkg/cal
317    o pkg/profiles:
318     - added option ALLOW_PROFILES_GENERICGRID
319         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
320         that interpolation information (grid points and coefficients) is provided
321         within the netcdf input files.
322         -> sample matlab scripts can be found in MITgcm_contrib/gael
323         that allow you to prepare netcdf input files.
324     - also modified: cleaner include statements, cleaner error print statements,
325       cleaner stops when error, and more tests of the netcdf input files consistency.
326    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
327    o pkg/seaice:
328     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
329       requires a new routine: seaice_diagnostics_fill.F
330     - make sure that seaice does not move if not forced (pressure replacement
331       method, Hibler and Ip, 1995), changes results
332     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
333     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
334       It is turned off by default (=-1.), because it changes the results.
335     - make it possible to read AREA from a file, too.
336    
337    checkpoint59c
338    o add S/R and diagnostics for oceanic mixed-layer depth
339    o move GMRedi call after all vertical mixing schemes (including KPP)
340    o pkg/thsice:
341     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
342      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
343    o pkg/obcs:
344     - bug fix for balance code
345    o pkg/seaice:
346      - allow values of SEAICE_elasticParm > 1
347      - add new parameter SEAICE_evpTauRelax as an alternative
348        to SEAICE_elasticParm
349      - make lsr boundary conditions free slip (by default), changes result
350      - add code for no slip boundary conditions for lsr
351      - set minimum of zeta to zero (and not 4e8) (changes results)
352      - add a cap on AREA after advecting AREA if seaice_growth is not called
353    o change calculation of Visbeck K:
354      - no longer depend on tapering scheme; instead, compute slope (limited
355        by GM_maxSlope). this is equivalent to what was comuted before with
356        clipping or linear tappering.
357      - fix vertical averaging (wrong by 1/2 level)
358      - leave the old version (but will not be maintained) within
359        #ifdef OLD_VISBECK_CALC / #endif
360      - update output of exp. ideal_2D_oce
361    o change error catch in calc_r_star to improve vectorization
362    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
363      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
364    o adjoint:
365      Re-organized adjoint checkpointing according to Matt Mazloff
366      (but with modifs/completions/cleanups)
367      Storing is now bundled into large arrays to optimized I/O
368      (and second step in cleanup of the_main_loop)
369    
370    checkpoint59b
371    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
372      - export/import (between ocean & coupler) fields needed for ocean DIC.
373    o pkg/seaice:
374      - get rid of three more exchanges seaice_calc_viscosities (required
375        different loop boundaries in seaice_lsr and seaice_ocean_stress)
376      - bug fix in seaice_ocean_stress (update of lab_sea required)
377      - reduce loop boundaries to necessary minimum also in seaice_evp
378      - go back to the old way of computing deltaC/Z as the adjoint likes that
379        better
380    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
381      passive tracer to an Age Tracer) + update output.txt
382    o pkg/exf:
383      - implement A-grid / C-grid selection for wind-stress input files.
384      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
385      for now, in exf_bulk_largeyeager04.F only :
386      - change implementation for case where windspeed + 2. components wind-stress
387        are read-in. AND use rhoConstFresh to convert evap.
388    o pkg/seaice:
389      - use correct EXCH_UV for wind-forcing (on A-grid).
390      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
391        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
392    o pkg/exf:
393      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
394      EXF_INTERPOLATION:
395      - merge global_with_exf/code version of exf_interp_read.F
396        to the main code ;
397      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
398        reading the file ; Important: This options needs to be defined to recover
399        previous code.
400        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
401      - no longer loose real*8 precision along the way when using exf_iprec=64.
402    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
403      - change discretisation of evp-solver in order to avoid another exchange
404        (changes lab_sea) and clean up a little
405      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
406        help the adjoint (this also changes the results slightly)
407      - add a few "_d 0" where they had been missing in seaice_evp.F
408      - cleaning up: remove unused seaice_calc_rhs.F
409    o pkg/exf: some cleaning-up:
410      - change various "constants" into runtime parameters
411      - cleaned-up Large&Yeager04 routine which should eventually
412        replace exf_bulkformulae.F (changed names of S/R and CPP)
413        and merged various ALLOW_ATM_WIND options
414     only used with thsice pkg (in thsice_get_exf.F):
415      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
416        which are used when useStabilityFct_overIce=TRUE (= the default)
417      - change default values of ice & snow emissivity and scale downward LW
418        by ice & snow emissivity.
419    o pkg/thsice:
420     fix few little problems, in thsice_calc_thickn.F:
421      - growth vertically (and not laterally) if iceFrac == iceMaskMax
422      - melt only laterally if hIce < hThinIce (as the comments say)
423      and in thsice_extend.F:
424      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
425      - start to form ice as soon as the minimum ice-volume is reachable.
426     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
427      and cpl_aim+ocn
428    o pkg/kpp
429     - move computation of surface related input fields to KPP into a new
430       subroutine kpp_forcing_surf.F
431     - remove wrong (within bi,bj loops) EXCH calls.
432     - little cleaning (add argument myThid in last position, cvs header ...)
433     - for now, fix conservation problem by exchanging KPPviscAz (may not
434       be the best fix)
435    o pkg/seaice
436     - check for inconsistent evp parameter/cpp-flag combination
437     - remove leftover errIO flat for obsolete name list error handling
438    o OpenAD
439     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
440    
441    checkpoint59a
442    o pkg/seaice: some parameter clarifications and a little bit of clean up
443    o pkg/thsice: rename run-time parameters:
444       himin       -> hIceMin
445       himin0      -> hThinIce
446       hihig       -> hThickIce
447       i0          -> i0swFrac
448       transCoef   -> bMeltCoef
449       frac_energy -> fracMelting
450      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
451       with default values (for now) that do not change the results.
452      remove old version of thsice vars advection in pkg/seaice.
453    o in FFIELDS.h:
454      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
455      - make pLoad & sIceLoad always available (but still only used if
456         ATMOSPHERIC_LOADING is #define).
457    o pkg/kpp: replaced _KPP_RL with _RL
458    o bug fixes for vertical diffusivity computations when both KPP and
459        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
460        are no longer updating the vertical diffusivity array
461        (passed as argument) but are (re-) setting those arrays.
462    o pkg/seaice: fix bug in evp solver, while doing that
463      - change (improve?) discretization of stress computations for both
464        cgrid-lsr and evp solver
465      - add a new routine to compute strain rates
466      - the above changes lab_sea results
467      - add no slip conditions for evp solver (off by default), lsr-version
468        may follow
469      - fix exchange for shear at Z-points (does not change lab_sea)
470      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
471        (to force the user to pick a time step since there is not "safe" way
472        of choosing it)
473      - add principal stress diagnostics
474      - rearrange fields for evp a little to avoid having to call a: too many
475        exchanges and b: exchanges for stress trensor components which we do
476        not have.
477      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
478        of evp, complete rewrite for lsr case (latter is does not yet work
479        in all cases)
480    o pkg/kpp: add code to have mixing in shelf ice caverns
481      - add myThid to all kpp routines (long overdue)
482    
483    checkpoint59
484    o pkg/exf:
485      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
486        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
487      - move exf header files from lower_case.h to UPPER_CASE.h ;
488        add missing cvs Header & Name
489      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
490      - add namelist param. selectStressGridPosition, exf_monFreq
491      - retire many _CLIM routines, and remove data.exf_clim
492        + params moved to data.exf
493        + climsst, climsss now handled by exf_set_gen, i.e.
494          climss?period=0 refers to constant field,
495          climss?period=-12 to monthly forcing
496      - split up namelists in data.exf
497    o pkg/seaice:
498      - remove seaice_exch and seaice_exch_uv
499      - remove superfluous exchange of theta
500      - add myThid to seaice_budget_ocean/ice
501      - add new interface for atmospheric wind forcing (C-grid only)
502        + new routine
503        + two new field (taux, tauy for stress over ice)
504        + removed one global field (DAIRN) for C-grid case only
505    o pkg/thsise
506      - 2nd set of modifs for thsice adjoint in conjunction with exf
507    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
508    
509    checkpoint58y_post
510    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
511      vertical diffusivity, similar to that in MOM4; turned on using
512      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
513      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
514    o Added capability for 3D specification of background vertical diffusion
515      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
516      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
517      "data" file that contains the 3D vertical diffusivity coefficients.
518    o ice dynamics (pkg/seaice) with thsice thermodynamics:
519      - add code within pkg thsice to advect & diffuse sea-ice fields
520      similar to (and will replace) what has been added in  seaice_advdiff.F,
521      but: - conserving Mass, Heat & Salt.
522           - better when using non-linear advection scheme (not yet fully tested)
523           - can also be used in atmospheric set-up (for now, only the diffusion).
524    
525    checkpoint58x_post
526    o IO option for global-file compact format:
527      - add options when generating topology (utils/exch2/matlab-topology-generator)
528      - add I/O capability (pkg/mdsio).
529      - adapt utils/matlab/rdmds.m to read this format.
530      for now long-line format not yet supported by pkg/mdsio (& exch2).
531    o shelfice: add a few diagnostics
532    
533    checkpoint58w_post
534    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
535      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
536      (and replace horiVertRatio in NH code).
537      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
538                         and tutorial_plume_on_slope (sensitive to truncation)
539    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
540      directly to drive seaice model (C-grid only)
541    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
542     - reintroduce computation of wind from stress,
543     - compute tau (in exf_bulkformulae.F) from windstress averaged to
544       mass points to avoid tau = 0
545     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
546    o rdmnc.m: make it work with "global" files created with gluemnc
547    o rdmnc.m : some improvements in dealing with singleton dimension
548      (tested on all testreport mnc output files).
549    o genmake2: disable pkg/profiles if netcdf test fails.
550    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
551    o move call to cal_readparms up to make calendar parameters/variable available
552      to all packages
553    
554    checkpoint58v_post
555    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
556      useDynP_inEos_Zc tested.
557    o pkg/exf: changes to properly interpolate/mask/scale initial fields
558    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
559      and portions thereof.  See read_cs.txt for description and examples.
560    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
561      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
562      following the great-circle arc between those 2 points.
563    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
564      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
565    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
566     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
567     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
568     - still needs work (not working with some options ; efficiency to improve)
569       and serious testing.
570     - use this scheme for temperature & salinity in 2 advection test exp.:
571       advect_xy & advect_xz, respectively.
572    
573    checkpoint58u_post
574    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
575    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
576    o testreport: add option "-skipdir" to skip some test.
577    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
578      momentum calculation.
579    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
580    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
581      remove checkpoint.F and the_correction_step.F (no longer used);
582      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
583    o add option (linFSConserveTr) to correct for tracer source/sink due to
584      Linear Free surface
585    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
586    o pkg/thsice: fix reading mnc-pickups
587    
588    checkpoint58t_post
589    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
590    o pkg/mdsio:
591     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
592       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
593       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
594     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
595     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
596       either MDS_READ_FIELD or MDS_WRITE_FIELD )
597     - new S/R (to replace MDSWRITEMETA), which allows to write more
598       informations (variable names, time ...) to meta files.
599     - modify rdmds.m to give back the meta file content.
600    o pkg/diagnostics: change vertical interpolation to be safer, and more
601       flexible (define p-levels to interpolate to in data.diagnostics);
602      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
603       diagnostic pointer.
604    o pkg/seaice: more cleaning up of seaice_growth, added many comments
605    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
606    o fix multi-category seaice:
607     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
608       SEAICE_MULTICATEGORY
609     - fix short wave heat flux
610    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
611       and allow to use EVP solver. Change forward lab_sea: test both EVP
612       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
613    o Initial check-in of lab_sea adjoint
614      (very similar to natl_box_adjoint/code_seaice)
615      * used C-grid and EVP solver
616      * used KPP, GM/Redi
617      * uses inAdExact=.TRUE.
618      * gradient checks fail for both ADM and TLM
619        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
620        f.d. gradients actually seem more problematic than ADM, TLM gradients;
621        issue is related to forward mismatch between g77 an ifort
622    o pkg/seaice: overhaul of thermodynamics
623     - growth.F and groatb.F are replaced by new routine seaice_growth.F
624     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
625     - move a few global fields out of SEAICE.h into seaice_growth.F and
626       make them 2D (FICE/QNETO/ ...)
627     - remove FO (it is the same as QNETO)
628     - introduce a few local fields to avoid modifying external fields such
629       as atemp, etc.
630    
631    checkpoint58s_post
632    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
633      changed exf_set_gen.F so that
634        genperiod=0 means input file is one time-constant field and
635        genperiod=-12 means input file contains 12 monthly means
636    o CG2D: use pre-computed solver main-diagonal (stored in common block);
637      this affects truncation error ; generate new output file for exp. which
638      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
639        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
640        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
641        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
642        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
643        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
644    o start implementation of deep-atmosphere and anelastic formulation
645    o verification: remove 2nd copy of input files and use script "prepare_run"
646      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
647    o mom_common/vecinv/fluxform: fix a few initialisation isssues
648    o profiles: fix for multithreaded case
649    
650    o diagnostics: rename few diags:
651      s/'PRESSURE'/'RCENTER '/g
652      s/'TICE    '/'oceFreez'/g
653      s/'TAUX    '/'oceTAUX '/g
654      s/'TAUY    '/'oceTAUY '/g
655      s/'SWFLUX  '/'oceQsw  '/g
656      s/DIFx/DFxE/g
657      s/DIFy/DFyE/g
658      and add few ocean-forcing diagnostics:
659      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
660    o modifications to pkg/seaice/growth.F and budget.F, which change results of
661      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
662      as actual snow thickness.  It now refers everywhere to effective snow
663      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
664    
665    checkpoint58r_post
666    o modifications to pkg/seaice/growth.F, which change results of
667      lab_sea experiment: fixes pertain to melting snow over open water, to
668      masking EVAP under sea ice, and to using the correct AREA variable for
669      computations of EVAP, PRECIP, HSNOW, and GHEFF
670    o add ability to read bathy, salt, and theta using MNC (off by def)
671    o add flooding algorithm and advection of HSNOW for pkg/seaice;
672      both are turned off by default and do no change any results
673    o seaice advection with pkg/thsice: a step toward the use of non-linear
674      advection scheme, but #ifdef or commented out for now (requires more EXCH).
675    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
676      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
677      in natl_box (affects results @ truncation level: update output.txt)
678    o multi-threading and IO:
679      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
680      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
681        (needed to work with SingleCpuIO): tested in all verif. exp.
682    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
683      affects the results (but none of the verification test uses this scheme).
684    o Adding some pkg/diagnostics capability to pkg/seaice
685      (will certainly be subject to changes)
686    o ctrl: adding new control variables:
687      lwflux, lwdown, evap, snowprecip, apressure, runoff
688    
689    checkpoint58q_post
690    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
691      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
692      high_res_cube configuration by 4% on Columbia.
693    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
694      add (in global_with_exf/code) a version of EXF_INTERP_READ without
695      dynamical allocation (seems to work in multi-threaded).
696    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
697      single CPU io) so that TAF does not have to see EESUPPORT.h
698    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
699    
700    checkpoint58p_post
701    o obcs: stop if obcs is used with useCDscheme = .true.
702    o shelfice:
703     - fix a sign error so that no slip at shelfice interface works
704     - remove stop for combination non-hydrostatic code and shelfice. That does
705       not mean, that the results are correct, but at least they are numerically
706       stable
707    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
708    o added adjoint exch routined for all exch*3d* routines
709      and updated flow directives
710    
711    checkpoint58o_post
712    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
713      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
714    o change controling S/R for writing pickup file (new S/R do_write_pickup)
715      and clean-up reading/writing of pickup files.
716    o fix local version of read/write pickup (NH part) in rotating_tank/code
717    o simplify EXCH interface:
718     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
719     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
720    o added the regrid package
721    o shelfice:
722     - add a simple boundary layer scheme to reduce noise
723     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
724    
725    checkpoint58n_post
726    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
727       local variable (not in common block).
728    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
729      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
730      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
731        to work with SingleCpuIO.
732    o add "_d 0" to real constant of pkg/cfc subroutines ;
733       update exp. cfc_exemple & tutorial_cfc_offline output files.
734    o multi-threading and IO:
735      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
736        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
737      - barrier before and after reading.
738      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
739      - avoid using MDS_WRITELOCAL for LAND pkg output.
740      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
741        common-block variables ; Allows multi-threading with master-thread IO.
742    o change default MAX_NO_THREADS from 32 to 4 ;
743      and stop cleanly when MAX_NO_THREADS is too small.
744    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
745    
746    checkpoint58m_post
747    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
748       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
749    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
750       keep global_ocean.90x40x15 (for AD testing) with former secondary test
751       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
752    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
753        add MITgcm_tutorials (= code + all the tutorials)
754    o ecco, option to compute cost for total ssh (mean+anom)
755    o consistent with addition of ptracer and ssh in pkg/profiles
756    o profiles: adding ptracer and ssh
757    o testreport: change multi-test output-file name
758      (from output.txt.{name} to output.{name}.txt)
759    o profiles: now ok for mutli-tiles case
760    o seaice: add 4 parameters for different advection schemes for area,
761      (effective) seaice thickness, enthalphy, and snow height. Their default
762      is the standard parameter SEAICEadvScheme
763    o calc_gw:
764     - add cosFacU in zonal viscous flux (harmonic.visc.).
765     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
766       of tutorial_plume_on_slope.
767    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
768    o calc_gw: true flux-form, account for horizontal grid spacing.
769      update rotating_tank results, but not plume_on_slope (affected at
770      truncation level, 11 digits).
771    
772    checkpoint58l_post
773    o calc_gw:
774     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
775     - remove side-drag for now (need to fix it); update plume_on_slope results.
776     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
777    o commit code to make SST/SSS weights spatially variable
778      (based on either variable in-situ or variable initial T/S weights)
779    o pkg/ecco:
780      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
781        now based on horizontally varying weights wthetaLev, wsaltLev
782      * cost_averagesflags now returns year indices in addition to day, month
783      * sflux balance is performed on annual basis
784        (sflxumm, sfluxmm2, bal_sfluxmm)
785      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
786        including separate counting and multipliers
787    o pkg/rbcs
788      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
789    
790    checkpoint58k_post
791    o testreport:
792     - always build in dir. "build" (if not there, mkdir build instead of building
793       & running in input)
794     - run in dir run (if it exists), in build otherwise.
795     - call prepare_run (if input/prepare_run exists)
796     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
797    o pkg/exf modifications to interpolation and rotation routines for more
798       reasonable treatment of North Pole singularity: for tracers North Pole
799       value is set to northernmost zonal-mean value, for zonal velocity it is
800       set to zero, and for meridional velocity it is set to northernmost value.
801    o pkg/exf/exf_check_range.F
802     - add tile index to diagnostics and move stop statement to the very
803       end of the routine.
804    o pkg/diagnostics: (diagnostics_main_init.F)
805      define title of isomorphic variables according to the current config.
806    o pkg/thsice with pkg/seaice dynamics:
807    - fix domain of computation (interior only, required for exf) and do exchanges
808    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
809    o towards a standard way of dealing with multi-threading in MONITOR
810      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
811  o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)  o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
812     to W momentum equation in nonhydrostatic and quasihydrostatic runs.       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
813  o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.  o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
Legend:
Removed from v.1.685  
changed lines
  Added in v.1.935
  ViewVC Help
Powered by ViewVC 1.1.22