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Merging from release1_p5 (cf. tag-index for checkpoint46).
* need to call UPDATE_SURF_DR even if momStepping=F (RealFreshWater)
Included CPP option ALLOW_AUTODIFF_MONITOR to enable/disable use of adcommon.h/g_common.h
add argument myIter & myTime to S/R routine solve_for_pressure
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
small changes associated with NonLin_FreeSurf option : * initialization (ini_psurf.F); * dump hFac fields (write_state.F); * avoid unnecessary re-computation (forward_step.F initialise_varia.F calc_surf_dr.F);
Transfering major checkpoint store directive blocks to separate header files. Files are included in the_main_loop (lev3, lev2) and forward_step (lev1).
add options to select where the filters apply in the time-step
o Bugfix in adcommon.h: commen blocks were adjusted to latest common block structure in DYNVARS.h o placed a do_field_blocking_exchanges after dummy_in_stepping to ensure that addummy_in_stepping is preceded by exchanges.
#ifdef autodiff removed for future generalizations.
apply Shapiro filter on T,S before computing Phi_Hyd when stagger time stepping is used.
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 package "flt". o pkg/flt o verification/flt_example o visualization of trajectories supplied o works but output not available to testscript
Added some missing conditionals so that fixed/flow passive tracer experiments don't do any dyunamics.
modified to incorporate NonLin-FreeSurf
Moved TR1.h headers between ifdef ALLOW_PASSIVE_TRACER.
Modification for adjoint.
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.
Moved dummy_in_stepping routine to different place.
Commented out calls for Shapiro and zonal filters. JMC had moved these from the_main_loop.F to the_correction_step.F but had disabled them in the_main_loop.F by overriding CPP options. When PH re-instated forward_step.F the options weren't overridden. Commenting out seems safer.
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
See doc/tag-index and doc/notes_c37_adj.txt Preparation for stand-alone autodifferentiability.
separate the state variable "eta" from the 2D solver solution cg2d_x
apply shap_filter to U,V when Crank-Nickelson time step is used
use "zonal_filt_lat < 90." as a running flag for zonal FFT filter
move the IO at the end of a time step
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!
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
Rescaling of forcing fields done immediately after reading fields.
Change call to load_external_fields -> external_fields_load Tested for exp(0,2,4).
Moved the writing of time-averages to do_the_model_io().
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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