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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 verification: |
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- change (for now, only fwd test) offline_exf_seaice experiment: |
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use a re-entrant channel with idealized costline (trapezoidal shape) |
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at southern boundary to explore seaice dynamics and thermodynamics |
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with simple forcing. Main set-up has dynamics+thermo and SST relaxation; |
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secondary test (input.thsice) use thermodynamics only with SST relaxation. |
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- add seaice-dynamics only secondary test using LSR and pkg/thsice advection. |
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o pkg/exf: |
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- disable "sstExtrapol" when Nr=1 |
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o verification: |
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- add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble) |
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to test pkg/cheapaml. |
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o pkg/aim_v23 & pkg/shap_filt: |
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- fix dissipation heating (erroneous gravity multiplication factor). |
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o pkg/seaice: |
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- remove unused field pressPre from jfnk solver |
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- rename two subroutines in seaice_preconditioner.F |
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o eesupp/src: |
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- S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...) |
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o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again |
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- remove wrong parts of the rhs and the lhs (were in there |
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because I did not understand the concept of this preconditioner) |
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- add an exchange between u- and v-sweep. This increases communication |
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by a factor of two but improves the convergence of jfnk. Ideally, |
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one would like the u- and v-sweep to be independent. So far within |
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undocumented ifdefs |
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- reorganize the extra computations for printing the residuals |
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o tools/genmake2: |
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- comment out the "mpif.h" include in NetCDF test programm (for MPI built) |
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since it's not necessary (and was preventing to use MNC in some cases). |
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checkpoint64a (2012/11/16) |
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o pkg/autodiff: |
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- improve pkg-internal logical parameter switch (inAd/inFwd mode) so that |
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autodiff_readparms.F no longer depends on calling order (within |
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packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h): |
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rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd |
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and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd. |
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o pkg/obcs: |
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- adding tidal velocity forcing capability to obcs |
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for usage example, see verification/seaice_obcs/input.tides |
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o pkg/seaice: |
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- turn the LSR-relaxation parameters WFAU/V into runtime parameters |
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SEAICE_LSRrelaxU/V |
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- introduce runtime parameter SEAICEetaZmethod (=0 by default) |
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o pkg/aim_v23: |
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- implement heating from friction (bottom friction and stratospheric drag). |
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o pkg/shap_filt: |
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- fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from |
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dissipation but only for Shap_funct=2, active when addFrictionHeating=T. |
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o model/src: |
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- move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in |
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time-constant addMass field from file (addMassFile); |
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- support for heating due to friction (and Kinetic Energy dissipation): |
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add option, run-time switch and 3-D field array + support code ; each pkg |
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or S/R can add heating contribution (if there is a sink of KE); the sum is |
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accounted for as a Temperature tendency term (EXTERNAL_FORCING_T). |
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o pkg/seaice: |
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- complete merge of ITD code into seaice_growth.F |
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from MITgcm_contrib/torge/itd/code/ |
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no verification so far, but Torge Martin tested |
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"1-D test case and Beaufort set up; |
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deliver okay results after 1 model year." |
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- complete merge of SEAICE_SIZE.h into all relevant routines |
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- move computation of eta at Z-points into calc_viscosities |
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+ introduce global field etaZ |
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+ add different methods for computing etaZ, for now the old |
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method (simple averages of eta to Z-points) is hardwired |
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+ replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual, |
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seaice_preconditioner |
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- simplify computations for SEAICE_ZETA_SMOOTHREG |
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- seaice_preconditioner: |
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+ replace one remaining press by pressLoc (mistake) |
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+ adjust printing of residuals |
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- improve I/O of diagnostics of JFNK in seaice_jfnk.F: |
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+ add (SEAICE.h) and rename some counters (initiliased in |
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seaice_init_fixed.F) |
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+ add _BEGIN/END_MASTER (myThid) around print statements |
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+ print total number of iterations and failures over SEAICE_monFreq |
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interval to STDOUT |
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- move control over output-messages by fgmres to seaice_jfnk to save |
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some operations |
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- move resetting initial guess for fgmres outside of seaice_fgmres_driver |
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in order to make restarts with sol .ne. zero (fgmres with restarts) |
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(seaice_jfnk.F, seaice_fgmres.F) |
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- seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes |
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a serious convergence problem when open boundaries are involved |
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o pkg/ggl90: fix computation of control volumes for the case of |
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ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes |
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up half a grid cell from C-centered to W-centered (pointed out by C. Eden) |
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o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC |
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o pkg/autodiff |
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- Add inAdMode switch for SEAICEuseDYNAMICS: |
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SEAICEuseDYNAMICSinAdMode |
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(extend logic in ADAUTODIFF_INADMODE_SET) |
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o pkg/seaice |
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- Step 1 of merging ice-thickness distribution (ITD) code from |
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MITgcm_contrib/torge/itd/ (author: Torge Martin) |
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The code implements concept laid out in Thorndike et al. (1975); |
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code is enabled via CPP flag SEAICE_ITD |
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nITD (in SEAICE_SIZE.h) defines number of ice thickness categories; |
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code is not complete yet!! |
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- SEAICE_SIZE.h now included in almost all seaice routines |
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o verification (using seaice): |
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- switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp. |
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global_ocean.cs32x15.seaice ; update results. |
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- compile B-grid dynamics in FW test exp 1D_ocean_ice_column ; |
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- compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp |
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offline_exf_seaice (previously compiling B-grid). |
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o pkg/exf: |
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- fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow |
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to specify neither just 1 comp of wind or wind-stress, nor no surface momentum |
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forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind. |
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o pkg/layers (adjust changes from Sept 19): |
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- do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F) |
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this allows to remove "layers_maxNum" dimension from all layers arrays. |
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o pkg/layers (adjust changes from Sept 19): |
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- remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ; |
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- snap-shot extended to all type of layers (not just the 1rst type); |
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- remove layers variables when corresponding CPP option is undef. |
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o pkg/layers: |
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- rename pkg/layers variable and add new output (layer exist & un-weighted |
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velocity in layer) |
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o pkg/seaice: |
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- simplify (?) ocean-drag coefficent computations by using |
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the same routine in all three solvers (saves some code lines) |
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- remove global fields DRAGA and DRAGS from C-grid code and |
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declare them locally in lsr.F (the only place where they are |
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still used) |
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- update AD output of lab_sea.evp (very sensitive anyway). |
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o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics |
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(Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK |
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and SEAICEuseJFNK=.true. A few things to note: |
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- involves a FGMRES, that is parallel but very inefficient, |
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because of many scalar products (global sums) in the Gram-Schmidt |
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orthogonalization method. Needs to be replaced. Original code |
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from J.-F. Lemieux |
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- preconditioner for FGMRES is a stripped down version of LSOR |
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- SOLV_MAX_ITERS is now used for LSOR as a solver and as a |
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preconditioner. For the preconditioner, the default is set to 10. |
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- Jacobian times vector is computed with finite differences |
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- marginally related to JFNK-solver: add a smooth regularization for |
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zeta with tanh that will improve convergence (Lemieux and Tremblay, |
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2009) for any implicit solver (not implemented for EVP because EVP |
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does not need this regularization in the first place). Define |
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SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use. |
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o eesupp/src: |
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- check in genmake2 that intrinsic S/R flush is available. |
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- add S/R to flush IO unit (if intrinsic S/R flush is available) |
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- flush standard & error msg unit before MPI termination |
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- if debugMode, flush IO unit after printing msg |
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o pkg/ctrl: |
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- ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call |
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to ctrl_set_unpack_xyz. |
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checkpoint64 (2012/10/09) |
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o pkg/shelfice |
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- in mom_fluxform.F, mom_vecinv.F: |
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CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid) |
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Bug fix KappaRU -> KappaRV |
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does not change verification/isomip but may change other setups |
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(presumably constant KappaRU=KappaRV) |
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- fix diagnostics SHIU/Vdrag (thanks to Tom Millgate) |
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o pkg/obcs: |
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- fixed some indexing bugs in obcs_seaice_sponge.F |
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- added obcs relaxation subroutines for HSALT and HSNOW |
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- changes verification/seaice_obcs/results/obcs_seaice_sponge.F |
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o pkg/seaice: |
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- add "multicategory" parameterization for snow in analogy to ice, |
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default is off for now. |
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o pkg/obcs: |
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- added obcs_seaice_sponge.F for obcs relaxation of seaice variables; |
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see verification/seaice_obcs/input.seaiceSponge for example application. |
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- remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB |
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index setting by master-thread. This fix multi-threads Pb in previous modifs. |
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o pkg/layers : |
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- add diagnostics to pkg/layers |
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- move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F |
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(from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly. |
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o pkg/generic_advdiff/gad_implicit_r.F : |
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- fix ADVr diagnostics in case of both implicit vertical advection and diffusion. |
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o pkg/seaice/seaice_growth.F: |
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- fix SItflux diagnostics in virtual salt flux + balanceEmpmr case. |
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o pkg/obcs: |
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- change default setting of OBCS_UVICE_OLD from defined to undef; |
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- use new parameter OB_indexNone for null index value (instead of hard-coded 0) |
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in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F; |
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- pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z; |
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- change OB null index value (OB_indexNone) to -99 ; this fix the problem |
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with Southern & Western OB at a tile edge (at least in a simple set-up). |
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o pkg/obcs: |
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- change settings of OB index in case OB coincides with tile edge (shared by |
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2 tiles), so that common OB location is registered by both tiles (instead of |
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only 1). However, for Southern and Western OB, index value = 0 is not |
| 201 |
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recognized as valid OB index (=default null value) and needs to be fixed. |
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- modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting) |
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- new parameter "OB_indexNone" for null index value (for now, still zero) |
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to replace hard-coded null index value of zero. |
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o pkg/exch2: |
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- improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON: |
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always check buffer-size (but outside the loop); move checking for valid |
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index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON, |
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print each tile and point connection only if |W2_printMsg|>= 2 and 3. |
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o pkg/ctrl (pack & unpack): |
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- in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable |
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(locally defined) for different variables (+ remove the variable-specific |
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file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL |
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(to be extended to other local file names in ctrl.h). |
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o pkg/flt: |
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- add a FLT_Iter0 option (similar to PTRACERS_Iter0). |
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o pkg/mdsio: |
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- fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing |
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o tools/genmake2: |
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- add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE |
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(added by Alistair in version 1.51 for building without make depend); |
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- remove Header files list (H_SRC_FILES) from the dependence of targets |
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ad_input_code.f & ftl_input_code.f (not clear why it was added in the first |
| 224 |
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place in version 1.23): this save going through staf when unrelated header |
| 225 |
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file has been modified. |
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Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without |
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"make depend" step, still need to do "make links" before "make adtaf". |
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o eesupp/src (+ few pkg src files) & genmake2: |
| 229 |
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- finish to remove ALWAYS_USE_MPI in source code that TAF does not see; |
| 230 |
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- no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2). |
| 231 |
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- improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish |
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upper/lower case ; account for space between "#" and undef/define) |
| 233 |
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o pkg/flt (with exch2): |
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- cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F; |
| 235 |
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- simplify threads synchronisation; fix (many issues) multi-threaded with MPI. |
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|
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checkpoint63s (2012/09/05) |
checkpoint63s (2012/09/05) |
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o pkg/ecco: |
o pkg/ecco: |
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- remove #ifdef ALLOW_SMOOTH_CORREL3D brackets. |
- remove #ifdef ALLOW_SMOOTH_CORREL3D brackets. |
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