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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/ctrl: |
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- remove extra 2D field "for good measure" when initializing in |
| 9 |
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ctrl_set_globfld_[xy/xz/yz].F |
| 10 |
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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 |
| 15 |
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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). |
| 20 |
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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 |
| 24 |
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at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
| 25 |
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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. |
| 62 |
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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) |
| 82 |
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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 |
| 85 |
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o pkgs _fields_load: |
| 86 |
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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 |
| 89 |
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rbcs to get interpolation weights and time reccord number. |
| 90 |
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- fix multi-threading in aim_fields_load.F |
| 91 |
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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: |
| 93 |
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new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear |
| 94 |
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interpolation weights) to use in a periodic time-series ; do not divide by |
| 95 |
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time-step to convert to integer: |
| 96 |
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- this fixes case where externForcingPeriod is not multiple of time-step |
| 97 |
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(Thanks to Christopher L. Wolfe) |
| 98 |
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- this fixes case where externForcingPeriod is an odd multiple of time-step |
| 99 |
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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 ; |
| 102 |
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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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|
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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 |
| 108 |
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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. |
| 113 |
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This will affect the results if using obcs+biharmonic diffusion. |
| 114 |
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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 |
| 118 |
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in Interior region. No impact on solution but affects Velocity monitor stats. |
| 119 |
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o pkg/ptracers (adjoint) |
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New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate |
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tape file for each tracer |
| 122 |
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o model/inc/src and pkg/autodiff: add parameters that allow to turn |
| 123 |
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of parts of the adjoint code at run time. For now, there are only |
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useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These |
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parameters are set in data.pkg. |
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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 |
| 128 |
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pkg/autodiff. |
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o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at |
| 130 |
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the end; this fixes the adjoint balancing code for open boundaries. |
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o pkg/ctrl: |
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- 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 |
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xx_${varname}period = -12., means one-year-periodic monthly control part |
| 135 |
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- introduce helper routine ctrl_init_rec (part of ctrl_init.F) to |
| 136 |
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clean up ctrl_init a little, remove unused variables |
| 137 |
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- ctrl_init: fixed the handling of the start/endrec for obcs-variables |
| 138 |
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- move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec |
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|
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checkpoint62u (2011/03/15) |
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o model/src: |
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- for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in |
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h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ; |
| 144 |
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- in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to |
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INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF. |
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o pkg/ctrl/obcs/ecco: |
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- remove obsolete, unused, and partially broken code: |
| 148 |
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ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within |
| 149 |
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ALLOW_CTRL_OBCS_BALANCE |
| 150 |
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- put a stop statement into ecco/cost_obcsvol.F, but also add |
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cost_obcsvol to ecco_ad_diff.list |
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o pkg/ecco: fix counting cost function contributions for obcs (code |
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by Matt M.) and diffkr for diagnostics |
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o pkg/ecco, pkg/ctrl, pkg/grdchk: |
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add cost penalty terms for initial uvel, vvel, eta controls |
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and I/O for prior error files |
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o pkg/mdsio: |
| 158 |
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move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option |
| 159 |
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(new argument) to check for tiled file in mdsioLocalDir : this fix the |
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restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir. |
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o pkg/ctrl: |
| 162 |
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- ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by |
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ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove |
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unused and superfluous variables |
| 165 |
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- ctrl_get_gen_rec.F: catch the case of xx_genperiod=0. |
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o pkg/ecco |
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- enable adjoint of Stevens OB |
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o pkg/ctrl/ecco/grdchk: |
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- remove global declaration of tmpfldx/yz and tmpfldx/yz2. |
| 170 |
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Fortunately, we do not have any tests for the numerous cpp-flagged |
| 171 |
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option of "obcs as control parameters" so we will never know |
| 172 |
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if this is an improvement (but at least now things compile). |
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- remove an obsolete initialization from ecco_cost_init_barfiles.F |
| 174 |
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- fix some problems within never used ifdefs to make the code compile |
| 175 |
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o pkg/obcs: |
| 176 |
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- Refine Interior mask definition to work with more complex OB (e.g. |
| 177 |
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if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to |
| 178 |
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read in Interior mask from file. Check if Interior mask is consistent |
| 179 |
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with OB list of indices. |
| 180 |
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o pkg/seaice |
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- beginning code for a seaice tracer package, |
| 182 |
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but currently only used for seaice age: SEAICE_AGE |
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SEAICE_num = 4 |
| 184 |
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iTracer = 1: area-weighted ice age |
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= 2: volume-weighted ice age |
| 186 |
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= 3, 4: template for one-year vs. multi-year ice |
| 187 |
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data.seaice has new namelist SEAICE_PARM03 for arrays related to |
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SEAICE_num |
| 189 |
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|
| 190 |
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checkpoint62t (2011/03/05) |
| 191 |
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o pkg/obcs: |
| 192 |
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- obcs_apply_uv.F: change to a 2 steps method, first tangential component; |
| 193 |
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then normal component. This ensures that the normal component is set |
| 194 |
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correctly even when it conficts with tangential setting from an other OB. |
| 195 |
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Affects results of test-experiment seaice_obcs: update the output.txt |
| 196 |
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o pkg/obcs: |
| 197 |
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- add code to monitor statistics of dynamical fields at OB. |
| 198 |
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- take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW : |
| 199 |
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- fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection). |
| 200 |
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- change default: balance the Net inflow through all OB (instead of balancing |
| 201 |
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each OB separately); keep the old method if setting OBC_balanceFacX < 0. |
| 202 |
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- switch on useOBCSbalance in dome experiment: only correct Western OB outflow |
| 203 |
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to match Nortern OB inflow (OBCS_balanceFacN=0). |
| 204 |
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o pkg/seaice: |
| 205 |
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- redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL |
| 206 |
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o pkg/seaice (seaice_growth v 1.113): |
| 207 |
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- reverting seaice_growth to v 1.111 in order to have code with exact bit |
| 208 |
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compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge |
| 209 |
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CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced |
| 210 |
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runtime flag SEAICEareaFormula is kept but is inactive |
| 211 |
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o model/src: |
| 212 |
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- add new param to scale curvilinear grid distance and area when using |
| 213 |
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a different sphere radius from the grid-files. |
| 214 |
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- test/check multi-threads EXCH applied to local variable (cg2d_x) |
| 215 |
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o adjoint: |
| 216 |
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- enable adjoint of Stevens OB |
| 217 |
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- add dummy_in_dynamics to enable extraction of ADJrhoinsitu |
| 218 |
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(a bit delicate because of potentially modified adj. common block structure; |
| 219 |
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current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later) |
| 220 |
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|
| 221 |
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checkpoint62s (2011/02/15) |
| 222 |
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o pkg/seaice (seaice_growth v 1.112): |
| 223 |
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- introduce SEAICEareaFormula run time parameter, which selects the recipe for |
| 224 |
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computing the ice cover tendency from effective thickness tendencies. Include |
| 225 |
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Ian Fenty's formula. |
| 226 |
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- remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using |
| 227 |
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SEAICEareaFormula. |
| 228 |
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- simplify notations for the various d_HEFF/d_AREA terms. |
| 229 |
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o pkg/gmredi: |
| 230 |
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- add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code |
| 231 |
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from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative; |
| 232 |
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add a verification test-run (front_relax.bvp) to test GM_useBVP. |
| 233 |
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o pkg/seaice (seaice_growth v 1.111): |
| 234 |
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- for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's. |
| 235 |
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- the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to |
| 236 |
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also melt ice. |
| 237 |
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o pkg/seaice: |
| 238 |
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- McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty). |
| 239 |
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- can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h |
| 240 |
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o pkg/cheapaml: |
| 241 |
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- from Nico Wienders: New version of this package. |
| 242 |
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o pkg/flt: |
| 243 |
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- add CPP options to prevent floats to re-enter the opposite side of |
| 244 |
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a periodic domain (default: keep periodicity) |
| 245 |
o pkg/gmredi: |
o pkg/gmredi: |
| 246 |
- apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners |
- apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners |
| 247 |
(needed for multi-dim advection). |
(needed for multi-dim advection). |
| 248 |
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- switch on GM Advective form in global_ocean.cs32x15 and update output.txt |
| 249 |
o model/src: |
o model/src: |
| 250 |
- fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run. |
- fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run. |
| 251 |
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o tutorial_tracer_adjsens |
| 252 |
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- extend to NLFS and replace maskC by hFacC |
| 253 |
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(change reference output accordingly) |
| 254 |
|
|
| 255 |
checkpoint62r (2011/01/24) |
checkpoint62r (2011/01/24) |
| 256 |
o testreport: |
o testreport: |
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