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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 model/inc: |
| 8 |
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- move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from |
| 9 |
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8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) |
| 10 |
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o pkg/kpp & aim_v23: |
| 11 |
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- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
| 12 |
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o pkg/seaice: |
| 13 |
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- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
| 14 |
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undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
| 15 |
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- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
| 16 |
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o eesupp/src: |
| 17 |
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- fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) |
| 18 |
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in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). |
| 19 |
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o switch to TAF version-2: |
| 20 |
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- add flow directives to "freeze" naming convention for ad-routines that |
| 21 |
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are used in I/O routines of adjoint state and associated common blocks |
| 22 |
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that are used in adcommon.h (backward compatible with version-1) |
| 23 |
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- update all ad-optfiles (in tools/adjoint_options + few local to some |
| 24 |
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verification exp) to switch to latest TAF version (currently 2.5.5); |
| 25 |
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merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented |
| 26 |
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out except for diva). |
| 27 |
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- the major change with TAF version-2 is that both the differentiated |
| 28 |
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routines and the forward routines (new) are returned as part of the TAF |
| 29 |
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output source code. Update genmake2 accordingly. |
| 30 |
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- new output for AD experiment tutorial_global_oce_biogeo (better AD gradient |
| 31 |
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with version-2 when compared to TLM or FWD gradient); other experiments |
| 32 |
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output show minor changes (machine truncation level); update the few AD & |
| 33 |
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TLM output with 12 matching digits only (some prior to version-2 switch). |
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|
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checkpoint64l (2013/08/05) |
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o model/src: |
| 37 |
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- in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F |
| 38 |
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- main_do_loop.F: no longer includes additional (AUTODIFF) header files |
| 39 |
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when using TAF but only if using OpenAD. |
| 40 |
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o pkg/mom_common+fluxform+vecinv: |
| 41 |
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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); |
| 44 |
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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 |
| 46 |
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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 |
| 48 |
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- store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, |
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useBiharmonicVisc & useVariableVisc. |
| 50 |
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- fix old bug (already in 1rst implementation of variable horizontal viscosity |
| 51 |
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in calc_gw.F, version 1.27, 2006/06/20): |
| 52 |
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horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 |
| 53 |
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even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. |
| 54 |
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- change background horiz viscosity in vertical momentum (gW) to always be |
| 55 |
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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) |
| 57 |
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- change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of |
| 58 |
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viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing |
| 59 |
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horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since |
| 60 |
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default viscAh,viscA4 is zero). |
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o model/src: |
| 62 |
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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: |
| 64 |
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- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
| 65 |
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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. |
| 67 |
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|
| 68 |
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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 |
| 71 |
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and remove it from genmake2. |
| 72 |
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o tools/build_options: |
| 73 |
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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: |
| 78 |
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- remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken); |
| 79 |
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- only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set; |
| 80 |
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- add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in |
| 81 |
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Makefile, which is set by genmake2, and check which mpi-headers are needed. |
| 82 |
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Note: need to update adjoint_options/adjoint_diva_mpi accordingly. |
| 83 |
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- update target "CLEAN" (to also remove ./mpi_headers/ dir). |
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o testreport: |
| 85 |
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- changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, |
| 86 |
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perform additional runs (number of additional runs is "add_DIVA_runs" taken |
| 87 |
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from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h"). |
| 88 |
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o verification/lab_sea (AD test): |
| 89 |
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- change to test Divided Adjoint Run in this set-up (both standard AD test |
| 90 |
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and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test. |
| 91 |
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o pkg atm_ & ocn_compon_interf: |
| 92 |
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- remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old |
| 93 |
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staggerTimeStep implementation) and disable (retired) corresponding |
| 94 |
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parameter. |
| 95 |
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o pkg/offline: |
| 96 |
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- comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01]; |
| 97 |
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- add S/R OFFLINE_CHECK to print offline parameter summary |
| 98 |
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and stop if loading a file that is not used; |
| 99 |
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- enable to calculate GMRedi tensor, KPP mixing and convective index |
| 100 |
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when the corresponding file(s) is/are not specified (but pkg is used). |
| 101 |
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- comment out resetting of monitorFreq (to endTime) since it still useful |
| 102 |
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for monitoring CFL numbers and checking offline fields. |
| 103 |
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o OpenAD: |
| 104 |
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- do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get |
| 105 |
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smaller standard output) and generate new (smaller) output (on baudelaire |
| 106 |
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using gfortran with -ieee) for exp. tutorial_tracer_adjsens |
| 107 |
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o model/src: |
| 108 |
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- call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F), |
| 109 |
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(where external_forcing_adjust was called) and change list of arguments; |
| 110 |
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- merge external_forcing_adjust.F into external_forcing_surf.F |
| 111 |
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- put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F) |
| 112 |
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which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX, |
| 113 |
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previously in file "balance_relax.F", now removed); remove corresponding |
| 114 |
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arrays in FFIELDS.h. |
| 115 |
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- EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement |
| 116 |
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a hack for getting back surfaceForcingS (loaded from file) when using |
| 117 |
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ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up. |
| 118 |
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- update output of AD test experiment global_ocean.cs32x15.seaice_dynmix |
| 119 |
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(was getting only 11 digits for AD-grad, due to different truncation |
| 120 |
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error in AD code). |
| 121 |
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|
| 122 |
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checkpoint64j (2013/07/04) |
| 123 |
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o pkg/offline: |
| 124 |
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- to enable the use of other features with pkg offline (e.g., obcs), |
| 125 |
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also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come. |
| 126 |
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- comment out "allowFreezing" (now active) in 2 offline testing exp. |
| 127 |
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o pkg/exf ALLOW_RUNOFTEMP |
| 128 |
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- fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL |
| 129 |
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- ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice |
| 130 |
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- changes verification/global_ocean.cs32x15/results/output.seaice.txt |
| 131 |
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o pkg/atm_phys: |
| 132 |
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- allows to add some damping on uVel,vVel (strength only function of k). |
| 133 |
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o verification, ad-tests: |
| 134 |
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- reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, |
| 135 |
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global_ocean_ebm and offline_exf_seaice.thsice. |
| 136 |
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o verification/halfpipe_streamice: |
| 137 |
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- found a bug in s/r pkg/streamice/streamice_advect_thickness which caused |
| 138 |
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flux input boundary conditions to be ignored; a fix for this bug changed |
| 139 |
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verification results for forward test. |
| 140 |
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- add adjoint test. |
| 141 |
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o pkg/ptracers: |
| 142 |
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- allow to restart without SOM pickup (resetting SOM to zero). |
| 143 |
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o pkg/gmredi: |
| 144 |
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- New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added. |
| 145 |
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- It uses mixing length theory and suppression by steering level effects to |
| 146 |
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calculate a diffusivity used in the Redi tensor (see Bates et al., submitted |
| 147 |
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to JPO, for more details). |
| 148 |
|
- It also uses the diffusivity to calculate an eddy induced streamfunction |
| 149 |
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based on a PV closure (rather than a buoyancy closure as in GM). |
| 150 |
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- New files added to pkg/gmredi: |
| 151 |
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gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy |
| 152 |
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induced overturning streamfunction (called from gmredi_calc_tensor) |
| 153 |
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gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required |
| 154 |
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for use in gmredi_k3d |
| 155 |
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gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate |
| 156 |
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the eddy diffusivity |
| 157 |
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|
| 158 |
|
checkpoint64i (2013/06/18) |
| 159 |
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o pkg/cheapaml: |
| 160 |
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- take src files from MITgcm_contrib/verification_other/offline_cheapaml/code |
| 161 |
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that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics) |
| 162 |
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with pkg/cheapaml. |
| 163 |
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o utils/python: add subpackage for cubed sphere function, first example is |
| 164 |
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simple cs.pcol to plot 2D fields on a map |
| 165 |
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o pkg/streamice: |
| 166 |
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- This is a new package in MITgcm, which solves dynamic equations for ice |
| 167 |
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sheets and ice streams |
| 168 |
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- At the moment it is independent of atmosphere/ocean dynamics, or any |
| 169 |
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other physical packages in MITgcm, even ShelfIce (although it is anticipat- |
| 170 |
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ed that this will change) |
| 171 |
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- There is a new verification exercise that tests it, halfpipe_streamice, |
| 172 |
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evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a |
| 173 |
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rectangular embayment |
| 174 |
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- halfpipe_streamice is forward-only for now, will have TAF test soon |
| 175 |
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- for questions, email dgoldber@mit.edu |
| 176 |
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o pkg/thsice: |
| 177 |
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- fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing |
| 178 |
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of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40); |
| 179 |
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- remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new |
| 180 |
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call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect ); |
| 181 |
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- allow precip from pkg/cheapaml to make snow over seaice. |
| 182 |
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o pkg/cfc: |
| 183 |
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- move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC |
| 184 |
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- remove atmos CFC 2-D arrays from common bloc (now local variables) |
| 185 |
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- change some hard-coded constant to run time parameter for reading and |
| 186 |
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and interpolating atmospheric CFC ; keep same default as previously. |
| 187 |
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- more flexible reading of Atmos CFC (number of records no longer hard-coded) |
| 188 |
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- put arguments in standard order: myTime, myIter, myThid |
| 189 |
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- use standard S/R GET_PERIODIC_INTERVAL for time interpolation of |
| 190 |
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atmospheric CFC ; fix for the case myIter < PTRACERS_iter0. |
| 191 |
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- fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf |
| 192 |
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- new routine to print summary of CFC params and check for consistency. |
| 193 |
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o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff, |
| 194 |
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similar to thsice_advdiff. |
| 195 |
|
Note that for the B-grid case the routine parameters uc/vc are overwritten. |
| 196 |
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o pkg/cfc: |
| 197 |
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- change time interpolation for atmospheric CFC-11 (now same as for CFC-12); |
| 198 |
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update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline. |
| 199 |
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- fix interpolation of atmphspheric CFC between Sorthern and Northern |
| 200 |
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hemisphere value. |
| 201 |
|
o pkg/seaice: |
| 202 |
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- allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml) |
| 203 |
|
o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics; |
| 204 |
|
so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE. |
| 205 |
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- requires an additional time level that is stored in the pickup |
| 206 |
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- you can start with AB2 from a pickup without this time level with |
| 207 |
|
pickupStrictlyMatch = .false. |
| 208 |
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|
| 209 |
|
checkpoint64h (2013/05/26) |
| 210 |
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o pkg/cheapaml: |
| 211 |
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- replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux); |
| 212 |
|
affect machine truncation (but exp cheapAML_box still pass with 13 digits). |
| 213 |
|
- consistent treatment of uWind,vWind location: assume everywhere in |
| 214 |
|
pkg/cheapaml that they are on C-grid (@ uVel,vVel location) |
| 215 |
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(Note: was already the case for Tair,Qair advection); |
| 216 |
|
add option (INCONSISTENT_WIND_LOCATION) to recover old results. |
| 217 |
|
- compute diabatic forcing only in the interior (excluding overlap regions) |
| 218 |
|
- fill in array "Qsw" (for short-wave heating); |
| 219 |
|
- add diagnostic for precip ; fill-in diagnostics for cheapAML state vars |
| 220 |
|
before any update (consistent with MITgcm state var diagnostics); |
| 221 |
|
- cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if |
| 222 |
|
non periodic ; + adjusted for uWind,vWind (C-grid). |
| 223 |
|
o pkg/seaice: |
| 224 |
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- remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and |
| 225 |
|
add explicitly pkg/exf in experiments that currently use pkg/seaice. |
| 226 |
|
- allows to compile pkg/seaice without pkg/exf. |
| 227 |
|
o tools/OAD_support: |
| 228 |
|
- use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds |
| 229 |
|
of array "ourStepOf" in function rvNextAction (revolve.F90). |
| 230 |
|
o pkg/aim_compon_interf renamed to pkg/atm_compon_interf |
| 231 |
|
- change pkg name (to be used with other atmospheric physics pkg) |
| 232 |
|
but by-pass CVS when making the new pkg so that we keep the CVS history. |
| 233 |
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o pkg/offline: |
| 234 |
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- call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F |
| 235 |
|
(previously called from pkg/dic_surfforcing_init.F) |
| 236 |
|
o model/src: |
| 237 |
|
- re-order sequence of calls within packages_init_variables.F, using |
| 238 |
|
standard order, except for: |
| 239 |
|
DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top), |
| 240 |
|
CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom) |
| 241 |
|
o new pkg: atm_phys |
| 242 |
|
- add entry point and source code (previously in contrib |
| 243 |
|
verification_other/atm_gray/code_gray/) for new pkg "atm_phys" |
| 244 |
|
(atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008). |
| 245 |
|
- re-order sequence of calls within packages_readparms.F, |
| 246 |
|
packages_init_fixed.F and packages_write_pickup.F |
| 247 |
|
(but skip packages_init_variables.F because of TAF issues). |
| 248 |
|
- update contrib/*/atm_gray/ experiment. |
| 249 |
|
o pkg/seaice (ITD code): |
| 250 |
|
- simplify and fix the writing of pickup-files for ITD case |
| 251 |
|
o pkg/seaice (ITD code): |
| 252 |
|
- introduce floe size dependent lateral melt for ITD case; |
| 253 |
|
- cleaning (avoid division by zero, change to f77 syntax, remove tabs) |
| 254 |
|
- update seaice_itd experiment main output. |
| 255 |
|
o pkg/thsice: |
| 256 |
|
- remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and |
| 257 |
|
declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F; |
| 258 |
|
changed accordingly pkg/atm2d. |
| 259 |
|
|
| 260 |
|
checkpoint64g (2013/05/01) |
| 261 |
|
o pkg/exf ALLOW_RUNOFTEMP |
| 262 |
|
- if defined, river and glacier runoff temperature can be read-in from |
| 263 |
|
runoftempfile; runoftempfile needs to have same format as runofffile |
| 264 |
|
o pkg/thsice (& pkg/bulk_force): |
| 265 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
| 266 |
|
for energy content of Precip + RunOff & Evap (like with pkg/exf). |
| 267 |
|
- change computation domain to always be the interior (without overlap). |
| 268 |
|
- fix bug (wrong overlap) when using EXF and stressReduction > 0. |
| 269 |
|
o verification/tutorial_global_oce_biogeo: |
| 270 |
|
- add preliminary OpenAD setup (still has problems) |
| 271 |
|
o pkg/seaice: |
| 272 |
|
- turn some parameters for choosing the convergence criterion of |
| 273 |
|
the inexact Newton method (JFNK) into runtime parameters for convenience |
| 274 |
|
- clean up seaice_calc_viscosities.F: remove/retire two options for |
| 275 |
|
SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes |
| 276 |
|
the results of lab_sea/input because a division has been replaced by |
| 277 |
|
a multiplication with the reciprocal (sumNorm) |
| 278 |
|
- modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve |
| 279 |
|
convergence of solver (changes results, of course), and to test some |
| 280 |
|
new features |
| 281 |
|
o model/src: |
| 282 |
|
- remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call. |
| 283 |
|
- remove unused forcing field "dQdT" and associated parameter "dQdTFile". |
| 284 |
|
- move forcing adjustment (balancing surface forcing) in specific S/R |
| 285 |
|
where might also be applied exchanges (if needed) to forcing arrays. |
| 286 |
|
o pkg/shelfice: |
| 287 |
|
- allow to specify the Ice-Shelf mass per unit area (instead of |
| 288 |
|
shelficeLoadAnomaly) and do the conversion from one to the other |
| 289 |
|
- move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA |
| 290 |
|
to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and |
| 291 |
|
(b) will be loaded in time (before calling INI_PRESSURE) in case it is |
| 292 |
|
needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc |
| 293 |
|
- update isomip experiment forward output (get machine truncation error |
| 294 |
|
from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly) |
| 295 |
|
o verification/offline_exf_seaice: |
| 296 |
|
revise data.seaice in input.thermo and input_ad and update results accordingly |
| 297 |
|
HO = 0.2, SEAICE_areaLossFormula = 2, |
| 298 |
|
SEAICE_growMeltByConv = .TRUE., |
| 299 |
|
SEAICE_doOpenWaterMelt = .TRUE., |
| 300 |
|
Improve consistency with input.thsice and fix the spurious 500m ice corners |
| 301 |
|
o verification/global_ocean.cs32x15: |
| 302 |
|
- set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0., |
| 303 |
|
in icedyn (thsice+seaice-dyn) test and update output. |
| 304 |
|
o verification/offline_exf_seaice: |
| 305 |
|
- adjust list of tested variables (with testreport) and update |
| 306 |
|
standard test output with better slection of monitored fields. |
| 307 |
|
o pkg/cd_code: |
| 308 |
|
- swtich off Adams-Bashforth on the 1rst iteration. Update output of |
| 309 |
|
experiment lab_sea.hb87 |
| 310 |
|
o tools/genmake2: |
| 311 |
|
- change default makedepend from the system default to tools/xmakedepend: |
| 312 |
|
When no makedepend is specified, select tools/xmakedepend it the test pass, |
| 313 |
|
otherwise select the system default (if exist and pass the test) or |
| 314 |
|
try to build cyrus-makedepend ; stop if none of the 3 works. |
| 315 |
|
o pkg/exf & pkg/thsice: |
| 316 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
| 317 |
|
for energy content of Precip + RunOff & Evap. Assumes: |
| 318 |
|
1) Rain has same temp as Air. |
| 319 |
|
2) Snow has no heat capacity (consistent with seaice & thsice pkgs) |
| 320 |
|
3) Run-Off comes at the temp of surface water (with same Cp) |
| 321 |
|
4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be |
| 322 |
|
put directly into Latent Heat flux & should use water-vapor heat capacity. |
| 323 |
|
5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent |
| 324 |
|
with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL). |
| 325 |
o pkg/seaice: simplify the use of CPP flags in JFNK-related files |
o pkg/seaice: simplify the use of CPP flags in JFNK-related files |
| 326 |
(compile when SEAICE_ALLOW_JFNK is defined) |
(compile when SEAICE_ALLOW_JFNK is defined) |
| 327 |
o pkg/thsice: |
o pkg/thsice: |
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