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checkpoint58b_post
o AIM+thSIce: fix sign of Short-Wave through the Ice ; update output.txt of exp. aim.5l_cs.thSI
various mnc cleanups and improvements: + shrink lookup tables by factor of ~4 + better error reporting when running out of lookup space + able to handle longer path/file names (up to 500 chars)
o Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. o TBD: "hidden" mom_vecinv recomp. in dynamics
change forcing_In_AB to affects both T,S forcing and Momentum forcing and add new flag to put Dissipation tendency out of Adams-Bashforth.
updating
o updating
remove the BUILD_INFO.h include from CPP_EEOPTIONS.h
updating
updating
o Apply mask on Fresh-Water flux (needed for SSH forcing). update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
updating
Adding parameter to remove on-the-fly global mean and trend from exf forcing and ctrl control adjustments
o change the default rotation period to 86164.s = the Earth rotation
o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) and based on a reference stratification. Tested within hs94.cs-32x32x5.
updating
forgot to commit an earlier comment, sorry
updating
taggin before I commit seaice changes
updating
updating
updating
o fix bug (typo) in obcs_apply_eta.F
o updating
updating
updating
o AIM pkg: change threshold on large-scale condensation to conserve Heat.
o pkg/diagnostics: add options and parameters for regional-statistics diagnostics ; define regions by reading a region-mask from a file (might add other options later)
o pkg/bulk_force: - add option and parameters to use AIM surface-flux formulae. + some cleaning.
checkpoint58
add "--embed-source"
Updating
tag checkpoint57z_post
Updating
Updating
o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): affects output (@ truncation level) of exp. plume_on_slope ; updated.
o updating
o no AB-2 on Gw at the first iteration (consistent with Gu,Gv,Gt,Gs ...) affect results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) o transfert surface NH pressure to eta field (if exactConserv).
Adding unfinished 3-dim. relaxation code.
o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
and update lab_sea output.txt file.
Updating
Update
o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
o adding new package rbcs
o gchem/dic/cfc/offline changes
checkpoint57x_post
o cleanup our namelist syntax in verification: - make it more F95 standards compliant (some work still needed) - allows the vast majority of our tests to work with gfortran
o Disable useVariableViscosity for adjoint for time being (there are a number of extensive recomputations) o Initialize certain variables needed for adjoint
o Non-Hydrostatic: - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
o Allow to apply AB on T,S rather than on AB(gT,gS): - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 - use the same arrays (gtNm,gsNm) to hold tracer field at previous time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). - need a "clever" read_pickup to restart from the other AB formulation
o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h o remove some unused variables (reduces number of compiler warnings)
checkpoint57w_post
pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
fix the singleCpuIO RS version of MDSWRITEFIELD
and add a WARNING if using globalFiles=T with multi-processors.
o write grid-file(s) in only one format (MDS or MNC): default=MNC (if using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
o tracer advection scheme: add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, was not very convenient). add implicit version for DST-3 & DST3_Flux_Limit vertical advection; (further tests needed for the implicit DST & Flux-Limiter schemes)
o updating: add namelist parameter PTRACERS_ref in analogy to tRef and sRef for convenience, handy, when you want to initialize ptracers in a large domain with a constant non-zero value. Also, untangle ptracers_init.F a little.
checkpoint57v_post o change dome exp. to use variable viscosity in side-drag terms.
o add new parameter: sideDragFactor to enable half-slip-side BC and change side-drag S/R to use viscosity from mom_calc_visc (can switch back by setting sideDragFactor=0.); affects results at truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
o remove all the files from the cfc_offline test since they are now incorporated into tutorial_cfc_offline which has been producing identical results for a few days of testing
o vorticity & strain are now computed without masking, to account for no-slip-side BC in variable viscosity calculation ; mask is applied anyway later on, before computing advection/coriolis terms.
updating
o Updating: fix behavior of ptracers_monitor when monitor output is written to a netcdf-file; still not independent of monitor.F (writes in the same file).
o change default value of tRef (put a uniform, meaningful value for ocean & atmos) and initialize sRef (was missing, as Martin mentioned).
Fix bug and add to tag_index.
fix typo (oh, well)
Updating: new tag
Updating:
o OBCS and PTRACERS: add open boundary support for passive tracers
- either use homogenous (pseudo) v.Neumann conditions or prescribe
OB-values from file; this is not different from the way theta and salinity
are treated
- however, Orlanski-radiation conditions are not supported, and the model
will stop if you use pTracers and Orlanski at the same time.
- beefed up the rountine obcs_external_fields_load: now only those open
boundary values are overwritten with values from files for which there
are really files, otherwise the OB-fields remain untouched. This makes
it possible to use different OBs at different ends of the domain (as
with EXF)
- TODO: add support for OB?w and OB?eta, which can currently not be read
from a file.
o reduce number of exch calls in shap_filt (s2).
o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ truncation level) 4/5 MLAdjust test results (11&12 digits match).
checkpoint57t_post
o new test: global_ocean.cs32x15.viscA4 o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum.
o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); note that biharmonic viscosity + no-slip is not tested in any experiment.
o fix bug in non-linear free-surf side-drag ; generate new output for global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
o make mnc honor the writeBinaryPrec flag for all the non-pickup and non-diagnostics output types
o mention eesupp changes
o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
o add brackets in multi-terms sum to get same truncation, independent of the face number (manage to get exactly same value of gU,gV at the cs-edge) affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
Adding clean version of mom_calc_visc and viscAhRemax and viscA4Remax params.
checkpoint57s_post
Update tags to reflect corrections to viscosity calculations.
o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
o In response to JMC's bug report, genmake2 now ignores any soft-links that it finds in the *current* directory when searching for files. Soft-links found in any other source directories will still work as they did before. And regular (non-soft-link) files will also work as before.
o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
a C routine to unlimit the stack size
- very helpful on clusters of workstations since the ulimit/limit
behavior can (otherwise) only be inherited from parent processes
which is difficult with some MPI-over-ssh/rsh implementations
o mention aim
o mnc-ify pkg/land as requested by Daniel
o various changes to mnc including:
- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
- output can now be grouped so that all files within a group
change the ITER portion of their names in lock-step together
- can now read ("global") PER-FACE (in addition to PER-TILE) files
and works with both EXCH1 and EXCH2 (but needs more testing)
- writing works for all verification test cases w/ g77 on Linux
checkpoint57r_post
o make MNC variable initialization happen earlier
o add diagnostics for (almost) each term of the momentum Eq.
Updating
Updating.
o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) o remove MINIMAL_TAVE_OUTPUT option ; add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
Updating
o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) update exp. cpl_aim+ocn output.
o mention seaice mnc/mdsio bug
Updating
checkpoint57p_post
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
(already the case for some pkgs, including recent MNC_init, e.g. thsice)
o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F (was already the case for dissipation with mom_vecinv, and also the case for grad.PhiHyd when staggered-timeStep) This will allow to put dissipation out-off the AB time-stepping. Unfortunately, affects truncation error. Update output of exp. that "fails" (cg2d matching number) and leave the others for later: front_relax(10), global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
Updating & tagging
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and (2) its ready to be documented during the 20050801 DocFest
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc for ideal_2D_oce and lab_sea on linux_ia32_g77
Updating & tagging
Updating
Updating
Updating
Updating
Adding precip control
Tagging for pre-checkin
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) and advect_cs (use EXCH-2 and standard cs-32 grid files).
o pkg/exch2: filling of face-corner halo regions is optional (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
checkpoint57l_post tag before updating tutorials (pre-release-2)
o add cos & sin of grid-direction orientation angle (curvilinear grid only, for output and interpolation of input fields onto model grid) o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). Affects results of exp. rotating_tank ; update output.txt.
update the previous comment.
o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
and/or using a fraction-weight field.
o add mnc output capability to diagnostics/diagstat and update our cvsignore files for the ACSII output generated
Tagging c57k_post to provide tag for lab_sea with diagnostics
tagging checkpoint57j_post
o add matlab scripts for CS-grid vectors (in utils/cs_grid)
o diagnostics pkg: change pointers so that 1 diagnostic can be used several times with different frequencies.
o mnc-ify the thsice package as requested by Daniel Enderton - the monitor--MNC output needs work - many attributes need to be added (most are currently blank) - does not break testreport (at least on IA32)
o mnc-ify aim_v23 as requested by Daniel Enderton - sets sane default flags (unchanged behavior) - does not break aim.5l_cs or aim.5l_LatLon verification tests
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
o add Sadourny like discretization to the 4th.O vorticity advection scheme
updated.
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
update output.txt from: aim.5l_cs (& .thSI), fizhi-gridalt-hs
and global_ocean.cs32x15 (& .thsice).
o fix few little things to avoid floating error with -ftrapuv (ifort v9) (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
tag checkpoint57i_post
Changes in diagnostics package behavior
o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; add 1rst Order upwind vertical Shear.
o add a quick fix for A/B checkpointing in OFFLINE mode
o add IGNORE_TIME define and -ignore_time option to genmake2 as an end-run around the C/Fortran linking horror in eesup/src/timers.F
Logged addition of pkg/runclock and nh_am2
added a few "_d 0" and D0 (in PARAMETER statements) in a desperate effort to make vermix.my82 pass on a Sun, unfortunately no success; but for cleaner code I check it in anyway.
o for mnc output, fill the 'T' coordinate var with myTime and create a separate 'iter' variable for iteration count
o pkg/diagnostics: Global statistics tested against monitor output. o make seaice-pkg I/O type flags (MNC/MDS) more standard.
o pkg/diagnostics: add new capability: output of Global/Regional & per-level statistics
checkpoint57h_done tag after changing user customized files (DIAGNOSTICS_SIZE.h, data.diagnostics, data.gchem, data.ptracers) is done.
o pkg/diagnostics: prepare for Global/Regional statistics. add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE and rename it: DIFFERENT_MULTIPLE
checkpoint57h_post o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
o pkg/diagnostics: change output frequency, now in seconds (instead of Nb of iterations). This requires to change data.diagnostics.
make a tag before changing diagnostic frequency.
o in mnc, let the user create the output dir if both mnc_outdir_date and mnc_outdir_num are false
o add fflags() to pkg/diagnostics which allows one to specify, on a per-file basis, the file precision [default behavior is unchanged]
o added diagnostics to pkg/kpp, including computation of mixed layer depth based on a temperature/density criterion o updated verification/natl_box to test the new pkg/kpp diagnostics
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, not mnc -- this mistake was found by JMC and is now corrected
checkpoint57g_post o add Adams-Bashforth 3rd Order time stepping: - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
tag checkpoint57g_pre before Adams-Bashforth-3
checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
updating
updating
checkpoint57f_post o add parameter "baseTime" = model base time = time at iteration zero new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to account for baseTime shift o move Coriolis arrays from PARAMS.h to GRID.h
checkpoint57f_pre
updating
o mnc-ifying the seaice package
Alternative length scale calculation in mom_vi_hdissip.F
updating
Add tag on LeithD.
o add "d0" in getcon.F to reduce differences between compilers/platforms update output.txt of exp. fizhi-gridalt-hs
o change port_rand funtion to allow to set the seed.
o fix obscure MNC bug involving conversion between reals and integers
- it caused no problems with certain (eg. gcc, ifc) compilers but the
new version is now more standards-compliant
updating
updating
o fizhi pkg: fix AtoC and CtoA when called with same input & output array update output.txt of exp. fizhi-gridalt-hs
o add more "Z" dimensions and associated coordinate vars to MNC
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
o parameter calendarDumps: when set, approximate months (30-31 days) and years (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar months and years. Requires pkg/cal.
o diagnostics: add pickup functionality - off by default for backwards compatibility - current version only uses MDSIO -- MNC will be added
updated (Shapiro tendency diagnostics)
o allow to use pkg diagnostics for LAND pkg output.
o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
checkpoint57d_post o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
o modify verification/ideal_2D_oce so that it tests the creation of mnc output from the diagnostics package
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
o make genmake2 more portable by using ".$FS" instead of ".f" for more of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
o add coordinate variables to the MNC output from the diagnostics package
o change MNC-flags default value: true when useMNC=TRUE
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F the ability (off by default) to read the grid information using MNC
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
o do snap-shot diagnostics at the middle of the time-interval (instead of at the end).
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add new test for AIM with thSIce + slab-ocean
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
o move state variable diagnostics to the beginning of the time step ; (note: still needs some work specially for snap-shot diagnostics) duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
checkpoint57c_post o Change testing option (-ieee) to get closer agreement between g77 & ifort o generate new output.txt files on faulks with g77 & the new -ieee option
tag before changing default testing option with g77
o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT"; update output.txt of exp. global_ocean.90x40x15
o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
updating
updating
add saltFlux(+File) forcing capability with periodicExternalForcing
o allow to use pkg diagnostics for GM-Redi & ThSIce output o diagnostics_fill: fill-in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
o improvements for the MNC output from DIAGNOSTICS:
- correct handling of the unlimitied dimension
- all dims now have associated coordinate variables
- variables located at U, V, and Corner ("Z") points are now written
with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
*all* data points are output
o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
o added pkg/seaice/seaice_monitor.F
o mdsio_readfield.F can now read files visible only to master process
o pkg/seaice: some test code for ice-modified ocean stress
o exf_getffields interpolation defaults to bilinear for all scalar forcing fields (remains bicubic for wind velocity and stress). This avoids, e.g., spurious negative numbers for precipitation and humidity. Will cause some small numerical differences for integrations using pkg/exf/exf_interp.F.
checkpoint57b_post o simplify options in diagnostics_fill arguments (remove weird combinations)
o fix MNC coordinate variables so that they now contain per-face index values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in general, EXCH2 grids are only aligned to a "local" coordinate system
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) o Implement instantaneous output within pkg diagnostics: setting a negative frequency in data.diagnostics produces "snap-shot" output (as opposed to time-average if freq > 0)
o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
NOTE: change ptracer diagnostics name: use 2 characters to work with
more than 9 tracers. Add also diagnostics of advect & diffus flux.
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it becomes the coordinate variable for the 'T' dimension
o add CF-style coordinate variables to MNC
- just a first cut: numbers are meaningless on the cubesphere and
missing along the T axis but otherwise it works!
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) this is based directly on what the model compute, so that the content of each diagnostics might be affected by switching options (e.g., implicitDiffusion) o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
o updating
o updating
o changes per discussion of AM, JMC, & EH3 today:
- move redundant "grid" variables out of "state" -- in preparation of
creating proper CF-style coordinate variables and in recognition
that any/all grid variables can be easily copied (eg. w/NCO) from
the grid files into any of the other NetCDF files
- *always* output grid variables with MDSIO (this will eventually be
changed)
- output MNC grid file if useMNC is true
o every instance of _END_MASTER() has been found and replaced with _END_MASTER( myThid ) in order to satisfy certain picky Sun preprocessors
re-arrange diagnostics pkg initialisation: - allow each package to extend the available diagnostics list - add some checking and fix small problems (multi-threaded, ...) - new S/R diagnostics_fill (replace fill_diagnostics): look through the short list of active diag. (instead of the long list) create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
close bracket
Open bracket for TAMC-related changes
checkpoint57
updating
o updating
- switch back to "sflux = sflux - runoff" in exf_getforcing.F - use bilinear instead of bicubic interpolation for runoff, to avoid negative numbers.
o implement Implicit Vertical advection for pTracers
updating
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) (implemented also for implicit vertical diffusion & advection)
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) (not yet implemented for implicit vertical diffusion & advection)
o updating
o updating
o updating
o updating
o updating
o updating
o document changes (hopefully), to be done: regenerate dic_example output, because it was wrong, and check in an example that test the cfc-pkg.
o add PTRACERS (PTR0[1-5]) to testreport output
o updating
updating
o GMredi: - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
o small cleaning of exch2: remove files that are also in eesupp/src
o updating
o GCHEM: move call to GCHEM_FORCING_SEP, so that it is now called before the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
updating and tagging
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
o cleanup full files
checkpoint55j_post
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
o add build dirs
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
o make all subroutines 30 or less characters in length for certain older compilers to work
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
was supposed to be checkpoint55i_post (instead of g)
checkpoint55g_post o change arrays for total vertical diffusivity (2.D if explicit, 3.D if implicit) ; each ptracer uses its own background value.
o add comments about ocn_compon_interf, mnc, and ITRDA
fixed wayward endif in mom_fluxform that messed up cyclindrical configuration
o give MNC the ability to create additional files rather than
exceeding a specified file size limit
- run-time configurable (in data.mnc) as "MNC_MAX_FSIZE"
- the default is just less than 2GB which is a practical limit
on many systems (eg. Baylor's and Helen's recent problems)
- tested and works on Linux/g77 -- needs testing elsewhere
Compute the non-local term using either KPP vertical diffusivity (default)
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
checkpoint55h_post o add verification test "vermix" o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS o useMNC moved from data.mnc to data.pkg
o remove all the *_ioinc flags and replace them with the single global outputTypesInclusive flag
o allow to set a vertical profile of vertical diffusivity for T & S
sorry, yet another tag, checkpoint55g_post
o checkpoint55f_post
o some delicate re-shuffle of store directives to avoid one extra call of do_oceanic_physics o NB: this may break global_ocean adjoint temporarily, but it is clear how to fix it. Will do later, need this now.
updating
o add ability of MNC to write local and "partial" (eg. 2D slices where the full 3D field is never actually stored) arrays to NetCDF files with the correct (that is, the complete multi-dimensional) set of array indicies - used in mom_vecinv() to write the diagFreq output - tested (demonstrated) in verification/aim.5l_cs
o further mnc-ification - add kpp to mnc output (both snapshot and timeave) - add verification/lab_sea to the list with mnc setups o reformat files for ProTeX
o non-hydrostatic code:
- add new parameter viscAhW, replaces viscAh in calc_gw, defaults to
viscAh. Useful when viscAh=0 in non-hydrostatic simulations
o fixed about 35 bugs
extend simple cost functions to treat time mean quantities o cost_tile called from forward_step o cost_accumulate_state called from cost_tile
modified argument list of CALL OBCS_CALC to myTime+deltaTclock
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
be 2 times larger than the minimum size the advection scheme requires.
now get a perfect conservation of salt in advect_cs test-exp (updated)
o updating
- add horizontal diffusion of TKE, requires exchanges in
do_fields_blocking_exchanges, horizontal diffusivity is zero by
default. In OPA there is no horizontal diffusion of TKE but the
mixing coefficients are computed from a horizontal average of TKE of
6 points or so. I think that diffusion has a little more physical
justification.
- clean up ggl90_calc in the hope of reducing memory usage (this hope
was in vain)
- mask tke-variable in ggl90_init
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) o fix biharmonic diffusion on CS-grid.
o updating
Adding obcs exchanges for useOBCSprescribe
updating obcs
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments which simplifies the calls and passes the ifc check-bounds test
checkpoint55b_post o add a 2D scalar, Z location, exchange_2 routine.
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] affects advect_cs results (for the wrong reason): update output.txt
o use a more standard discretization for biharmonic viscosity ; (original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) affects results of dome set-up: update output.txt o fix gad_advection.F (CubedSphere part), back to version 1.23 o fix bug in mom_vi_del2uv.F (CubedSphere part).
o merged code to
* prescribe/read time-dependent open boundaries
(works in conjunction with exf, cal)
* sponge layer code for open boundaries
* each boundary N/S/E/W now has its own CPP option
(healthy for the adjoint)
sheduling c55 so that john can write more adjoint papers without crediting the developers!
tagging checkpoint54f_post
o updating tag-index
o add comments about IO
o BUILD_INFO.h comment
o added two new packages o create a new tag
o add offline package
o add dic_example
o genmake2: add ability to search for C compilers and cleanup test output - fixes recent SX-6 problems and should help with others (eg. HP-UX)
checkpoint54d_post o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, leading to additional shift by 5 days each year of integration (i.e. leading to considerable offset over the years)
Added feature: - if levels() is ommitted from namelists in data.diagnostics then ALL levels are diagnosed instead of none
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep o start with no AB and no initial filtering (staggerTimeStep): change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F (external loading & cpl import/export stay in forward_step.F) o update coupling interface to work with new staggerTimeStep o change MDSIO ptracers_pickup.
update (few bugs fixed)
o netcdf (mnc) now compiles and runs on halem
checkpoint54c_post
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr this affects (truncation error) output.txt of test-exp: global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
o change Qnet to always be the net heat flux, (+upward). affects (truncation error) output of natl_box exp.: updated
o define the max number of passive tracers in PTRACERS_SIZE.h o start to test routinely pkg/mnc in exp0 o add sea-ice loading (sIceLoad) as a new forcing field.
add "checkpoint54b_post", created yesterday but missing in tag-index
o add testreport "-j JOBS" for parallel builds -- gives impressive speedup on Altix, Opteron, and other SMP machines
o add diagnostics/mnc
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
o staggerTimeStep & NLFS: rescale T & S surface tendencies. affects (truncation error) output of lab_sea & natl_box exp.: updated o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
checkpoint54a_post o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) + internal_wave (shift in writing cg2d_ini_res)
o tag before changing staggerTimeStep : checkpoint54a_pre
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice - modified verification/lab_sea and natl_box_adjoint accordingly
updating
update
o prepare splitting of thermodynamics: store convect.counter in common block
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
o new parameter "nShapS": allow to treat differently S from T (nShapT) o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
checkpoint53f_post o modifications that affect AIM experiment results (update output.txt): - no advection of S at top interface Nr (pkg/generic_advdiff) - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
o AIM pkg: - include stability function into surf.Flux derivative relative to Tsurf - calculate clear-sky radiation & surface temp. change (for diagnostics)
added checkpoint53e_post notes
o about to check in some rotating tank merges
checkpoint53d_post
o faulks upgraded: re-generate output.txt that has changed: global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
Added vertical diffusivity profile (T/S) due to Bryan and Lewis, 1979. New parameters: diffKrBL79surf - surface diffusivity diffKrBL79deep - deep diffusivity diffKrBL79Ho - turning depth for arctan function diffKrBL79scl - depth scale for arctan function This diffusivity is added to all other diffusivities. The defaults are set so as to give zero diffusivity.
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
Added Sadourny discretization of Coriolis in V.I. mode - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h - re-enabled use of omega3 in mom_vecinv.F
Added variable viscosity for the vector invariant equations based on Leith, 1968, Phys. Fluids (10) 1409-1416 - the use of the variable viscosty in the no-slip boundary conditions has not been implemented (but should be) - new parameters viscC2leith and viscC4leith are non-dimensional - I decided to modulate the variable viscosuty with the same viscAhMax and viscA4max; ideally we should have another maximum based on dx^2/dt etc.
o add comment
Bug fix for mom_*_sidedrag.F
Fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation of mom_common/ - simple re-arrangement of instructions within computing loop
updating
o new version of coupler for AIM+thSIce and Ocean models - new fields (SSS,h_MixLayer ...) are exchanged through the coupler - land: change Evaporation of snow - aim with thSIce: fix bug in snow-precip.
ebm package wasnt quite up to the parallel task. Fixed that.
o updating
tagging
updating
Created pkg/mom_common/ o changed pkg_groups and pkg_depend o moved duplicate files in mom_vecinv and mom_fluxform to mom_common/ This is in preparation for checking in Smagorinsky and Leith type variable viscosities.
o pkg/land: only liquid water can diffuse or run-off o AIM with land: soil wetness availability account for snow
o added printMapIncludesZeros to EEPARMS namelist
added comments for mods to verification/natl_box_adjoint
updating
Added comments for checkpoint53
o about to create checkpoint52n_post
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
- changed proxy for geostrophic velocity and updated
verification/lab_sea/results/* accordingly
- changed proxy for geostrophic velocity and updated
verification/lab_sea/results/output.txt accordingly
o removed ADI dynamic solver from pkg/seaice
o replaced all occurrences of 1/CSTICE or 1/CSUICE - they caused a segmentation fault under certain circumstances - removed unused field WATR
o bug fix in exf-package:
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask
now reflect that.
- fortuitously this change does not affect any of the verifaction
experiments
o small fixes in the cal-package:
- set reference date to first of January for the 'model'-calendar
- failing of cal_CheckDate in cal_FullDate now actually results in a
warning
o small modifications in exf-package to increase flexibility:
- change climtempfreeze from a constant to a runtime parameter that
is specified in data.exf_clim (default = -1.9)
- introduce runtime parameter windstressmax (default = 2.0) that is
specified in data.exf
fix in pkg/thsice ; update (global_ocean.cs32x15/) output.txt.thsice
make checkpoint52m_post
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; this does not change any of the results, because myIter=0 in swfrac always lead to jwtype=2 (the default anyway), but the call makes little sense as a default
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow atmospheric model (AIM) to use it ; add a "slab ocean" component. o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
o extending useSingleCpuIO option to work with new exch2 I/O format
- old-style, missing-tile I/O is still accessible by defining CPP
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
o add notes
o added api_reference comments
updating
o C code to create a directory (eg. "mnc_20040322_0001") with a name based on the creation date and a sequence number
o add mnc comments
o thermodynamics sea-ice (thsice) is now tested with testreport. o test exp. advect_cs: use the standard cs32 grid ; update output.
checkpoint52l_post
o new land formulation:
a) use ground enthalpy as prognostic variable to ensure exact
energy conservation.
b) account for water temperature and for latent heat of freezing
in all processes (rain, run-off, ground storage)
c) compute surface and ground temperature implicitly.
o aim_v23 modification for new land model:
a) Treat separately land / ocean / sea-ice surface fluxes
to allow implicit computation of land & sea-ice surface temp.
b) add snow precipitation.
checkpoint52l_pre before checking in new land model.
o fix problem (when 1 tile is empty) in min/max monitor. o fix bug in timeAve (u,vZetatave in common block)
o no restoring terms under ice for pkg/seaice o modfied EXF_EXTERNAL_FLUXES option o added exf_albedo parameter
o moved SEAICE_DO_DIAGS to S/R do_the_model_io o bug fix for pkg/seaice pickups
o MNC changes
updating
o mask vorticity at the corner ; affects global_ocean.cs output o fix ini_curvilinear_grid ; test CS experiments with mpi
aim.5l_cs: modify sea-ice fraction input file ; update output
updating
c52k_post
Logging monitor bug fix and tidy up of diags
updating
gave pkg/mdsio/mdsio_readfield.F more useful logic and error messages
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating debug output
o modified mdsio_writefield to handle non-global files under exch2
o update AIM Cubed-Sphere exp (aim.5l_cs): use land, p*, and Franco.M forcing fields with fractional land-sea mask. o update AIM Equatorial Channel exp: use standard aim_v23 pkg and change the SST fields to be more realistic.
o limit timeave output for hi-res integrations
o modified mdsdio_readfield and mdsio_writefield to make exch2 do globalFile -- but *not* usesingleCPUIO
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and mon_vort3.F to make exch2 friendly with >1 tile per cube face
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of the old pkg/aim).
New tag checkpoint52i_pre/post
Modified doc/tag-index and verification/lab_sea/README
shortened offending lines in exch2_send_rx?.template
Modified W2_EXCH2_TOPOLOGY.h to reflect current topo generator
o added temporary hack for sea-ice dynamics on the cube: metric terms are ignored and it is assumed that there is no sea-ice on cube faces 1, 2, 4, and 5.
o genmake2: add build & execute test for NetCDF code
aim.5l_cs and global_ocean.cs32x15 now using exch2, grid file cleanup
o added useSingleCPUIO flag to monitor.F and mon_out.F
remodified tag entry
Added exch2 routines and pointed hs94.cs-32x32x5 at them
checkpoint52e_post o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) to work with implicit vertical advection and AB ; o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. o update output (gad_calc_rhs.F changes affect truncation error) of exp: front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
o first attempt to solve vertical advection (momemtum & T,S) implicitly: for now, only implemented with Lax-Wendroff (tracer) and VecInv (mom)
tag checkpoint52e_pre before adding implicit vertical advection
o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
fix for long (>60 years) integrations
Missed entry for last tag
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 ocean exp. that uses NLFS: global_ocean.cs32x15 & global_ocean_pressure
added exf_offset_atemp for Celsius to Kelvin conversion of atemp
o Updated tag index file for fizhi infrastructure changes
tag checkpoint52d_post
o new experiment, cpl_aim+ocn: coupled ocean - AIM atmosphere on cs32 grid.
first version of the coupler + interfaces for multi-components set-up.
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code to conform to the common rule.
o changes to permit hi-res, cubed-sphere, configuration
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
of surface winds for the cube
(A verification experiment, based on global_ocean.cs32x15, but with
pkg/seaice turned on and with on-the-fly interpolation from the NCEP
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
complete with example surface forcing files and matlab scripts to look
at the output and compare it with that of global_ocean.cs32x15.)
added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
added tag checkpoint52d_pre
add call to AIM pendant S/R in external_forcing & external_fields_load.F
o surface flux time-av diagnostic modified for NLFS & RealFreshWater
Reverse mode: 53 -> 52
tagging checkpoint52c_post
updating
updating
checkpoint52b_post
o new version: "thsice" of thermodynamic sea-ice pkg:
- only 1 call from "forward_step"; conserve energy, fresh-water & salt.
- modify fluxes but do not change theta directly;
- light cleaning of bulk_force pkg (still needed with thsice).
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice
+ output_thsice.txt to test thsice & bulk_force pkgs.
o put back grid & coriolis monitor output.
tag checkpoint52b_pre before checking-in new ThermSeaIce (ThSIce) pkg
updating
updating
FREEZE_SURFACE is the new version of FREEZE and limits only surface temperature; keep the old version of FREEZE to reproduce old results.
o modifications to make FREEZE flux visible to pkg/kpp
- moved surfaceTendencyTice from pkg/seaice to main code
- FREEZE moved to FORWARD_STEP
- subroutine FREEZE now limits only surface temperature
this means new output.txt for global_ocean.90x40x15,
global_ocean.cs32x15, and global_with_exf, but note
that results for these three experiments remain
bit-identical to before if allowFreezing=.FALSE.
o added surface flux output variables to TIMEAVE_STATVARS
o time-averaged output for pkg/ptracers
o some bug fixes for #undef REAL4_IS_SLOW
tagging checkpoint52 = ecco_c52_e35
updating
o creating checkpoint51s_post
o created checkpoint51r_post
tagging checkpoint51q_post
o creating new tag
o updated and tested version of the cd_code package o almost all of the cd_code functionality has been moved into the package but some cleanups (read/write checkpoints) remain
o add a "cd_code" package and update all the verification tests so that they use the new package instead of "INCLUDE_CD_CODE"
updating old info
tagging checkpoint51o_post
o undid all of the cp51 checkin pending some ongoing code cleanups and discussion
o modifications to make FREEZE flux visible to pkg/kpp
- moved surfaceTendencyTice from pkg/seaice to main code
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
- subroutine FREEZE now limits only surface temperature
(this means new output.txt for global_ocean.90x40x15,
global_ocean.cs32x15, and global_with_exf)
o added surface flux output variables to TIMEAVE_STATVARS
o added the [#include "AD_CONFIG.h"] statement to all files that need it for adjoint/tl #defines o re-worked the build logic in genmake2 to support AD_CONFIG.h o removed tools/genmake since it no longer works
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
Output on faulks using -ieee with of=linux_ia32_g77: Y Y Y Y 13 16 16 16 0 16 16 16 16 16 16 16 16 13 13 13 16 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 14 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 16 13 13 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 16 16 16 16 13 16 pass aim.5l_LatLon Y Y Y Y 13 16 16 16 16 16 16 16 16 16 13 13 13 13 13 22 16 pass exp0 Y Y Y Y 14 16 16 16 16 16 16 16 22 16 16 16 16 16 13 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 13 16 16 13 13 16 16 13 13 16 16 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 13 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 13 13 16 pass global_with_exf Y Y Y Y 16 16 16 16 16 16 16 16 16 13 13 13 13 16 16 9 16 pass hs94.128x64x5 Y Y Y Y 13 16 16 16 16 16 16 16 16 13 16 16 16 13 13 22 16 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 9 10 16 13 13 16 16 16 22 16 16 12 13 13 13 22 12 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 13 16 16 16 13 16 16 13 12 13 13 13 12 13 FAIL lab_sea Y Y Y Y 11 16 16 16 16 16 13 16 13 13 13 12 13 12 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
o first version of genmake2 that works with TAF -- note that only the "ad_taf" target has been confirmed to work and the others are in progress
changes to pkg/cal and pkg/exf that allow and speed-up long integrations
o add salt flux to forcing fields (used when salty sea-ice forms or melts) o enable to apply restoring on S & T only in a latitude band. o update output (external_forcing_surf modif. change truncation errors) global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
checkpoint51k_post
o change default to: useNHMTerms=.FALSE.
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
- new output.txt for idealized oceanic exp (NHMTerms are now turned off):
exp1, ideal_2D_oce
- change data file of oceanic exp (leave the results unchanged for now)
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
o set gravitySign automatically according to the vertical coordinate used
(and change sign: back to "logical" value: +1 when R increases downward)
*** empty log message ***
tagging checkpoint51j_post
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
New tag before merging genmake2 branch
forgot to commit tag-index for c51g_post
tag c51h_pre
updating
o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation of tracer Green's fucntions for ocean inversion project.
o Mods and bug fixes to pkg/cal and pkg/exf needed for computation of tracer Green's fucntions for ocean inversion project.
o Added on-the-fly spatial interpolation capability
"USE_EXF_INTERPOLATION" to pkg/exf.
- This is a temporary Cartesian-grid hack until
the super-duper ESMF coupler becomes available.
- See verification/global_with_exf/README for usage example.
- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
flags and modified pkg/seaice accordingly.
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
non-local transport term.
checkpoint51f_post
o Added on-the-fly spatial interpolation capability
"USE_EXF_INTERPOLATION" to pkg/exf.
This is a temporary Cartesian-grid hack until
the super-duper ESMF coupler becomes available.
Usage example is in verification/global_with_exf.
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
non-local transport term.
checkpoint51e_post
o pkg/mom_vecinv:
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
- add time-ave diagnostic of vorticity advection.
o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
o atmospheric geopotential: - include water vapor effect;
- use p^kappa in p* scaling.
AIM: add stratospheric drag ; LAND : read initial state from files.
tagging checkpoint51d_post
fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
o introducing integer flag debugLevel o introducing pathname variable mdsioLocalDir for mdsio
tagging checkpoint51b_post
creating checkpoint51a_post
tagging checkpoint51
preparing c51
updating
tagging checkpoint50h_post
o new package "land": provides surface BC for AIM. o pkg/ptracers: apply exchange to all tracers after reading a pickup.
New variable in PARM03: pickupSuff is a string that can be set to indicate the suffix on pickup files. This allows us to avoid renaming the temporary pickup files.
o AIM: use true log-P extrapolation for near surface temp (= as in
F.Molteni paper) ; update aim.5l_cs output.
checkpoint50g_post
o merged with release1_p17 (pkg/seaice and verification/lab_sea)
- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
- LSR sea-ice dynamic solver moved to SouthWest B-grid location and
made the default because of faster convergence than ADI
tagging checkpoint50f_post
tagging checkpoint50f_pre
o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
+ change Evap over land. (update aim.5l_cs output)
Recorded updates by AJA
o make KPP work with PTRACERS - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is nearly a copy of kpp_transport_s - there is no analogue to SurfaceTendencyS, so I have to use gPtr(of the surface layer) instead o add a new platform SunFire+mpi (SunFire 15000) to genmake o make new tag checkpoint50e_post
o change kpp output from multiple-record state files to single-record state files analogous to write_state.F o reduce the output frequency of cg3d-related stuff to the monitor frequency, analogous to the cg2d-related output. o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, so that o make tag checkpoint50d_post
checkpoint50c_post o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
o add time-average diagnostic of U*V and vertical diffusive flux for theta. o bug fixed in convective adjustment diagnostic (multi-tile set-up). o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
checkpoint50c_pre Merging from release1_p13: o bug fix for pkg/seaice dynamic solver o Added SEAICE_initialHEFF to pkg/seaice
checkpoint50b_post o store u*,v* in gU,V instead of in guNm1,gvNm1 o in order to put the momForcing out of the Adams-Bashforth: move forcing & CD-scheme calls from mom_fluxform & mom_vecinv to timestep.F o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays o re-generate output for highly sensitive test-exp: global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
tag checkpoint50b_pre before modifying momentum timestep.
o restore the use of momAdvection & useCoriolis flags (mom_vecinv).
updating.
updating
tagging half a century.
updating.
updating.
tagging checkpoint49
tagging checkpoint48h_post before commiting AD-related changes.
Modified File doc/tag-index
o SEAICE_WRITE_PICKUP needs to be called before WRITE_CHECKPOINT
o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F o Added SEAICE_initialHEFF to pkg/seaice
checkpoint48g_post --- EOS: o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF store total Potential in totPhyHyd for diagnostics & EOS. o fix restart and overlap Pb when using Z-coord and EOS funct. of P --- Pressure/geopotential gradient: o use Ro_surf & R_low instead of hFac in cal_phi_hyd: o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind ( changes results of global_ocean_pressure ) o NLFS + z-coord.: add eta*Rho' contribution. o accurate phiHyd when using interface-W at the middle between 2 centers ( changes results of ideal_2D_oce ) o includes r* 2nd term in potential gradient.
Merging from release1_p12: o Modifications for using pkg/exf with pkg/seaice - improved description of the various forcing configurations - added basic radiation bulk formulae to pkg/exf - units/sign fix for evap computation in exf_getffields.F - updated verification/global_with_exf/results/output.txt o Added pkg/sbo for computing IERS Special Bureau for the Oceans (SBO) core products, including oceanic mass, center-of-mass, angular, and bottom pressure (see pkg/sbo/README.sbo). o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F to avoid negative values in shallow regions. - updated verification/natl_box/results/output.txt - updated verification/lab_sea/results/output.txt o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F o Added useSingleCpuIO option (see PARAMS.h). o Updated useSingleCpuIO option in mdsio_writefield.F to work with multi-field files, e.g., for single-file pickup. o pkg/seaice: - bug fix in growth.F: QNET for no shortwave case - added HeffFile for specifying initial sea-ice thickness - changed SEAICE_EXTERNAL_FLUXES wind stress implementation o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, kpp_transport_t.F, forward_step.F, and the_main_loop.F o pkg/seaice: - adjoint-friendly modifications - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
tag checkpoint48e_post
o dynamics: change definition of computational domain & adapt mom_fluxform
accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
o following exp works with Olx=Oly=2 (and pass through checkbounds option):
adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5
global_ocean.90x40x15 global_with_exf global_ocean_pressure
inverted_barometer solid-body.cs-32x32x1
(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
checkpoint48d_post
o in preparation for r*:
a) use pre-computed gradient of hydrostatic potential:
changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
=> affects results of glob_oce_pressure (different truncation error)
update output.txt of ideal_2D_oce & global_ocean_pressure
checkpoint48d_pre o in preparation for r*: new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. pass the 2 comp. of the grad. as arguments to momentum S/R. but for the moment, only used if it does not change the results. o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
tagging checkpoint48c_post purely adjoint-related (bracketed between 48c_pre/post)
Logging addition of tidal_basin_2d
o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
checkpoint48b_post
o r* coordinate added in #ifdef NONLIN_FRSURF block. (modification to pressure gradient not yet implemented) o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports (for U & V) that are used for vertical advection of momentum.
checkpoint48a_post
o In preparation for r*, use temp. array to compute vertical transport
in flux-form momentum pkg. => change results of few test-exp.
Update output of: exp4, exp5, front_relax, global_ocean_pressure,
lab_sea, natl_box & plume_on_slope
checkpoint48
tagging checkpoint47j_post
add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
checkpoint47i_post
o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
default= 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
Duplicate tag of PH's c48
pkg/gmredi: fix few bugs and restore parameter values (e.g., Small_Number=1.D-12) and scheme (e.g., Large_SlopeSqr=1.D+48) of checkpoint47f_post
creating checkpoint48
creating checkpoint47g_post
time-average AIM output: becomes independent from statvars time-average (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
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
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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