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checkpoint47e_post o created a tag prior to creating a branch
o updated tag-index after creating a new tag: checkpoint47d_post I still have to remove the experiments goz and gop, because they are obsolete
A new tag because a verification experiment was added.
o allow to run AIM physics with SPEEDY input files (from Franco Molteni) o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) when using P-coordinate; only implemented for atmospheric config. o OCEANICP & realFreshWater: include P-E direct effect on wVel ; NOTES: requires option NONLIN_FRSURF to be "#define". o update advect_xz/results/output.txt (left from checkpoint44g_post)
checkpoint47b_post Merging from release1_p9: o pkg/seaice - removed GOTO's and added taf directives - double precision constants to reduce the g77 (Linux) to F77 (SGI) differences reported in release1_p8 o tools/genmake - added SGI options o verification/testscript - updated to that of checkpoint47a_post o verification/global_ocean.90x40x15/input/eedata - modified for SGI f77 compatibility o verification/lab_sea - added description of sea-ice model - added missing matlab routines - added test of thermodynamics parallelization Modified Files: doc/tag-index pkg/seaice/SEAICE_FFIELDS.h pkg/seaice/SEAICE_PARAMS.h pkg/seaice/adi.F pkg/seaice/advect.F pkg/seaice/budget.F pkg/seaice/diffus.F pkg/seaice/dynsolver.F pkg/seaice/groatb.F pkg/seaice/growth.F pkg/seaice/lsr.F pkg/seaice/ostres.F pkg/seaice/seaice_do_diags.F pkg/seaice/seaice_get_forcing.F pkg/seaice/seaice_init.F pkg/seaice/seaice_model.F pkg/seaice/seaice_readparms.F tools/genmake verification/global_ocean.90x40x15/input/eedata verification/lab_sea/README verification/lab_sea/matlab/lookat_exp1.m verification/lab_sea/matlab/lookat_exp2.m verification/lab_sea/matlab/lookat_exp3.m verification/lab_sea/matlab/lookat_exp4.m verification/lab_sea/matlab/lookat_exp5.m verification/lab_sea/matlab/lookat_exp6.m verification/lab_sea/results/AREAtave.0000000010.data verification/lab_sea/results/HEFFtave.0000000010.data verification/lab_sea/results/UICEtave.0000000010.data verification/lab_sea/results/VICEtave.0000000010.data verification/lab_sea/results/output.txt Added Files: verification/lab_sea/seaice.ps verification/lab_sea/matlab/lookat_exp7.m verification/lab_sea/matlab/mmax.m verification/lab_sea/matlab/mypcolor.m verification/lab_sea/matlab/myquiver.m verification/lab_sea/matlab/readbin.m verification/lab_sea/matlab/wysiwyg.m Removed Files: verification/lab_sea/code/KPP_OPTIONS.h
Adding comment for therm_seaice and bulk_force.
make tag checkpoint47a_post
o new pkg: aim_v23 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. for now, keep the same surface forcing as before. - Part-Cell implemented into AIM; check that Heat & Water are conserved - aim.5l_cs: use new aim pkg (run 10yr & get better results than before) - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg o add diagnostic of surface correction term in monitor output
Given that we soon run out of single-character letters I take the liberty of creating checkpoint47.
Preparing checkpoint46n_post
New tag to delimit quasi-hydrostatic modifications.
Added catch for cases when experiments are checked in with insufficient monitor output for testscript to use. Instead of a 16 d.p. match testscript now returns "--" and N/O instead of "pass".
Added new routine quasihydrostaticterms() and flag "quasihydrostatic" which is false by default and enables QH mode. Exlcusive with nonhydrostatic flag.
Added non-hydrostatic Coriolis term to U equation - needs new PARAMS.h arraya fCoriCos(i,j,bi,bj) - new routine: mom_u_coriolis_nh()
Fixed sign of non-hydrostatic metric terms of form u*w/r and v*w/r. - now depends on sign of gravitySign which in P coordinates should be -1 and otherwise +1.
Added work.pc* to .cvsignore since switch from pgf77 to g77/ifc.
Added new flag "useNHMTerms" which controls appearance of non-hydrostatic metric terms: - defaults to TRUE but is set to false when metricTerms is false. This means no output is currently affected since N-H metric terms have always been associated with spherical metric terms to date. - note that N-H metric terms are both incomplete and disctetized incorrectly and are not fixed as yet. - turning off useNHMTerms affects these experiments adjustment.128x64x1, aim.5l_Equatorial_Channel, exp1, exp2, global_ocean.90x40x1, hs94.128x64x5, hs94.1x64x5, natl_box which means they all have non-hydrostatic metric terms in them.
Removed second appearance of gravitySign in a namelist.
No longer using PGI compiler (pgf77) since it does work even on our own machines! - use g77 where it works otherwise ifc
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
updating tag-index
fixed the verification/global_ocean.90x40x15 experiment: - new bathymetry (the world according to A., JMC, and M.) - new initial fields and forcing fields (*.bin files) - new POLY3.COEFFS (for the next release one should switch to a full equation of state: JMD95P or MDJWF) - fixed several errors and redundancies in the data file - experiment uses looped cells - added matlab directory with diagnostic scripts for plotting of output
* S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: - read AIM physics parameters from a file (data.aimphys) - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
* 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
Clean up AIM package (and keep the results unchanged). make tag checkpoint46i_post
o cleaned up the use of rhoNil and rhoConst. - rhoNil should only appear in the LINEAR equation of state, everywhere else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst and the dynamical equations are all divided by rhoConst o introduced new parameter rhoConstFresh, a reference density of fresh water, to remove the fresh water flux's dependence on rhoNil. The default value is 999.8 kg/m^3 o cleanup up external_forcing.F and external_forcing_surf.F - can now be used by both OCEANIC and OCEANICP
o Include a new diagnostic variable phiHydLow for the ocean model - in z-coordinates, it is the bottom pressure anomaly - in p-coordinates, it is the sea surface elevation - in both cases, these variable have global drift, reflecting the mass drift in z-coordinates and the volume drift in p-coordinates - included time averaging for phiHydLow, be aware of the drift! o depth-dependent computation of Bo_surf for pressure coordinates in the ocean (buoyancyRelation='OCEANICP') - requires a new routine (FIND_RHO_SCALAR) to compute density with only Theta, Salinity, and Pressure in the parameter list. This routine is presently contained in find_rho.F. This routine does not give the correct density for 'POLY3', which would be a z-dependent reference density. o cleaned up find_rho - removed obsolete 'eqn' from the parameter list. o added two new verification experiments: gop and goz (4x4 degree global ocean, 15 layers in pressure and height coordinates)
tagging checkpoint46f_post
Fixing Martin's tagging errors
o Added new equation of state -> MDJWF - EOS of McDougall et al., 2002, JAOT, submitted - caveat: the equation of state is only valid for a smaller (more realistic?) range of values than JMD95P/Z and UNESCO - added masks to the calculation of pressure in store_pressure - added more check values for density in check_eos (ini_eos.F), some of the old check values are out of the range of the MDJWF-eos, so don't expect perfect matches for those
o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and 'OCEANICP', also initialised field pressure correctly in ini_eos in the case of pressure coordinates. eosType='JMD95Z' in combination with buoyancyRelation='OCEANICP' now causes an error. o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) in find_alpha/beta.
Changes necessary for ocean in p-coordinates - Added new buoyancy relation = 'OCEANICP' - Added new parameters = gravitySign (this used to be contained inside the factor dRdZ which I added when we first switched to R coordinates). X GM/Redi is not compatible (yet) X bottom drag and no-slip need to be debugged.
o Added new equation of state -> JMD95Z and JMD95P - EOS of Jackett and McDougall, 1995, JPO - moved all EOS parameters into EOS.h - new routines ini_eos.F, store_pressure.F o Added UNESCO EOS, but not recommended because it requires in-situ temperature (see JMD95) o Modified formatting for knudsen2.f in utils/knudsen2 and added unesco.f to be used with POLY3
Added pressure loading term and experiment based on Wunsch and Stammer (1997) o new field in FFIELDS.h, etc... o new cpp flag ATMOSPHERIC_LOADING o Changed hFacC to _hFacC in calc_phi_hyd.F o Added SHORTWAVE_HEATING to some files for consistency
Preparing checkpoint46
import 2 fixes from release1_p5
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S (affects plume_on_slope "cg2d" output)
rescaling gNm1 (NLFS + A-B) improve the global conservation of tracer
change phiMin in exp1 (to agree with documentation) and add few flags ...
Creating yet another checkpoint: checkpoint45c_post
Creating checkpoint45b_post
checkpoint45a_post o compute Rho over the whole domain (extend iMin,jMin indices) o specific exchange for X-slice domain (case Ny=1)
add small fix (solve_for_pressure, obcs_calc in exp4 & internal_wave)
Creating checkpoint44h_post = checkpoint45
o vertical grid option: allow to put the Interface at the middle between 2 cell-centers ; replace delZ in pkg/kpp by drF.
o GM Advective form: Tracers are advected using the residual transport (= Euler+GM-bolus); set GM_AdvSeparate=T to return to previous form.
create checkpoint44g_post : o fix surface correction term in multiDimAdvection (affects plume_on_slope results) ; ifdef missing in thermodynamics.F
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.
Document testscript -cleanup.
modification in pkg/shap_filt (affects allmost all S/R): a) new shap_filt S/R to use no-slip BC with S2 filter b) enable to filter 2D fields.
Document checkpoint44e_pre,post
Creating chkpt44d_post (I forgot to create chkpt44d_pre, but chkpt44d_pre = chkpt44c_post).
updated: o real fresh water flux implemented with non-linear free-surface.
chkpt44c_pre,post 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
updated
updated
Creating checkpoint44
updated
Annotation of c43.
Creating checkpoint42
Annotation for c41
Annotations for c40
Annotation for c40pre9
Checkpoint40pre8 (postponing c40)
Creating checkpoint40 --- no pre, no post, no nothin'
Creating checkpoint40pre7.
New tag checkpoint40pre6.
New tag: checkpoint40pre5
checkpoint40pre4
Doc. for checkpoint40pre3
Doc. for checkpoint40pre2
checkpoint39
checkpoint39
See doc/tag-index and doc/notes_c37_adj.txt Preparation for stand-alone autodifferentiability.
new tag
add a new tag (checkpoint36)
New checkpoint
Checkpoint34 (update).
Checkpoint34.
New tag (checkpoint32)
Notes for checkpoint32 added.
Comments for checkpoint31.
New tag.
New checkpoint (29).
Included documentation of changes from c27 to c28. (P.H.)
New checkpoint.
New checkpoint
Checkpoint 25
New checkpoint
New checkpoint
Entered checkpoint22 into tag-index.
New entry in tag-index for checkpoint21
Creating checkpoint20
Notes for tag checkpoint19.
Updates to tag0index for checkpoint18
Record updates for checkpoint17
Checkpoint16 documentation updates
CHanges to exchange routines for general tile <-> tile connectivity, DMA and shared memory communication hooks, variable width overlaps and TAMC reverse mode flag.
Consistent isomorphism changes
Added tag-index record for checkpoint13
Creating a tag in order to make a branch. See tag-index for info.
*** empty log message ***
New tag checkpoint11
Making tag checkpoint10
o General tidy-up. o MPI fix. Filename changes (meta/data). salbin*y stuff. o SST.bin SSS.bin added to verification/exp2
New tag and tag-index.
Fairly coplete 4 degree global intercomparison setup. Includes changes to make convective adjustment and hydrostatic pressure correct as well as IO for climatological datasets
Added tag-index record for checkpoint6
Added tag description
Added notes for new tag - checkpoint4
Added tag-index file for recording "release" information associated with a tag.
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