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o few modif.'s to get latest version adjointed (mainly kick out code in ini_linear_phisurf) o modif's to run adjoint with exactConserv o case GM_BOLUS_ADVEC should be cleaned S/R gmredi_slope_psi should be cleaned o verification/carbon now has exactConserv=.TRUE.
checkpoint47f_post
Merging from release1_p10:
o modifications for using pkg/exf with pkg/seaice
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
and SEAICE_EXTERNAL_FLUXES
- pkg/exf CPP options EXF_READ_EVAP and
EXF_NO_BULK_COMPUTATIONS
- usage examples are Experiments 8 and 9 in
verification/lab_sea/README
- verification/lab_sea default experiment now uses
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
Two packages: bulk_force (Bulk forcing) and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 Earlier integration from Stephaine Dutkiewicz and Patrick Heimbach. Two ifdef statements for compile time, ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE Two switches in data.pkg to turn on at run-time: cat data.pkg # Packages &PACKAGES useBulkForce=.TRUE., useThermSeaIce=.TRUE., & WARNING: useSEAICE and useThermSEAICE are mutually exclusive. The bulk package requires an additional parameter file with two namelists, data.ice and data.blk. c ADAPTED FROM: c LANL CICE.v2.0.2 c----------------------------------------------------------------------- c.. thermodynamics (vertical physics) based on M. Winton 3-layer model c.. See Bitz, C. M. and W. H. Lipscomb, 1999: "An energy-conserving c.. thermodynamic sea ice model for climate study." J. Geophys. c.. Res., 104, 15669 - 15677. c.. Winton, M., 1999: "A reformulated three-layer sea ice model." c.. Submitted to J. Atmos. Ocean. Technol. c.. authors Elizabeth C. Hunke and William Lipscomb c.. Fluid Dynamics Group, Los Alamos National Laboratory c-----------------------------------------------------------------------
differentiable version of checkpoint46n_post o external_fields_load now part of differentiation list o pressure needs multiple storing; would be nice to have store_pressure at beginning or end of forward_step, e.g. by having phiHyd global (5-dim.) (NB: pressure is needed for certain cases in find_rho, which is also invoked through convective_adjustment). o recomputations in find_rho for cases 'JMD95'/'UNESCO' or 'MDJWF' are OK. o #define ATMOSPHERIC_LOADING should be differentiable o ini_forcing shifted to begining of initialise_varia
Merging from release1_p8 branch:
o GAD:
- generated new common blocks to account for call of
same gad routines with differing traceridentities
(needed to modify tracerIdentity indices in GAD.h)
- generated separate common blocks for case useCubedSphereExchange
(Department of Futurology)
- parameter lists to gmredi_?transport: added tracerIdentity
- added new key indices to tamc.h
Moved call to packages_init_varia before call convective_adjustment_ini. Corresponding adjustment of tape init. for TAF.
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
* Updated adjoint/makefile
o removed "_ecco" from names
o added/modified forward mode options
o added dependent vector option
o tried SVD matrix computation (doesn't work;
too much memory use by TAF)
* Updated flow directives related to FTL
* removed global_sum__g.F (not necessary)
* initialise forward mode anomalies in ctrl_unpack.F
(so far "crude" initialization only).
* Added flag ALLOW_TANGENTLINEAR_RUN complememting
ALLOW_ADJOINT_RUN
* driver routine the_model_main.F needs separate call
to FTL routine G_THE_MAIN_LOOP with parameter list
identical to THE_MAIN_LOOP (TAF doesn't remove arguments).
* added template file tangentlinear_model.F
for forward mode.
Transfering major checkpoint store directive blocks to separate header files. Files are included in the_main_loop (lev3, lev2) and forward_step (lev1).
#ifdef ALLOW_COST_TRACER replaced by ALLOW_PASSIVE_TRACER (required)
Preparing adjoint of Held-Suarez: - bugfix for storing in absence of CD code - adding EXACT_CONSERV to AD list - new routine ini_autodiff to add TAMC-specific initialisations - adding Shapiro filter to AD list
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 single apostrophy (').
Bringing comments up to data and formatting for document extraction.
o New package pkg/rw/ needed new flow directives for TAMC. o Replacement of calc_mom_rhs by mom_fluxform and mom_vecinv needed update of adjoint/makefile and additional store directives in the_main_loop.F to cover all cases.
Moved TR1.h headers between ifdef ALLOW_PASSIVE_TRACER.
Cleanup of store directives for TAF.
Added a few re-initialisations for TAF.
o Extracted core part of the_main_loop and re-created forward_step
N.B.: Time-dependent part of cost function should remain in
the_main_loop (or contributions must be stored)
o Added some parameter recomputations of nIter0
o Added grdchk package handling o Added passive tracer handling
the default is now to call the filter after solve_for_pressure
Corrected all the timer labels (for the non-adjoint sections).
Added Kinetic energy monitoring.
Adding skeleton "monitor" routines. The default is to do it every time-step. monitorFreq=0 disables.
Modifications/fixes to support TAMC differentiability (mostly missing or wrong directives).
See doc/tag-index and doc/notes_c37_adj.txt Preparation for stand-alone autodifferentiability.
remove "include CG2D.h"
move the IO at the end of a time step
set initial Time & Iteration counter in the_model_main and pass them as argument to the_main_loop
Made sure each .F and .h file had the CVS keywords Header and Name at its start. Most had header but very few currently have Name, so lots of changes!
Restructered the calling tree between THE_MODEL_MAIN()
and DYNAMICS(). Two calling levels have been inserted
to better split the "fixed" initialization phase from
the main time-loop for easier connectivity with the adjoint
infrastructure.
The calling tree now looks like:
the_model_main:
initialise_fixed()
the_main_loop()
the_main_loop:
initialise_varia()
do i=1,nIters
forward_step()
enddo
forward_step()
forward_step:
load_external_fields()
dynamics()
do_the_model_io()
solve_for_pressure()
do_gterm_blocking_exchanges()
write_checkpoint()
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