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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 pkg/obcs: |
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- split header file "OBCS.h" into 4 separated files: |
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OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h |
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Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h |
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(contain no conditional statement that depends on OBCS options). |
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o ctrl, cost, grdchk & autodiff pkgs: |
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- make options file more standard (like other {PKG}_OPTIONS.h file but |
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with AD_CONFIG.h); clean-up some of the included header files. |
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o pkg/obcs: |
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- do not mask tracer when applying OB (tracer == 0 could generate problems) |
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- apply tracer OB values to tracer field only at OB location (instead of |
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over a band of OLx width) |
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- clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R) |
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- remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove |
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obcs_apply_tloc.F & obcs_apply_sloc.F |
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o obcs in model/src: |
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- call OBCS_APPLY_W only if NonHydrostatic. |
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- call OBCS_APPLY_ETA only if NonLinFreeSurf. |
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- reset dEtaHdt and wVel to zero outside OB interior region ; |
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- leave tracer unchanged outside OB interior region: This has no effect |
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on the solution but just to prevent unrealistic tracer value outside OB. |
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- zero out velocity outside OB interior region: This has no effect on |
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the solution but just to prevent unrealistic velocity outside OB. |
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o obcs and non-lin free-surf: |
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move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F |
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and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F |
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+ add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR: |
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this fixes missing EXCH + get consistent eta OB value (+ fix restart). |
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update results of test-exp. exp4(nlfs). |
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o exp4 (nlfs) test-exp: |
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use OBC for Eta at Western & Eastern OB (to test prescribing Eta |
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with NonLin-FreeSurf); update output.nlfs.txt |
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o obcs and 2d/3d solver norm: |
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use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB |
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and outside OB interior region (will allow to place OB further inside the |
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domain). Depending on the domain, can affects cg2d-Norm (previous |
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cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl, |
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and cg3d-Norm (previous Norm was computed before canceling OB terms), |
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e.g. in tutorial_plume_on_slope. |
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- update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope. |
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o pkg rbcs: |
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- split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h |
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- add capability to apply relaxation to horizontal velocity uVel & vVel. |
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o pkg/grdchk: add gradient check for control variable xx_shifwflx |
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o pkg/shelfice/shelfice_init_fixed.F |
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fix CPP-flag combinations |
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o pkg/seaice: Merge iceage code of Pierre Rampal |
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* update/change/correct ice age calculations |
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* add age updates for pathological cases |
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Probably needs more testing... |
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checkpoint62x (2011/05/13) |
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o pkg/mom_vecinv: |
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high-order vorticity scheme: use interior masks (maskInW & S) |
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to zero-out (outside OB) gradient of vorticity. |
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o verification exp.: |
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turn on "useEnergyConservingCoriolis" (better discretisation) in exp. |
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hs94.128x64x5 and seaice_obcs ; update results. |
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o pkg/obcs: |
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fix bug in OBeta for YZ sections in obcs_exf_load.F |
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o pkg/ctrl, pkg/shelfice, and optim: |
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- add new control variable xx_shifwflx (fresh water flux underneath ice |
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shelves). This is almost as tedious as obcs-ctrl, because the |
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variables needs its own mask. |
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- add a cost function term that penalizes the deviation of xx_shifwflx |
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from the first guess (zero) in analogy to other control variables |
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o pkg/shelfice: |
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- start basic adjoint |
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o pkg/ctrl: |
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- remove extra 2D field "for good measure" when initializing in |
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ctrl_set_globfld_[xy/xz/yz].F |
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- replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec |
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- improve error messages in ctrl_set_unpack_* |
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o OBC implementation in momentum: |
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use interior masks (maskInC,W & S) in momentum S/R: |
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- multiply divergence, tension and some del^i.u or del^j.v by maskInC |
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- multiply del2u,del2v by maskInW/S (biharmonic viscosity) |
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- multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) |
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- multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) |
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Motivation: fix/clean implementation of OBC with biharmonic-viscosity |
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(and also with Leith/Smagorinsky harmonic-viscosity). |
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Update output of experiment dome and exp4 (+nlfs). |
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o exp4 test-exp: |
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- turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) |
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and prescribe time-varying OB (without pkg/exf) for zonal-velocity |
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at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
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time-varying OB at Western-side for wVel (NonHyd); update output. |
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- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
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and biharmonic-viscosity ; also use prescribed time varying OB. |
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o pkg/obcs: |
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fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
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o model/src: |
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- fix startTime setting when baseTime<>0 & nIter0=0 are specified ; |
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- initialise startTime & nIter0 with unlikely values: allows to set one |
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from the other without ambiguity. |
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o seaice_obcs test-exp.: |
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add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output. |
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o pkg/obcs: |
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- remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: |
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no longer needed with maskInC,W,S in pkg/generic_advdiff. |
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o pkg/seaice: |
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- retired SEAICE_SALINITY and SEAICE_salinity in favor of |
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SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively. |
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- fixed bug in the initialization of sea ice salinity variable HSALT |
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in seaice_init_varia.F (removed dependence on ICE2WATR) |
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o fizhi-cs test exp.: |
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switch reference output convention for these 2 non-standard test-exp, |
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from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5) |
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to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11) |
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reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran |
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o model/inc: |
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- change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4") |
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of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS) |
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o pkg/seaice: |
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- fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY |
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o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15 |
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- updated output*.txt files due to bug fixes in salt, saltPlumeFlux, |
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and initial HSALT |
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checkpoint62w (2011/04/26) |
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o pkg/mom_fluxform: |
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- fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf. |
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- use parameter "sideDragFactor" in no-slip BC side-drag part. |
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- update output of exp. global_ocean.90x40x15 |
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o pkg/mom_vecinv: |
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mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform) |
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o update seaice exp.: |
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use more consistent parameter values (remove "backward compatability only": |
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ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh) |
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related to thermodynamics seaice. Update output (fwd+AD) of exp.: |
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1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs |
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o update test-exp global_ocean.90x40x15: |
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o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis). |
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o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.) |
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o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params) |
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o turn on zStar & viscA4 in standard set-up (dir input/) |
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and update output files: output.txt & output.dwnslp.txt |
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o new AD-test experiment: obcs_ctrl |
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(From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector. |
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o pkg/dic: |
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fix two bugs in handling water vapour pressure in carbonate chemistry |
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and air-sea fluxes. Found by Val Bennington and Galen McKinley |
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(add DIC Option = WATERVAP_BUG to recover old results) |
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update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline |
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o adding allowInteriorFreezing option to check for water below freezing point |
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at depth and bring the negative heat anomaly to the surface level |
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o pkgs _fields_load: |
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- extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs) |
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- use new S/R GET_PERIODIC_INTERVAL in pkgs: |
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bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and |
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rbcs to get interpolation weights and time reccord number. |
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- fix multi-threading in aim_fields_load.F |
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- apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F |
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o external_fields_load: |
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new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear |
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interpolation weights) to use in a periodic time-series ; do not divide by |
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time-step to convert to integer: |
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- this fixes case where externForcingPeriod is not multiple of time-step |
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(Thanks to Christopher L. Wolfe) |
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- this fixes case where externForcingPeriod is an odd multiple of time-step |
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(was wrong by half of time-step); update results of tutorial_global_oce_in_p. |
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store index of time-record which is currently loaded: |
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- works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ; |
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- needed for the adjoint but not yet used because of extensive recomputations; |
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(to be fixed soon) |
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checkpoint62v (2011/04/02) |
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o verification/1D_ocean_ice_column added to test Ian Fenty's |
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pkg/seaice_growth.F modifications for improving sea ice code differentiability |
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o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope |
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(new velocity statistics after changing maskInW & maskInS definition) |
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o pkg/generic_advdiff with OBCS: |
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use maksInW & maskInS in advective flux and in biharmonic diffusion calculation: |
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equivalent to assumption of no tracer gradient outside the OB region. |
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This will affect the results if using obcs+biharmonic diffusion. |
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update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc) |
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o pkg/obcs: |
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change definition of maskInW & maskInS: leave OB edges inside (maskIn=1) |
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(e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still |
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in Interior region. No impact on solution but affects Velocity monitor stats. |
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o pkg/ptracers (adjoint) |
o pkg/ptracers (adjoint) |
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New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate |
New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate |
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tape file for each tracer |
tape file for each tracer |
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o model/inc/scr and pkg/autodiff: add parameters that allow to turn |
o model/inc/src and pkg/autodiff: add parameters that allow to turn |
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of parts of the adjoint code at run time. For now, there are only |
of parts of the adjoint code at run time. For now, there are only |
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useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These |
useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These |
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parameters are set in data.pkg. |
parameters are set in data.pkg. |
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This is the lazy coward's version of doing this, but still useful for |
This is the lazy coward's version of doing this, but still useful for |
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debugging. In order to do it right, everything needs to be moved to |
debugging. In order to do it right, everything needs to be moved to |
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pkg/autodiff. |
pkg/autodiff. |
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o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at |
o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at |
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the end; this fixes the adjoint balancing code for open boundaries. |
the end; this fixes the adjoint balancing code for open boundaries. |
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o pkg/ctrl: |
o pkg/ctrl: |
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- change behavior of xx_${varname}period to be analogous to exf-conventions: |
- change behavior of xx_${varname}period to be analogous to exf-conventions: |
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xx_${varname}period = 0., means time-independent control part |
xx_${varname}period = 0., means time-independent control part |
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xx_${varname}period = -12., means one-year-periodic monthly control part |
xx_${varname}period = -12., means one-year-periodic monthly control part |
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- introduce helper routine ctrl_init_rec (part of ctrl_init.F) to |
- introduce helper routine ctrl_init_rec (part of ctrl_init.F) to |
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clean up ctrl_init a little, remove unused variables |
clean up ctrl_init a little, remove unused variables |
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- ctrl_init: fixed the handling of the start/endrec for obcs-variables |
- ctrl_init: fixed the handling of the start/endrec for obcs-variables |
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