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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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checkpoint64o (2013/09/25) |
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o added SINGLE_DISK_IO option because reading of parameter files on |
| 9 |
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very large number of processors did not work with existing set-up |
| 10 |
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o pkg/atm_phys & atm_compon_interf: |
| 11 |
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- allows for coupling of gray-atmosphere (atm_phys) with ocean. |
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o tools/build_options: |
| 13 |
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- switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran |
| 14 |
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& linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also |
| 15 |
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remove CPP setting (was identical to genmake2 default). |
| 16 |
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o pkg/gmredi & model/src: Some updating and work done on the residual model. |
| 17 |
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- created new file model/src/calc_eddy_stress.F to calculate the eddy stress. |
| 18 |
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- fixed up the calculation of the eddy stress and how it is added to the |
| 19 |
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external forcing via taueddy_external_forcing.F |
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- at the moment, it is very experimental and only works with the variable eddy |
| 21 |
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diffusivity calculated in gmredi_k3d.F |
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o pkg/seaice/seaice_check.F: add a check to catch the case of specifying |
| 23 |
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lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice |
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o testreport (& tools/do_tst_2+2): |
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- for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}' |
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o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11: |
| 27 |
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- remove CPP='cpp -traditional -P' (this is genmake2 default) |
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- add switch (for big setups) to use 'medium' memory-model (but leave it |
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commented out for now). Note: needed with FC 19 to compile big setups. |
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o pkg/atm_compon_interf: |
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- regroup per field origin (model & pkgs) the coupling storage routines |
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(which accumalate in time each coupling field) |
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- move bi,bj loops inside atm_store_my_data.F and store also wind-stress; |
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update accordingly + simplify aim_do_physics.F |
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|
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checkpoint64n (2013/08/26) |
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o pkg/bbl: |
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- update formulation to reduce dispersion of tracer properties in bbl |
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- replaced horizontal and vertical transport parameters with velocities |
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- changes results for verification/global_with_exf.yearly |
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o verification/halfpipe_streamice: |
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- change to matrix construction; update both Fwd & AD output. |
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o verification/tutorial_tracer_adjsens: |
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- OpenAD test: switch to vector-invariant momentum since fluxform with |
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rStar causes problems with OpenAD; update output. |
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o tools: |
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- genmake2: define a common prefix for all temp-file names ; move them |
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to local /tmp disk (but would be easy to move them back); |
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- xmakedepend: apply the same switch for temp-files. |
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o pkg/offline: |
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- changes for use with rStar (NLFS): assume that we continue to provide |
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UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid |
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output files) and apply r* scaling at each time-step (function of the time |
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varying Eta field); use normal pickup files (needed for restart with NLFS). |
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o adjoint with OpenAD: |
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- move OpenAD-specific files from verification/OpenAD/code_oad_all to a new |
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package openad. This package has to be compiled for all runs with OpenAD |
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instead of specifying code_oad_all as a modification directory. |
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- link the fortran templates from tools/OAD_support to the build directory |
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for preprocessing to avoid conflicts between different setups compiled |
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simultaneously and simplify cleanup. |
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o pkg/exf: |
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- in exf_getforcing.F: comment out most of the EXCH calls (fields used by |
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main model or other pkgs are exchanged in EXF_MAPFIELDS). |
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o model/src: |
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- do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline |
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(similar to do_fields_blocking_exchanges.F). |
| 68 |
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o tools/genmake2: |
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- remove TAF output src code just before calling staf (when not doing a fresh |
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built, will stop if things go wrong with staf). |
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- fix target "adobj" (left from TAF version-2 transition) |
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o pkg/diagnostics: |
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- add a parameter to track the status of pkg/diagnostics activation; |
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this replace/extend the use of logical param "settingDiags" (to check |
| 75 |
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when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call. |
| 76 |
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New S/R to print error message and stop when pkgStatus is not right. |
| 77 |
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- to try: add a warning when "data.diagnostics" exist but useDiagnostics=F. |
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|
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checkpoint64m (2013/08/13) |
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o model/inc: |
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- move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from |
| 82 |
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8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) |
| 83 |
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o pkg/kpp & aim_v23: |
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- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
| 85 |
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o pkg/seaice: |
| 86 |
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- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
| 87 |
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undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
| 88 |
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- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
| 89 |
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o eesupp/src: |
| 90 |
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- fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) |
| 91 |
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in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). |
| 92 |
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o switch to TAF version-2: |
| 93 |
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- add flow directives to "freeze" naming convention for ad-routines that |
| 94 |
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are used in I/O routines of adjoint state and associated common blocks |
| 95 |
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that are used in adcommon.h (backward compatible with version-1) |
| 96 |
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- update all ad-optfiles (in tools/adjoint_options + few local to some |
| 97 |
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verification exp) to switch to latest TAF version (currently 2.5.5); |
| 98 |
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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 |
| 102 |
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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 |
| 105 |
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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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|
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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. |
| 113 |
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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 |
| 116 |
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only when using variable horiz. viscosity (useVariableVisc=T); |
| 117 |
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- simplify mom_vecinv.F (only 1 block for momViscosity). |
| 118 |
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o pkg/mom_common: variable horiz. viscosity in NH code |
| 119 |
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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 |
| 121 |
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- store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, |
| 122 |
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useBiharmonicVisc & useVariableVisc. |
| 123 |
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- fix old bug (already in 1rst implementation of variable horizontal viscosity |
| 124 |
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in calc_gw.F, version 1.27, 2006/06/20): |
| 125 |
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horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 |
| 126 |
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even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. |
| 127 |
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- change background horiz viscosity in vertical momentum (gW) to always be |
| 128 |
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viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using |
| 129 |
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any type of variable viscosity, e.g., viscAh/4Grid) |
| 130 |
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- change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of |
| 131 |
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viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing |
| 132 |
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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). |
| 134 |
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o model/src: |
| 135 |
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- extend length of drC & recip_drC from Nr to Nr+1. |
| 136 |
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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. |
| 138 |
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- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
| 139 |
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and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h. |
| 140 |
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|
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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 |
| 144 |
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and remove it from genmake2. |
| 145 |
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o tools/build_options: |
| 146 |
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- remove MPI_HEADER_FILES_INC setting (no longer used) and comment out |
| 147 |
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MPI_HEADER_FILES list (let genmake2 find the missing headers) |
| 148 |
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o verification/halfpipe_streamice: |
| 149 |
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- change to driving stress formulation; update both Fwd & AD output. |
| 150 |
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o tools/genmake2 and Divided Adjoint with MPI: |
| 151 |
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- remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken); |
| 152 |
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- only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set; |
| 153 |
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- add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in |
| 154 |
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Makefile, which is set by genmake2, and check which mpi-headers are needed. |
| 155 |
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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: |
| 158 |
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- changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, |
| 159 |
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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"). |
| 161 |
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o verification/lab_sea (AD test): |
| 162 |
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- change to test Divided Adjoint Run in this set-up (both standard AD test |
| 163 |
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and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test. |
| 164 |
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o pkg atm_ & ocn_compon_interf: |
| 165 |
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- remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old |
| 166 |
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staggerTimeStep implementation) and disable (retired) corresponding |
| 167 |
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parameter. |
| 168 |
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o pkg/offline: |
| 169 |
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- comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01]; |
| 170 |
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- add S/R OFFLINE_CHECK to print offline parameter summary |
| 171 |
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and stop if loading a file that is not used; |
| 172 |
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- enable to calculate GMRedi tensor, KPP mixing and convective index |
| 173 |
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when the corresponding file(s) is/are not specified (but pkg is used). |
| 174 |
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- comment out resetting of monitorFreq (to endTime) since it still useful |
| 175 |
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for monitoring CFL numbers and checking offline fields. |
| 176 |
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o OpenAD: |
| 177 |
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- do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get |
| 178 |
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smaller standard output) and generate new (smaller) output (on baudelaire |
| 179 |
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using gfortran with -ieee) for exp. tutorial_tracer_adjsens |
| 180 |
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o model/src: |
| 181 |
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- call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F), |
| 182 |
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(where external_forcing_adjust was called) and change list of arguments; |
| 183 |
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- merge external_forcing_adjust.F into external_forcing_surf.F |
| 184 |
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- put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F) |
| 185 |
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which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX, |
| 186 |
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previously in file "balance_relax.F", now removed); remove corresponding |
| 187 |
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arrays in FFIELDS.h. |
| 188 |
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- EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement |
| 189 |
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a hack for getting back surfaceForcingS (loaded from file) when using |
| 190 |
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ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up. |
| 191 |
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- update output of AD test experiment global_ocean.cs32x15.seaice_dynmix |
| 192 |
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(was getting only 11 digits for AD-grad, due to different truncation |
| 193 |
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error in AD code). |
| 194 |
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|
| 195 |
|
checkpoint64j (2013/07/04) |
| 196 |
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o pkg/offline: |
| 197 |
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- to enable the use of other features with pkg offline (e.g., obcs), |
| 198 |
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also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come. |
| 199 |
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- comment out "allowFreezing" (now active) in 2 offline testing exp. |
| 200 |
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o pkg/exf ALLOW_RUNOFTEMP |
| 201 |
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- fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL |
| 202 |
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- ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice |
| 203 |
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- changes verification/global_ocean.cs32x15/results/output.seaice.txt |
| 204 |
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o pkg/atm_phys: |
| 205 |
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- allows to add some damping on uVel,vVel (strength only function of k). |
| 206 |
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o verification, ad-tests: |
| 207 |
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- reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, |
| 208 |
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global_ocean_ebm and offline_exf_seaice.thsice. |
| 209 |
|
o verification/halfpipe_streamice: |
| 210 |
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- found a bug in s/r pkg/streamice/streamice_advect_thickness which caused |
| 211 |
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flux input boundary conditions to be ignored; a fix for this bug changed |
| 212 |
|
verification results for forward test. |
| 213 |
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- add adjoint test. |
| 214 |
|
o pkg/ptracers: |
| 215 |
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- allow to restart without SOM pickup (resetting SOM to zero). |
| 216 |
|
o pkg/gmredi: |
| 217 |
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- New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added. |
| 218 |
|
- It uses mixing length theory and suppression by steering level effects to |
| 219 |
|
calculate a diffusivity used in the Redi tensor (see Bates et al., submitted |
| 220 |
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to JPO, for more details). |
| 221 |
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- It also uses the diffusivity to calculate an eddy induced streamfunction |
| 222 |
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based on a PV closure (rather than a buoyancy closure as in GM). |
| 223 |
|
- New files added to pkg/gmredi: |
| 224 |
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gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy |
| 225 |
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induced overturning streamfunction (called from gmredi_calc_tensor) |
| 226 |
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gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required |
| 227 |
|
for use in gmredi_k3d |
| 228 |
|
gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate |
| 229 |
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the eddy diffusivity |
| 230 |
|
|
| 231 |
|
checkpoint64i (2013/06/18) |
| 232 |
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o pkg/cheapaml: |
| 233 |
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- take src files from MITgcm_contrib/verification_other/offline_cheapaml/code |
| 234 |
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that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics) |
| 235 |
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with pkg/cheapaml. |
| 236 |
|
o utils/python: add subpackage for cubed sphere function, first example is |
| 237 |
|
simple cs.pcol to plot 2D fields on a map |
| 238 |
|
o pkg/streamice: |
| 239 |
|
- This is a new package in MITgcm, which solves dynamic equations for ice |
| 240 |
|
sheets and ice streams |
| 241 |
|
- At the moment it is independent of atmosphere/ocean dynamics, or any |
| 242 |
|
other physical packages in MITgcm, even ShelfIce (although it is anticipat- |
| 243 |
|
ed that this will change) |
| 244 |
|
- There is a new verification exercise that tests it, halfpipe_streamice, |
| 245 |
|
evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a |
| 246 |
|
rectangular embayment |
| 247 |
|
- halfpipe_streamice is forward-only for now, will have TAF test soon |
| 248 |
|
- for questions, email dgoldber@mit.edu |
| 249 |
|
o pkg/thsice: |
| 250 |
|
- fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing |
| 251 |
|
of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40); |
| 252 |
|
- remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new |
| 253 |
|
call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect ); |
| 254 |
|
- allow precip from pkg/cheapaml to make snow over seaice. |
| 255 |
|
o pkg/cfc: |
| 256 |
|
- move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC |
| 257 |
|
- remove atmos CFC 2-D arrays from common bloc (now local variables) |
| 258 |
|
- change some hard-coded constant to run time parameter for reading and |
| 259 |
|
and interpolating atmospheric CFC ; keep same default as previously. |
| 260 |
|
- more flexible reading of Atmos CFC (number of records no longer hard-coded) |
| 261 |
|
- put arguments in standard order: myTime, myIter, myThid |
| 262 |
|
- use standard S/R GET_PERIODIC_INTERVAL for time interpolation of |
| 263 |
|
atmospheric CFC ; fix for the case myIter < PTRACERS_iter0. |
| 264 |
|
- fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf |
| 265 |
|
- new routine to print summary of CFC params and check for consistency. |
| 266 |
|
o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff, |
| 267 |
|
similar to thsice_advdiff. |
| 268 |
|
Note that for the B-grid case the routine parameters uc/vc are overwritten. |
| 269 |
|
o pkg/cfc: |
| 270 |
|
- change time interpolation for atmospheric CFC-11 (now same as for CFC-12); |
| 271 |
|
update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline. |
| 272 |
|
- fix interpolation of atmphspheric CFC between Sorthern and Northern |
| 273 |
|
hemisphere value. |
| 274 |
|
o pkg/seaice: |
| 275 |
|
- allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml) |
| 276 |
|
o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics; |
| 277 |
|
so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE. |
| 278 |
|
- requires an additional time level that is stored in the pickup |
| 279 |
|
- you can start with AB2 from a pickup without this time level with |
| 280 |
|
pickupStrictlyMatch = .false. |
| 281 |
|
|
| 282 |
|
checkpoint64h (2013/05/26) |
| 283 |
o pkg/cheapaml: |
o pkg/cheapaml: |
| 284 |
- replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux); |
- replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux); |
| 285 |
affect machine truncation (but exp cheapAML_box still pass with 13 digits). |
affect machine truncation (but exp cheapAML_box still pass with 13 digits). |
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