CVS log for MITgcm/doc/tag-index
	Help

Request diff between arbitrary revisions / Display revisions graphically

checkpoint61c

o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
  to add mass source/sink of fluid in the interior (3-D generalisation
  of oceanic real-fresh water flux).

o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)

o new pkg: down_slope

o move kSurfC,kSurfW 7 kSurfS from SURFACE.h to GRID.h (next to kLowC)

o change FIND_RHO to FIND_RHO_2D :
  pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
o new pkg: cheapaml

checkpoint61b

exch2:
  change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
  comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
  (both are no longer needed) in exch_uv: no effect in forward run; but
   get truncation error differences with adjoint exch.

o exch2:
 - change index-bounds storage (moved from target to local tile,
   more intuitive this way) ; rename/remove some variables.
 - change utils/exch2/matlab-topology-generator accordingly.

checkpoint61a

o exch2/matlab-topology-generator:
  fix bug in index bounds for N-S internal exchange

make sure that the stuff that is written to msgbuf in mnc_handle_err
is not too long for msgbuf, in order to get a little more meaningfull
error messages ...

fix syntax of awk so that testreport works smoothly even in the sun

Tagging checkpoint61
  Change default for TAF usage by removing argument '-nonew_arg'
  This changes TAF subroutine argument list (ordering of active var.)
  Omission of this flag leads to incompatibility w.r.t. TAMC
  To restore TAMC-compatibility, need following modifs:
  * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
  * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
  Tested TAF version is 1.9.22

o autodiff
  Change default for TAF usage by removing argument '-nonew_arg'
  This changes TAF subroutine argument list (ordering of active var.)
  Omission of this flag leads to incompatibility w.r.t. TAMC
  To restore TAMC-compatibility, need following modifs:
  * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
  * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
  Tested TAF version is 1.9.22
  N.B.: exch2 hand-written adjoint code currently not TAMC compatible

checkpoint60
--->>> This is the last checkpoint for which generating the adjoint
--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
--->>> by default.
--->>> Future checkpoints will ommit this flag by default.

os7mp changes

*** empty log message ***

*** empty log message ***

*** empty log message ***

*** empty log message ***

*** empty log message ***

checkpoint59r

pkg/mdsio/mdsio_facef_read.F & ini_cori.F: fix reading option for CS-grid

updating

updating

describe recent changes: let's see how this missing value business is
accepted by the user(s)

pkg/thsice/thsice_ini_vars.F added default initial values so that
thermodynamics sea ice solver does not blow up when some initial fields
are missing.  The important one is reasonable default values for enthalpy.

o move from external_forcing_surf.F to ini_forcing.F
  the p-coord. hack consisting in using pLoad to set phi0surf ;
  update output of tutorial_global_oce_in_p (affected @ truncation level).

*** empty log message ***

  change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
  applies to files where Temperature & Salinity 2nd Order moments are used.

update

checkpoint59q

o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
   (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)

Refresh tutorial_global_oce_biogeo

*** empty log message ***

updating

updating

*** empty log message ***

o remove "exp5" (replaced by tutorial_deep_convection).

updating

o tutorial_deep_convection : updated

add a flag for restoring T and S underneath sea ice

updating

merge netcdf-support and diagnostics from Patrick Rosendahl into code

*** empty log message ***

checkpoint59p

o pkg/dic: test for "pickup_dic" file when restarting ;
  if no pickup-file, can restart with a re-initialised pH (same as it did
  before) providing pickupStrictlyMatch is set to False.

o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
  + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP

o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
  and staggerTimeStep is off (needed for stability of Internal-wave dynamics).

o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
   scheme to use for vorticty-term ;
 - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
   (with default selectVortScheme, return to original discretisation)
 - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)

updating

o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
  bottom ; only used with variable horizontal viscosity and non-hydrostatic.
  also fix diagnostics VISCAHW & VISCA4W.

tag checkpoint59o

o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).

improve vectorizability by moving a few statements out of the main loop

  - convert potential temperature into in-situ temperature. This changes the
    isomip tests => update tests

first round of fixes to pkg/shelfice
  - sort out freshwater flux; convert freshwater fluxes to mass fluxes
    (kg/m^2/s), does not break tests, because in verification/isomip,
    rhoConstFresh=rhoConst (by accident)

document: add a flag writePickupAtEnd (default=true) to be able to suppress
writing a pickup at the last timestep

*** empty log message ***

o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
  conditions that have a different sampling frequency than S/T/U/V obcs

o pkg/diagnostics (stats-diags):
  - fix global Min/Max in case 1 processor get only empty tiles

replace (4 times)
     make genmake_tc_1.o >> genmake_warnings 2>&1
with
     COMM="$CC $CFLAGS -c genmake_tc_1.c"
     echo $COMM >> genmake_warnings
     $COMM >> genmake_warnings 2>&1
to make genmake2 always see the value of CC as specified in the
optfile. This change may break testreport or building the code on some
platforms where the default value of CC does not point to anything
useful. In that case, setting CC will fix the problem.

o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
  - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
  - modify verification advect_cs test to test SOM-advection on CS-grid.

*** empty log message ***

checkpoint59n

o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
  number in dedicate array "hdiag":
  - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
    with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
  - many small changes (integer format) for large number of diagnostics
  - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
    a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.

 add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
 usingSphericalGrid, this allows to define the rotated grid coordinates
 via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
 geographical coordinates according to the inverse of the rotation defined
 by the Euler angles, so that Coriolis parameter and online-interpolation by
 exf works with the geographical coordinates on XC/YC/XG/YG.

 The three Euler angles PhiEuler, ThetaEuler, and PsiEuler
 define the rotation about the original z-axis (of an sphere
 centered cartesian grid), the new x-axis, and the new z-axis,
 respectively.
 Naturally, this feature does not work with all packages, so the
 some combinations are prohibited in config_summary (flt,
 flt_zonal, ecco, profiles), because there the coordinates are
 assumed to be regular spherical grid coordinates.

*** empty log message ***

have mnc create marginally meaning full coordinate variables if
usingCurvilinearGrid and NOT EXCH2 (that is the grid indices)

add a verification experiment that tests useEXFyearlyFields with
USE_EXF_INTERPOLATION defined

o pkg/mypackage:
  - add example of read/write pickup for state-var ;
  - add entry points to the main code for state-vars diags & write-pickup.

  - add new subroutine that determines the file to read from for
    use*YearlyFields = .TRUE. and .FALSE.

o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
  transitions for useExfYearlyFields

o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
  analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
  subroutines (which could be generated from a template, because they are
  almost identical) to save a few lines of code and may make it easier to
  change this bit; for now they are included in obcs_prescribe_read.F for
  simplicity

o finish vectorization of exf_interp for TARGET_NEC_SX
  by unrolling short inner k-loops by hand (arghhh!)

o pkg/exf:
  - add a little more diagnostic to exf_interp_read (in analogy to
    mds_read_field, can be turned off with debugLevel < debugLevA=1)
  - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
    ugly but fast (vectorization is not yet complete)

o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice

o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
  http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html

o verification/seaice_obcs: updated for restart test and latest options

  add a new flag SEAICEuseTEM to use a slightly different
  ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
  for now this is only available for the C-grid code and also within
  #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
  default is to not use it.

tag "checkpoint59m" (before the next "DocFest" or the next snow-storm ?)

reinserted comment that was accidentally deleted.

o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
  and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature

o pkg/seaice/seaice_growth.F: use a different time constant for freezing
  ice due to supercooled sea water, hardwired to SEAICE_deltaTtherm/0.1

o gad_som : fix flux output (& diagnostics) to have same units as other
  advection scheme fluxes (was previously multiplied by deltaT).

o added verification/seaice_obcs both to test seaice open boundaries
  and to provide an example matlab scrpt for generating them

o added verification/lab_sea/input.salt_plume

o pkg/salt_plume: clean up salt_plume_frac.F

o pkg/kpp: added saltplume diagnostics

o pkg/obcs and pkg/seaice:
  - do not set uice and vice to zero when OB*icefile are unspecified
  - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
  - moved seaice tracer obcs after call to seaice_growth

tag checkpoint59l was done before changes in pkg/salt_plume

o pkg/salt_plume: added various options for salt plume depth
  criterion and for vertical distribution of the salt

checkpoint59l

o pkg/ptracers: new version of ptracers pickup:
  read meta file and write only fields which are needed to restart.
  ( same logic as main pickup file ; also using pickupStrictlyMatch )

  - reformulated availHeat in seaice_growth.F to be independent of AREA

updating

replaced EXF_OPTIONS.h CPP option EXF_SUBTRACT_UVVEL_FROM_UVWIND
with EXF_PARAM.h runtime parameter useRelativeWind

o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
C     When the prescribed open boundary conditions are incosistent with
C     forcing, for example, six-hourly forcing and daily or monthly sea
C     ice boundary conditions, ice convergence at edges can cause model
C     to blow up.  The above CPP option fixes problem, hence it is
C     turned on by default, but this is at the expense of less accurate
C     boundary conditions.

pkg/seaice: removed some unused halos

forgot to document my little change: Compiler directive for NEC SX computers

o pkg/seaice: removed SEAICE_FFIELDS.h and seaice_get_forcing.F
  seaice forcing fields can now be read only through pkg/exf

no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP

o pkg/exf: added CPP option EXF_SUBTRACT_UVVEL_FROM_UVWIND for subtracting
  UVEL and VVEL from UWIND and VWIND prior to applying bulk formulae.

checkpoint59k

o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
  dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.

o fix un-initialised variable problem (in mom_vecinv & shap_filt):
  all experiments pass when compile with un-initilised var. checking option.

added pkg/salt_plume by gathering code, which were previously
spread around various files in model/inc and model/src
results remain numerically identical to before, as a first step
towards adding more options, etc., to this package

o script to test restart (for now, in MITgcm_contrib/jmc_script)
o pkg/seaice: new read/write pickup version.
  read meta file and write only fields which are needed to restart.
  ( same logic as main pickup file ; also using pickupStrictlyMatch )

updating

o lab_sea.hb87: modify the domain & update output.hb87.txt :
o pkg/rw: cleaning-up:
o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
  a set of consecutive levels in/from a 3-D array.

o pkg/ptracers:
  use use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
  to-do: fix pkg/diagnostics when large number of diagnostics are defined.

checkpoint59j

o in pkgs: dic, obcs, offline, rbcs:
  standard way to compute coeff. for time interpolation between 2 time reccords
  which retains full precision (& make results less dependent on compiler).
  update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.

updating

split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
 (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
  to allow to compile customized code before the update)

o cleaning-up:
  - fix CPP instruction syntax in pkg/obcs
  - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
    add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
  - fix some threads issue in IO parts.

add more comments about EmPmR units changes in coupled set-up

About modifying pkg/dic

o pkg/mom_fluxform: special version of momentum advection.

Added open boundary conditions capability for seaice UICE, and VICE
UICE and VICE are reset at the edges after calling the solver and
before advection/diffusion.  Needs testing.

o new read/write pickup version:
  - for now, only implemented for main (mdsio) pickup file.
  - write out only what is needed to restart; merge pickup_nh , pickup_ph
    and main pickup together.
  - read meta file; read only what is needed to restart; stop if a field
    is missing (if pickupStrictlyMatch=T, = the default) or try to restart
    if it make sense (even if the restart is not perfect).
  - if no meta file, assume that pickup to read corresponds exactly to
    a pickup that would currently be written.
   - read pickup written in the old format (until checkpoint59i) if it
    recognizes an old meta file (no field-list).
  - add a meta file in exp. which starts from a pickup: 2 cases:
    a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
     e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
    b) a meta file describing the content of the associated pickup file
     e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
o pkg/mdsio & pkg/rw:
  - new routine to read a meta file ; new set of routine to read
    Multiple-fields file (with meta file).

added open boundary conditions capability for seaice HSNOW and HSALT
(code contributed by Michael Schodlok)

checkpoint59i

Update

o pkg/kpp: add "_d 0" to real constant (if missing);
  update output of exp: natl_box (10.digits); vermix (std, 7.digits)
  and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).

o prepare for "clever pickup" implementation: add new header file "RESTART.h"
  for internal parameters related to restart process (formerly from PARAMS.h)
  and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
  as argument. (only atm2d & obcs write_pickup have not yet been updated)

o pkg/monitor:
  - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
  - fix mon_stats_rs (statistics over the full domain, even where field is zero)
  - account for deep Atmosphere factor and density factor (anelastic)

o Added open boundary conditions capability for seaice HEFF and AREA
For time being this capability requires pkg/exf, pkg/obcs, and pkg/seaice
UICE and VICE are masked at the southern and western open boundaries, if
any, of the domain.  Eventually needs to be extended to SALT and SNOW.

updating

o add missing cvs $Header:$ or $Name:$ in eesupp/*, pkg/* & verification/code*

document recent changes

o add new diagnostics to seaice: advective, diffusive fluxes (only for
  multidim-advection, for scheme 2 they are not filled) and transports,
  thermodynamic growth rates

o change units of EmPmR (inside the code) from m/s to kg/m2/s (mass flux) but
  leave input file unchanged. Affects results @ truncation level (cg2d match)
   and update output of experiments: lab_sea(6), global_ocean.90x40x15(10),
   global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
  + adjoint results: global_ocean_ebm(11) and lab_sea (12).
  Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).

checkpoint59h

update

Added comments, which describe the changes made in kpp_calc_diff_s & _t.F on
April 23, 2007.  These routines no longer update the vertical
diffusivity array (passed as argument) but are (re-) setting those
arrays.  Also changed order GMREDI_CALC_DIFF & KPP_CALC_DIFF_T in
calc_diffusivity.F and ptracers_calc_diff.F since now the order matters.

improve vectorization by moving if-statement out of loops

added the salt plume scheme (ALLOW_SALT_PLUME) to pkg/kpp
(code conttributed by An Nguyen)

o testreport:
  - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
    monitor & update offline_exf_seaice exp. output.
  - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)

finally document this:
o pkg/seaice:
  - bug fix in the evp solver: boundary conditions were affected be
    masking of zMax/zMin (changes results)
  - minor bug fix in boundary conditions in seaice_calc_strainrates
    (changes results for no_slip)
  - seaice_lsr.F: make interpolation of eta dependent on boundaries
  - replace hardcoded lower limit for zeta (zMin) by runtime parameter
  - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
    stress formulation and no-slip boundary conditions

o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
  in gad_calc_rhs.F ; add few safety stops in initialisation phase.

A simple HSALT time stepping equation has been checked in.

o pkg/thsice: use continuous power-law function for partition of energy