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usePickupBeforeC35 no longer supported ; remove this option.
do not refer to gxNm1 if unnecessary (to work also with AB-3)
remove parts that were not in checkpoint35 version
- set up forward_step for a call to gchem_forcing, that will replace
gchem_forcing_int in ptracers_forcing
- cleaning up, in particular CPP-flags and call to ptracer_statvars
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) (adjoint stuff still has some tr1 names, but all use ptracer arrays)
o prepare addition of new packages GGL90 and OPPS - new parameters useGGL90 and useOPPS - include call to the new routines at the (hopefully) right places
o first check-in for the "branch-genmake2" merge
o verification suite as run on shelley (gcc 3.2.2):
Wed Oct 8 23:42:29 EDT 2003
T S U V
G D M c m s m s m s m s
E p a R g m m e . m m e . m m e . m m e .
N n k u 2 i a a d i a a d i a a d i a a d
2 d e n d n x n . n x n . n x n . n x n .
OPTFILE=NONE
Y Y Y Y 13 16 16 16 0 16 16 16 16 16 16 16 16 13 12 0 0 pass adjustment.128x64x1
Y Y Y Y 16 16 16 16 0 16 16 16 16 16 16 0 0 16 16 0 0 pass adjustment.cs-32x32x1
Y Y Y Y 16 16 16 16 0 16 16 16 16 16 16 22 0 16 16 22 0 pass adjust_nlfs.cs-32x32x1
Y Y Y Y -- 13 13 16 16 13 13 13 13 16 16 16 16 16 16 16 16 N/O advect_cs
Y Y Y Y -- 22 16 16 16 16 16 16 13 16 16 16 16 16 16 16 16 N/O advect_xy
Y Y Y Y -- 13 16 13 16 16 16 16 16 16 16 22 16 16 16 16 16 N/O advect_xz
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 pass aim.5l_cs
Y Y Y Y 14 16 16 16 16 16 16 16 16 13 16 16 16 16 16 13 16 pass aim.5l_Equatorial_Channel
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 13 16 16 13 13 16 pass aim.5l_LatLon
Y Y Y Y 13 16 16 16 16 16 16 16 16 16 13 12 13 13 16 13 16 pass exp0
Y Y Y Y 14 16 16 16 16 16 16 16 22 16 16 16 13 16 16 22 16 pass exp1
Y Y Y Y 13 13 16 13 16 16 16 16 16 13 13 16 16 13 13 13 13 pass exp2
Y Y Y Y 16 16 16 16 16 16 16 16 22 16 16 16 16 16 16 16 16 pass exp4
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 22 16 16 16 22 16 pass exp5
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 pass front_relax
Y Y Y Y 14 16 16 13 13 16 16 13 13 16 13 13 16 12 13 13 16 pass global_ocean.90x40x15
Y Y Y Y 10 16 16 13 13 16 13 16 16 13 13 13 13 16 16 13 16 FAIL global_ocean.cs32x15
Y Y Y Y 6 11 12 13 13 12 13 16 13 9 9 9 9 10 9 9 11 FAIL global_ocean_pressure
Y Y Y Y 14 16 16 13 16 16 16 13 13 13 13 13 16 12 16 13 16 pass global_with_exf
Y Y Y Y 14 16 16 16 16 16 16 16 16 11 13 22 13 16 16 9 16 pass hs94.128x64x5
Y Y Y Y 13 16 16 16 16 16 16 16 16 11 16 16 16 13 16 22 13 pass hs94.1x64x5
Y Y Y Y 14 16 16 16 16 16 16 16 16 13 16 13 13 16 16 22 13 pass hs94.cs-32x32x5
Y Y Y Y 10 10 16 13 13 16 16 16 22 16 13 13 13 13 13 22 13 FAIL ideal_2D_oce
Y Y Y Y 8 16 16 16 16 16 16 16 16 13 13 8 16 16 16 16 16 FAIL internal_wave
Y Y Y Y 14 16 16 16 16 16 16 16 16 13 13 22 13 13 13 22 16 pass inverted_barometer
Y Y Y Y 12 16 16 16 16 16 16 16 16 16 13 12 13 13 13 13 13 FAIL lab_sea
Y Y Y Y 11 16 16 16 16 16 16 16 13 13 13 12 13 16 13 12 13 FAIL natl_box
Y Y Y Y 16 16 16 16 16 16 16 16 22 16 16 16 16 16 16 16 16 pass plume_on_slope
Y Y Y Y 13 16 16 16 16 13 16 16 16 16 16 16 16 13 16 16 16 pass solid-body.cs-32x32x1
fix bug in ptracers time averaging if gchem forcing is done separately (ie #define PTRACERS_SEPARATE_FORCING)
o included PACKAGES_CONFIG.h in all files where the ALLOW_${PKG_NAME}
defines are used
o added comments where IF ( use${PKG_NAME} ) statements will probably
be needed -- or need to be edited
additions for biogeochemistry packages
Merging from c51
store u*,v* in gU,V instead of in gu,vNm1.
merging c49 and e27
made convective adjustment work with pressure coordinates: - changed the direction of k-loop in convective_adjustment.F for the case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) - adjusted the reference pressure k-index in convective_adjustment.F - adjusted the convection condition in convect.F (in analogy to calc_ivdc.F) - convective_adjustment no longer computes anything on the halos - removed the warnings about negative salinity from find_rho.F and find_alpha.F; instead the new routine look_for_neg_salinity, called at the beginning of find_rho, find_alpha, and find_beta, does a check of the entire slice, if CPP-option CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
* split calc_exact_eta in 2 S/R : integr_continuity & update_etaH * move wVel computation at the end of the time step, in S/R integr_continuity * create specific S/R to exchange T,S before DYNAMICS (for stagger time step) * update timeave pkg for wVel diagnostic ; put convertEmP2rUnit in PARAMS.h
Changes encapsulated by checkpoint43a-release1mods and chkpt44d_post
on the main trunk.
These are:
o added missing EXCLUDE_MONITOR flags
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
(incompatible typ in MIN/MAX expressions caused problems
on IBM SP3)
o in genmake added variable MAKEDEPEND
plus resetting for case SunOS
o added timer_stats.c routine for IBM SP3
o removed variables in dynamics
o real fresh water flux implemented with non-linear free-surface.
o few fix (mask in shap_s2, EmPmR in external_field_load,
USE_NATURAL_BCS in solve_for_P);
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
o merge of relevant stuff from the ecco-branch:
- genmake: removed $S64 overwrite for case SunOS
- pkg/exf: update and corrections for field swapping and obcs
- pkg/ecco: parameter lists for the_model_main, the_main_loop
harmonized between ECCO and MITgcm
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
updated checkpointing_lev... lists for obcs
- model/src: minor changes in forward_step, plot_field
added directive for divided adjoint in the_main_loop
- pkg/mdsio: added mdsio_gl_slice
o check parameters & config (chkpt44a_pre,post)
o OBC and NonLin_FrSurf.
o fix bug in mom_vi_del2uv
o select when filters are applied ; add options to zonal_filter (data.zonfilt)
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
o update AIM experiments (NCEP input files)
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
o added some stuff for AD
These were merged with
cvs co -r release1 -P MITgcm
cd MITgcm
cvs update -kk
cvs update -j checkpoint43a-release1mods -j chkpt44d_post -d -P -kk
Added PTRACERS package
This allows an arbitrary number of passive tracers to be integrated
forward simultaneously with the dynamicaly model.
+ Implemented so far:
- basic forward algorithm (time-stepping, advection, diffusion, convection)
- I/O and checkpointing
- GM/Redi *but* using the GM/Redi coefficient of Salt
+ Not implemented so far:
- KPP
- OBCS
+ No specific example supplied (yet) but global_ocean.90x40x15 has the
necessary data.ptracer file. Simply use -enable=ptracers and uncomment
line in data.pkg. PTRACER01 then reproduces Salt exactly.
+ This package is disabled by default since it increases storage.
Merging changes on MAIN between checkpoint43 and checkpoint43a-release1mods
Command: cvs -q update -jcheckpoint43 -jcheckpoint43a-release1mods -d -P
These changes are most of the changes between c43 and c44 except those
that occured after "12:45 11 Jan 2002". As far as I can tell it is
checkpoint43 with the following mods:
o fix bug in mom_vi_del2uv
o select when filters are applied ; add options to zonal_filter (data.zonfilt) o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
o update AIM experiments (NCEP input files)
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
o added some stuff for AD
o Jamar wet-points
This update does not contain the following mods that are in checkpoint44
o bug fix in pkg/generic_advdiff/
- thread related bug, bi,bj arguments in vertical advection routines
o some changes to pkg/autodiff, pkg/cost, pkg/exf, pkg/ecco,
verification/carbon and model/src/ related to adjoint
o some new Matlab scripts for diagnosing model density
- utils/matlab/dens_poly3.m and ini_poly3.m
The list of exclusions is accurate based on a "cvs diff". The list of
inclusions is based on the record in doc/tag-index which may not be complete.
Merge changes from main trunk: o changed param. list for call obcs_calc in thermodynamics o flow directives in the_correction_step not needed anymore Remove forward_step for ecco-branch
remove some store directives
Updating ecco-branch-mod1 to checkpoint44. Will be tagged ecco-branch-mod2.
add options to select where the filters apply in the time-step
Fixed AD-related problems: o Store directives up-to-date with re-arranged Adams-Bashforth (mainly thermodynamics.F) o New store directives for multi-dim. advection schemes * new CPP flag ALLOW_MULTI_DIM_ADVECTION * new common block and key passkey (mainly gad_advection.F) o Modified store directives for split of dynamics/thermodynamics for the case ALLOW_KPP o Cleaned argument list for timestep_tracer.F
Bringing comments up to data and formatting for document extraction.
"Volume exact-Conservation" modified for non-linear free-surface + Crank-Nickelson
Added CPP option ALLOW_PASSIVE_TRACER for TR1.h related fields.
o Added grdchk package handling o Added passive tracer handling
the default is now to call the filter after solve_for_pressure
Merge from branch pre38: o essential mods for cubed sphere o debugged atmosphere, dynamcis + physics (aim) o new packages (mom_vecinv, mom_fluxform, ...)
rewrite calc_exact_eta.F to be independant of the 2D solver. allow to filter Velocity uVel,vVel instead of u,v_Star (1rst guess)
Modifications/fixes to support TAMC differentiability (mostly missing or wrong directives).
correct type writing error
allow to re-compute eta to conserve exactly the total volume
Modifications and additions to enable automatic differentiation. Detailed info's in doc/notes_c37_adj.txt
calc_grad_phi_surf (replace calc_grad_eta_surf) to get directly gradient of Phi_Surf
change in calling Time-Average routine (new package) ; and add etaN as argument of calc_grad_eta_surf
recover (after checkpoint35) time average output
Added conditional for calling CORRECTION_STEP() to facilitate fixed flow, passive trac expts.
Merged changes from branch "branch-atmos-merge" into MAIN (checkpoint34) - substantial modifications to algorithm sequence (dynamics.F) - packaged OBCS, Shapiro filter, Zonal filter, Atmospheric Physics
Packaged OBCS (open boundary conditions) o source code now in pkg/obcs o controlled by namelist in data.obcs o includes Orlanski radiation condition (in same directory) o affects exp4 and internal_wave
Tentative implimentatin of OBCs.
Moved "correction" phase of algorithm from top of dynamcs() to end of forward_step(). - allows deletion of ini_predictor - need convective adjustment of initial conditions for backward compatibility. - exchange fields instead of tendancies, called in forward_step() - encapsulated convective adjustment for convenience: convective_adjustment()
file the_correction_step.F was initially added on branch branch-atmos-merge.
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