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o Adding package parameters and hooks to MITgcm for new seaice package. o Adjusting KPP package for use with seaice package.
o added Eliassen-Palm flux hook (dynamics) o removed unused TAF keys iikey, idkey (dynamics,thermodynamics)
Included CPP option SINGLE_LAYER_MODE to configure barotropic setup (Martin Losch).
Preparation & fixing to avoid recomputation in reverse mode: o thermodynamics: fixed o impldiff: prepared
These changes constitute a patch to release1. They were made on a development branch called "release1_final" and are on the main trunk between chkpt44d_post and checkpoint44h_post along with other changes. This code is equivalent to chkpt44d_post with the following patches: - AD-related changes for GMRedi - fixes i KPP (delZ -> drF) - hook to OBCS songe layer code in external_forcing - errorMessageUnit non-zero in eeboot.F - modified test cost function and carbon verif.
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
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.
Removed CPP connection between DISABLE_MULTIDIM_ADVECTION and ALLOW_AUTODIFF_TAMC. o ie. removed #ifdef ALLOW_AUTODIFF_TAMC from GAD_OPTIONS.h o updated comments in thermodynamics.F to reflect this change
Switched sense of CPP macro for controlling multi-dimensional advection: o DISABLE_MULTIDIM_ADVECTION is set in GAD_OPTIONS.h o automatically set if differentiating code (comments around call to gad_advection point out how to re-enable it) o this avoids needing to add the former macro to CPP_OPTIONS.h - reason for this is there's no point in any of the new schemes without it.
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
Deleted apostrophies in comments: "Isn't" breaks cpp...
Bringing comments up to data and formatting for document extraction.
Corrected parameter lists for case tr1stepping.
Re-arranged sequence of operations for Adams-Bashforth o this does not change numbers o this makes it very easy to extract forcing/diffusion out of ABII by changing calling sequence in calc_gt, calc_gs,... Key modifications: o new s/r: ADAMS_BASHFORTH2 gT=3/2*gT-1/2*gTnm1 o changed TIMESTEP_TRACER from gTnm1=t+dt*(3/2*gT-1/2*gTnm1) to gT=T+dt*gT o changed CALC_GT,CALC_GS & CALC_GTR1 to calcuate "gT" defined by new timestep_tracer (ie. including forcing, ABII, N-L F-S, etc...) now calls ADAMS_BASHFORTH2 and FREESURF_RESCALE_G o changed CYCLE_TRACER appropriately T=gT only Other associated mods: o new s/r: FREESURF_RESCALE_G applies non-linear free-surface term this used to be in TIMESTEP_TRACER o added myIter as argument to CALC_GS,CALC_GT,CALC_GTR1
Reinstate calls to advection routines after gratuitous commenting removed them in previous update! :^)
Include initialisation of gTracer fields to break dependency for TAF.
Added multi-dimensional form of advection o available only for single step schemes (ie. can't be used with ABII) o stable for max(cfl_u,cfl_v,cfl_w)<=1 (without cfl_u+cfl_v+cfl_w <=1) o selected using multiDimAdvection=.T. (default) o had to hack some existing routines to work on local arrays
Added run-time control of advection schemes.
- advection scheme determines method of forward integration.
- unfortunately, we have to use integers in "data" since ENUM_CENTERED_2ND
doesn't mean anything to fortran
- defaults are centered second
- output differs due to these mods! This is due to the g77 optimization.
I have tested that using -ffloat-store, these mods do not affect
the output so am confident about changes.
T S U V
C D M c m s m s m s m s
n p a R g m m e . m m e . m m e . m m e .
f n k u 2 i a a d i a a d i a a d i a a d
g d e n d n x n . n x n . n x n . n x n .
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 22 16 16 pass adjustment.128x64x1
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 pass adjustment.cs-32x32x1
Y Y N N -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- N/O aim.5l_Equatorial_Channel
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 pass aim.5l_LatLon
Y Y N N -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- N/O aim.5l_zon-ave
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 22 16 pass exp0
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 22 16 pass exp1
Y Y Y Y 13 16 16 16 16 16 16 16 13 16 13 13 13 13 13 13 16 pass exp2
Y Y Y Y 12 16 16 13 16 16 16 16 16 13 16 16 16 16 13 13 16 FAIL 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 16 16 16 16 16 16 16 16 16 16 16 22 16 16 16 11 16 pass hs94.128x64x5
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 22 16 pass hs94.1x64x5
Y Y Y Y 14 16 16 16 16 16 16 16 16 16 13 16 16 16 16 16 13 pass hs94.cs-32x32x5
Y Y Y Y 16 16 16 22 16 16 16 16 16 16 16 22 16 16 16 16 16 pass internal_wave
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 pass natl_box
Y Y Y Y 16 16 16 16 16 13 16 13 16 16 16 16 16 16 16 16 16 pass solid-body.cs-32x32x1
Modifications related to split into thermodynamics.F, dynamics.F o missing initialisations in dynamics.F added o some fields no longer needed in dynamics/thermodynamics deleted o split of calc_diffusivity.F into calc_viscosity.F (plus split of kpp_calc_diff.F into kpp_calc_visc.F) o Modifications of some store directives for TAF
Split dynamics.F into dynamics.F and thermodynamics.F - idea is to make algorithm more transparent??? - probably less efficient - has exchanges at end of thermodynamics.F (which are needed if using staggered time-stepping with the cube OR using AIM.
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