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new tag: checkpoint66f
document addition to new run-time param "plotLevel"
document adding flag to add snow mass to seaiceMassC/U/V
Noting bug fix in bling production
document bug fixed in ini_masks_etc.F (for rStar with useShelfIce)
documents changes in pkg/rw (contribution from Jody Klymak: option to set mds file suffix)
document changes in pkg/mom_vecinv (highOrderVorticity & selectVortScheme=2 case)
documenting changes to bling package
new tag "checkpoint66e"
document update of exf_check.F & exf_summary.F
document change in pkg/exf (interpolation with #undef EXF_INTERP_USE_DYNALLOC)
- document recent changes
document update of lab_sea AD output and pkg/exf addition ({FLD}RepCyle)
MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat that is, there is one less increment needed than total number of latitudes
document bu fixed in exf_zenithangle.F
document changes in pkg/bling (USE_EXFCO2 code)
document changes in pkg/exf
document changes inverification exp. global_ocean.cs32x15.icedyn
- document change in pkg setting (useCAL no longer set to T if useEXF) - new tag (checkpoint66d)
document changes regarding EXF_READ_EVAP in pkg/exf
- document recent changes
document changes/addition to pkg dependency rules
adding ocean_basin routines for defining basin masks
document pkg/exf changes (addition of new S/R EXF_GETFFIELD_START).
document changes in pkg/exf (allowed to be used without pkg/cal)
updated
document changes in pkg/exf
- document recent changes
new tag "checkpoint66c"
document changes/addition to testreport
minor edit
- document recent changes
- update tag-index regarding mnc_utils
- document recent changes
- document recent changes.
document changes in pkg/exf check & summary
document addition to local xmakedepend
document change of hflux definition in pkg/exf
new tag "checkpoint66b"
document update of verification exp. global_ocean.cs32x15.thsice
document implementation of implicit bottom friction
document this:
add linear remapping scheme (Lipscomb 2001) to ITD model
- this is a first version that includes many regularisations that may
not all be necessary, to be sorted out,
- turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
- change one verification experiment in seaice_itd to use and test new code
- seaice_growth: catch a case where the argument of log can be zero
or smaller (important for code stability)
document changes in SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F & solve_pentadiagonal.F
new tag "checkpoint66a"
Document that apco2 is now read in bling package. And delete that it was added to exf
Documenting adding aPCO2 to EXF package. This code was originally from Holger Brix. Enable this code with USE_EXFCO2 in EXF_OPTIONS
document switch in S/R call for implicit vertical visc. & diffusion
document 2nd round of changes in implicit vertical routines
document some updates of implicit vertical routines
new tag "checkpoint65z"
update descript of multithreading fixes for seaice_fgmres.F
- document recent additions to the MITgcm manual
- document recent changes in pkg/ecco
document attempt to multithread seaice_fgmres.F
document bug fix in interpolation near South Pole.
document moving SGRunOff setting from pkg/exf to pkg/icefront
document changes in pkg/exf: "exf_output_interp" and in exf_set_uv.F
Noted bling pkg cleaning
forgot to document pkg/cal changes (on Jun 30) regarding calandar-dump
enable linear-free-surface correction by ptracer, default off
add this documentation: pkg/ptracers: add Bruno Deremble's code to complete the linear surface correction for tracer conservation
new tag "checkpoint65y"
document few fix for pkg/debug stats.
document addition to pkg/monitor
document bug fixed in obcs_balance_flow.F
document fix to compile coupled atm+ocn with seaice dynamics & dic
new tag "checkpoint65x"
updated
documenting addition of BLING BGC package
document fixing tensile stength computation
new tag "checkpoint65w"
document fix for ECCO_CTRL_DEPRECATED-code
document changes in secondary test exp.: global_ocean.cs32x15.viscA4
document changes related to non-hydrostatic free-surface: fix EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
document small changes to SEAICE_ITD related code
document fixing case: selectP_inEOS_Zc=3
document this: add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
describe basal/bottom stress as parameterisation for grounding ice (Lemieux et al. 2015)
document update of halfpipe_streamice ADM output.
new tag "checkpoint65v"
document update of verification experiments (removing Ro_SeaLevel + testing of new advection schemes in advect_xz exp.)
document changes in setting vertical axis origin
document this:
- simplify computation of deltaZ and zetaZ to simple averaging following
Bouillon et al. (2013). This removes a lot of code, but also changes
verification experiment lab_sea.hb87
new tag "checkpoint65u"
document addition of PPM and PQM advection schemes (from Darren)
document addition of variable gravity, Ideal-Gas in z-coords, options regarding pressure used in EOS with Z-coords.
- document recent change in pkg/exf
document changes in model/src (+ in PARAMS.h)
new tag "checkpoint65t"
document addition to pkg/atm_phys
ducument minor changes for anelastic formulation
document addition of hack in "remove_comments_sed" (for TAF)
document changing the termination criterion for seaice_fgmres
document recent change to pkg seaice, in particular:
- unify iteration parameters for implicit solvers (JFNK and Picard)
SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
SEAICEnonLinTol replaces JFNKgamma_nonlin
- remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
- add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
use with SEAICEuseKrylov
- pkg/seaice/seaice_lsr.F
fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
an effect.
document two new parameters
- SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
parameter is not in any namelist)
- SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
a preconditioner for the non-linear Newton iteration of the JFNK
solver
document changes related to replacing 1./SEAICE_deltaTdyn in seaice_lsr.F
document pkg/salt_plume changes related to coupling interface
document changes in pkg/ggl90, tools/adjoint_options and pkg/dic
document changes in pkg/atm_compon_interf related to atmSLPr.
new tag: checkpoint65s
document latest HAVE_ETIME modif
document changes in eesupp & genmake2 (etime), tools/tst_2+2, pkg/dic (rm USE_ATMOSCO2) and new flag to apply EXCH to U,V earlier.
document changes in coupling pkgs
document bug fixed in pkg/dic (dic_atmos.F, case dic_int1=3)
document changes in pkg/atm_compon_interf
document bug fixed in pkg/dic (dic_atmos.F)
document new parameter SEAICEpressReplFac
document changes in pkg/atm_phys
new tag checkpoint65r
updating
document bugfix in tridiagonal solvers for SEAICE_OLx/y>0
document fixing a bug
document additions to pkg/atm_phys.
document change in IDEMIX: add upper limit for horizontal group velocity to avoid instability problems in the explicit horizontal diffusion term for long time steps or high resolution
document changes to pkg/diagnostics (stat-diags)
document fix in seaice_growth.F
- catch potential division by zero in ITD code, does not change
verification results
- document latest changes.
document changes in pkg/atm_compon_interf (seaice fraction sent to coupler)
document ETIME fix (in timers.F & genmake2)
document change in seaice_evp.F: refine residual computation
new tag: checkpoint65q
document fix in seaice_readparms to be able to actually set new parameters SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
document fixing residual computations in seaice_evp.F
document fix for aimCO2 pickups and fixing wrong truncation with fct "FLOAT"
document addition of sequential-coupling option
document changes in coupler pkgs
document changes in MPI-global-sum default
add SHELFICETransCoeffTFile for initializing spatially varying heat and salt transfer coefficients Modified Files: doc/tag-index pkg/shelfice/SHELFICE.h pkg/shelfice/shelfice_init_varia.F pkg/shelfice/shelfice_readparms.F
document changes in coupler pkgs
document pkg/rbcs changes
new tag "checkpoint65p"
document this: change (fix?) store directives (move one and add one) and key computations; since there is no adjoint test for EVP, we don't know what it does to the adjoint solution, but at least there are no more recomputation warnings left
document this for seaice_evp.F: slight modification of averaging so that EVP stands a chance of giving the same results as a fully converged VP (JFNK) solver
minor adjustment
fix bug in Tang-Linear FLAGS setting for MPI + DIVA
update tag-index, streamice change
document changes in pkg/exf for constant-in-time wind/stress (period=0)
document change to EVP/aEVP
redefining uLoc/vLoc to u/v, instead of 2u/v
documentation for this:
introduce "adaptive EVP" by Madlen Kimmritz
- this is an intermediate state of a truely converging EVP that has
the potential of outperforming implicit VP methods, I do not recommend
using it yet.
- for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
and all parameters are hardwired
- for convergence it still requires very smooth regularisations, that means,
if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
specific averaging appears to be required, still subject to tuning
- still needs cleaning and I need to turn parameter into runtime parameters
- add code to compute and print residuals of iteration, compile with
defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
document this fix: bug in seaice_evp.F (factor of four in front of e12Csq) that entered with r1.54 on Sep04, 2015, -> update results of lab_sea.hb87 (again)
new tag "checkpoint65o"
allow to use Vector-Invariant form in deep atmos and anelastic formulation
document this: introduce fast ice parameterisation following Itkin et al. (2015) and Koenig-Beatty+Holland (2012) - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth - global 2D field tensileStrength, computed in seaice_calc_ice_strength - requires an extra input argument for S/R seaice_calc_viscosities - tensileStrength's depth dependence is different from Itkin et al. (2015)
o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
- if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
by AREA according to Connelly et al. (2004), JPO.
- For EVP and the LSR solver, the implicit part of the drag term is
the only non-zero term in the denominator when there is no ice (which
prevented running the model with zero ice-ocean drag). If
SEAICEscaleSurfStress = .TRUE., this results in a division by zero
(or zero main diagonals BU/BV) which need to be caught. A practical
consequence is that for open water, the momentum equation reduce
to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
they happen to be zero, often leading to a non-zero solution over
open water.
document this:
revise EVP code (pkg/seaice/seaice_evp.F) in preparation for a more
efficient EVP method.
- introduce area-weighted averages for e12 (analogously to
seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
remain, but also changing the order of terms in the previous average
changed the results as much) -> update experiment
- add SEAICE_DELTA_SMOOTHREG code
- disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
TEM-code
- adjust loop bounds so that only required fields are computed
- add new averaging code for zetaZ/deltaZ (again similar to
seaice_calc_viscosities.F), inactive by default for now (will change
results again), but will replace old code eventually
document new option for multi-proc GLOBAL_SUM to to always cumulate tile local-sum in the same order
new tag: checkpoint65n
update previous modif
document changes in pkg/offline
an other fix for pkg/offline where KPP is computed.
document changes related to offline pkg.
Update.
Update
Update.
documents this - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising delta with a smooth function in s/r seaice_calc_viscosity (no effect on EVP) - rename local suffix "sqr" into "sq" for more consistent variable names
document this: add new parameter SEAICE_deltaMin that is used ***only*** for regularizing Delta (and nothing else, like the parameter which is also used for all sorts of things SEAICE_EPS). Defaults to SEAICE_EPS for backward compatibility only.
document this: replace erroneously storing e12Csqr on the wrong tape with the wrong key by inialising it before use -> fixes a recomputation problem but does not fix the gradient
fixed a few bugs
document update of adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
document changes in pkg/layers
document the following changes
o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
computations; for SEAICE_VECTORIZE_LSR
- move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
sweep to the outside,
- remove store directives and add "CADJ loop sequential" directives
in analogy to model/src/solve_tridiagonal.F
- replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
boundaries to yield more readable code. This has also the charming side
effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
seaice_lsr_tridiagu/v now requires either of these flags, vectorization
still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
an additional option)
The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
but the adjoint gradients (which are affected by this change) still explode.
- Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
in lab_sea forward experiment (changes results -> updated)
- updating adjoint experiment will follow
document fix in coupler mapping with pkg/exch2
new tag "checkpoint65m"
document update of pkg/layers parameter checking
Added missing call to layers_fill for keeping track of tottend.
Added CPP flag LAYERS_FINEGRID_DIAPYCNAL to switch on/off refined grid binning of diapycnal velocities.
Reverted the messy, unnecessary changes to layers interpolation.
Fixed layers diagnostics naming issues.
- document recent change in pkg/ptracers
document changes in pkg/diagnostics (update of diag_pkgStatus in multi-threaded)
document changes in pkg/layers related to units of potential density.
document few fixes in pkg/layers
document changes seaice_calc_viscosity.F
new tag "checkpoint65l"
log updates to pkg/shelfice
document this for genmake2:
replace
FFLAGS = ${FFLAGS} ${FEXTRAFLAGS}
FOPTIM = ${FOPTIM}
by
FFLAGS = ${FFLAGS}
FOPTIM = ${FOPTIM} ${FEXTRAFLAGS}
document changes in seaice_growth.F: replace tmpscal1**1.36 by (hopefully) faster exp(1.36*log(tmpscal1))
document new testreport flag -small_f
new tag "checkpoint65k"
- document latest changes.
- document latest changes.
document new code in exf_interp.F that allows input grids with latitude starting in the north and modifications of verification/global_with_exf
document changes in testreport: replace "cat -n" by "nl" (two occurrences) replace "grep -A3" by an "sed" command (one occurrence)
add this: 3 functions, more or less a copy of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to convert from conservative to potential temperature. For now they are not called anywhere.
document idemix related changes in ggl90:
- re-organize code in s/r ggl90_calc a little to move computations that
are different for idemix into separate loops (changes verification
experiements at truncation level)
- requires 2 new 2D fields KappaM, verticalShear
- make hFacI and recip_hFacI local 3D variables that are passed to
s/r ggl90_idemix
- fix and improve some comments
new tag "checkpoint65j"
document changes to pkg/openad/seawater.F
document changes in salt vertical diffusivity default + pkg/mnc pickup default
fix documentation to only refer to Olbers, D. and Eden, C. (2013) and IDEMIX 1
Update.
document changes in testreport
update documentation of pkg/ggl90 idemix code
Update
document new option of genmake2 (for TAF ad built).
document IDEMIX in ggl90
shorter AD test run for few verification experiments
document changes to testreport:
- fix two non-POSIX sed statements so that there are no error messages
on Mac OS X
- replace hostname -s with hostname | sed 's/\..*$//'
- document changes in isomip.htd-verification experiment - new diagnostic SHIuStar (in pkg/shelfice) - changes in sw_temp
document changes in pkg/shelfice
document bug fixed in function/subroutine SW_TEMP (conversion from Theta to in-situ Temp)
document changes in pkg/shelfice for RealFreshWaterFlux
document little changes in pkg/shelfice
document the new option to prescribe a fixed thickness PDF for thermodynamic calculations
new tag "checkpoint65i"
document changes in Frictional-Heating
document changes (+ bug fixed) in frictional heating.
document changes related to ALLOW_EDDYPSI parts + gmredi_k3d.F diagnostics fixes
document changes in FFIELDS.h initialisation (fixes restart with selectAddFluid=1)
document (minor) changes in pkg/shelfice
document this:
o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
and last weeks modification that I obiously had forgotten about:
o pkg/seaice: two new runtime parameters:
- SEAICE_cStar replaces the hard wired "20" in the strength formulation,
long overdue
- SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
parameterization of tensil stress for fast ice (does not do anything yet)
o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
for LSR: move checking overlaps out of JFNK-if-block
document changes in pkg/atm_phys
document changes in mom_u/v_bottomdrag.F & shelfice_u/v_drag.F
document changes of vertical viscosity local arrays 3rd dimension
commit tag for pkg/shelfice changes
new tag "checkpoint65h"
- document recent changes (since last checkpoint).
document changes in momentum diagnostics (Um_Diss & Vm_Diss)
document this change in pkg/seaice/seaice_lsr.F: fix computation of BU/BV, make sure they are non-zero, only necessary for cubed sphere exchanges and SEAICE_OLx/y>0. This makes calling s/r fill_cs_corner_rl obsolete (removed).
document changes in verification/global_ocean.cs32x15/input.seaice
- add test for strong implicit coupling and restricted addtive Schwarz
methods for LSR
- update results/output.seaice.txt
document changes in pkg/dic (#undef ALLOW_OLD_VIRTUALFLUX by default)
document fixing inconsitent setting in tutorial_global_oce_biogeo AD & OAD set-up
documentation for this: o add eesupp/src/fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F) and call it in seaice_lsr when using nonzero SEAICE_OLx/y
document this: introduce strongly implicit coupling in seaice, intended for stabilizing LSR (following Hutchings et al. 2004)
domentation for this: add overlap for restrictive additive Schwartz method also to LSR, but turn it off by default (because it only seems to work for non-cubed sphere/llc topologies)
document ad-dump changes (extra exchanges for seaice adjoint variables and for mnc output), todo: ptracers_ad_dump.F
document addition to pkg/obcs (for diagnostics of Velocity-Potential)
document changes in diagnostics calculation of Velocity-Potential (with OBCS)
new tag checkpoint65g
document ALLOW_3D_DIFFKR fix in pkg/my82, pkg/pp81 & pkg/kl10.
document changes to evp code
add comment about adding diagnostics SIdelta (Delta, deformation parameter)
- document recent changes.
document addition of safety stop related to ALLOW_3D_DIFFKR.
- document recent changes.
document additions (from Hajoon) to pkg/dic
document cpp flag fix in seaice_preconditioner.F
- document latest changes.
- document latest changes.
- document recent changes.
new tag "checkpoint65f"
- document latest changes.
- document recent changes.
- document latest changes.
- document latest changes.
- document latest changes.
- document latest changes
- document recent changes
new tag "checkpoint65e"
replaced the just-added OBCS_OPTIONS.h CPP options with run-time variables see pkg/obcs/OBCS_PARAMS.h for details)
adding compile-time options for sponge boundary layers
- abbreviate previous log of pkg/ctrl,ecco,exf
add seasonal incoming solar radiation in pkg/atm_phys
- document latest changes
- document latest changes
- document latest changes
document latest cahnges
new tag checkpoint65d
- document latest changes
- document latest changes
document changes in/related to pkg/streamice
update
- document recent changes.
document changes in OpenAD verification experiments: ALLOW_AUTODIFF_TAMC undef in OpenAD test ; use pkg specific option file instead of ECCO_CPPOPTIONS.h
document changes in loop range in apply_forcing.F & gad_calc_rhs.F
document modification in pkg/dic for OBCS
new tag checkpoint65c
document changes in pkg/dic/dic_atmos.F
new experiment testing OBCS and DIC pkgs, derived from tutorial_global_oce_biogeo
document changes in ini_theta.F (apply allowFreezing @ all k only if checkIniTemp=T)
document changes in pkg/diagnostics for Stats-Diags (in diagstats_calc.F)
document changes in pkg/gchem for OBCS + DIC
update forcing code for Held & Suarez experiments (except Lat-Lon grid one)
document changes to allow to use AB on tracers (instead of on tendency) with AB-2 code and in pkg/ptracers
remove gT,gS and gPtr from common block.
document changes in several S/R argument list related to the use of local tendency array (without bi,bj) in S/R temp/salt/ptracers_integrate.F
document these changes:
- move computation of stress contributions to rhsU/V in s/r seaice_lsr
to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
- make u/vIceC local variables if SEAICE_CGRID is defined only to be used
in seaice_lsr
- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
in s/r seaice_lsr_calc_coeffs
new tag checkpoint65b
document fixing of geothermalFile initialisation + changes in pkg/matrix
document changes in S/R TIMESTEP_TRACER calls + S/R DWNSLP_APPLY calls. and changes in Stats-Diagnostics (DIAGNOSTICS_FILL called with bibjFlg < 0)
document changes in temp/salt/ptracer update: move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer_integrate.F
Upate doc
document changes in calc_phi_hyd.F for atmospheric set-up
fix some text
document change in seaice_lsr.F
- rename integer variable ilcall to ipass (that's what it is called
in the residual diagnostics
- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
default) for improved non-linear convergence of the first few
steps
- add a few comments and add new ones to explain some of the store
directives
update todays changes in seaice_lsr, etc.
o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
- add an auxilliary variable "bet" and fix store directives and keys in
seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
less exact gradients in my tests); but there are still
recomputation warning (although gradients are sort of OK), when
SEAICE_LSR_VECTORIZE is not defined, so this flag and
SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
- update verification experiments lab_sea.
- change some comments in S/R seaice_calc_viscosities
document changes in place where EXCH of velocity field is done when staggerTimeStep without multi-dim advection ; + some setting related to doAB_onGtGs=F.
new pkg "kl10" (thanks to Jody Klymak) for mixing due to internal wave breaking
update some experiments.
document my share of bugs for today:
- reduce the number of include files and store directives in
S/R seaice_lsr_tridiagu/v
- change the order of loops in one case in S/R seaice_lsr_tridiagv
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
get rid off one store directive (a TAF bug?)
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
S/R seaice_lsr_tridiagv to change the loop range for consistency
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
S/R seaice_lsr_tridiagu/v (requires update of
offline_exf_seaice/input.dyn_jfnk)
new tag "checkpoint65a"
document changes in calc_surf_dr.F (Non-Lin Free-Surf in p/z coords) related to hFacW,S when using non-uniform kSurf (topo in p-coords, ice-shelf in z-coords); update output of tutorial_global_oce_in_p.
document changes related to APPLY_FORCING calls
document changes in ptracers diagnostics title and units
new tag: checkpoint65
fix description of changes in adjoint
document changes in pkg/fizhi/fizhi_tendency_apply.F
Add this:
o pkg/seaice: more clean up
- rename TAF common block tapes to be more consistent and remove
unnecessary duplicates
- add store directives to remove more recomputations,
but use smaller tapes (and adjust keys) when
SEAICE_LSR_ADJOINT_ITER is undefined. The idea behind this flag is
to reduce the memory footprint when the adjoint of the LSR is not
required. As of now, defining the flag SEAICE_LSR_ADJOINT_ITER
increase 4 common block tapes for 2D field by a factor of
SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). For experiment
offline_exf_seaice, this means on a linux box with gfortran nearly
a factor of 10 (but keep in mind there is mostly seaice code
in this experiment)
> size mitgcmuv_ad
text data bss dec hex
5100659 1216 220458952 225560827 d71c8fb
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
but only a moderate increase of 36% for global_ocean.cs32x15
text data bss dec hex
6695027 1648 1014578664 1021275339 3cdf6ccb
6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
- note: there are still recomputations in global_ocean.cs32x15 and
the gradient agreement changes (gets a little worse)
- in general, the AD gradients still are wrong
Update
document changes in pkg/down_slope (for NLFS) and in momentum (fluxform) time-stepping (NLFS with momDissip_In_AB=F)
document changes from external_forcing.F to apply_forcing.F
documentation for a little bit of clean up
- rearrange some code blocks, so that now all calculations for
setting up the right-hand-sides done within one single block
(I find that easier to read and understand)
- rearrange freedrift-code to reduce the number of ifdefs
- adjust some indentations and comments
new tag: checkpoint64z
document changes around external_forcing.F
document this:
- always initialize local arrays in seaice_lsr_tridiagu/v
- add more local tapes to seaice_lsr_tridiagu/v
- move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
keep it in bi/bj loop; this seems to be essential
- gradients are still wrong but only by 4-7 orders of magnitude
instead of 15 orders of magnitude, lab_sea improves a little
documentation for this:
- (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
generates unnecessary code in seaice_lsr_ad
- add more store directives in seaice_lsr to avoid unnecessary code
in seaice_lsr_ad
- exclude some residual computations in seaice_lsr when
ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
in seaice_lsr_ad
- add more storing, a new tape (model/src/the_main_loop.F) and
another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
and klockey should be checked by a specialist)
The above changes do not alter the verification results
- modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
and update lab_sea after previous changes in pkg/seaice below
adjust description of this: - remove some store directives and add new ones in an effort to get finally rid off the recomputation warnings. This is successful for SEAICE_VECTORIZE_LSR defined (i.e. no extensive recomputation warnings left), but there are still too many recomputations on the solver iteration level - adjoint results do not change (except for maybe lab_sea), because no experiment uses the adjoint of the dynamics solver
- document latest changes.
how often am I allowed to fix my comments?
forgot to add this: - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
add this to the tag-index:
- remove unnecessary u/vTmp from subroutine call of
seaice_lsr_tridiagu/v
- remove some store directives and add new ones in an effort to get
finally rid off the recomputation warnings. This is successful
for SEAICE_VECTORIZE_LSR defined (i.e. no extensive recomputation
warnings left), but there are still too many recomputations on the
solver iteration level
documentation these change in pkg/seaice
- move definition of MPSEUDOTIMESTEPS into TAMC-block in
SEAICE_SIZE.h
- add a store directive in S/R seaice_calc_viscosities to avoid
recomputations
document changes in seaice ITD code (+ exp seaice_itd)
documentation for - replacement of verification/seaice_itd - change of some defaults of ridging parameters in seaice_readparms.F
new tag "checkpoint64y"
documents this:
- modify the regularization of very small volumes of ice; only check
total volume HEFF, and do not apply correction to individual ice
classes because that leads to funny patterns in the heat and fw-fluxes
into the ocean. Adjust seaice_itd/results/output.txt
- replace nITD by SEAICE_multDim in loop-ranges
document changes in pkg/exf (fix for period = -12 in UV interpolation)
document changes in pkg/exf, pkg/cal and verification/global_with_exf.
document pkg/sbo updates (SBO in testreport + multi-threading)
document pkg/sbo update
more standard LAND pkg interface.
document packages_readparms.F & {pkg}_readparms.F (case where use{PKG}=F)
document changes in pkg/seaice:
- remove code that resets useThSice in S/R seaice_readparms and
replace by a warning in S/R seaice_check
- remove parameter MULTDIM, replace with nITD and runtime
parameter SEAICE_multDim (still hard-wired to nITD if
SEAICE_ITD is defined)
new tag: checkpoint64x
Modified output fullowing An Nguyen's changes to pkg/salt_plume (carry corresponding heat flux along with salt redistribution)
document pkg/sbo updates
document changes in pkg/atm_phys (dargan_bettsmiller_mod.F90)
describe modification of seaice_calc_ice_strength.F
document fixing seaice_do_ridging.F - fix a bug that was compensated by areaScaling (-> remove areaScaling code) - added SEAICEsnowFracRidge to redistributed snow (2nd bug) - set closing/openingRate to zero where no extra iteration is need (3rd bug) - add some debugging information and error messages (warnings)
modifications relatd to atmosphere p* (model/src) and update FWD output of of exp: aim.5l_cs (x2), 3 fizhi_ exp, tutorial_held_suarez_cs, and cpl_aim+ocn.
document bug fix in seaice_prepare_ridging.F
update
document this bug fix: replace SEAICE_rhoSnow by SEAICE_rhoIce in the Rothrock (1975)-type strength calculations
remove "recip_Cp" from common block ; add thetaConst (for pStar).
from Jeff Scott: add option EXF_CALC_ATMRHO
tag checkpoint64w
update 4 output_adm.txt (global_ocean.cs32x15 & lab_sea experiments).
store factor rStarFacC**atm_kappa (= pStarFacK) in common block
document fixing a restart problem for ITD with new ice strength parameterisation
document removing global variable TICE in pkg/seaice
new header file "CTRL_FIELDS.h"
documentation for some small modifications to the ridging code
- make fw2ObyRidge a global variable and add the freshwater flux to
seaice_growth
- pass actual thickness from seaice_prepare_ridging, so that it is
computed only in one place and compute it in the same way as in
seaice_growth
- initialise more fields in seaice_do_ridging that where cause floating
point exceptions over land
document preparations for ridging code and first real ridging code
- move most of "PART 1" of S/R seaice_growth into a new and separate
S/R seaice_reg_ridge that will both regularize the state variable after
advection call the actual ridging routine;
- requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
- remove ridging code from seaice_advdiff
- clean up remaining part 1 of seaice_growth in an attempt to make it
more readable (this is probably subjective)
- call seaice_itd_redist once in the initialisation phase to have the initial
conditions in the correct category
- finally: add new ridging routine for ITD code
new tag checkpoint64v
Document this: - add diagnostic for HSNOWITD - add opnWtrFrac as a global variable (required for ridging scheme)
add SALT_PLUME_IN_LEADS code to pkg/salt_plume + seaice_growth.F, rename "tpmean" to "mdt" and "topexmeanfile" to "mdtdatfile" in pkg/ecco
document changes to seaice: new way of computing ice strength (if SEAICE_ITD). Very experimental and not yet complete (no actual ridging so far, but coming soon)
verification/hs94.1x64x5: - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
fix conflicts
add atn recent changes to pkg/salt_plume and pkg/ecco
document Changes in CPP-Options setting for AutoDiff (TAF & OpenAD)
document this for seaice_growth.F
- fix a bug in the lateral melt parameterization for SEAICE_ITD
in seaice_growth; tempFrz needs to be computed inside the i/j-loop
- rearrange loop order for better vector code in the same code block
- rewrite the floeDiameter formula to have fewer divisions
- (miraculously) none of this changes the results of seaice_itd
document fix to pkg/streamice pickup
document changes in pkg/seaice:
- refine checks for jfnk-related parameters
- comment out if statement with SEAICEuseIMEX parameter as long as there
is no IMEX code to avoid confusion and surprises
new tag "checkpoint64u"
document changes in MLAdjust test experiment
document changes in pkg/mom_vecinv
document changes to allow to use thin-walls
forgot to document changes in tools/adjoint_options/adjoint_oad
document this:
- rename recently introduced parameters from (wrong name) AB to
BDF (backward difference time discretisation)
- retire runtime parameters SEAICEuseAB2, SEAICE_abEps
new tag "checkpoint64t"
Update.
ducument changes in genmake2 (OpenAD Makefile)
document changes in pkg/shelfice
Update
- document changes.
- document changes.
o pkg/exf/exf_check.F
- fix a small bug again (originally found by Wentao Liu, now found again)
- streamline error output
o pkg/streamice and aim_v23:
replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
Apple's /usr/bin/cpp knows what to do:
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
Target: x86_64-apple-darwin13.0.0
tag checkpoint64s
updated
document changes in thermodynamics.F and related S/R
updated (missing few little recent fixes)
useSingleCpuInput separates single-CPU input from single-CPU output
document the fix of an initialisation bug for the SEAICE_VECTORIZE_LSR_ZEBRA option
new tag "checkpoint64r"
document update of results reference output
document changes in thermodyanmics.F and tem/salt/ptracers_integrate.F
document changes in ATM/OCN coupler and coupling interface pkgs
document changes in calc_adv_flow (AUTODIFF only) and update of exp. results
document changes in pkg/exch2 and coupler interface
document changes in thermodynamics.F (removing k-loop) and others.
document changes in pkg/gmredi (GM_AdvForm); useOldFreezing removed and OAD_support/cb2mGetModules.csh + code_oad/CPP_OPTIONS.h
tag checkpoint64q
document output update.
remove kLev argument and use global_sum_tile_rl in tracer_meanarea
document changes in pkg/cost (related to GLOBAL_SUM_TILE)
isotropic 3-D Smagorinsky code moved to pkg/mom_common
document changes in pkg/dic/dic_cost.F and in smag3d code (in tutorial_deep_convection)
move setdir.c and remove old routines used for tape IO
document changes in verification/isomip and in optfile linux_amd64_ifort11
new tag: checkpoint64p
changes in adread_adwrite.F for mismatch with ALLOW_AUTODIFF_WHTAPEIO
document changes in tape IO subroutines
document changes in adread_adwrite.F
document pkg/exf changes
document addition to tutorial_deep_convection verification experiment.
Added SINGLE_DISK_IO option for use with MPI on very large number of processors and Lustre-type file systems.
tag checkpoint64o
document changes in some linux_amd64 optfiles
documentation for the residual model
updating
tools/build_options: update linux_amd64_gfortran & linux_amd64_ifort11
document changes in pkg/atm_compon_interf
update formulation to reduce dispersion of tracer properties in bbl replaced horizontal and vertical transport parameters with velocities changes results for verification/global_with_exf.yearly details in pkg/bbl/bbl_description.tex
tag checkpoint64n
halfpipe_streamice
updated (tutorial_tracer_adjsens OpenAD test)
document changes in genmake2 and pkg/offline (used with rStar)
log changes for adjoint with OpenAD
document changes in do_stagger_fields_exchanges.F & exf_getforcing.F (skip EXCH calls)
document pkg/diagnostics changes
tag checkpoint64m
updated
basic fixes in pkg/seaice thermodynamics code
start to document the switch to TAF version-2
tag checkpoint64l
document changes in included header files in main_do_loop.F
in dynamics.F, skip call to CALC_VISCOSITY if momViscosity=F
document changes in pkg/mom_common+fluxform+vecinv (horiz. viscosity)
document changes related to variable horiz. viscosity in NH code (calc_gw.F)
document modification of drC (& recip_drC)
updated
tag checkpoint64k
document changes related to DIVA+MPI and OpenAD in Makefile (genmake2) and in tools dir.
update halfpipe_streamice
changes in testreport for Divided Adjoint (DIVA) test + switch lab_sea to use DIVA
document removal of parameter cpl_earlyExpImpCall
update pkg/offline changes
document pkg/offline changes
changes in OpenAD + update tutorial_tracer_adjsens output_oadm.txt file
document changes related to EXTERNAL_FORCING_SURF
new tag, checkpoint64j
document changes for offline pkg
adding RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice wich changes verification/global_ocean.cs32x15/results/output.seaice.txt
fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
document pkg/atm_phys modif
document changes in 3 AD-tests (shorter simulations)
changed results for verification/halfpipe_streamice
document pkg/ptracers modif (restart without SOM pickup files)
Added a new eddy diffusivity parameterisation pkg/gmredi. More detailed description in tag-index.
Documenting changes in seaice_advdiff that happened 11 days ago. Sorry about this, but at least the description is at the right place (with the wrong tag)
just testing
tag checkpoint64i
document pkg/cheapaml addition
document new subdir in utils/python
new STREAMICE package and verification expt
document pkg/thsice modifs
document pkg/cfc changes/updates
document pkg/cfc changes (+ corresponding verification output update)
using seaice dynamics without pkg/exf
document AB2 for ice dynamics
tag checkpoint64h
document changes in pkg/cheapaml (+ dependence seaice / exf)
document modif in tools/OAD_support/revolve.F90
pkg/aim_compon_interf renamed to pkg/atm_compon_interf
update packages_init_variables.F changes + pkg/offline initialisation
update new pkg "atm_phys" doc
1rst step in adding new pkg: atm_phys
changes in writing pickup-file for pkg/seaice ITD code
document changes in pkg/seaice ITD code
document pkg/thsice modification (snowPrc)
tag checkpoint64g
document recent changes in pkg/seaice (already a couple of days ago,
but apparently I had forgotten to do this):
- turn some parameters for choosing the convergence criterion of
the inexact Newton method (JFNK) into runtime parameters for convenience
- clean up seaice_calc_viscosities.F: remove/retire two options for
SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
the results of lab_sea/input because a division has been replaced by
a multiplication with the reciprocal (sumNorm)
- modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
convergence of solver (changes results, of course), and to test some
new features
adding ALLOW_RUNOFTEMP
document changes in pkg/thsice (& pkg/bulk_force)
document new verification sub-experiment
document some cleaning in model/src
document changes in pkg/shelfice and isomip experiment output
forgot to check-in this 2 days ago.
*** empty log message ***
document fix in CD-scheme (no AB on 1rst iteration)
change default makedepend to tools/xmakedepend
document changes in exf & thsice pkgs for the case ERL is used (temp_EvPrRn=0)
document diagnostics fix in pkg/thsice
document change in cpp-flags
Update
document changes in pkg/thsice (ocean relative velocity in basal turb. flux)
tag checkpoint64f
Adding OpenAD verification experiment to isomip for shelfice package
- verification/offline_exf_seaice: replace adjoint experiment.
update
document change in seaice_evp
update some AD & TLM output
document new flag SEAICE_VECTORIZE_LSR_ZEBRA
tag checkpoint64e
Update
document changes in multi-dim advection (pkg/generic_advdiff).
document small changes in pkg/generic_advdiff SOM advection
document bug fix in the no-slip implementation in seaice_calc_strainrates
document recent change to seaice (jfnk-solver)
document fix in line search in s/r seaice_jfnk_update
document re-organization of seaice_lsr and seaice_preconditioner
Update
changes in S/R ADAMS_BASHFORTH2/3 (add 1 argument)
document changes in pkg/cheapaml
new tag checkpoint64d
document changes in horizontal-grid setting and in Angular-Momentum monitor
documentation of this: replace a hard coded parameter by a runtime parameter SEAICE_JFNK_tolIter
document RAS in the preconditioner of JFNK and the changes to seaice_fgmres.F (re-ordering option)
document changes in utils/matlab (rdmnc.m changes + cs_grid/bk_line/)
document bug fix in seaice_fgmres.F, s/r seaice_scalprod
documenting step 2 improving vectorization of layers_fluxcalc.F
pkg/diagnostics: change default missing_value from UNSET_RL to -999.
updating
- document recent changes.
updated (fizhi-cs reference output now generated using gfortran)
- account for moist thermodynamics in (dry) potential temperature equation;
1st step toward generic time-varying control variable (2D)
document changes in verification/global_ocean.cs32x15 (related to thsice).
pkg/ptracers: code from Ryan A. to reset a tracer.
document pkg/thsice changes
fix missing EXCH of sIceLoad in thsice_main.F for seaice diffusion only.
tag checkpoint64c
document new parameter JFNKres_tFac
update: add a little more text to explain the line search option and the associated changes
document this line search option of JFNK solver
ducument pkg/mdsio changes (writing missing value to meta files)
document Qsw diagnostics extension
document changes in verification/offline_exf_seaice
document changes in verification cfc_example & offline_exf_seaice + in pkg/layers
document changes in offline_exf_seaice verification experiment
document addition of Finite-Volume presure gradient form for atmosphere using sigma-coordinate
document implementation of EVP*
changes in pkg seaice & cheapaml to work when compiling with "-use_r4".
warning if select_rStar=2 with nonlinFreeSurf <> 4 ; update few AD experiments.
other pkg/cheapaml changes
document pkg/cheapaml changes.
*** empty log message ***
document pkg/cheapaml changes.
document changes (from last 2 days) in verification/cheapAML_box experiment.
- add thermodynamics only test.
- document SEAICE_MULTICATEGORY removal - new tag: checkpoint64b
pkg/cheapaml: fix the restart issue (related to AB-2)
- recent changes in lab_sea and offline_exf_seaice adjoint tests.
document addition of cg2d-param for selecting solution other than last iter.
document new S/R SEAICE_CALC_LSR_COEFFS
document this: - modify the computation of the residual so that the mass of sea-ice is not used twice; this simplyfies the calculations, but since the residual only used if LSR_mixIniGuess.ge.4, and this is never tested, it does not affect the testreport results.
disabling SEAICE_GROWTH_LEGACY for verification/seaice_obcs
quasi-hydrostatic extended to p & p* coordinate
document changes in JFNK solver: new scalar product and some cleaning up
bug fixed in dissipation heating
add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver.
document this in pkg/seaice:
- first attempt at a multi-threaded fgmres solver for the JFNK solver:
introduce bi/bj loops and use global_sum_tile_rl instead of
mpi_allreduce in seaice_fgmres.F
- improve diagnostics output for fgmres solver (seaice_fgmres.F)
- replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F)
- add a verification experiment for JFNK in offline_exf_seaice
document verification/offline_exf_seaice cheanges
add new experiment "cheapAML_box"
fix dissipation heating in pkg/aim_v23 & pkg/shap_filt.
updating - rename two subroutines in seaice_preconditioner.F - remove unused field pressPre from jfnk solver
document mdsfindunit.F changes
document fixing the seaice_preconditioner once again
document genmake2 changes
checkpoint64a
pkg/autodiff: improve pkg-internal logical parameter switch (inAd/inFwd mode)
adding tidal velocity forcing capability to obcs Modified Files: model/src/dynamics.F forward_step.F the_main_loop.F pkg/obcs/OBCS_FIELDS.h OBCS_OPTIONS.h OBCS_PARAMS.h OBCS_SEAICE.h obcs_apply_eta.F obcs_apply_r_star.F obcs_apply_surf_dr.F obcs_apply_ts.F obcs_apply_w.F obcs_calc.F obcs_check.F obcs_init_variables.F obcs_readparms.F verification/seaice_obcs/code/OBCS_OPTIONS.h Added Files: pkg/obcs/obcs_add_tides.F verification/seaice_obcs/input.tides/* verification/seaice_obcs/results/output.tides.txt
updating: introduce runtime parameter SEAICEetaZmethod (=0 by default)
updating
document addition of frictional heating in pkg shap_filt and aim_v23
document adMass Changes + addition of frictional heating support
Update
- move computation of eta at Z-points into calc_viscosities
+ introduce global field etaZ
+ add different methods for computing etaZ, for now the old
method (simple averages of eta to Z-points) is hardwired
+ replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
seaice_preconditioner
- simplify computations for SEAICE_ZETA_SMOOTHREG
updating: - replace one remaining press by pressLoc (mistake) - adjust printing of residuals
updating:
- move control over output-messages by fgmres to seaice_jfnk to save
some operations
- improve I/O of diagnostics of JFNK in seaice_jfnk.F:
+ add (SEAICE.h) and rename some counters (initiliased in
seaice_init_fixed.F)
+ add _BEGIN/END_MASTER (myThid) around print statements
+ print total number of iterations and failures over SEAICE_monFreq
interval to STDOUT
updating
updating
updating
updating
Update
Add commentes re. ITD code.
document changes in seaice verification experiments.
pkg/exf/exf_check.F: same conditional stop as before Aug 28 changes
update verification output: lab_sea/results/output_adm.evp.txt
document latest pkg/layers changes
document pkg/layers changes.
document this:
- simplify (?) ocean-drag coefficent computations by using
the same routine in all three solvers (saves some code lines)
- remove global fields DRAGA and DRAGS from C-grid code and
declare them locally in lsr.F (the only place where they are
still used)
a little documentation about the JFNK-solver, which is still very much work in progress
document addition of intrinsic S/R flush calls + fix ctrl_unpack.F (ALLOW_GENARR3D_CONTROL)
tag checkpoint64
update: fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
#ifdef ALLOW_SHELFICE CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid) Bug fix KappaRU -> KappaRV
- fixed some indexing bugs in obcs_seaice_sponge.F - added obcs relaxation subroutines for HSALT and HSNOW - changes verification/seaice_obcs/results/obcs_seaice_sponge.F Modified Files: pkg/obcs/OBCS_SEAICE.h obcs_readparms.F obcs_seaice_sponge.F verification/seaice_obcs/input.seaiceSponge/data.obcs verification/seaice_obcs/results/output.seaiceSponge.txt
updating: add multicategory snow to sea ice
Added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
see verification/seaice_obcs/input.seaiceSponge for example application.
Modified Files:
doc/tag-index
pkg/obcs/OBCS_OPTIONS.h OBCS_SEAICE.h
obcs_apply_seaice.F obcs_check.F obcs_readparms.F
verification/seaice_obcs/code/OBCS_OPTIONS.h
Added Files:
pkg/obcs/obcs_seaice_sponge.F
verification/seaice_obcs/input.seaiceSponge/data.obcs
verification/seaice_obcs/results/output.seaiceSponge.txt
pkg/obcs/obcs_readparms.F : fix previous modifs when multi-threading
*** empty log message ***
document changes in pkg/obcs
document changes in pkg/obcs
pkg/exch2: improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON
document FLT_Iter0 addition & changes in ctrl_pack/unpack
fix missing STOP in mdsio_readvec_loc.F
document changes in Makefile (genmake2)
- some fixes in pkg/flt with exch2 ; finish to remove ALWAYS_USE_MPI which is no longer set in Makefile (was done by genmake2).
change indentation (+ try to re-tag this file).
- document, although a little late, some changes that went into checkpoint63s.
tag checkpoint63s
document changes in eesupp/src (related to usingMPI) and in pkg/exch2
- fix bug/typo in pkg/flt (FLT_WITHOUT_Y_PERIODICITY) - fix bug in pkg/ggl90 (ALLOW_GGL90_SMOOTH with useCubedSphereExchange)
- AD & TL output: comment out the nasty "writeBinaryPrec = writeStatePrec" line - add 1 line of doc on pkg/cheapaml changes
document changes in genmake2 (AD_CONFIG.h & MAKE)
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document changes in genmake2 (source genmake_local after processing args)
document changes in grdchk_main.F
move call to COST_INIT_VARIA to initialise_varia.F
pkg/dic: move initialisation of freefe from dic_biotic_forcing.F to fe_chem.F
*** empty log message ***
*** empty log message ***
document testreport changes
option in testreport to test TLM set-up
checkpoint63r
*** empty log message ***
document recent changes + the last bit to be checked-in today.
- document changes related to ECCO_CPPOPTIONS.h - genmake2: check for lapack
*** empty log message ***
- changes made to ECCO_CPPOPTIONS.h in all code_ad verification experiments. - modification of EXF_OPTIONS.h (ECCO_CPPOPTIONS_H replaces ALLOW_AUTODIFF_TAMC in controling whether options are set here or in ECCO_CPPOPTIONS.h)
*** empty log message ***
*** empty log message ***
*** empty log message ***
pkg/shelfice
add to EEPARAMS.h Real-type constant for simple number (0,1,2,1/2)
*** empty log message ***
pkg/autodiff: new generic active_read/write S/R. one for each type (RS/RL)
pkg/autodiff: active_read/write "_lov" version: update and simplify
document active_read/write changes in pkg/autodiff
pkg/thsice: option to balance atmos fresh-water flux
Update
tag checkpoint63q
document adjoint-experiment output update (ad-monitor)
document changes in pkg/autodiff rlated to monitor and snap-shot of AD-vars
Update
pkg/exf: fix checking of surface-relaxation setting
- bottom drag: split loops (only compute quadratic bottom drag if it's used) - reduce length of simulation by half in few AD tests.
describe replacement of KE.ne.0 with KE.gt.0 in mom_u/v_bottomdrag and shelfice_u/v_drag
document changes in CG2D_NSA (+ experiments using it)
update verification/tutorial_tracer_adjsens parameters (more consistent)
-fix exch2 compact format definition with empty facet -fix large-size domain format when reading meta file
model/src: refine CS-grid check.
*** empty log message ***
*** empty log message ***
*** empty log message ***
document changes related to automatically generated file AD_CONFIG.h
tag checkpoint63p
- update according to june 29 model/src and pkg/seaice modifs.
new run-time parameter in autodiff_readparms.F
new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
Update doc
tag checkpoint63o
document changes in vertical mixing schemes interface
document testreport changes
document changes in initialise_varia.F
Update
HAVE_NETCDF added to the DEFINES list
document changes (eosType setting in data, model/src changes)
*** empty log message ***
*** empty log message ***
fix UPDATE_CG2D and update bottom_ctrl_5x5 results
implement vertical bi-harmonic diffusion
Update
For verification purposes, the exact adjoint rather than an approx. should be used (e.g., to comare against F.D. or TLM). Update results/ accordingly.
changes in pkg/cal (cal_getdate.F) + fix calendarDumps for non-zero phase-lag
document changes of calendarDumps implementation in pkg/diagnostics
tag checkpoint63n
updated
document changes in ni_masks_etc.F (useShelfIce) and in calc_r_star.F
document changes to shelfice
document new DISCONNECTED_TILES option
document CG solvers changes
Update
tag checkpoint63m
document changes in hydrostatic pressure calculion below ice-shelf + isomp update
add snowPrecip to HSNOW in seaice_growth
document changes in local AD option files
Update doc
new S/R PACKAGES_CHECK
avoid calling a S/R with 2 times the same arg
document new internal flag uniformFreeSurfLev + changes in CALC_PHI_HYD
document changes in ctrl_init.F: - add a formal parameter to s/r ctrl_init_rec to print xx_$(ctrl_valiable)_file for easier debugging - move call of cal_* routines into the if-block where they are really needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having to specify a startdate
turn on seaice Multi-category in global_ocean.cs32x15.seaice
document more changes in pkg/cal.
document changes in pkg/cal
tag checkpoint63l
fix in pkg/bbl (case multi-tiles per proc) + update output.yearly.txt
pkg/cal: fix for case baseTime <> 0 (+ some cleaning)
start to implement clean wait to stop in initialization S/R.
o pkg/bbl: - replace deltaT with dTtracerLev(k) for asynchronous time stepping - global_with_exf/input.yearly verification; changes output.yearly.txt
modification so it can work with z*
document various little changes in eesupp/src
cleaning of pkg/fizhi turbulence cold-start switch
changes in pkg/exch2 [fix problem with sNx <> sNy and GCD(sNx,sNy) < 2*Olx]
move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
updating
Update
more pkg/fizhi modifs
pkg/fizhi: fix update_earth_exports.F for multi-tile per proc
add 1 gmredi diagnostic
fix few initialisation and multi-tile Pb in pkg/fizhi
document fix in mom_vecinv
fixing initialization bug and changing loop order in pkg/icefront/icefront_init_varia.F
document small changes in ini/update_masks_etc.F: move k-loop outside of i/j-loops when (re-)computing R_low in in order to avoid -O3 optimization problems with some compilers (gfortran 4.6.0 on MacOS)
momentum: separate fVer kUp/kDown in argument list of MOM_FLUXFORM & MOM_VECINV
tag checkpoint63k
document fix in ALLOW_ADDFLUID momentum part and SOLVE_DIAGONAL default.
changes in verification exp. global_ocean.90x40x15/input_ad
solve_*diagonal.F story continues
Update
Update
little changes to testreport
describe changes in shelfice
Some doc re. solve_...diagonal.F changes.
document fwd lab_sea experiment update
document changes in pkg/seaice parameter setting
document pkg/obcs addition.
document pkg/ptracers changes (parameter to decide when to start a tracer)
move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h
document pkg/ecco cost output-file fix
document changes in pkg/seaice/dynsolver.F
*** empty log message ***
fix some initialisation issues for adjoint recomputation
generating updated verification/global_with_exf/results/output.yearly.txt on forge
added verification for pkg/frazil in global_with_exf/input.yearly changes results/output.yearly.txt
changing pkg/frazil forcing terms from K/s to W/m^2
*** empty log message ***
adding pkg/frazil - see frazil_description.tex for details
document changes in shelfice_thermodynamics.F:
- fix exponents for velocity dependent exchange coefficients: change
from 2/3(=0) to 0.66666666666666667
- move computation of velocity dependent exchange coefficients into
separate loop, so that it applies to both thermodynamics
- move some divisions by constants out of loops
tag checkpoint63j
*** empty log message ***
update list of modified output_adm*.txt
document changing global_ocean.cs32x15.seaice because of differences at truncation level. Let's hope that the adjoint is not too bad.
updating
pkg/seaice clean up...
pkg/seaice and global_ocean.cs32x15
fix and simplify interface between pkg/thsice and pkg/salt_plume
- document latest pkg/seaice commit.
document pkg/seaice changes
document changes in pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY)
- add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice. - move untested set-up to MITgcm_contrib/verification_other.
reitired seaice agetr
docuemnt changes in seaice_solve4temp.F and seaice_freedrift.F
document changes in pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef)
document seaice_solve4temp.F changes and updated output.
apply mask to taux,tauy (in seaice_get_dynforcing.F); this affects results when using SEAICEuseFreeDrift and/or using useHB87stressCoupling =T.
updating
document vectorized salt_plume
fix option "-makefile NAME" in genmake2
tag checkpoint63i
updating
change default celsius2K from 273.16 to 273.15
update: small changes in find_rho/alpha and seaice_evp
document fixing of diagstats_calc for TARGET_NEC_SX
document changes in pkg/obcs OB indices setting when using exch2
update previous changes
change default EXF_LWDOWN_WITH_EMISSIVITY and update exp. using pkg/exf default emissivities
ducument bugs fixed in pkg/seaice
Update
updating
document exf-interpolation changes regarding near poles treatment.
pkg/exf: fix masking of wind-stress (was wrong if interpolated or read on A-grid) and update results of exp. global_with_exf (x2).
updating
document changes in esf_interp.F (no effect on results)
forgot to document this: pkg/seaice: change declaration of UVM from _RL to _RS
tag checkpoint63h
pkg/offline related changes
update CS-32 grid-files with grid-angle generated using cubeCalcAngle.m
-pkg/exf (vertor interpolation): use grid-angles for rotation. -pkg/seaice: remove stop if exf option ALLOW_RUNOFF is undef.
document changes in pkg/PKG_OPTIONS.h files.
updating
describe changes in pkg/seaice: sort out emissivity and long wave radiation step 2
changes in exf_readparms.F (simplify default setting of interpolation parameters)
document pkg/exf (interpolation) changes.
updating
explain ocean_emissivity*lwdown in exf_radiation
document changes in pkg/seaice: FV B-LSR solver and SEAICE_emissivity
updating
describe changes in pkg/seaice/seaice_readparms.F and model/src
tag checkpoint63g
- recent changes
useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
document changes in obcs_calc_stevens/obcs_apply_ts
- change non-curvilinear grid setting to also work with exch2 + blank tiles - switch to exch2 test-exp. global_ocean.90x40x15 and remove 1 blank-tile
fix initialisation of sigma-coordinates
new run-time switch "doResetHFactors" (default=false) to reset (or not) thickness factors (hFac*) at the beginning of forward_step.F
update advect_xz test exp
IES cost term
pkg/rbcs: fix missing relaxUFile & relaxVFile in namelist advect_xz: update and add a seconddary test (using implicit vertical advection)
updating
document changes related to tracer vertical implicit implementation
tag checkpoint63f
updating
document fixing a bug in code for northern and southern boundaries
updating
document bug fix in seaice metric terms and more
change S/R INTEGR_CONTINUITY, now called directly from forward_step.F
changes in do_oceanic_phys.F + change diagnostic WRHOMASS
updating
document new cpl_aim+ocn test exp. output.
updating
add diagnostics for Adams-Bashforth tendency increment.
updating
tag checkpoint63e
update
Update
simplify exp4+stevens
document seaice-LSR changes
updating
document updated Stevens code and also a few more things that I did describe in the cvs messages
updating
tag checkpoint63d
updating (also older changes about gad-routines, that I obviously forgot to document)
update seaice_obcs output (switch off OBCS_UVICE_OLD)
-new obcs implementation in seaice-dynamics
little changes in pkg/seaice dynamics + update test exp output
Document changes in packages layers and dic
document this:
- improve vectorization also for adjoint code of
solve_tridiagonal and solve_pentadiagonal. As this requires up to
5 new 3D-fields, this code is only turned on for the combination of
ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX.
- remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
ALLOW_AUTODIFF. !!!!! THIS FLAG NOW NEEDS TO BE SET OUTSIDE OF
SOLVE_TRI/PENTADIAGONAL.F !!!!