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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o switch to TAF version-2: |
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- add flow directives to "freeze" naming convention for ad-routines that |
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are used in I/O routines of adjoint state and associated common blocks |
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that are used in adcommon.h (backward compatible with version-1) |
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- update all ad-optfiles (in tools/adjoint_options + few local to some |
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verification exp) to switch to latest TAF version (currently 2.5.5); |
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merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented |
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out except for diva). |
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- the major change with TAF version-2 is that both the differentiated |
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routines and the forward routines (new) are returned as part of the TAF |
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output source code. Update genmake2 accordingly. |
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- new output for AD experiment tutorial_global_oce_biogeo (better AD gradient |
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with version-2 when compared to TLM or FWD gradient); other experiments |
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output show minor changes (machine truncation level); update the few AD & |
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TLM output with 12 matching digits only (some prior to version-2 switch). |
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checkpoint64l (2013/08/05) |
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o model/src: |
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- in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F |
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- main_do_loop.F: no longer includes additional (AUTODIFF) header files |
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when using TAF but only if using OpenAD. |
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o pkg/mom_common+fluxform+vecinv: |
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- always set horiz. viscosity arrays to background value before calling |
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MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC |
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only when using variable horiz. viscosity (useVariableVisc=T); |
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- simplify mom_vecinv.F (only 1 block for momViscosity). |
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o pkg/mom_common: variable horiz. viscosity in NH code |
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- move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F) |
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from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h |
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- store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, |
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useBiharmonicVisc & useVariableVisc. |
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- fix old bug (already in 1rst implementation of variable horizontal viscosity |
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in calc_gw.F, version 1.27, 2006/06/20): |
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horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 |
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even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. |
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- change background horiz viscosity in vertical momentum (gW) to always be |
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viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using |
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any type of variable viscosity, e.g., viscAh/4Grid) |
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- change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of |
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viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing |
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horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since |
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default viscAh,viscA4 is zero). |
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o model/src: |
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- extend length of drC & recip_drC from Nr to Nr+1. |
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o Divided Adjoint (DIVA) with MPI: |
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- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
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- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
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and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h. |
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checkpoint64k (2013/07/23) |
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o tools/OAD_support: |
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- avoid the need for file "oadtempflile" in insertTemplateDir.bash |
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and remove it from genmake2. |
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o tools/build_options: |
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- remove MPI_HEADER_FILES_INC setting (no longer used) and comment out |
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MPI_HEADER_FILES list (let genmake2 find the missing headers) |
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o verification/halfpipe_streamice: |
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- change to driving stress formulation; update both Fwd & AD output. |
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o tools/genmake2 and Divided Adjoint with MPI: |
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- remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken); |
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- only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set; |
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- add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in |
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Makefile, which is set by genmake2, and check which mpi-headers are needed. |
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Note: need to update adjoint_options/adjoint_diva_mpi accordingly. |
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- update target "CLEAN" (to also remove ./mpi_headers/ dir). |
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o testreport: |
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- changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, |
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perform additional runs (number of additional runs is "add_DIVA_runs" taken |
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from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h"). |
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o verification/lab_sea (AD test): |
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- change to test Divided Adjoint Run in this set-up (both standard AD test |
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and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test. |
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o pkg atm_ & ocn_compon_interf: |
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- remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old |
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staggerTimeStep implementation) and disable (retired) corresponding |
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parameter. |
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o pkg/offline: |
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- comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01]; |
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- add S/R OFFLINE_CHECK to print offline parameter summary |
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and stop if loading a file that is not used; |
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- enable to calculate GMRedi tensor, KPP mixing and convective index |
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when the corresponding file(s) is/are not specified (but pkg is used). |
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- comment out resetting of monitorFreq (to endTime) since it still useful |
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for monitoring CFL numbers and checking offline fields. |
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o OpenAD: |
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- do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get |
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smaller standard output) and generate new (smaller) output (on baudelaire |
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using gfortran with -ieee) for exp. tutorial_tracer_adjsens |
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o model/src: |
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- call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F), |
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(where external_forcing_adjust was called) and change list of arguments; |
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- merge external_forcing_adjust.F into external_forcing_surf.F |
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- put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F) |
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which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX, |
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previously in file "balance_relax.F", now removed); remove corresponding |
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arrays in FFIELDS.h. |
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- EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement |
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a hack for getting back surfaceForcingS (loaded from file) when using |
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ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up. |
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- update output of AD test experiment global_ocean.cs32x15.seaice_dynmix |
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(was getting only 11 digits for AD-grad, due to different truncation |
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error in AD code). |
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checkpoint64j (2013/07/04) |
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o pkg/offline: |
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- to enable the use of other features with pkg offline (e.g., obcs), |
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also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come. |
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- comment out "allowFreezing" (now active) in 2 offline testing exp. |
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o pkg/exf ALLOW_RUNOFTEMP |
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- fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL |
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- ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice |
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- changes verification/global_ocean.cs32x15/results/output.seaice.txt |
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o pkg/atm_phys: |
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- allows to add some damping on uVel,vVel (strength only function of k). |
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o verification, ad-tests: |
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- reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, |
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global_ocean_ebm and offline_exf_seaice.thsice. |
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o verification/halfpipe_streamice: |
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- found a bug in s/r pkg/streamice/streamice_advect_thickness which caused |
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flux input boundary conditions to be ignored; a fix for this bug changed |
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verification results for forward test. |
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- add adjoint test. |
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o pkg/ptracers: |
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- allow to restart without SOM pickup (resetting SOM to zero). |
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o pkg/gmredi: |
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- New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added. |
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- It uses mixing length theory and suppression by steering level effects to |
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calculate a diffusivity used in the Redi tensor (see Bates et al., submitted |
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to JPO, for more details). |
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- It also uses the diffusivity to calculate an eddy induced streamfunction |
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based on a PV closure (rather than a buoyancy closure as in GM). |
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- New files added to pkg/gmredi: |
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gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy |
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induced overturning streamfunction (called from gmredi_calc_tensor) |
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gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required |
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for use in gmredi_k3d |
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gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate |
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the eddy diffusivity |
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checkpoint64i (2013/06/18) |
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o pkg/cheapaml: |
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- take src files from MITgcm_contrib/verification_other/offline_cheapaml/code |
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that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics) |
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with pkg/cheapaml. |
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o utils/python: add subpackage for cubed sphere function, first example is |
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simple cs.pcol to plot 2D fields on a map |
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o pkg/streamice: |
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- This is a new package in MITgcm, which solves dynamic equations for ice |
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sheets and ice streams |
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- At the moment it is independent of atmosphere/ocean dynamics, or any |
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other physical packages in MITgcm, even ShelfIce (although it is anticipat- |
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ed that this will change) |
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- There is a new verification exercise that tests it, halfpipe_streamice, |
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evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a |
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rectangular embayment |
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- halfpipe_streamice is forward-only for now, will have TAF test soon |
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- for questions, email dgoldber@mit.edu |
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o pkg/thsice: |
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- fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing |
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of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40); |
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- remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new |
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call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect ); |
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- allow precip from pkg/cheapaml to make snow over seaice. |
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o pkg/cfc: |
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- move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC |
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- remove atmos CFC 2-D arrays from common bloc (now local variables) |
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- change some hard-coded constant to run time parameter for reading and |
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and interpolating atmospheric CFC ; keep same default as previously. |
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- more flexible reading of Atmos CFC (number of records no longer hard-coded) |
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- put arguments in standard order: myTime, myIter, myThid |
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- use standard S/R GET_PERIODIC_INTERVAL for time interpolation of |
| 178 |
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atmospheric CFC ; fix for the case myIter < PTRACERS_iter0. |
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- fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf |
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- new routine to print summary of CFC params and check for consistency. |
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o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff, |
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similar to thsice_advdiff. |
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Note that for the B-grid case the routine parameters uc/vc are overwritten. |
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o pkg/cfc: |
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- change time interpolation for atmospheric CFC-11 (now same as for CFC-12); |
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update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline. |
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- fix interpolation of atmphspheric CFC between Sorthern and Northern |
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hemisphere value. |
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o pkg/seaice: |
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- allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml) |
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o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics; |
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so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE. |
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- requires an additional time level that is stored in the pickup |
| 194 |
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- you can start with AB2 from a pickup without this time level with |
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pickupStrictlyMatch = .false. |
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|
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checkpoint64h (2013/05/26) |
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o pkg/cheapaml: |
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- replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux); |
| 200 |
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affect machine truncation (but exp cheapAML_box still pass with 13 digits). |
| 201 |
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- consistent treatment of uWind,vWind location: assume everywhere in |
| 202 |
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pkg/cheapaml that they are on C-grid (@ uVel,vVel location) |
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(Note: was already the case for Tair,Qair advection); |
| 204 |
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add option (INCONSISTENT_WIND_LOCATION) to recover old results. |
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- compute diabatic forcing only in the interior (excluding overlap regions) |
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- fill in array "Qsw" (for short-wave heating); |
| 207 |
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- add diagnostic for precip ; fill-in diagnostics for cheapAML state vars |
| 208 |
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before any update (consistent with MITgcm state var diagnostics); |
| 209 |
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- cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if |
| 210 |
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non periodic ; + adjusted for uWind,vWind (C-grid). |
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o pkg/seaice: |
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- remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and |
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add explicitly pkg/exf in experiments that currently use pkg/seaice. |
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- allows to compile pkg/seaice without pkg/exf. |
| 215 |
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o tools/OAD_support: |
| 216 |
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- use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds |
| 217 |
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of array "ourStepOf" in function rvNextAction (revolve.F90). |
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o pkg/aim_compon_interf renamed to pkg/atm_compon_interf |
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- change pkg name (to be used with other atmospheric physics pkg) |
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but by-pass CVS when making the new pkg so that we keep the CVS history. |
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o pkg/offline: |
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- call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F |
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(previously called from pkg/dic_surfforcing_init.F) |
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o model/src: |
| 225 |
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- re-order sequence of calls within packages_init_variables.F, using |
| 226 |
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standard order, except for: |
| 227 |
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DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top), |
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CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom) |
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o new pkg: atm_phys |
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- add entry point and source code (previously in contrib |
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verification_other/atm_gray/code_gray/) for new pkg "atm_phys" |
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(atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008). |
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- re-order sequence of calls within packages_readparms.F, |
| 234 |
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packages_init_fixed.F and packages_write_pickup.F |
| 235 |
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(but skip packages_init_variables.F because of TAF issues). |
| 236 |
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- update contrib/*/atm_gray/ experiment. |
| 237 |
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o pkg/seaice (ITD code): |
| 238 |
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- simplify and fix the writing of pickup-files for ITD case |
| 239 |
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o pkg/seaice (ITD code): |
| 240 |
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- introduce floe size dependent lateral melt for ITD case; |
| 241 |
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- cleaning (avoid division by zero, change to f77 syntax, remove tabs) |
| 242 |
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- update seaice_itd experiment main output. |
| 243 |
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o pkg/thsice: |
| 244 |
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- remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and |
| 245 |
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declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F; |
| 246 |
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changed accordingly pkg/atm2d. |
| 247 |
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|
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checkpoint64g (2013/05/01) |
checkpoint64g (2013/05/01) |
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o pkg/exf ALLOW_RUNOFTEMP |
o pkg/exf ALLOW_RUNOFTEMP |
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- if defined, river and glacier runoff temperature can be read-in from |
- if defined, river and glacier runoff temperature can be read-in from |
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