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$Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.1577 2012/01/20 14:35:03 mlosch Exp $ |
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$Name: $ |
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|
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Notes on tags used in MITgcmUV |
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============================== |
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|
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o model/src: add a little initialisation trick to find_rho.F and find_alpha.F |
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to make TAF generate vectorizable code |
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o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows. |
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Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers |
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have flags that do this more efficiently. |
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o pkg/diagnostics/diagstats_calc.F |
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- for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact |
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o pkg/obcs (with exch2): |
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- derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F) |
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and remove code (in obcs_readparms.F) which was based on EXCH of indices |
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(through buffer) and did not account for exch2 (e.g., CS-grid) topology. |
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o pkg/exf and seaice exp: |
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- change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0) |
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so that switching off area & heff advection flags does not affect results. |
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- change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h |
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- keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef |
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EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update |
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results of verification experiments: 1D_ocean_ice_column(fwd), |
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global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8) |
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and offline_exf_seaice (all 4). |
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o pkg/seaice: |
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- remove array YNEG, RIVER, TMIX (replaced by local var) from common block; |
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remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef. |
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- fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY) |
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but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and |
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not multi-dim advection; |
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- fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and |
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SHORTWAVE_HEATING #undef. |
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o optim: make Makefile more robust (?) |
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o pkg/obcs: |
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* fix treatment of obcs_read_pickup for TAF |
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o pkg/shelfice: |
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* add missing initialisation of num_shifwflx |
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* new adjoint verification exp. for isomip |
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* change Prandtl and Schmidt numbers from generic formulations |
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(in terms of model diffus. and visc.) to separate runtime |
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parameters, with Holland and Jenkins (1999) default values. |
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o pkg/exf (interpolation): |
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- extended input field (2 rows) near the N & S poles: |
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* fill in with the symetric value (when even Nb of data in longitude) |
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* add average value at the poles only for scalar quantities ; for vector |
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component interpolation, skip the averaging and keep duplicated values, |
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unless the 2 components have same location (uvInterp=T) in which case |
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interpolate the 2 components together using S/R EXF_INTERP_UV. |
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- new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field |
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together: this allows to account properly for local orientation when |
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averaging at N & S pole. |
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- add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding |
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exf-interpolation near N & S poles. Undef by default. |
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- add debug check/print on 1rst iter if debugLevel >=2. |
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o pkg/exf: |
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- change masking flags definition (no longer "parameter"), put them in |
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common block and set them in S/R EXF_INIT_FIXED. |
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- change recognized masking flag from s,u,v to c,w,s since the mask |
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to use (maskC,W,S) depends on position on model grid and has little to |
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do with scalar/vector difference; fix masking if using P-coordinates. |
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- fix masking of wind-stress (was wrong if interpolated or read on A-grid) |
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and update results of exp. global_with_exf (x2). |
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- fix setting of zenith-angle table when SHORTWAVE_HEATING is undef. |
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o pkg/obcs |
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- S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate) |
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o pkg/exf (interpolation): |
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- assume periodicity in X only if input field cover full longitude range. |
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- improve search for lat. index (supposed to be faster, in ~log2(ny) steps, |
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and should vectorise). |
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- fix input lat of the 2 added row (in case we provide N.pole data). |
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|
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checkpoint63h (2011/12/30) |
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o pkg/seaice: |
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- change declaration of UVM from _RL to _RS in order to get B-grid |
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uIce,vIce monitor when _RS = real*4 |
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o pkg/offline: |
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- new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags); |
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- compute vertical velocity if not read from file (switch on exactConserv |
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& staggerTimeStep); |
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- fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq. |
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o verification: |
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- update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input) |
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with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m": |
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fix Pb in yG definition @ 2 missing corners (previously yG was averaged); |
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- update output of exp. global_ocean.cs32x15.viscA4 after changing |
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grid-file angles (used here for coriolis-3d); |
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- remove (or gzip) few files not needed to run fizhi-cs experiments. |
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o pkg/exf (vector interpolation): |
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- rotate vector component toward local grid-axis orientation using grid-angles |
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(stored in GRID.h) instead of locally computed rotation angle; keep old code |
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available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default). |
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o pkg/seaice: |
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- allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION |
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undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined. |
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o pkg/PKG_OPTIONS.h files: |
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- move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h", |
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outside of the #ifdef ALLOW_THISPKG / #endif block. |
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- update verification/*/code/PKG_OPTIONS.h files. |
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o add a verification experiment (offline_exf_seaice/input.seaice) that test |
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the B-grid LSOR solver |
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o pkg/seaice: sort out emissivity and long wave radiation step 2: |
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- add emissivity for snow and ice as new run-time parameters |
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(unfortunately) that default to the corresponding exf values; this |
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changes results in most verification experiments so that for backward |
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compatibility these parameter have to be set explicitly to inconsistent |
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values (ugly); |
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- the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired |
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emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp |
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until we agree how to handle this bug properly |
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o pkg/exf (interpolation): |
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- add a set of run-time param ({inputfield}_interpMethod), one for |
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each interpolated input field, to select the interpolation method |
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with a value of zero switching off the interpolation; |
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- print interpolation parameters to standard output; |
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- refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined |
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(to use instead runoff_interpMethod=0 in data.exf). |
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- simplify default setting of interpolation parameters (for all fields, |
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set position to match model grid cell-center position, leading to trivial |
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interpolation in case of regular Lat-Lon grid) and fix for the case of |
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non-uniform delY. |
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o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for |
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within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1. |
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this factor is absolutely required, because the lw exitance (= out-going |
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long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown, |
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where the reflectivity rho = 1-emissivity for conservation reasons. Once |
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this is established, we can remove the CPP-Flag (if we want to). |
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o pkg/seaice: |
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- qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and |
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ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined |
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- sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity |
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what the name implies (and not emissivity*BoltzmannConstant), this means |
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the old default value of 5.5e-8 now means |
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5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in |
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S/R exf_readparms |
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- FV-discretization of the B-grid LSOR solver, turn on with |
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SEAICE_LSRBNEW. This new solver also involves a slight re-organization |
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of the calling routine dynsolver, so that B and C-grid code look a |
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little more alike. |
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- fix index bugs in ostres.F (B-grid code) |
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o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better |
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o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the |
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default for SEAICE_emissivity, if useEXF; requires setting a wrong |
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parameter value in global_ocean.cs32x15/input.seaice/data.seaice for |
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backward compatiblity |
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o model/src: use sigmaR in calc_ivdc |
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|
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checkpoint63g (2011/12/16) |
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o pkg/seaice/seaice_growth.F: |
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fix heat conservation of the coupled ocean-seaice system. |
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when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of |
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solid vs liquid water treatment is resolved via QNET. |
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o pkg/seaice/seaice_growth.F: |
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add missing term for sublimation in saltFlux, which was breaking conservation. |
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o pkg/seaice/seaice_model.F: |
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Remove this patholigical case treatment in evolution branch, |
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where it is un-necessary and breaks conservation. |
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Update global_ocean.cs32x15/results accordingly for |
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output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt |
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o model/src: |
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useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in |
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external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE. |
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o pkg/obcs: |
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modify Stevens boundary conditions so that S/R obcs_calc_stevens computes |
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tendency for temperature and salinity that is then applied to update |
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theta and salt in S/R obcs_apply_ts; this requires proper masking of all |
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horizontal advection and diffusion contributions on the boundary (in |
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S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and |
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removing the mask in S/R timestep_tracer. The advantage of this approach is |
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that the updated tracer values include contributions from the surface |
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forcing and vertical diffusion. |
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This modification changes exp4.stevens because of vertical diffusion. |
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o model/src: |
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change non-curvilinear grid setting to also work with exch2 + blank tiles: |
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- move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst |
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face dimensions. |
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- new S/R INI_LOCAL_GRID to define model tile-local grid (using same units |
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as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID |
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and INI_SPHERICAL_POLAR_GRID. |
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change test-experiment global_ocean.90x40x15: |
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- split the domain in many more tiles (9x4 tiles of 10x10 each); |
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- switch to exch2 and remove 1 blank-tile (but only for MPI test). |
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- update results of both test (std & dwnslp). |
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o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in |
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tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation |
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o model/src: |
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- take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS |
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and fix initialisation when using sigma-coords. |
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o model/src: |
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- improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc. |
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to their current value at the beginning of forward_step.F": add a new run-time |
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switch "doResetHFactors" (default=false) and use it to do (or not) the resetting. |
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- set doResetHFactors=T in the following test exp: |
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global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS), |
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global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS) |
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and tutorial_global_oce_in_p (nonLinFS in p) |
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o pkg/ecco |
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- added IES cost term |
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o verification/advect_xz |
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- scale down the depth by 1/100 (from 200 km to just 2.km) |
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- add secondary test using divergent flow, r-star and implicit vertical advection. |
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- add note (check_conserve_TS.txt) and matlab script to check global |
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conservation of T & S with NonLin-FreeSurf and Adams-Bashforth. |
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o pkg/rbcs: |
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- add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F). |
207 |
o pkg/obcs (Stevens BCs): |
208 |
- fix various problems in the phase speed computations of the Stevens |
209 |
boundary conditions: |
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- sign error for western and southern boundaries, |
211 |
- time tendencies were underestimated by factor of dTracerLev and some just |
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zero (for multidim advection schemes) -> now estimate time tendencies |
213 |
from difference between previous (n) time level and the one before (n-1); |
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this requires storing a field per tracer per boundary, also in the pickup |
215 |
files. |
216 |
- replace deltaTmom in cflMer/Zon computation with dTracerLev |
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- set default phase velocity to cflMer/Zon |
218 |
- update verification experiment exp4.stevens |
219 |
o pkg/generic_advdiff (implicit_r): |
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- fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf |
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(remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F); |
222 |
- fix implicit vertical diffusion or advection with NonLin FreeSurf |
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(was using current recip_hFacC instead of future recip_hFacC): set future |
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recip_hFac in thermodynamics.F and pass & use it in all vertical implicit |
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solver S/R ; |
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- fill diagnostics of vertical advective fluxes (computed from tendency) |
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when using implicit vert. advection; |
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- update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion: |
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global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD), |
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tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD) |
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and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5. |
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o pkg/diagnostics: |
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- add diags for T & S tendency which goes through Adams-Bashforth. |
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|
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checkpoint63f (2011/11/30) |
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o pkg/obcs/obcs_calc_stevens.F: |
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- join some loops to reduce number of if-statements |
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- fix a bug in code for northern and southern boundaries. |
239 |
o pkg/seaice/seaice_init_varia.F |
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- undo resetting UVM=0 that has slipped in unnoticed in r1.49 and |
241 |
caused zero ice-velocities for the B-grid code |
242 |
o pkg/seaice/seaice_init_fixed.F |
243 |
- fix a bug in the initialisation of the second metric terms |
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k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0. |
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- this affects all seaice configurations with useCurviLinearGrid = .true. |
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and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms |
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= .true. (default) |
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- the only verification experiment affected is global_ocean.cs32x15: |
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icedyn, seaice, and seaice_dynmix (AD) |
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o pkg/thsice/thsice_diagnostics_state.F |
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- only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does |
252 |
not contain garbage that can lead to surprises in diagstats_calc.F |
253 |
o model/src: |
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- move bi,bj loops inside INTEGR_CONTINUITY ; |
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- call INTEGR_CONTINUITY directly from forward_step.F |
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(previously called from momentum_correction_step.F) |
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- call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F, |
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forward_step.F and pkg/ecco/the_main_loop.F |
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o model/src/do_oceanic_phys.F: |
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- reset addMass to zero only if useICEFRONT ; |
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- separated k-loop for rhoInSitu calculation ; |
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- add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P) |
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and at constant T,S (= WdRHOdP); |
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NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport |
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of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical |
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transport of locally-referenced potential density); |
267 |
to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP) |
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o gluemnc: |
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- replace ncrcat with ncks when adding variables to *.glob.nc |
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- change the way variables without record dimensions are handled so that |
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files that have variables with and without record variables can be glued: |
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add a record dimension with a new unique name to be able to differentiate |
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between variable with and without a-prior record dimensions. Remove |
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this record dimension before adding the variable to the *.glob.nc file. |
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This procedure automatically works also for grid.*.nc files that do not |
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have any record dimension. |
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o verification/cpl_aim+ocn: |
278 |
- generate new reference output on baudelaire (gfortran, mpich2) (previously |
279 |
from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script. |
280 |
o pkg/obcs/obcs_calc_stevens.F: |
281 |
- add code for northern and southern boundaries. |
282 |
- reorder some loops to save some operations and so that drFBar can be scalar |
283 |
o model/src: |
284 |
- re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine |
285 |
truncation) and add diagnostics for Adams-Bashforth tendency increment. |
286 |
- update test-exp. AD output: |
287 |
1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl; |
288 |
and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20, |
289 |
front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5), |
290 |
global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4), |
291 |
matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre, |
292 |
tutorial_global_oce_in_p, tutorial_global_oce_latlon and |
293 |
tutorial_plume_on_slope. |
294 |
o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX |
295 |
that vectorises. This code uses 3 extra 2D fields, F90 array assignments |
296 |
and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX |
297 |
does not even come with an F77 compiler anymore, this should not be |
298 |
a limitation |
299 |
|
300 |
checkpoint63e (2011/11/06) |
301 |
o pkg/seaice adjoint of LSR: |
302 |
- substantially rework STORE dirs. |
303 |
- add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED |
304 |
this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields |
305 |
and only perform SOLV_MAX_FIXED adjoint iters. |
306 |
If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration |
307 |
always goes to same record, meaning that the last forward field will be |
308 |
the one used in the adjoint - an approximation. |
309 |
- now produces non-zero LSR-related gradients, and acceptable gradients for |
310 |
An's zonal (x-z) test case (to be checked in) |
311 |
- lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR |
312 |
(but these are screwed up by the thermodynamics in the first place); |
313 |
reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution; |
314 |
output_adm.txt also reflects changes to seaice_lsr |
315 |
- global_ocean.cs32x15: |
316 |
* the "default" input_ad.seaice has been re-defined to always exclude dynamics |
317 |
(output_adm.seaice.txt was updated) |
318 |
* new input_ad.seaice_dynmix tests a forward LSR / backward free-drift |
319 |
(output_adm.seaice_dynmix.txt) |
320 |
o test-exp. exp4+stevens: |
321 |
- switch off pTracers and nonHydrostatic (restart problems with NH); update output |
322 |
o pkg/seaice (lsr solver): |
323 |
- put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only); |
324 |
update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15 |
325 |
- fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD) |
326 |
- new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution |
327 |
into initial guess for linearised solver; use weight ~ (1/err)^2,4. |
328 |
- compute (with new S/R) and print initial (+ free-driff sol. if available) |
329 |
and final residual of linearised system. |
330 |
o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity |
331 |
(requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F) |
332 |
o pkg/obcs: Stevens BCs (still only for east and west) |
333 |
- fix Stevens BCs by using intermediate velocities of previous |
334 |
time step as "baroclinic" contribution rather velocity of one grid cell |
335 |
inside the boundaries; more consistent but makes the entire treatment |
336 |
more complicated, requires new pickup files and two new S/Rs: |
337 |
obcs_copy_uv_n and obcs_save_uv_n |
338 |
keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY |
339 |
(undefined by default) |
340 |
- silently move computation of some grid factors into separate loops to |
341 |
save some recomputations |
342 |
- add a hack for non-linear free surface |
343 |
- add a verification experiment to exp4 that tests this code |
344 |
o make gluemnc/xplodemnc work with (moron) non-GNU shell tools |
345 |
|
346 |
checkpoint63d (2011/10/25) |
347 |
o pkg/obcs + seaice-dynamics: |
348 |
- new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before |
349 |
solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB |
350 |
values (consistent with an implicit method). |
351 |
- add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to |
352 |
return to older implementation (same results as before); note that none of |
353 |
the "experimental" OBCS_SEAICE options are implemented in the new version. |
354 |
- switch test exp. seaice_obcs to use new version (update output). |
355 |
o pkg/seaice: |
356 |
- add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS) |
357 |
- add parenthesis in Water-Ice drag calculations (evp & lsr); |
358 |
- in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1; |
359 |
and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice) |
360 |
- update output of test exp lab_sea that uses evp or lsr (fwd+ad) |
361 |
and global_ocean.cs32x15 (icedyn & seaice fwd+ad). |
362 |
o pkg/layers: |
363 |
- Include potential density as new coordinate (Thanks to David Munday) |
364 |
o pkg/dic: |
365 |
- Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add |
366 |
carbonate computation/output to CALC_PCO2_APPROX |
367 |
o pkg/generic_advdiff |
368 |
- make TAF generate code that vectorizes: |
369 |
gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F |
370 |
o model/src: |
371 |
- improve vectorization also for adjoint code of |
372 |
solve_tridiagonal and solve_pentadiagonal. As this requires up to |
373 |
5 new 3D-fields, this code is only turned on for the combination of |
374 |
ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message |
375 |
for singular matrix check (only for TARGET_NEC_SX). |
376 |
- remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to |
377 |
ALLOW_AUTODIFF. This flag now needs to be set outside of |
378 |
solve_tri/pentadiagonal.F |
379 |
o pkg/exf: |
380 |
- fix previous modif in exf_readparms.F (revision 1.66: treatment of |
381 |
optional namelist EXF_NML_OBCS). |
382 |
- add many debug-print (to trace down where pkg/cal error msg comes from) |
383 |
o pkg/mom_vecinv/mom_vi_hdissip.F |
384 |
- rearrange loops so that vectorization is improved and in particular |
385 |
the adjoint routine vectorizes. The code is a little longer now, but I |
386 |
think easier to read. |
387 |
Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested. |
388 |
o pkg/seaice: |
389 |
- allow to specify initial seaice velocity from files (uIceFile,vIceFile) |
390 |
o pkg/exch2: |
391 |
- alternative code (without tile x tile matrix) for cumulated (global) sum; |
392 |
used as default; keep using matrix version in adjustment.cs-32x32x1. |
393 |
o tools/build_options: |
394 |
- after merging some MPI and/or multi-threads specific optfiles so that |
395 |
the modified default optfile support both built (using genmake2 -mpi |
396 |
for the MPI built, using genmake2 -omp for OpenMP built), |
397 |
move now obsolete optfiles to tools/build_options/unsupported/ |
398 |
(add copy of email sent to support list in doc/optfiles_changes.txt) |
399 |
|
400 |
checkpoint63c (2011/09/28) |
401 |
o pkg/ebm: |
402 |
- fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of |
403 |
test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d) |
404 |
o pkg/seaice (SItracer pickup) |
405 |
* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER) |
406 |
To be done: |
407 |
- thorough testing of missing fields in S/R seaice_read_pickup |
408 |
- thorough matching between generic tracers and specific fields used |
409 |
(e.g. volume-weighted age, area-weighted age, salinity, ...) |
410 |
o pkg/grdchk: |
411 |
- all procs calculate and print finite-difference gradient (for testreport) |
412 |
- change description output used by testreport; |
413 |
- AD testing: also compare and report Finite-difference gradient; |
414 |
=> update all output_adm*.txt |
415 |
o test exp. global_ocean_ebm: |
416 |
- switch back useRealFreshWaterFlux (no problem anymore with run-off); |
417 |
and turn on exactConserve; update (fwd) output. |
418 |
o pkg/seaice (LSR): |
419 |
- print to STDOUT number of solver iterations at SEAICE_monFreq interval. |
420 |
- modify solver to deal cleanly with u/v switch at face edges (CS-grid): |
421 |
* identical results with non-CS topology (but save up to half of EXCH calls) |
422 |
* no much changes in cs-32 verification tests since no ice at face edges |
423 |
(differences due to convergence criteria, since nb of iterations changed) |
424 |
* expect some differences on lat-lon-cap grid. |
425 |
update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice) |
426 |
o pkg/exch2: |
427 |
- add new CPP option to disable Cumul-Sum matrix (to save storage when using |
428 |
many tiles); until alternative coding is added, just add a stop. |
429 |
o pkg/kpp: |
430 |
- move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F |
431 |
to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list). |
432 |
o optfiles: |
433 |
- merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles |
434 |
into corresponding standard one, which now support different build: |
435 |
(when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built) |
436 |
- add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael) |
437 |
o pkg/obcs (seaice): |
438 |
- add missing EXCH for uIce,vIce after applying OBCS; |
439 |
- remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding |
440 |
argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R |
441 |
EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F; |
442 |
- fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared) |
443 |
- verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi |
444 |
and eedata.mth for MPI and mutlti-threaded testing. |
445 |
o pkg/flt: |
446 |
- make FLT EXCH working with multi-threads (and MPI + multi-threads); |
447 |
- use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h; |
448 |
- fix pickup and trajectories + profiles output with multi-threads; |
449 |
- add parameter to select group of fields to write along trajectory and |
450 |
profile (default unchanged); |
451 |
- only call PORT_RAND* function when flt_noise <> 0; |
452 |
- add multi-threaded test for verification exp. flt_example. |
453 |
o eesupp/src: |
454 |
- fix S/R ALL_PROC_DIE for MPI+multi-threads. |
455 |
- USE_OMP_THREADING: check that number of threads (from eedata) matches |
456 |
actual number (from env.var. setting). |
457 |
o pkg/ebm: |
458 |
- fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file. |
459 |
- add multi-threaded test for verification exp. global_ocean_ebm |
460 |
|
461 |
checkpoint63b (2011/08/29) |
462 |
o pkg/ebm: |
463 |
- fix sign of runoff; |
464 |
- update directly forcing fields (Qnet,EmPmR) to use standard |
465 |
external_forcing_surf.F (remove ebm_forcing_surf.F); |
466 |
- avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F); |
467 |
- set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm) |
468 |
and apply relaxation towards corresponding SST field (2-D map or ZonAver). |
469 |
- update global_ocean_ebm parameters file data and update output (fwd+ad). |
470 |
o verification/matrix_example: |
471 |
- split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for |
472 |
MPI and mutlti-threaded testing. |
473 |
o pkg/matrix: |
474 |
- change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ; |
475 |
- fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter); |
476 |
- fix for multi-threaded (remove DATA statement); |
477 |
- use standard DIFFERENT_MULTIPLE function; |
478 |
- add MATRIX_OPTIONS.h |
479 |
o verification/matrix_example: |
480 |
To allow to split the domain in several tiles, change the domain size |
481 |
from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on |
482 |
Western side) of land points. |
483 |
o (*_)write_pickup: |
484 |
- fix few bugs in mypackage_read/write_pickup.F |
485 |
- in MDS_WR_METAFILES calls, replace "myTime" by a local copy into |
486 |
array of length 1 (was caught by compiler syntax-check). |
487 |
o pkg/diagnostics (velocity potential solver): |
488 |
- fix initialisation of main diagonal matrix (for overlap values) |
489 |
o tools/build_options: |
490 |
- towards single optfile for MPI and non-MPI built: merge few +mpi optfile |
491 |
into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11) |
492 |
- linux_amd64_gfortran: merge +mpi_generic version into standard optfile: |
493 |
* move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ; |
494 |
* FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list; |
495 |
and use "-devel" testreport option for standard testing on baudelaire. |
496 |
o pkg/grdchk: |
497 |
- Assume that all gradient-check position are within the same tile |
498 |
corresponding to global indices (iGloTile,jGloTile) and that |
499 |
positions (i,j indices or nbeg) are local to this tile; |
500 |
- set tile local-indices and proc. number according to tile global-indices; |
501 |
- remove grdchkwhichproc from namelist (retired param); |
502 |
- send adjoint gradient to all procs so that all procs print it to STDOUT; |
503 |
- switch on MPI test for global_ocean.90x40x15 AD test experiment. |
504 |
o adding package bbl (Bottom Boundary Layer) |
505 |
description in MITgcm/pkg/bbl/bbl_description.tex |
506 |
example/test experiment in MITgcm_contrib/bbl |
507 |
o adjoint verifications |
508 |
- changed 5 experiments to multi-tiles |
509 |
* global_ocean.90x40x15 |
510 |
* obcs_ctrl |
511 |
* offline_exf_seaice |
512 |
* tutorial_dic_adjoffline |
513 |
* tutorial_tracer_adjsens |
514 |
changed reference output for those that crossed tile boundaries |
515 |
(changed choices of gradient check positions) |
516 |
- with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi) |
517 |
- temporary bug fix in grdchk_loc.F for obcs |
518 |
o genmake2 & testreport |
519 |
- add target "obj" (just for OBJFILES files) to Makefile; |
520 |
- add option to specify FEXTRAFLAGS on command line. |
521 |
o pkg/mypackage: |
522 |
- remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS |
523 |
|
524 |
checkpoint63a (2011/08/02) |
525 |
o pkg/diagnostics (velocity potential): |
526 |
- fix velocity-potential calculation when using OBCS: balance net inflow |
527 |
at each level (new S/R OBCS_DIAG_BALANCE). |
528 |
- fix some of the problems with OBCS in stream-function calculation. |
529 |
o pkg/exf/exf_readparms.F |
530 |
- make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF, |
531 |
EXF_NML_OBCS) more consistent, so that you need not have these lists |
532 |
in data.exf when they are not used. |
533 |
o optim/optim_readdata.F: |
534 |
- add some output about obcs variables that might help debugging |
535 |
- add a check about nvarlength |
536 |
o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec |
537 |
o pkg/diagnostics (velocity potential): |
538 |
- fix mask for OBCS (still problems in stream-function with OBCS); |
539 |
- add specific parameter (default = main code CG2D params) for solver; |
540 |
- in case of poor convergence, use solution corresponding to lowest residual. |
541 |
o pkg/seaice/seaice_growth.F: small changes that permit vectorizable |
542 |
adjoint code. In general statements like tmpscal=fld(i,j) are problematic |
543 |
and should be avoided where possible. |
544 |
o model/src (rStar): |
545 |
- include r* effect on reference-state (PhiRef) in totPhiHyd |
546 |
(so that it's really the potential anomaly at the cell center); |
547 |
affect solution only if z* with full pressure in EOS. |
548 |
- test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and |
549 |
update output (because of z* in totPhiHyd and viscA4 changes); |
550 |
- keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly |
551 |
@ constant r) until interpolation at constant r is implemented. |
552 |
o pkg/diagnostics |
553 |
- fix RCENTER diagnostics in case cell center is not at interface middle |
554 |
o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use |
555 |
this eos with eosType = 'TEOS10', in data (PARM01). This eos implies |
556 |
that THETA and SALT are "conservative temperature" and "absolute |
557 |
salinity" |
558 |
o pkg/ctrl |
559 |
- fix computation of endrec in s/r ctrl_init_rec |
560 |
- ctrl_pack/unpack_*: remove unused variables and some obsolete code |
561 |
o pkg/seaice/seaice_growth.F |
562 |
- fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code, |
563 |
remove then obsolete STORE directives |
564 |
- fix STORE directives for tice and tices, so that only the |
565 |
appropriate part of the fields are stored (and not the entire |
566 |
field); update global_ocean.cs32x15.seaice AD output. |
567 |
- cosmetic changes: adjust CPP flags and indentation for better |
568 |
legibilty |
569 |
o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by |
570 |
Chris Wilson) |
571 |
o pkg/gmredi: |
572 |
Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF), |
573 |
and test it in verification exp. "front_relax.bvp" (update output.bvp.txt) |
574 |
|
575 |
checkpoint63 (2011/07/11) |
576 |
o pkg/exch2: |
577 |
- rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h |
578 |
- exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the |
579 |
(2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y |
580 |
increments, calculates Cumul-Sum @ tile origin and sends results to each tile. |
581 |
o pkg/diagnostics: |
582 |
- deal with pairs of post-processed diags which are computed together; in |
583 |
particular, re-order list of diags within 1 file to save 2nd computation. |
584 |
- add S/R to compute velocity stream-function (called after velocity-potential |
585 |
calculation) from divergence free transport -> new diagnostics "PsiVEL". |
586 |
- add parameter to select grid-point location where PsiVEL == 0. |
587 |
o eesupp/src: |
588 |
new S/R to calculate cumulated sum on tiled array, corner grid-cell location |
589 |
(specific S/R needed with exch2 topology - for now, just print an error msg) |
590 |
o pkg/shelfice |
591 |
- Implement friction velocity-dependent transfer coefficients following |
592 |
Holland and Jenkins, JPO, 1999 |
593 |
Original code by M. Losch with small modifs. |
594 |
Enable with CPP option SHI_ALLOW_GAMMAFRICT |
595 |
and runtime flag SHELFICEuseGammaFrict |
596 |
o verification lab_sea & global_ocean.cs32x15: |
597 |
- use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local): |
598 |
does not miss some dependencies (but is slower) and also works with many files |
599 |
(default makedepend limitation for AD built). |
600 |
- use cyrus_makedepend in adjustment.128x64x1 (so that it still tested). |
601 |
o pkg/diagnostics: |
602 |
- add run-time parameter "useMissingValue" (def=False) to fill land-point |
603 |
(i.e., where mask=0) with MissingValue ; used only in MNC output file. |
604 |
This replaces CPP-option DIAGNOSTICS_MISSING_VALUE. |
605 |
- Extend the use of "missing_value" setting from data.diagnostics for the case |
606 |
of counter-diagnostics (where fraction-weight is zero). This applies both to |
607 |
MNC and MDS output files. |
608 |
o pkg/seaice/seaice_growth.F: |
609 |
- add 'a priori' cap of latent heat flux based on actual mass considerations |
610 |
when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the |
611 |
non-legacy seaice_solve4temp. |
612 |
- add diagnostic of the residual sublimation freshwater flux (the freshwater |
613 |
flux taken from the ocean if the total actual latent heat fluxes exceed |
614 |
the maximum) |
615 |
- remove the CPP switch around the *_FWbySublim unit change and move diagnostic |
616 |
fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F. |
617 |
- add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef |
618 |
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim). |
619 |
- bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET. |
620 |
- bug fix : missing part to Martin's r_FWbySublim pathological case fix. |
621 |
o verification 1D_ocean_ice_column: |
622 |
made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet |
623 |
update results |
624 |
o pkg/diagnostics: |
625 |
- Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P') |
626 |
which are not filled-up but computed from other diags ; In this case, the mate |
627 |
diag points to the primary (filled-up) diag to used for post processing. |
628 |
- Update Velocity-potential computation using post-processed diag framework. |
629 |
==> Change the ordering of fields and time-periods in MDS output file |
630 |
when using periodic averaging: now writes one time record with the full set |
631 |
of fields for this time period, then the next time reccord (it used to be |
632 |
one field with the full set of time records then the next field). |
633 |
Note: this is now similar to NetCDF (MNC) output file. <== |
634 |
|
635 |
checkpoint62z (2011/06/21) |
636 |
o adjoint monitor: |
637 |
- Add adjoint monitor output for packages exf, seaice |
638 |
and update relevant testreport output |
639 |
o pkg/seaice: |
640 |
- re-order diags inits so that they appear in order in available_diagnostics.log |
641 |
- added diags: hsnow thermo. rates of change, area preceeding ridiging process, |
642 |
area/heff/hsnow preceeding thermodynamic growth/melt. |
643 |
- modified diag: SIdA; output actual effect, as the description states. |
644 |
- modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. |
645 |
- retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. |
646 |
(SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; |
647 |
and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) |
648 |
- modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. |
649 |
- added diagnostics for seaice generic tracers (SItr*). |
650 |
- added SItrUnit and SItrNameLong run time param (for SItr* diags). |
651 |
- in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. |
652 |
I. Fenty: 18-Jun-2011: |
653 |
Minor changes to seaice package: |
654 |
1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and |
655 |
added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) |
656 |
- Differentiated "regularization variables" from "floor variables" |
657 |
* areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor |
658 |
* hiceMin became SEAICE_hice_reg (old hiceMin) |
659 |
(with _reg meaning regularization variable) |
660 |
- SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion |
661 |
so as to ensure energy conservation when going between phases |
662 |
- A22 was not used anywhere |
663 |
2) Changed regularization procedure for heffActual and hsnowActual to ensure |
664 |
well-boundedness and smooth adjoint in seaice_growth.F |
665 |
3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells |
666 |
because the old regularization always set heffActual >= 0.05 cm |
667 |
4) Changed the model so that the default behavior is to put a small (10^-5) "floor" |
668 |
on AREA when HEFF > 0. |
669 |
- went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to |
670 |
requiring that DISABLE_AREA_FLOOR *not* be defined |
671 |
Affected verifications: |
672 |
- 1D_ocean_ice_column (output.txt output_adm.txt) |
673 |
- global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) |
674 |
o pkg/diagnostics: |
675 |
- move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). |
676 |
- rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument |
677 |
(was _RL, now integer) with option = 0 to retrieve all levels. |
678 |
- add pieces of code to compute velocity potential at each level (new diagnostics |
679 |
PhiVEL, works only when UVELMASS & VVELMASS are also turned on); |
680 |
for now, using same params as CG2D (target-resisual, max Nb of iter ...). |
681 |
- fix few issues with counter diagnostics in diagnostics_setdiag.F & |
682 |
diagstats_setdiag.F (if diagnostic counter is itself a counter diag) |
683 |
and in diagnostics_fract_fill.F (do not need a valid pointer for the |
684 |
diagnostics counter-mate); check that definition of counter-diagnostic |
685 |
includes a valid counter-mate (in diagnostics_set_levels.F). |
686 |
o model/src (rStar): |
687 |
- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
688 |
affect solution only if z* with full pressure in EOS; |
689 |
update output of test-exp global_ocean.90x40x15. |
690 |
o pkg/seaice: |
691 |
- introduce siEps=1e-5 parameter |
692 |
- use areaMax in AREA update (part 4), consistent with ridging step (part 2.5). |
693 |
- re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code. |
694 |
- introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer. |
695 |
For now it covers, and was tested for, ice salinity and age (attached to HEFF), |
696 |
as well as ice cover age and ridging index (attached to AREA). |
697 |
For now the run time parameters (in data.seaice/SEAICE_PARM03) are |
698 |
SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA'). |
699 |
Up to SItrMaxNum=3 tracers can be used simultaneously. |
700 |
o pkg/salt_plume: |
701 |
-introduce SPsalFRAC run time parameter that sets the fraction of the |
702 |
salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically) |
703 |
that gets vertically redistributed (fluxed down) by pkg/salt_plume. |
704 |
o model debug options: |
705 |
- Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored |
706 |
in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h). |
707 |
- Refine debug-msg printing selection (3 new levels): |
708 |
debugMode : controls printing of debug messages (sequence of S/R calls). |
709 |
debugLevel : controls printing of algorithm-relevant auxiliary/debug messages |
710 |
debLevZero = 0 ; /* level of disabled aux. msg printing */ |
711 |
debLevA = 1 ; /* level of minimum aux. msg printing */ |
712 |
debLevB = 2 ; /* level of low aux. print (report read-file opening)*/ |
713 |
debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */ |
714 |
debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */ |
715 |
debLevE = 5 ; /* level of extensive debug printing */ |
716 |
New debugLevel default: with default debugMode value (=F), |
717 |
= 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.; |
718 |
and if debugMode=T, default debugLevel = 4 (debLevD). |
719 |
Relation with previous settings: |
720 |
debLevB (=2) corresponds to former debLevA (=1) |
721 |
debLevD (=4) corresponds to former debLevB (=2) |
722 |
Note: |
723 |
a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before); |
724 |
b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs); |
725 |
to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5) |
726 |
- Add new parameter (printResidualFreq, read from PARM02 namelist) to print |
727 |
detailed CG solvers convergence; off (=0) by default, except if debugLevel=5. |
728 |
o pkg/obcs: |
729 |
- change OBCSfixTopo default from True to False (should not change the results); |
730 |
keep OBCSfixTopo=T in verification-exp. seaice_obcs. |
731 |
o pkg/thsice: |
732 |
- fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in |
733 |
2nd layer seaice sublimation (unlikely to happen) |
734 |
- use Interior mask for OBCS in thsice_advection.F (similar to what is |
735 |
done in gad_advection & seaice_advection). |
736 |
o adjoint: |
737 |
bug fix spotted by Gael Forget: |
738 |
seaice_advection and thsice_advection still had |
739 |
legacy CPP options to avoid CS corner updates for adjoint |
740 |
o pkg/seaice: |
741 |
=> Change some of the defaults (2011/05/29): |
742 |
- change SEAICEuseFluxForm default (from False to True) |
743 |
- change DIFF1 default (from 0.004 m/s to 0. m/s) |
744 |
And print warnings if DIFF1 is not set in data.seaice and centered |
745 |
avection scheme is used without any diffusion. |
746 |
also: |
747 |
- fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F; |
748 |
- set SEAICEdiffKh[] default in the same way as SEAICEadvSch[] |
749 |
- stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any |
750 |
other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with |
751 |
#undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE. |
752 |
update results of test exp.: |
753 |
lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20) |
754 |
output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200) |
755 |
output_adm.noseaicedyn (SEAICEuseFluxForm=T) |
756 |
offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T) |
757 |
seaice_obcs: output (SEAICEuseFluxForm=T) |
758 |
and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004) |
759 |
for standard fwd & AD lab_sea tests (to keep the same output). |
760 |
o pkg/seaice/seaice_growth.F: |
761 |
- use Ian Fenty's capping formulas for actual ice |
762 |
thickness thoughout EVOLUTION branch. |
763 |
- put treatment pathological case #2) in CPP brackets |
764 |
(ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). |
765 |
- update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. |
766 |
o pkg/seaice: |
767 |
- seaice_diffusion.F : remove the min(DX,DY) factor permanently; |
768 |
pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter; |
769 |
also pass fac as a param, which can be 1. (to update the tendency |
770 |
field) or the time step (to update the field itself). |
771 |
- seaice_advdiff.F: for multidim, call seaice_diffusion with |
772 |
e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call |
773 |
seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. |
774 |
- SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : |
775 |
hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
776 |
o pkg/seaice: |
777 |
diffusion with centered advection scheme (diffus.F & advect.F): |
778 |
- simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) |
779 |
to just compute the laplacian of input-field. |
780 |
- unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call. |
781 |
- fix flux-form version in diffus.F to conserve tracer. |
782 |
update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects |
783 |
machine truncation) and lab_sea.salt_plume (conservative flux-form modif) |
784 |
|
785 |
checkpoint62y (2011/05/26) |
786 |
o pkg/seaice: |
787 |
- seaice_growth.F : in EVOLUTION branch, always include |
788 |
a_QSWbyATM_cover in qnet (as it should be). |
789 |
- verification/global_ocean.cs32x15 : update results accordingly |
790 |
(output.seaice.txt output_adm.seaice.txt). |
791 |
o pkg/seaice + obcs: |
792 |
- use maskInW & maskInS in multi-dim advection and biharmonic diffusion: |
793 |
equivalent of assuming no tracer gradient outside the OB region. |
794 |
update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion) |
795 |
- remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed |
796 |
after changes above); |
797 |
- obcs+seaice cleaning: apply seaice-tracer OB values to tracer field |
798 |
only at OB location (instead of over a band of OLx width). |
799 |
o pkg/seaice: |
800 |
- fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F |
801 |
(dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid) |
802 |
o pkg/obcs: |
803 |
- split header file "OBCS.h" into 4 separated files: |
804 |
OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h |
805 |
Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h |
806 |
(contain no conditional statement which depends on OBCS options). |
807 |
- move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h) |
808 |
to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h). |
809 |
o ctrl, cost, grdchk & autodiff pkgs: |
810 |
- make options file more standard (like other {PKG}_OPTIONS.h file but |
811 |
with AD_CONFIG.h); clean-up some of the included header files. |
812 |
o pkg/obcs: |
813 |
- do not mask tracer when applying OB (tracer == 0 could generate problems) |
814 |
- apply tracer OB values to tracer field only at OB location (instead of |
815 |
over a band of OLx width) |
816 |
- clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R) |
817 |
- remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove |
818 |
obcs_apply_tloc.F & obcs_apply_sloc.F |
819 |
o obcs in model/src: |
820 |
- call OBCS_APPLY_W only if NonHydrostatic. |
821 |
- call OBCS_APPLY_ETA only if NonLinFreeSurf. |
822 |
- reset dEtaHdt and wVel to zero outside OB interior region ; |
823 |
- leave tracer unchanged outside OB interior region: This has no effect |
824 |
on the solution but just to prevent unrealistic tracer value outside OB. |
825 |
- zero out velocity outside OB interior region: This has no effect on |
826 |
the solution but just to prevent unrealistic velocity outside OB. |
827 |
o obcs and non-lin free-surf: |
828 |
move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F |
829 |
and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F |
830 |
+ add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR: |
831 |
this fixes missing EXCH + get consistent eta OB value (+ fix restart). |
832 |
update results of test-exp. exp4(nlfs). |
833 |
o exp4 (nlfs) test-exp: |
834 |
use OBC for Eta at Western & Eastern OB (to test prescribing Eta |
835 |
with NonLin-FreeSurf); update output.nlfs.txt |
836 |
o obcs and 2d/3d solver norm: |
837 |
use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB |
838 |
and outside OB interior region (will allow to place OB further inside the |
839 |
domain). Depending on the domain, can affects cg2d-Norm (previous |
840 |
cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl, |
841 |
and cg3d-Norm (previous Norm was computed before canceling OB terms), |
842 |
e.g. in tutorial_plume_on_slope. |
843 |
- update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope. |
844 |
o pkg rbcs: |
845 |
- split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h |
846 |
- add capability to apply relaxation to horizontal velocity uVel & vVel. |
847 |
o pkg/grdchk: add gradient check for control variable xx_shifwflx |
848 |
o pkg/shelfice/shelfice_init_fixed.F |
849 |
fix CPP-flag combinations |
850 |
o pkg/seaice: Merge iceage code of Pierre Rampal |
851 |
* update/change/correct ice age calculations |
852 |
* add age updates for pathological cases |
853 |
Probably needs more testing... |
854 |
|
855 |
checkpoint62x (2011/05/13) |
856 |
o pkg/mom_vecinv: |
857 |
high-order vorticity scheme: use interior masks (maskInW & S) |
858 |
to zero-out (outside OB) gradient of vorticity. |
859 |
o verification exp.: |
860 |
turn on "useEnergyConservingCoriolis" (better discretisation) in exp. |
861 |
hs94.128x64x5 and seaice_obcs ; update results. |
862 |
o pkg/obcs: |
863 |
fix bug in OBeta for YZ sections in obcs_exf_load.F |
864 |
o pkg/ctrl, pkg/shelfice, and optim: |
865 |
- add new control variable xx_shifwflx (fresh water flux underneath ice |
866 |
shelves). This is almost as tedious as obcs-ctrl, because the |
867 |
variables needs its own mask. |
868 |
- add a cost function term that penalizes the deviation of xx_shifwflx |
869 |
from the first guess (zero) in analogy to other control variables |
870 |
o pkg/shelfice: |
871 |
- start basic adjoint |
872 |
o pkg/ctrl: |
873 |
- remove extra 2D field "for good measure" when initializing in |
874 |
ctrl_set_globfld_[xy/xz/yz].F |
875 |
- replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec |
876 |
- improve error messages in ctrl_set_unpack_* |
877 |
o OBC implementation in momentum: |
878 |
use interior masks (maskInC,W & S) in momentum S/R: |
879 |
- multiply divergence, tension and some del^i.u or del^j.v by maskInC |
880 |
- multiply del2u,del2v by maskInW/S (biharmonic viscosity) |
881 |
- multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) |
882 |
- multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) |
883 |
Motivation: fix/clean implementation of OBC with biharmonic-viscosity |
884 |
(and also with Leith/Smagorinsky harmonic-viscosity). |
885 |
Update output of experiment dome and exp4 (+nlfs). |
886 |
o exp4 test-exp: |
887 |
- turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) |
888 |
and prescribe time-varying OB (without pkg/exf) for zonal-velocity |
889 |
at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
890 |
time-varying OB at Western-side for wVel (NonHyd); update output. |
891 |
- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
892 |
and biharmonic-viscosity ; also use prescribed time varying OB. |
893 |
o pkg/obcs: |
894 |
fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
895 |
o model/src: |
896 |
- fix startTime setting when baseTime<>0 & nIter0=0 are specified ; |
897 |
- initialise startTime & nIter0 with unlikely values: allows to set one |
898 |
from the other without ambiguity. |
899 |
o seaice_obcs test-exp.: |
900 |
add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output. |
901 |
o pkg/obcs: |
902 |
- remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: |
903 |
no longer needed with maskInC,W,S in pkg/generic_advdiff. |
904 |
o pkg/seaice: |
905 |
- retired SEAICE_SALINITY and SEAICE_salinity in favor of |
906 |
SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively. |
907 |
- fixed bug in the initialization of sea ice salinity variable HSALT |
908 |
in seaice_init_varia.F (removed dependence on ICE2WATR) |
909 |
o fizhi-cs test exp.: |
910 |
switch reference output convention for these 2 non-standard test-exp, |
911 |
from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5) |
912 |
to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11) |
913 |
reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran |
914 |
o model/inc: |
915 |
- change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4") |
916 |
of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS) |
917 |
o pkg/seaice: |
918 |
- fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY |
919 |
o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15 |
920 |
- updated output*.txt files due to bug fixes in salt, saltPlumeFlux, |
921 |
and initial HSALT |
922 |
|
923 |
checkpoint62w (2011/04/26) |
924 |
o pkg/mom_fluxform: |
925 |
- fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf. |
926 |
- use parameter "sideDragFactor" in no-slip BC side-drag part. |
927 |
- update output of exp. global_ocean.90x40x15 |
928 |
o pkg/mom_vecinv: |
929 |
mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform) |
930 |
o update seaice exp.: |
931 |
use more consistent parameter values (remove "backward compatability only": |
932 |
ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh) |
933 |
related to thermodynamics seaice. Update output (fwd+AD) of exp.: |
934 |
1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs |
935 |
o update test-exp global_ocean.90x40x15: |
936 |
o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis). |
937 |
o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.) |
938 |
o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params) |
939 |
o turn on zStar & viscA4 in standard set-up (dir input/) |
940 |
and update output files: output.txt & output.dwnslp.txt |
941 |
o new AD-test experiment: obcs_ctrl |
942 |
(From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector. |
943 |
o pkg/dic: |
944 |
fix two bugs in handling water vapour pressure in carbonate chemistry |
945 |
and air-sea fluxes. Found by Val Bennington and Galen McKinley |
946 |
(add DIC Option = WATERVAP_BUG to recover old results) |
947 |
update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline |
948 |
o adding allowInteriorFreezing option to check for water below freezing point |
949 |
at depth and bring the negative heat anomaly to the surface level |
950 |
o pkgs _fields_load: |
951 |
- extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs) |
952 |
- use new S/R GET_PERIODIC_INTERVAL in pkgs: |
953 |
bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and |
954 |
rbcs to get interpolation weights and time reccord number. |
955 |
- fix multi-threading in aim_fields_load.F |
956 |
- apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F |
957 |
o external_fields_load: |
958 |
new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear |
959 |
interpolation weights) to use in a periodic time-series ; do not divide by |
960 |
time-step to convert to integer: |
961 |
- this fixes case where externForcingPeriod is not multiple of time-step |
962 |
(Thanks to Christopher L. Wolfe) |
963 |
- this fixes case where externForcingPeriod is an odd multiple of time-step |
964 |
(was wrong by half of time-step); update results of tutorial_global_oce_in_p. |
965 |
store index of time-record which is currently loaded: |
966 |
- works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ; |
967 |
- needed for the adjoint but not yet used because of extensive recomputations; |
968 |
(to be fixed soon) |
969 |
|
970 |
checkpoint62v (2011/04/02) |
971 |
o verification/1D_ocean_ice_column added to test Ian Fenty's |
972 |
pkg/seaice_growth.F modifications for improving sea ice code differentiability |
973 |
o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope |
974 |
(new velocity statistics after changing maskInW & maskInS definition) |
975 |
o pkg/generic_advdiff with OBCS: |
976 |
use maksInW & maskInS in advective flux and in biharmonic diffusion calculation: |
977 |
equivalent to assumption of no tracer gradient outside the OB region. |
978 |
This will affect the results if using obcs+biharmonic diffusion. |
979 |
update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc) |
980 |
o pkg/obcs: |
981 |
change definition of maskInW & maskInS: leave OB edges inside (maskIn=1) |
982 |
(e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still |
983 |
in Interior region. No impact on solution but affects Velocity monitor stats. |
984 |
o pkg/ptracers (adjoint) |
985 |
New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate |
986 |
tape file for each tracer |
987 |
o model/inc/src and pkg/autodiff: add parameters that allow to turn |
988 |
of parts of the adjoint code at run time. For now, there are only |
989 |
useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These |
990 |
parameters are set in data.pkg. |
991 |
This is the lazy coward's version of doing this, but still useful for |
992 |
debugging. In order to do it right, everything needs to be moved to |
993 |
pkg/autodiff. |
994 |
o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at |
995 |
the end; this fixes the adjoint balancing code for open boundaries. |
996 |
o pkg/ctrl: |
997 |
- change behavior of xx_${varname}period to be analogous to exf-conventions: |
998 |
xx_${varname}period = 0., means time-independent control part |
999 |
xx_${varname}period = -12., means one-year-periodic monthly control part |
1000 |
- introduce helper routine ctrl_init_rec (part of ctrl_init.F) to |
1001 |
clean up ctrl_init a little, remove unused variables |
1002 |
- ctrl_init: fixed the handling of the start/endrec for obcs-variables |
1003 |
- move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec |
1004 |
|
1005 |
checkpoint62u (2011/03/15) |
1006 |
o model/src: |
1007 |
- for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in |
1008 |
h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ; |
1009 |
- in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to |
1010 |
INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF. |
1011 |
o pkg/ctrl/obcs/ecco: |
1012 |
- remove obsolete, unused, and partially broken code: |
1013 |
ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within |
1014 |
ALLOW_CTRL_OBCS_BALANCE |
1015 |
- put a stop statement into ecco/cost_obcsvol.F, but also add |
1016 |
cost_obcsvol to ecco_ad_diff.list |
1017 |
o pkg/ecco: fix counting cost function contributions for obcs (code |
1018 |
by Matt M.) and diffkr for diagnostics |
1019 |
o pkg/ecco, pkg/ctrl, pkg/grdchk: |
1020 |
add cost penalty terms for initial uvel, vvel, eta controls |
1021 |
and I/O for prior error files |
1022 |
o pkg/mdsio: |
1023 |
move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option |
1024 |
(new argument) to check for tiled file in mdsioLocalDir : this fix the |
1025 |
restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir. |
1026 |
o pkg/ctrl: |
1027 |
- ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by |
1028 |
ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove |
1029 |
unused and superfluous variables |
1030 |
- ctrl_get_gen_rec.F: catch the case of xx_genperiod=0. |
1031 |
o pkg/ecco |
1032 |
- enable adjoint of Stevens OB |
1033 |
o pkg/ctrl/ecco/grdchk: |
1034 |
- remove global declaration of tmpfldx/yz and tmpfldx/yz2. |
1035 |
Fortunately, we do not have any tests for the numerous cpp-flagged |
1036 |
option of "obcs as control parameters" so we will never know |
1037 |
if this is an improvement (but at least now things compile). |
1038 |
- remove an obsolete initialization from ecco_cost_init_barfiles.F |
1039 |
- fix some problems within never used ifdefs to make the code compile |
1040 |
o pkg/obcs: |
1041 |
- Refine Interior mask definition to work with more complex OB (e.g. |
1042 |
if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to |
1043 |
read in Interior mask from file. Check if Interior mask is consistent |
1044 |
with OB list of indices. |
1045 |
o pkg/seaice |
1046 |
- beginning code for a seaice tracer package, |
1047 |
but currently only used for seaice age: SEAICE_AGE |
1048 |
SEAICE_num = 4 |
1049 |
iTracer = 1: area-weighted ice age |
1050 |
= 2: volume-weighted ice age |
1051 |
= 3, 4: template for one-year vs. multi-year ice |
1052 |
data.seaice has new namelist SEAICE_PARM03 for arrays related to |
1053 |
SEAICE_num |
1054 |
|
1055 |
checkpoint62t (2011/03/05) |
1056 |
o pkg/obcs: |
1057 |
- obcs_apply_uv.F: change to a 2 steps method, first tangential component; |
1058 |
then normal component. This ensures that the normal component is set |
1059 |
correctly even when it conficts with tangential setting from an other OB. |
1060 |
Affects results of test-experiment seaice_obcs: update the output.txt |
1061 |
o pkg/obcs: |
1062 |
- add code to monitor statistics of dynamical fields at OB. |
1063 |
- take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW : |
1064 |
- fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection). |
1065 |
- change default: balance the Net inflow through all OB (instead of balancing |
1066 |
each OB separately); keep the old method if setting OBC_balanceFacX < 0. |
1067 |
- switch on useOBCSbalance in dome experiment: only correct Western OB outflow |
1068 |
to match Nortern OB inflow (OBCS_balanceFacN=0). |
1069 |
o pkg/seaice: |
1070 |
- redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL |
1071 |
o pkg/seaice (seaice_growth v 1.113): |
1072 |
- reverting seaice_growth to v 1.111 in order to have code with exact bit |
1073 |
compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge |
1074 |
CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced |
1075 |
runtime flag SEAICEareaFormula is kept but is inactive |
1076 |
o model/src: |
1077 |
- add new param to scale curvilinear grid distance and area when using |
1078 |
a different sphere radius from the grid-files. |
1079 |
- test/check multi-threads EXCH applied to local variable (cg2d_x) |
1080 |
o adjoint: |
1081 |
- enable adjoint of Stevens OB |
1082 |
- add dummy_in_dynamics to enable extraction of ADJrhoinsitu |
1083 |
(a bit delicate because of potentially modified adj. common block structure; |
1084 |
current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later) |
1085 |
|
1086 |
checkpoint62s (2011/02/15) |
1087 |
o pkg/seaice (seaice_growth v 1.112): |
1088 |
- introduce SEAICEareaFormula run time parameter, which selects the recipe for |
1089 |
computing the ice cover tendency from effective thickness tendencies. Include |
1090 |
Ian Fenty's formula. |
1091 |
- remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using |
1092 |
SEAICEareaFormula. |
1093 |
- simplify notations for the various d_HEFF/d_AREA terms. |
1094 |
o pkg/gmredi: |
1095 |
- add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code |
1096 |
from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative; |
1097 |
add a verification test-run (front_relax.bvp) to test GM_useBVP. |
1098 |
o pkg/seaice (seaice_growth v 1.111): |
1099 |
- for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's. |
1100 |
- the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to |
1101 |
also melt ice. |
1102 |
o pkg/seaice: |
1103 |
- McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty). |
1104 |
- can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h |
1105 |
o pkg/cheapaml: |
1106 |
- from Nico Wienders: New version of this package. |
1107 |
o pkg/flt: |
1108 |
- add CPP options to prevent floats to re-enter the opposite side of |
1109 |
a periodic domain (default: keep periodicity) |
1110 |
o pkg/gmredi: |
1111 |
- apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners |
1112 |
(needed for multi-dim advection). |
1113 |
- switch on GM Advective form in global_ocean.cs32x15 and update output.txt |
1114 |
o model/src: |
1115 |
- fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run. |
1116 |
o tutorial_tracer_adjsens |
1117 |
- extend to NLFS and replace maskC by hFacC |
1118 |
(change reference output accordingly) |
1119 |
|
1120 |
checkpoint62r (2011/01/24) |
1121 |
o testreport: |
1122 |
- add option -deloutp (-do) to remove output file after successful run |
1123 |
- add option -mfile (-mf) for MPI machile-file and for each test-exp, |
1124 |
extract exact list of procs from this file ; adjust COMMAND by |
1125 |
replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs. |
1126 |
o pkg/ecco: replace old ineffective way of penalizing deviations from |
1127 |
first guess (of obcs) with code by Matt Mazloff |
1128 |
o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without |
1129 |
exf/cal |
1130 |
- ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl |
1131 |
and handle case of obcs?period == 0 |
1132 |
Not affected by these changes: There is still an inconsistency in |
1133 |
the computation of start/endrec for the obcs variables for ALLOW_CAL |
1134 |
defined (see comment by Menemenlis, 7-Mar-2003) |
1135 |
- make S/R ctrl_get_gen_rec return something meaningful even if |
1136 |
ALLOW_CAL is not defined |
1137 |
- ctrl_getobcs?: simplify code so that it does not need to use |
1138 |
S/R exf_swapfields |
1139 |
o testreport: |
1140 |
allow to test MPI with different number of processors for each experiment: |
1141 |
create file "SIZE.h.mpi" in each build dir. |
1142 |
Note: update of "-command" argument not yet implemented. |
1143 |
o model/src, pkg/autodiff, pkg/ecco, pkg/seaice: |
1144 |
alleviate the need for additional 3D tapes when using |
1145 |
the non-inear free surface in the adjoint. This is done |
1146 |
by adding an 'update' of hfacc etc. to their current |
1147 |
value at the beginning of forward_step.F. |
1148 |
o pkg/seaice |
1149 |
seaice_lsr: move stress-divergence computations out of outer pseudo- |
1150 |
timestepping loop |
1151 |
o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD' |
1152 |
up, so that the calls of the ctrl_* subroutines are really at the end |
1153 |
of the routine. |
1154 |
o pkg/gmredi: |
1155 |
allow to specify a 2-D horizontal map and a 1-D vertical profil |
1156 |
as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity. |
1157 |
o pkg/seaice: |
1158 |
move lsr iterations from seaice_dynsolver to seaice_lsr. |
1159 |
o pkg/seaice: |
1160 |
reduce memory footprint of seaice mutldim advection tapes, |
1161 |
by using a 2D tape independent of the generic_advdiff ones, |
1162 |
and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc. |
1163 |
|
1164 |
checkpoint62q (2010/12/29) |
1165 |
o model/src: |
1166 |
- check horizontal grid-spacing for unset or zero/negative values. |
1167 |
- change AD test hs94.1x64x5 to be truly a 2-D set-up. |
1168 |
o pkg/flt: |
1169 |
- use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR |
1170 |
- precision of input and output files set according to readBinaryPrec |
1171 |
and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits. |
1172 |
- initial float position from tiled file was not converted to index space |
1173 |
(looks like a bug): fixed to make it similar to initial pos. global file. |
1174 |
o global_ocean.cs32x15: |
1175 |
change SIZE.h of AD set-up to get same tiling as with MPI. |
1176 |
Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11) |
1177 |
o model/src: |
1178 |
add flag to control printing of domain fields (bathymetry, hFac ...) in |
1179 |
ini_mask_etc (call to plot_fieds_xy*). |
1180 |
o pkg/thsice: |
1181 |
if useEXF, some forcing fields are not valid in overlap: fixed by computing |
1182 |
over the interior only + apply EXCH at the end (like with SEAICE advection). |
1183 |
o pkg/mdsio: |
1184 |
- add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer |
1185 |
to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS. |
1186 |
- change barrier call for safe multi-threads access to 3-D shared buffer. |
1187 |
- MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones) |
1188 |
- replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and |
1189 |
remove the 4 S/R MDS_PASS_WH_R4/8toRL/S. |
1190 |
o pkg/flt: |
1191 |
- add fourth-order Runge-Kutta integration |
1192 |
- add basic exch2 support (only 1 facet supported so far!) |
1193 |
o pkg/mdsio+rw: |
1194 |
new S/R to read local (or tile independent) vector (read counterpart of |
1195 |
mds_writevec_loc, and front-end write_glvec_rl/rs). |
1196 |
o global_ocean.cs32x15: additional input_ad.seaice experiment |
1197 |
that uses pkg/seaice rather than pkg/thsice. |
1198 |
(using multidim advection for seaice) |
1199 |
o towards more F95 syntax for array specification in namelist: |
1200 |
- change "data.diagnostics" (data.ptracers was changed before checkpoint62p) |
1201 |
of all verification experiments. |
1202 |
e.g.: line: fields(1,3)='ETAN ','ETANSQ ', |
1203 |
was changed to: fields(1:2,3)='ETAN ','ETANSQ ', |
1204 |
- finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles |
1205 |
o global_ocean.cs32x15: additional input.seaice experiment |
1206 |
that uses pkg/seaice rather than pkg/thsice. |
1207 |
|
1208 |
checkpoint62p (2010/12/17) |
1209 |
o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it |
1210 |
to THSICE_SIZE.h to avoid conflict with pkg/seaice. |
1211 |
o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint. |
1212 |
allow for use of multim. advection in seaice adjoint. |
1213 |
o pkg/seaice: add diagnostics for snow precipitation and sublimation flux |
1214 |
- first attempt to close budgets by taking into account the freshwater |
1215 |
flux implied by the sublimation of snow and ice. So far only the |
1216 |
volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag |
1217 |
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET |
1218 |
o eesupp/src: |
1219 |
new S/R with new option (NML_EXTENDED_F77) to change array specification |
1220 |
from F95 standard to commonly accepted extended F77 form. |
1221 |
This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5) |
1222 |
and to revert back to the original syntax (with -DNML_EXTENDED_F77) |
1223 |
for less tolerant f77 compiler (e.g., pgf77, g77). |
1224 |
o globalFiles: |
1225 |
commented out in parameter file "data" since it's not safe with MPI |
1226 |
(e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much |
1227 |
in this case); no longer commented out in restart test (tst_2+2). |
1228 |
o add adTapeDir to specify a special directory where adjoint tapes are |
1229 |
written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05 |
1230 |
and cannot be used together with mdsioLocalDir. |
1231 |
o nesting pkgs: |
1232 |
- packages_init_variables : put call to OBCS_INIT_VARIABLES in last position |
1233 |
- update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) |
1234 |
- add parameter files + utils dir + output from short run on beagle. |
1235 |
o pkg/seaice: |
1236 |
fix seaice_growth.F store directives; update results of exp. lab_sea.ad |
1237 |
o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid |
1238 |
unnecessary copying in adjoint code, requires new parameter NMAX_ITER |
1239 |
|
1240 |
checkpoint62o (2010/11/25) |
1241 |
o pkg/exf: |
1242 |
- change CPP option EXF_VERBOSE to run-time logical param exf_verbose. |
1243 |
o pkg/seaice: |
1244 |
- seaice_ocean_stress: split a loop for better vectorization of the |
1245 |
adjoint code |
1246 |
- seaice_growth.F: fix bug in conservation of freshwater connected to |
1247 |
capping of heff, put contribution into d_HEFFbyNEG |
1248 |
- replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat |
1249 |
by something more sensible (parameters that are what their name implies) |
1250 |
- change some defaults, so that by default exf-parameters are used for |
1251 |
things like rhoAir, cpAir,latent/sensible heat parameters, in order |
1252 |
to reproduce the old results, many data.seaice now contain funny values |
1253 |
for cpAir and latent heat of sublimation |
1254 |
o packages_readparms.F: move exf_readparms up in line so that |
1255 |
exf-parameters are visible for other packages (e.g. seaice) |
1256 |
o debugMode & debugLevel=2: |
1257 |
- differentiate between debugMode & debugLevel=2: |
1258 |
debugMode: controls printing of debug messages (sequence of S/R calls). |
1259 |
debugLevel: controls printing of algorithm intermediate results and stats. |
1260 |
- remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2"; |
1261 |
=> allows to print debug-stats without all sequence of call messages. |
1262 |
- switch control of debug print from debugLevel to debugMode in many S/R. |
1263 |
o pkg/obcs (obcs-sponge): |
1264 |
fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the |
1265 |
call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge) |
1266 |
o pkg/generic_advdiff: |
1267 |
- record overlap minimum size for each advection scheme; |
1268 |
- refine criteria on overlap minimum size; |
1269 |
- check and stop (in gad_check) if overlap size is too small. |
1270 |
o pkg/obcs: |
1271 |
- with ptracers: remove multiple calls to obcs_apply_ptracer (only done |
1272 |
once, in ptracers_implicit.F) |
1273 |
- with seaice: remove test on empty file name in obcs_apply_seaice (always |
1274 |
apply OB values when tile has OB) |
1275 |
o model/src, coriolis setting: |
1276 |
- integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical |
1277 |
useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from |
1278 |
files (selectCoriMap=3) with any grid. |
1279 |
- add parameter "fPrime" for constant second Coriolis coeff (default=0). |
1280 |
o pkg/seaice/seaice_growth.F: |
1281 |
a few cosmetic changes that reduce the number of lines of code |
1282 |
o pkg/obcs: add boundary conditions following Stevens (1990) |
1283 |
- the code follows old MOM/NAOSIM code |
1284 |
- so far it is only implemented for the eastern and western boundaries |
1285 |
and NOT for pTracers |
1286 |
o pkg/rbcs: |
1287 |
- replace rbcsInIter by rbcsForcingOffset, the time in seconds at the |
1288 |
beginning of the first rbcs forcing period. |
1289 |
- add option rbcsSingleTimeFiles that makes rbcs read forcing data like the |
1290 |
offline package, i.e., one file per time, labeled by iteration number; |
1291 |
deltaTrbcs sets the timestep with which the data was generated; |
1292 |
rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset. |
1293 |
- rbcsForcingCycle=0 makes forcing non-cyclic. |
1294 |
- make arithmetic safe for negative times and odd forcing periods. |
1295 |
|
1296 |
checkpoint62n (2010/11/09) |
1297 |
o pkg/seaice: |
1298 |
fix masking in free-drift S/R ; update results of exp. lab_sea.fd |
1299 |
o pkg/obcs: |
1300 |
New S/R to copy tracer value from the OB location to narrow band region |
1301 |
(width = same as overlap) beyond the OB: preserve OB value (needed for |
1302 |
high-order scheme) which were overwritten by EXCH call if in overlap |
1303 |
region. Applied to theta, salt, ptracer and advected seaice variables. |
1304 |
With seaice: use maskInC in similar way as in gad_advection.F, |
1305 |
in seaice_advection.F and advect.F. |
1306 |
Update output of experiment seaice_obcs and change exp4 to test OBCS with |
1307 |
4th order Adv.Scheme. for pasive salt and ptracer. |
1308 |
o tools/genmake2: |
1309 |
- when looking for an optfile (not specified), only search for Fortran compiler |
1310 |
(remove sym-link test + setting of CPP + makedepend check + C-compiler check) |
1311 |
- in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm |
1312 |
(instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong) |
1313 |
- set default for CPP to "cpp -traditional -P" (was the case without specifying |
1314 |
an optfile, but otherwise default was just "cpp". |
1315 |
- comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from) |
1316 |
- when "CC" is not set in the optfile, look for possible C compiler |
1317 |
(instead of just setting CC=cc) |
1318 |
- put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes: |
1319 |
=> add a ".F" to ".o" rule for source files with no "#include" (such as |
1320 |
port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS. |
1321 |
- move gfortran before g77 in list of possible Fortran compiler (consistent |
1322 |
with reference compiler switch from g77 to gfortran) |
1323 |
o pkg/seaice: |
1324 |
o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to |
1325 |
seaice_check that stops the model, when the CPP flag is used. |
1326 |
o seaice_growth.F: make capping of ice volume conserving by returning the |
1327 |
capped ice as freshwater to EmPmR. This does not change the verification |
1328 |
experiments but will change runs where the capping is acutally active |
1329 |
o change reference platform+compiler from faulks+g77 to baudelaire+gfortran |
1330 |
(except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5, |
1331 |
global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD), |
1332 |
lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd) |
1333 |
o tools/genmake2: |
1334 |
- merge genmake_warnings & genmake_errors into 1 log file: "genmake.log") |
1335 |
- change DUMPSTATE default to false (can use "-ds" option to switch it to T) |
1336 |
- clean previous genmake log files before anything else. |
1337 |
- change Makefile to remove testreport log files (*.tr_log) and genmake log |
1338 |
files only with "CLEAN" target (instead of "Clean"); |
1339 |
o pkg/generic_advdiff: |
1340 |
Change OBCS in multiDim advection (gad_advection.F): |
1341 |
Use maskInC to prevent intermediate update of tracer-field in OB regions, |
1342 |
thus keeping current-time-step OB values; and remove the call to OBCS_APPLY |
1343 |
which were applying future time-step OB values. |
1344 |
This way, all explicit calculations use current-time-step OB values |
1345 |
(simpler and more consistent). |
1346 |
Affects results when set-up uses time-varying OBC and multi-dim advection; |
1347 |
update output of experiment seaice_obcs. |
1348 |
o pkg/seaice: |
1349 |
move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h: |
1350 |
this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH & |
1351 |
SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY. |
1352 |
Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY |
1353 |
but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp |
1354 |
unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h) |
1355 |
o pkg aim (2010/10/26): |
1356 |
- Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation |
1357 |
formulation with obliquity, eccentricity, ... as run-time parameters, |
1358 |
- Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and |
1359 |
upward shortwave radition at the surface (all-sky and clear-sky). |
1360 |
o pkg/obcs: |
1361 |
- writing sections with globalFiles=T does not work: switch to tiled-files |
1362 |
when writing sections for OBCS (change pkg/rw/write_rec.F accordingly). |
1363 |
- fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F |
1364 |
- apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs |
1365 |
|
1366 |
checkpoint62m (2010/10/21) |
1367 |
o pkg/seaice: vectorize seaice_solve4temp.F |
1368 |
- move iterations loops outside of i/j-loops |
1369 |
- requires 2D arrays for TB and effConduct |
1370 |
- add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is |
1371 |
modified in this routine |
1372 |
- a little bit of clean up, adjusting indentation, etc. |
1373 |
- replaced a few TEN**a by exp(a*log(10.)) in new code for better |
1374 |
performance and '**TWO' by '**2' (because TWO is a float), |
1375 |
replaced ONE, ZERO |
1376 |
o eesupp/src: |
1377 |
fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube |
1378 |
o pkg/seaice/seaice_growth.F |
1379 |
Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and |
1380 |
merging process. The merged routine has two branches, and one activates the 'evolution' |
1381 |
branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now). |
1382 |
In summary, here is what the '10/10 revision' did consist of |
1383 |
part 1: seaice_growth.F revisions 1.71 to 1.75 |
1384 |
- Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged. |
1385 |
The emphasis here was on improving readability (e.g. by trying to use meaningful |
1386 |
variable names) and modularity (e.g. by adding arrays to store heff etc. updates). |
1387 |
part 1.5: |
1388 |
- revising the lab_sea experiment to make it a more useful (i.e. stable |
1389 |
and representative of an actual model run). This was done by generating a |
1390 |
(winter) pickup to start from, switching back the main experiment dynamic |
1391 |
solver from evp to lsr, having one of the experiments use the free drift solution. |
1392 |
part 2: seaice_growth.F revisions 1.76 to 1.85 |
1393 |
- Sorting out hard-coded constants that prevented heat and fresh water conservation. |
1394 |
- Sorting out the various fields units and sign (set early on and reset at the end) |
1395 |
to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and |
1396 |
fresh water stock is 'effective ice meters', and >0 implies more ice/snow. |
1397 |
- Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks, |
1398 |
and simplifying logical expressions to further improve readibility. |
1399 |
part 3: seaice_growth.F revisions 1.86 to 1.89 |
1400 |
- Re-organize the blocks of code more logically. |
1401 |
- Merging the '_if.F' pieces that add something new. |
1402 |
o pkg/thsice: |
1403 |
- vectorize thsice_solve4temp and thsice_get_exf. |
1404 |
Problem: thsice_solve4temp has an unvectorizable statement that |
1405 |
might also be problematic for TAF |
1406 |
- thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This |
1407 |
does not change the verifcation experiment, but will change all |
1408 |
experiments that have this flag undefined (not tested in verification); |
1409 |
a little reorganization to save a few 2D fields and recomputations |
1410 |
- 1st step of revisiting thsice adjoint (major recomp. sorted out) |
1411 |
- 2nd step: fix some store dirs |
1412 |
o seems to work somewhat, i.e. using ifort but not g77 |
1413 |
o likely cause are incomplete init. or recomputation |
1414 |
o start verification/global_ocean.cs32x15/input_ad.thsice |
1415 |
o pkg/obcs: add support for exch2 |
1416 |
- the position of the boundary and prescribed values are specified using |
1417 |
a global domain with exch2 facets stacked |
1418 |
- in x for N,S boundaries (like W2_mapIO=-1) |
1419 |
- in y for E,W boundaries (so E,W boundaries do not overlap) |
1420 |
o pkg/mdsio: add support for writing global sections with exch2 |
1421 |
file layout is as for obcs described above: |
1422 |
- for x-z sections, facets are stacked in x (like W2_mapIO=-1) |
1423 |
- for y-z sections, facets are stacked in y |
1424 |
o pkg/thsice: |
1425 |
- change a few routines for better vectorization: thsice_albedo.F, |
1426 |
thsice_step_temp.F, and in thsice_calc_thickn.F. Results are |
1427 |
not affected, but in particular the latter routine has changed |
1428 |
dramatically (not necessarily easier to read now). |
1429 |
- re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops |
1430 |
iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF. |
1431 |
o verification/lab_sea: |
1432 |
- overhaul of the forward model experiments. The main motivation |
1433 |
for this revision is that lab_sea has proven quite fragile (when |
1434 |
changing the sea-ice code, and switching platforms) to a point |
1435 |
when failures were very hard to attribute to specific code problems. |
1436 |
- the suspected reason for this fragility is noise amplification by evp so, |
1437 |
to start with, we decided to replace evp with lsr in the main experiment. |
1438 |
- the input.lsr experiment thus became obsolete and was removed. |
1439 |
- it was replaced with the input.fd experiment that uses an |
1440 |
analytical "free drift" solution as the ice velocity field. |
1441 |
- Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp) |
1442 |
will hopefully allow us to discriminate problems due to dynamic solvers |
1443 |
from problems due to the thermodynamic code. input.salt_plume (lsr) allows |
1444 |
us to test additional options, along with the salt plume package. |
1445 |
- Finally a pickup was generated (at the end of a one year run) to |
1446 |
make the tests more representative of an actual model run. Previously |
1447 |
the tests starting point was a 1m thickness of ice everywhere. |
1448 |
o pkg/seaice: |
1449 |
- introducing S\R seaice_freedrift.F that compute the |
1450 |
analytical solution to an approximate ice momentum |
1451 |
equation (i.e. the simple stress/coriolis balance). |
1452 |
- define SEAICE_ALLOW_FREEDRIFT to trigger the computation |
1453 |
of the free drift velocity field, and enable its use. |
1454 |
To actually use the free drift solution as the model ice |
1455 |
velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice. |
1456 |
o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata" |
1457 |
|
1458 |
checkpoint62l (2010/10/04) |
1459 |
o pkg/seaice: |
1460 |
-fix the USE_ORIGINAL_SBI version (for variable freezing point); |
1461 |
-use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new |
1462 |
version (with USE_ORIGINAL_SBI undef); |
1463 |
o add hooks for new packages OASIS, the package will follow |
1464 |
(hooks exclude the seaice pkg for now) |
1465 |
o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO |
1466 |
Option to use mdsio_read_whalos.F/mdsio_write_whalos.F, |
1467 |
rather than mdsio_readvector.F/mdsio_writevector.F, within |
1468 |
adread_adwrite.F to read/write adjoint-related tapes to disk. |
1469 |
o eesupp and pkg/mdsio: ALLOW_WHIO |
1470 |
Option to write/read 2D fields to files including tiles halos. |
1471 |
The main purpose is for adjoint related "tape I/O". |
1472 |
The secondary purpose is for debugging phases. |
1473 |
A word on those rather specifically intended purposes. |
1474 |
The code was meant to be stripped down to the bare minimum. |
1475 |
Typically, there is a unique and basic mapping to the global |
1476 |
buffer (tile by tile, then proc by proc, then level by level), and |
1477 |
byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not |
1478 |
meant to generate user friendly outputs of various shapes and forms. |
1479 |
Rather it is intended, for the knowledgeabale developers, |
1480 |
to be largely independent of the many mdsio options, to allow |
1481 |
outputs of tiles+halos in debugging phases and in adjoint runs, |
1482 |
and to allow some flexibility in tuning (adoint) I/O depending on each |
1483 |
file system behavior. With regard to tuning, most of the potential knobs |
1484 |
(to leave files open, to allocate the I/O indep. of usesinglecpuio, |
1485 |
to specify directories, to specify the typical size of I/O calls, etc.) |
1486 |
are not yet included, and will be added if they prove useful. |
1487 |
o pkg/seaice: |
1488 |
fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F |
1489 |
o pkg/seaice: |
1490 |
new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty |
1491 |
code (seaice_budget_ice_if.F) which enable to recover old standard |
1492 |
code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined. |
1493 |
temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F. |
1494 |
o model/src (rStar): |
1495 |
use simple average (not area weighted) of rStarFac at U,V point when using |
1496 |
vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection) |
1497 |
update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20. |
1498 |
|
1499 |
checkpoint62k (2010/09/17) |
1500 |
o adjoint |
1501 |
* changed verification/global_ocean.cs32x15 ; adjoint now tests |
1502 |
Adams-Bashforth 3 + NLFS + RSTAR |
1503 |
* some more modifs required for ECCO-GODAE v4 |
1504 |
o pkg/seaice |
1505 |
add SEAICE_AGE_VOL option to use volume instead of area for |
1506 |
integrating SEAICE_AGE |
1507 |
o model/src: |
1508 |
first check-in of sigma & hybrid-sigma coordinate code ; also includes |
1509 |
non-linear free-surface parts ; but pressure-gradient not yet coded. |
1510 |
o pkg/ptracers: |
1511 |
option for ptracer to convert Salt Relax into additional EmP. |
1512 |
tested in exp. global_ocean.90x40x15.dwnslp (update output) |
1513 |
|
1514 |
checkpoint62j (2010/08/25) |
1515 |
o pkg/ggl90: |
1516 |
other minor changes: remove 3-D temp array gTKE (+ add argument myIter) |
1517 |
o pkg/dic: car_flux.F, phos_flux.F |
1518 |
- reduce number of exp-calls in order to improve performance |
1519 |
- clean up a little (replace fields by their macros, etc., fix |
1520 |
typo in CPP-flag) |
1521 |
o pkg/ggl90: minor changes |
1522 |
- GGL90diffKrS was removed --> always use GGL90diffKr |
1523 |
- GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV |
1524 |
- hack of mxlMaxFlag=2 --> ensure mixing between first and second level |
1525 |
(commented out for now) |
1526 |
- change in max/min operations to ensure that smoothing is ok |
1527 |
- smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr) |
1528 |
- always use diffKrNrT as background profile (i.e. never use diffKr field) |
1529 |
o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj) |
1530 |
o pkg/dic: |
1531 |
- model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better |
1532 |
vectorization |
1533 |
- small bug fix in insol for the unlikely case of a cartesian grid |
1534 |
- towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F |
1535 |
+ now vectorize, which also removes adjoint recomputations; |
1536 |
+ replace integer maksp1 by _RL maskp1 |
1537 |
+ replace a**x by exp(x*log(a)) in phos_flux.F for speed |
1538 |
|
1539 |
checkpoint62i (2010/07/21) |
1540 |
o pkg/flt: |
1541 |
- with OBCS: stop floats which enter the OB region |
1542 |
o model/src: |
1543 |
- use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones) |
1544 |
for implicit vertical advection. |
1545 |
o pkg/seaice: |
1546 |
- account for melting in seaice age evolution. |
1547 |
- remove double counting of seaice ridging effect on seaice age. |
1548 |
|
1549 |
checkpoint62h (2010/06/18) |
1550 |
o pkg/exch2: |
1551 |
- remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1). |
1552 |
o tools/genmake2 |
1553 |
- remove "-pdefault" option: redundant with the use of "packages.conf"; |
1554 |
- remove file pkg/pkg_default : set the default as a pkg group |
1555 |
("default_pkg_list") defined in pkg/pkg_groups; |
1556 |
- fix for case pkg/pkg_depend is missing (was hanging before); |
1557 |
- add option "-pgroups" to specify a different pkg_groups than the default. |
1558 |
o verification/adjustment.cs-32x32x1: |
1559 |
add a "minimal" set-up test (code_min & input_min) which only compiles |
1560 |
eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc. |
1561 |
o tools/genmake2 |
1562 |
- extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg])) |
1563 |
- fix details of checking for mnc & profile pkg when NetCDF is unavailable. |
1564 |
o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these |
1565 |
files are nearly the same anyway. |
1566 |
Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04: |
1567 |
- redefinition of tau(i,i) (by a factor of ustar) |
1568 |
- 1./exf(Const/T) -> exf(-Const/T) (big change in the results) |
1569 |
- replace rhonil by rhoConstFresh in computation of evap (bug fix) |
1570 |
- replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results) |
1571 |
- replace |
1572 |
rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh ) |
1573 |
shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j) |
1574 |
by |
1575 |
shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh ) |
1576 |
(changes results) |
1577 |
-> exf_bulkformulae v1.22, |
1578 |
update verification experiments lab_sea, offline_exf_seaice, seaice_obcs |
1579 |
(lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13, |
1580 |
output.txt 1.63 |
1581 |
offline_exf_seaice: output.seaicetd.txt 1.7 |
1582 |
seaice_obcs: output.txt 1.10) |
1583 |
Step 2: do the actual merge and remove exf_bulk_largeyeager04.F |
1584 |
-> exf_bulkformulae v1.23, |
1585 |
unfortunately requires updating lab_sea.salt_plume (6 matching digits), |
1586 |
and global_ocean.cs32x15.icedyn (only 11 matching digits) |
1587 |
Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice. |
1588 |
o adjoint of exch-1: |
1589 |
- pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list) |
1590 |
(note: was already like this when using EXCH-2) and remove flow dir |
1591 |
and hand-written AD version of high-level EXCH S/R (pkg/autodiff); |
1592 |
- provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow); |
1593 |
- update pkg/exch2 diff list. |
1594 |
|
1595 |
checkpoint62g (2010/05/19) |
1596 |
o eesupp/src (exch-1): |
1597 |
- split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F) |
1598 |
and remove argument "simulationMode"; same thing for all exch_*rx_cube.F |
1599 |
(renamed to exch1_*rx_cube.F). |
1600 |
- change accordingly exch_*_rx.template and AD version in pkg/autodiff |
1601 |
to call new exch1 S/R ; update Makefile and .cvsignore. |
1602 |
- replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove |
1603 |
exch2_xy_rx later) |
1604 |
Note: after updating your code, need to run "make clean" in eesupp/src |
1605 |
o test experiment bottom_ctrl_5x5: |
1606 |
new output_adm.txt with fewer grdchk & less monitor output. |
1607 |
o model/src: |
1608 |
remove the call to ini_cori in initialise_varia.F (just keep the usual one |
1609 |
in initialise_fixed.F). More consistent with coriolis & horizontal grid |
1610 |
beeing treated in the same way (ini_grid is not called a 2nd time). |
1611 |
o pkg/exf: |
1612 |
- rewrite exf_bulk_largeyeager04.F for better vectorization, changes |
1613 |
global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated |
1614 |
- fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now) |
1615 |
- cosmetic changes to exf_bulkformulae.F to make it look more like |
1616 |
exf_bulk_largeyeager04.F |
1617 |
o eesupp/src (exch-1): |
1618 |
- Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1). |
1619 |
- Separate buffer filling and MPI sending: allow EXCH-1 to work for local |
1620 |
array (non-shared) when using MPI+MTH. Also reduces number of BARRIER |
1621 |
(even without using MPI). |
1622 |
- Message mode: move RecvAck setting (indicator of buffer being ready) |
1623 |
from send_put to recv_get S/R (was useless before, but not sure if |
1624 |
it's much more useful now); |
1625 |
- Switch the order of sync: MPI-proc 1rst and then threads; |
1626 |
- take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead. |
1627 |
- fix AD code for communication mode ='get' (but not used). |
1628 |
o model/src: |
1629 |
initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does |
1630 |
not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp). |
1631 |
o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API |
1632 |
o pkg/ctrl: require a specific set of control variables and exf-flags for |
1633 |
adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied) |
1634 |
o model/src: |
1635 |
a) 1rst version of a new driver S/R to turn-off output freq and flags after the |
1636 |
1rst forward sweep, to avoid over-writing output files during recomputations |
1637 |
recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?) |
1638 |
b) 2nd version: |
1639 |
- add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO); |
1640 |
- switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast, |
1641 |
writePickupAtEnd) + seaice & ptracers output; |
1642 |
- do not switch off MNC flags (otherwise, won't get admonitor netcdf file) |
1643 |
o model/src: |
1644 |
- new S/R rotate_uv2en_rl (..._rs) that rotates vector fields. |
1645 |
o pkg/exch2: |
1646 |
- remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ; |
1647 |
- add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch). |
1648 |
o pkg/autodiff & exch2: |
1649 |
process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF |
1650 |
(for now, only if ALLOW_EXCH2 is defined). |
1651 |
o pkg/autodiff: |
1652 |
- include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F |
1653 |
(not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly. |
1654 |
+ clean-up comments (_RS is not always real*4) |
1655 |
- fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R) |
1656 |
- add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2: |
1657 |
was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs. |
1658 |
o testreport (AD-tests): |
1659 |
no longer link files from dir "../input" (1rst link files from |
1660 |
"../input_ad.[xx]" if secondary test "xx" and then from "../input_ad") |
1661 |
|
1662 |
checkpoint62f (2010/04/29) |
1663 |
o model/src/the_main_loop.F: |
1664 |
adjust store directives for seaice evp and multicategory according to |
1665 |
pkg/ecco/the_main_loop.F |
1666 |
o adjoint: |
1667 |
global_sum_ad was incomplete (noted many times by many people ;) |
1668 |
nice description by Jean U. as follows: |
1669 |
* allreduce(var) in global_sum.F can be interpreted as |
1670 |
reduce(sum) followed by broadcast of sum. |
1671 |
* The adjoint of that is |
1672 |
sum(adjoint) followed by broadcast(summed adjoint value) |
1673 |
or in other words, allreduce(sum, adjoint vars) |
1674 |
We were missing the sum(adjoint)! |
1675 |
Benign, except(!) for "global" scalars appearing in tile loops (bi,bj) |
1676 |
(noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset). |
1677 |
The fix should produce 16-digit accuracy between |
1678 |
single-CPU multi-tile (e.g. nSx=2, nPx=1) and |
1679 |
multi-CPU single-tile (e.g. nSx=1, nPx-2) |
1680 |
We'll probably change this yet again shortly |
1681 |
o eesupp/src: |
1682 |
- fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?) |
1683 |
o pkg/icefront |
1684 |
- ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving |
1685 |
specification of addmass array based on a 2D field, which is added |
1686 |
at bottommost wet level at each horizontal location. |
1687 |
o model/src: |
1688 |
horizontal grid initialisation (other than curvilinear): add code for Exch2 IO |
1689 |
layout; (not always compatible with delX,delY setting; commented out for now). |
1690 |
o pkg/exch2: |
1691 |
change tile to processor setting (case nSy*nPy > 1): allows default model mapping |
1692 |
(myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config. |
1693 |
|
1694 |
checkpoint62e (2010/04/15) |
1695 |
o pkg/obcs: |
1696 |
- fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert). |
1697 |
o pkg/dic: |
1698 |
-fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up; |
1699 |
(note: not presently tested in any forward verification exp.) |
1700 |
update tutorial_global_oce_biogeo AD output file. |
1701 |
o pkg/exf: |
1702 |
- account for the variation of albedo as a function of zenith angle |
1703 |
by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h |
1704 |
o build_options: |
1705 |
- rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas" |
1706 |
o pkg/dic: |
1707 |
change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart: |
1708 |
- use binary pickup file for restart; |
1709 |
- initialise atmos-CO2 box from dic_pCO2 parameter; |
1710 |
- fix multi-threaded. |
1711 |
o pkg/rbcs: |
1712 |
- clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ; |
1713 |
change (+ fix IO calls) type of array RBC_mask from _RL to _RS. |
1714 |
- add RBCS to exp4 passive tracer 01 (rbcs was previously untested) |
1715 |
and update output.txt |
1716 |
o pkg/kpp: |
1717 |
- add diagnostics for KPP non-local flux of Temp, Salinity and pTracers; |
1718 |
- change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS |
1719 |
(= ratio of KPP non-local (salt) flux relative to surface-flux) when |
1720 |
using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat '); |
1721 |
- change pkg/offline to read-in average KPPghat*KPPdiffKzS from file |
1722 |
KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile). |
1723 |
o pkg/offline: |
1724 |
fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor |
1725 |
(bug was added in version 1.10 on 2007-08-23). |
1726 |
o pkg/offline: |
1727 |
- no need to specify periodicExternalForcing, etc ... to use offline pack |
1728 |
- offline input files no longer just single prec --> parameter offlineLoadPrec |
1729 |
o verification/lab_sea: |
1730 |
change AD test to multi-tile setup and update all 4 AD output. |
1731 |
NOTE: while cost function values remain very similar, |
1732 |
gradients are very different, although gradient checks are self-consistent |
1733 |
Should try to get to the bottom of this (cost function summation order?) |
1734 |
o pkg/dic: |
1735 |
in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid |
1736 |
a weakness of TAF that drops part of double precision in log10 derivative. |
1737 |
<= changes removed since problem has been fixed in current TAF version 1.9.71 |
1738 |
update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo. |
1739 |
o pkg/ecco: |
1740 |
add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F |
1741 |
update all 4 lab_sea AD output. |
1742 |
|
1743 |
checkpoint62d (2010/03/22) |
1744 |
o build_options: |
1745 |
remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles. |
1746 |
o remove unbalanced quote (single or double) in commented line of source code |
1747 |
(may cause some warning with some preprocessor/makedepend versions). |
1748 |
o pkg/seaice: |
1749 |
fix seaice_model.F for adjoint (gael) and update AD results of experiments |
1750 |
lab_sea (std + evp + noseaicedyn) and offline_exf_seaice. |
1751 |
o testreport: |
1752 |
add option '-runonly' (short: '-ro') to just do the run part (without make). |
1753 |
o eesupp: remove JAM communication code (obsolete). |
1754 |
o add option to genmake2 & testreport to switch "_RS" type to "real*4" |
1755 |
(if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return |
1756 |
to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1 |
1757 |
(update also the output). |
1758 |
|
1759 |
checkpoint62c (2010/03/02) |
1760 |
o tools/build_options : |
1761 |
move (some) old optfiles from build_options/ to build_options/unsupported/ |
1762 |
o model/src and pkg/exf |
1763 |
surface relaxation -- separating data and data.exf options |
1764 |
The point is to ensure that we specify the surface relaxation |
1765 |
either in data or in data.exf (but not half and half) and to |
1766 |
avoid an accidental relaxation to 0 (which happened if a time |
1767 |
scale was specified but the file name was left empty) |
1768 |
o model/src model/inc and pkg/mom_common |
1769 |
ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity |
1770 |
=> addition to the viscosity field as computed by others schemes |
1771 |
o tools/build_options: |
1772 |
- rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile) |
1773 |
but keep the former optfile for few weeks for smooth transition |
1774 |
o pkg/ecco |
1775 |
- allow user defined cost function contributions |
1776 |
CPP: ALLOW_USERCOST_CONTRIBUTION |
1777 |
USAGE: compute contributions in cost_usercost_all.F |
1778 |
- note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. |
1779 |
the two options are complementary. |
1780 |
o pkg/smooth |
1781 |
- migration from contrib to the main repository |
1782 |
|
1783 |
checkpoint62b (2010/01/26) |
1784 |
o pkg/monitor: |
1785 |
- change back mon_printstats_rl.F & mon_stats_rl.F and add a stop |
1786 |
(in case someone forgot to update customized pieces of code) |
1787 |
o nonHydrostatic: |
1788 |
- add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested); |
1789 |
- add a simple 2-D experiment (short_surf_wave) to test it. |
1790 |
o pkg/icefront: |
1791 |
adding the shell of, and the hooks to, a new package that |
1792 |
will model melting and freezing of vertical glacier ice fronts |
1793 |
o momentum: |
1794 |
add diagnostics of momentum tendency from Hydrostatic pressure gradient |
1795 |
(without surf.pressure term: would need a 2nd filling since implicit term). |
1796 |
o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace |
1797 |
two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR |
1798 |
cannot deal with the former |
1799 |
o cleaning: |
1800 |
- remove all (except OpenAD) old TLM output from results_ad dirs. |
1801 |
- remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R) |
1802 |
- comment out maskH definition (replaced by maskInC) |
1803 |
o pkg/monitor: |
1804 |
- change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl |
1805 |
& mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs. |
1806 |
|
1807 |
checkpoint62a (2010/01/15) |
1808 |
o model/src: |
1809 |
- bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4) |
1810 |
o pkg/diagnostics: |
1811 |
- add optional level number diagnostics (i.e., level number to be define |
1812 |
explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X". |
1813 |
- strictly check for valid parser-code(10) ; |
1814 |
- check if adding diag to the list from the right place. |
1815 |
o pkg/longstep: |
1816 |
- change parameters and fix tracer conservation with rstar/nonlinear free surface |
1817 |
o diagnostics: |
1818 |
- in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer |
1819 |
S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics. |
1820 |
o pkg/diagnostics: |
1821 |
- Add option for writing vertical integral (sum of selected levels) of an output |
1822 |
field instead of writing output field levels. Activate this option on a per |
1823 |
output-file basis, by setting the 2nd character of fileflag to 'I'. |
1824 |
- Add field-specific information relative to level integral in 3rd postion |
1825 |
of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate |
1826 |
vertically (x level-thickness x hFac), "r"=same but without hFac. |
1827 |
o do_the_model_io: |
1828 |
- pass end-of-model-run flag as argument, from forward_step to diagnostics_write: |
1829 |
in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before |
1830 |
writing pickups and stopping. |
1831 |
o pkg/diagnostics (for now, only with mdsio): |
1832 |
- write time information to meta file (and modify accordingly rdmds.m) : |
1833 |
time-averaged diagnostics output: write starting and ending time of the |
1834 |
time-averaging interval ; snap-shot diagnostics output remains unchanged; |
1835 |
o pkg/timeave: |
1836 |
- S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously |
1837 |
always Nr), now assumed to be equal to number of levels of averaged field; |
1838 |
only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F |
1839 |
o pkg/sbo: |
1840 |
- fix ocean bottom pressure global-average & 2-D time-ave output (was |
1841 |
neither initialised nor filled). |
1842 |
- add starting iteration in suffix of global-average output file |
1843 |
(to avoid over-writing the file after a restart) |
1844 |
- use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb). |
1845 |
o time-average: |
1846 |
- use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj) |
1847 |
(pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf, |
1848 |
ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice) |
1849 |
this fix DIC_COST cumulative-time array (previously: bi,bj,k) |
1850 |
- fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice) |
1851 |
- fix missing accumulation for pkg/opps. |
1852 |
- cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0) |
1853 |
(pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81); |
1854 |
- fix initialisation of time-ave vars and do only full time-step increment |
1855 |
(i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81); |
1856 |
o pkg/layers: |
1857 |
- use standard RW pkg S/R to write the output |
1858 |
and remove local write_fld version (which had a problem). |
1859 |
- use simple cumulative-time array (no level index) to fix time-ave S/R calls. |
1860 |
- fix LAYERS_CALC argument list. |
1861 |
o pkg/timeave: |
1862 |
- store cumulative-time in a simple tiled array (drop the level index) |
1863 |
- add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array. |
1864 |
o pkg/ocn,aim_compon_interf |
1865 |
- changes for multi-threaded coupled run. (tested with ifort-11 on danton) |
1866 |
|
1867 |
checkpoint62 (2009/12/23) |
1868 |
o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output. |
1869 |
(was not previously tested in any other exp.) |
1870 |
o pkg/monitor: |
1871 |
- clean-up _RL/_RS version: add specific S/R for statistics with mask & volume: |
1872 |
mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one |
1873 |
(mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics. |
1874 |
- use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F). |
1875 |
- change del2 calculation. |
1876 |
- use interior masks (instead of maskH, <- to be remove). |
1877 |
- shorter monitor suffix for forcing stats ("forcing" instead of "extforcing"). |
1878 |
o mask & obcs: |
1879 |
- define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S). |
1880 |
- move global area computation from ini_masks_etc.F to ini_linear_phisurf.F |
1881 |
(called after packages_init_fixed) |
1882 |
o pkg/obcs: |
1883 |
- move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once. |
1884 |
Fixes bug in obcs+exf with nSx*nSy.GT.1 |
1885 |
- fix multi-tile handling in obcs balance code |
1886 |
o nonHydrostatic: |
1887 |
- Implement AB-3 for non-hydrostatic vertical momentum ; |
1888 |
(change ordering of var. stored in pickup file when using NH) |
1889 |
- move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D. |
1890 |
- add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x |
1891 |
(in prep. for new NH free surface form). |
1892 |
o pkg/obcs: |
1893 |
add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe |
1894 |
o model/src: |
1895 |
fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography |
1896 |
|
1897 |
checkpoint61z (2009/12/01) |
1898 |
o nonHydrostatic: |
1899 |
Fix missing vertical flux of vert. momentum near surface (k=1). This fixes |
1900 |
a spurious source of energy in simple baroclinic adjusment test case. |
1901 |
Update all non-hydrostatic exp output. |
1902 |
o model/src (3-d solver): |
1903 |
Change again 3-D solver free-surface RHS term when exactConserv=T: |
1904 |
simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1 |
1905 |
(which was not the case with previous formulation). |
1906 |
To recover previous version, just reset "oldFreeSurfTerm" to previous value. |
1907 |
Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW. |
1908 |
o nonHydrostatic: |
1909 |
- compatible with implicDiv2Dflow < 1 ; + implement implicit factor |
1910 |
for Non-Hydrostatic pressure gradient (similar to implicSurfPress). |
1911 |
- change 3-D solver to work with r* (for now, only with linear free-surf.) |
1912 |
- add few debug diagnostics (cg3d_x, residual) |
1913 |
o model/src: |
1914 |
fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b). |
1915 |
update output of exp. global_ocean.cs32x15.viscA4 |
1916 |
o update output of exp. global_ocean.cs32x15.icedyn after removing |
1917 |
#define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h |
1918 |
o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) |
1919 |
o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output |
1920 |
for complex grids, for now only to "state", "adstate", "adexf", "adseaice" |
1921 |
o model: add Christopher Wolfe's implemetation of the single reduction cg2d |
1922 |
(d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and |
1923 |
runtime flag useSRCGSolver. Modify verification experiment global_with_exf |
1924 |
to test this code |
1925 |
o pkg/cd_code: |
1926 |
Change defaut D-grid time-stepping to get the same for D-grid momentum as for |
1927 |
C-grid momentum. D-grid velocity used to be stepped forward in time with |
1928 |
Adams-Bashforth only on surface pressure term. Tests show that using AB on |
1929 |
D-grid coriolis term improves stability (as expected from CD-scheme paper). |
1930 |
To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h). |
1931 |
Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2), |
1932 |
lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD), |
1933 |
tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens. |
1934 |
Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2, |
1935 |
global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD. |
1936 |
o pkg/obcs: |
1937 |
- fix bug in initialisation (broken since Oct 1rst modification) |
1938 |
for useOBCSprescribe without useEXF. |
1939 |
|
1940 |
checkpoint61y (2009/11/15) |
1941 |
o pkg/seaice |
1942 |
- change (once again) the discretization for the evp solver: rather than |
1943 |
squaring the averages of strain rates, average the squares to give |
1944 |
a better approximation to VP behavior (in simple test); this breaks |
1945 |
verification experiments that use EVP (lab_sea and lab_sea.hb87) |
1946 |
--> update outputs |
1947 |
o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit) |
1948 |
to improve vectorization of adjoint code on TARGET_NEC_SX |
1949 |
o verification/vermix: |
1950 |
- change vermix to a more "classical" 1d column with high vertical |
1951 |
resolution, seasonal heat flux forcing and constant wind forcing |
1952 |
--> update outputs |
1953 |
o pkg/seaice |
1954 |
- fix diagnostics of principal stress components for EVP |
1955 |
- add optional diagnostics of non-linear convergence for LSOR solver |
1956 |
- make maximum zeta a runtime parameter |
1957 |
o model/src (3-d solver): |
1958 |
Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49), |
1959 |
which consisted in removing the Surf. Non-Hydrostatic pressure from the |
1960 |
whole column and adding it to Eta (inspired from Casualli, 1999): |
1961 |
Only affects 3-D solver initial guess and only if using ExactConserv, |
1962 |
but tests did show a degradation of solver convergence. For this reason, |
1963 |
decide to disable this piece of code. |
1964 |
to recover previous version, just set zeroPsNH = exactConserv (line 78). |
1965 |
Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW |
1966 |
o pkg/ggl90: |
1967 |
- fix previous modif (unfortunatly has not been documented here). |
1968 |
o pkg/seaice/autodiff: |
1969 |
- add CPP flag to include clipping of zeta in EVP code; |
1970 |
although clipping of zeta is not necessary for EVP and not recommended |
1971 |
it was done by default, now clipping is disabled by default |
1972 |
- modify computation and store zetaC/Z in seaice_evp for TAF |
1973 |
- add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default) |
1974 |
- change seaice_calc_viscosities/strainrates for better |
1975 |
vectorization after AD by TAF |
1976 |
- rearrange common blocks in SEAICE.h once again for easier dumps of |
1977 |
adjoint output, adjust adcommon.h and g_common.h |
1978 |
- change flux form of default advection scheme for better vectorization |
1979 |
of adjoint code |
1980 |
- modify lab_sea/input.lsr to test the flux form of default advection |
1981 |
scheme |
1982 |
o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level |
1983 |
transition in checkpoint61r) |
1984 |
|
1985 |
checkpoint61x (2009/10/19) |
1986 |
o adjoint: adding two new verification experiments |
1987 |
* tutorial_global_biogeo: an online dic sensitivity experiment |
1988 |
(work with G. Forget) |
1989 |
* tutorial_dic_adjoffline: an offline dic sensitivity experiment |
1990 |
(an update of the Dutkiewicz et al., 2006 paper) |
1991 |
Both use the same CO2FLUX cost function, but different controls |
1992 |
Gradient checks look good, but some recomp. could still be traightened out |
1993 |
Should add xx_dic control variable to test at some point |
1994 |
o model/src: |
1995 |
add run-time parameters to check and/or mask initial Temp & Salt |
1996 |
o pkg/ptracers: |
1997 |
apply zonal filter (if used) to all passive tracers |
1998 |
|
1999 |
checkpoint61w (2009/10/12) |
2000 |
o adjoint: |
2001 |
* update and finish work on adjoint of dic package (G. Forget) |
2002 |
* start adjoint of offline package |
2003 |
* bug fix for cube-sphere TLM code (active_file_g.F) |
2004 |
o tutorial_global_oce_optim: |
2005 |
now tested with 4 tiles (change data.grdchk and update output_adm.txt) |
2006 |
and add SIZE.h_mpi for MPI testing |
2007 |
o pkg autodiff |
2008 |
- fix bug in autodiff_restore |
2009 |
- make genmake2 remove comments and empty lines from ad_input_code.f in |
2010 |
order to reduce file size (new script file remove_comments_sed) |
2011 |
o allows to specify vertical profile of vertical viscosity (viscArNr) |
2012 |
o pkg autodiff |
2013 |
autodiff_ini_model_io: comment out writing of grid information to netcdf |
2014 |
files, because at this time the grid fields are a bunch of zeros |
2015 |
(this is analogous to ini_mnc_vars.F) |
2016 |
o pkg seaice/autodiff: |
2017 |
left-over from removing the 3-time-level fields: |
2018 |
- small rearrangement of common blocks (SEAICE.h) |
2019 |
- fix field declaration in order to get meaningful output in |
2020 |
adseaice.*.nc (adcommon.h) |
2021 |
o pkg obcs: |
2022 |
- go through NH code only if nonHydrostatic=T |
2023 |
- fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart) |
2024 |
- move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields |
2025 |
=> Update output of experiment seaice_obcs |
2026 |
- useOBCSbalance: code is wrong with multi-tile / proc: add a stop. |
2027 |
- fix NH+Orlanski restart (add wvel OBC value in pickup file) |
2028 |
- fix restart for useOBCSprescribe + useEXF |
2029 |
o pkg ctrl |
2030 |
- make obcs as control parameter work also with useSingleCPUio |
2031 |
- replace a few sny and snx by Ny and Nx to be consistent with |
2032 |
ctrl_set_globfld_x/yz.F |
2033 |
o pkg seaice |
2034 |
- re-introduce global field frWtrAtm for the case of |
2035 |
ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F) |
2036 |
- catch the case of an empty filename in seaice_cost_init_fixed.F |
2037 |
o pkg ecco: |
2038 |
- small bug fixes in the_main_loop |
2039 |
. fix order of monitor arguments |
2040 |
. change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY |
2041 |
. move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so |
2042 |
that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF |
2043 |
- replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the |
2044 |
imbalance diagnostics for wmean_h/sflux = 0 |
2045 |
- add actual values to f_obcsn/s/w/e in ecco_cost_final.F |
2046 |
- catch the case of empty filenames in ecco_cost_init_fixed.F |
2047 |
and ecco_readparms.F |
2048 |
- fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta) |
2049 |
to make this statement meaningfull in ecco_cost_weights.F |
2050 |
o pkg zonal_filt: |
2051 |
- change ZONAL_FILTER S/R interface (allows to filter 2-D fields) |
2052 |
- when using rStar, filter uVel*hFacW instead of uVel |
2053 |
(tested without topography: fix a Pb of growing instability with NLFS) |
2054 |
o pkg/aim/thsice: |
2055 |
-Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F |
2056 |
(works as SST restoring) |
2057 |
o pkg/thsice: |
2058 |
-add specific parameter for salt restoring in slab mixed-layer |
2059 |
(by default equal to the temperature restoring) |
2060 |
|
2061 |
checkpoint61v (2009/09/21) |
2062 |
o pkg/kpp: |
2063 |
-add double diffusive contributions as a hack, turned off by default |
2064 |
for now, and the code can be excluded with a CPP-flag |
2065 |
EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX |
2066 |
-add a verification experiments to "vermix" to test this code |
2067 |
o pkg/mom_common: |
2068 |
Move computation of length scales to mom_init_fixed.F (avoid recomputation |
2069 |
at each time-steps*levels). |
2070 |
o pkg/layers: |
2071 |
Created a new package for computing volume fluxes in temperature or |
2072 |
[not yet implemented] density layers, e.g. for calculating residual |
2073 |
overturning circulations. |
2074 |
o pkg/diagnostics: |
2075 |
implement a RS type version for the set of DIAGNOSTICS-FILL subroutines |
2076 |
o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option) |
2077 |
o pkg/mdsio (& pkg/rw): rework high level S/R interface: |
2078 |
To avoid mixing type (RS/RL) of input/output array argument, |
2079 |
replace single mixed-type array with a pair from each type (RS/RL). |
2080 |
o setting pickupSuff force to start from a pickup (even if nIter0=0): this |
2081 |
is now implemented for all pkgs (previously only done for the main pickup) |
2082 |
|
2083 |
checkpoint61u (2009/08/25) |
2084 |
o pkg/obcs: |
2085 |
- change OB?eta from _RS to _RL and put them into a separate commen block |
2086 |
- add code to read OB?eta from a file via obcs_prescribe_read: the code |
2087 |
compiles and does not destroy any other experiments, the data is read |
2088 |
properly, but the code is not tested in actual applications |
2089 |
o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to |
2090 |
create a meaningful unit attribute for the time coordinate variable |
2091 |
o pkg/ebm: add plenty of missing "_d 0" ; |
2092 |
update results of experiment global_ocean_ebm (fwd + adjoint tests) |
2093 |
Notes: several pieces of code only works for (very) specific set up |
2094 |
(domain size, lat range, etc ...); should be documented & stop if one |
2095 |
of those assumptions is not meet. |
2096 |
o pkg/seaice: add missing "_d 0" in HSNOW initialisation |
2097 |
update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests) |
2098 |
and offline_exf_seaice (seaicetd + adjoint). |
2099 |
o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC): |
2100 |
update results of experiments: lab_sea (4 fwd tests + 3 adjoint), |
2101 |
seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2). |
2102 |
o few changes to pass when compiling with strick checking of arguments |
2103 |
across S/R (allow to find few bugs in S/R calls). |
2104 |
o pkg/seaice: |
2105 |
- seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new |
2106 |
2d-fields, for slightly better performance |
2107 |
|
2108 |
checkpoint61t (2009/07/22) |
2109 |
o pkg/seaice: |
2110 |
- remove unused variables in seaice_evp |
2111 |
- reduce number of SQRT in seaice_evp and seaice_calc_viscosities |
2112 |
o eeset_parms.F, open_copy_data_file.F & ini_parms.F: |
2113 |
named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT): |
2114 |
each processor opens a different file (a fix from Matt). |
2115 |
o cg2d: |
2116 |
use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F : |
2117 |
this reduces number of EXCH calls by 2 when using exch2. |
2118 |
For now, keep previous size array for gc2d_nsa.F to avoid Pb with store |
2119 |
directives and missing simple EXCH (exch_s3d_rx) adjoint code. |
2120 |
o pkg/thsice: |
2121 |
add code for Near Infra-Red albedo (from Jeff) |
2122 |
(turned on with run-time flag: thSIce_calc_albNIR, in data.ice). |
2123 |
o ini_model_io: |
2124 |
move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F |
2125 |
MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F |
2126 |
to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice. |
2127 |
|
2128 |
checkpoint61s (2009/06/30) |
2129 |
o pkg/exch2 (exch2_rxN_cube*): |
2130 |
remove last BARRIER (no need to synchronise after getting data from shared |
2131 |
buffer (get) as long as any change to buffer (put,recv) is between BARRIER) |
2132 |
o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH |
2133 |
and generate new output (for the 2 tests) using default rotationPeriod. |
2134 |
o pkg/exch2: |
2135 |
- always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F |
2136 |
(was already the case with AUTODIFF_EXCH2 defined) |
2137 |
- add bj in exch2 arrays and S/R. |
2138 |
- can now use pkg/exch2 for regular (non CS) set-up; switch test experiment |
2139 |
MLAdjust to exch2 (identical results except with MPI -> truncation diff); |
2140 |
o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep |
2141 |
- adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY |
2142 |
GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT |
2143 |
- verification experiment natl_box.longstep |
2144 |
o build_options: ifort+mpi_aces optfile (following Constantinos advise): |
2145 |
allow different versions of ifort (8 or 9) and different versions |
2146 |
of mpi (mpich or mpich2) to be used with the same optfile. |
2147 |
requires to load a netcdf module and set MPI_INC_DIR (see comments inside |
2148 |
optfile). Change testing scripts (example_scripts/ACESgrid) accordingly. |
2149 |
o pkg/seaice: |
2150 |
fix previous modif (3-level field removed) for old-pickup reading |
2151 |
|
2152 |
checkpoint61r (2009/06/25) |
2153 |
o pkg/seaice: |
2154 |
- clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps: |
2155 |
1. introduce fields for time step (N-1) |
2156 |
2. do not use levels 2 and 3 anymore (but keep them) |
2157 |
3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This |
2158 |
includes changes to pkg/thsice/thsice_get_velocity.F, |
2159 |
model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and |
2160 |
pkg/obcs/obcs_apply_uvice.F. |
2161 |
- completely remove code for leap-frog time stepping for second order |
2162 |
advection |
2163 |
- adjusted adjoint accordingly; |
2164 |
gradient checks have improved by an order of magnitude! |
2165 |
|
2166 |
checkpoint61q (2009/06/22) |
2167 |
o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver |
2168 |
- the boundary conditions along open boundaries are unclear, because the |
2169 |
associated masks are set to zero and are thus treated as closed when |
2170 |
applying the slip-boundary conditions. |
2171 |
- move initialisation of grid variables from seaice_init_varia to _fixed |
2172 |
o adding doc/diags_changes.txt |
2173 |
o model/src: |
2174 |
do_the_model_io: rename few pkg S/R which are called from do_the_model_io, |
2175 |
to avoid "_diags" naming if no relation to pkg/diagnostics. |
2176 |
ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF |
2177 |
file and only call PLOT_FIELD_XYZ if debugMode=T. |
2178 |
remove few PLOT_FIELD_XY calls outside initialisation. |
2179 |
remove few unnecessary BARRIER. |
2180 |
o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling |
2181 |
of salt_plume package in Southern Ocean |
2182 |
o pkg/thsice: |
2183 |
- fix hOceMxL in overlap (needed for sea-ice advection); |
2184 |
update output of experiment global_ocean.cs32x15.icedyn. |
2185 |
o pkg/seaice: |
2186 |
- make the (placeholder-)tracer IceAge a little more meaningful |
2187 |
by avoiding ridging of age due to convergent ice flow |
2188 |
- add diagnostics for surface temperature, atmospheric and oceanic |
2189 |
heat flux, and atmospheric and oceanic ice growth |
2190 |
|
2191 |
checkpoint61p (2009/06/10) |
2192 |
o eesupp (global_max & global_sum): |
2193 |
- add one more element to buffer (start at index 0) for GL_MAX/SUM output; |
2194 |
- remove starting & endding barrier (no longer needed) |
2195 |
o pkg/mdsio, writelocal: |
2196 |
works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined |
2197 |
(remove the STOP): uses shared buffer IO to store data from all threads |
2198 |
and then let master-thread write nThreads tiles. |
2199 |
o pkg/mdsio (read/write field): |
2200 |
- tiled IO done in 1 piece (all levels at a time); |
2201 |
- new header file "MDSIO_BUFF_3D.h" with 3-D buffers. |
2202 |
- multi-threaded: allow to read/write local (non-shared) array |
2203 |
(was already working with singleCpuIO ; now works also without); |
2204 |
=> no longer needs barrier call after reading a file (added inside |
2205 |
mds_read/write field). |
2206 |
- move barrier calls outside gather/scatter_2d to mds_read/write_field |
2207 |
o pkg/obcs/exf |
2208 |
- exf_getffieldrec.F: add a few ". _d 0" and |
2209 |
add code to catch the case fldperiod = 0. |
2210 |
- obcs_precribe_read.F: change if statements so that they match |
2211 |
the variable type (_RL) |
2212 |
- add a separate exf_iprec_obcs to exf_set_obcs (by default equal to |
2213 |
exf_iprec) as part of namelist EXF_NML_01 |
2214 |
o pkg/mdsio: |
2215 |
- read/write tiled (local) files: read/write 1-level tile chunk at a time |
2216 |
(instead of segment of length sNx); expected to speed up tiled IO. |
2217 |
o pkg/exch2: |
2218 |
- take buffer copy from/to array out of S/R exch2_send/recv into new |
2219 |
S/R exch2_put/get ; Exch of local variable now works with MPI+MTH |
2220 |
(tested by removing commom block statement in SOLVE_FOR_PRESSURE.h). |
2221 |
- ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get) |
2222 |
- simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds |
2223 |
(which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by |
2224 |
including Topology header file (and common blocks). |
2225 |
- implement EXCH_IGNORE_CORNERS in scalar exchange (rx1); |
2226 |
remove 2nd exch call in exch2_s3d_rx (no longer needed). |
2227 |
- document S/R arg. list (+ update some comments) |
2228 |
o pkg/seaice: |
2229 |
- added SEAICE_CLIM_AIR code, which permits modulation of surface air |
2230 |
temperature and humidity over sea ice based on climatological values. |
2231 |
- clean up computation of Hibler+Bryan (1987) stress coupling for the case |
2232 |
of LSR (this change is expected to change the results slightly because now |
2233 |
it uses slightly difference moduli from the second last LSR solution, but |
2234 |
that is more consistent with the stress computations; this part of the code |
2235 |
is not tested in the verification experiments) |
2236 |
- fix diagnostics for flux of ice in case of B-grid |
2237 |
- turn strain rates eij and press into global fields within global |
2238 |
common block in SEAICE.h for more straighforward diagnostics |
2239 |
- fix diagnostics for principal stress components, press, zeta, eta |
2240 |
to give something meaning full |
2241 |
o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate |
2242 |
new output (all 4 tests) using default rotationPeriod. |
2243 |
o pkg KPP: |
2244 |
- add flag (LimitHblStable) to avoid limiting BL depth under stable conditions |
2245 |
- fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1 |
2246 |
and normal grid from 1 to Nr) |
2247 |
o Fix computations of L4rdt in mom_calc_visc.F |
2248 |
o eesupp: |
2249 |
new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg): |
2250 |
should be called before a "stop" if we know that all process are going |
2251 |
to stop; if one Proc does call this S/R, will hang in MPI_FINALISE. |
2252 |
|
2253 |
checkpoint61o (2009/05/26) |
2254 |
o pkg/exch2: change check_depths to issue just a warning (instead of error+stop) |
2255 |
o model/src/ini_curvilinear_grid.F: |
2256 |
compute angleSin/CosC when they are not read from a file |
2257 |
o pkg/seaice: |
2258 |
add pseudo time stepping for LSOR |
2259 |
o pkg/exch2: |
2260 |
temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW |
2261 |
o pkg/seaice: |
2262 |
Adding separate sea ice albedo, drag coefficients, and HO in Southern |
2263 |
Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h |
2264 |
o SingleCpuIO: |
2265 |
fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used. |
2266 |
o pkg/seaice: |
2267 |
put exchanged variable in (local) common block for MPI+Multi-Threads |
2268 |
to work (necessary with exch1, and for now with exch2 too). |
2269 |
o verification: to get more experiments tested with mpi, mth and mpi+mth, |
2270 |
change tiling of: |
2271 |
aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15, |
2272 |
hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope |
2273 |
update output of exp: |
2274 |
exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5), |
2275 |
tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod) |
2276 |
+ ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU |
2277 |
(note: output.txt generated on faulks using only 1 tile) |
2278 |
o eesupp & mdsio (SingleCpuIO): |
2279 |
- remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time |
2280 |
parameter "W2_useE2ioLayOut" (read from file "data.exch2"). |
2281 |
Note: was not effective for globalFile & useSingleCpuIO=F; now fixed. |
2282 |
- move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc). |
2283 |
- fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same |
2284 |
gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array). |
2285 |
o pkg/exch2: |
2286 |
- new code to set-up W2-Exch2 topology (replace matlab-topology-generator): |
2287 |
read parameter file "data.exch2" if it exists; otherwise try default regular |
2288 |
cube without blank-tile; new header file "W2_EXCH2_SIZE.h"; |
2289 |
- update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible |
2290 |
with new code (not to be used, just as a backup solution). |
2291 |
- add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2" |
2292 |
in utils/exch2/input. |
2293 |
|
2294 |
checkpoint61n (2009/05/12) |
2295 |
o eesupp & mdsio (SingleCpuIO): |
2296 |
- move mapping to global io-buffer inside gather_2d/scater_2d: this save |
2297 |
memory (1 less 2D global RL array); skip 1 buffer copy; and only send/ |
2298 |
receive real*4 array (instead of real*8) to read/write 32.bit files. |
2299 |
(new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S |
2300 |
and remove new mapping S/R) |
2301 |
o pkg/mdsio: in preparation for topology-generator within pkg/exch2: |
2302 |
- Change declaration of SingleCpuIO buffer, reduced to only 1 dim.: |
2303 |
xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h |
2304 |
when using exch2. Add S/R to map global io-buffer to global model array. |
2305 |
- uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt. |
2306 |
|
2307 |
checkpoint61m (2009/04/29) |
2308 |
o write_utils : change WRITE_1D_R8 to WRITE_1D_RL |
2309 |
and add 3 other S/R for other types (R4,R8,RS). |
2310 |
Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument. |
2311 |
o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros): |
2312 |
- ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ; |
2313 |
- reduce number of macro definitions (keep only those which are used); |
2314 |
can always call directly the corrresponding S/R if needed. |
2315 |
- everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix |
2316 |
_R4/_R8 to _RS/_RL when applied to _RS/_RL variable. |
2317 |
Fixed wrong type of arg in: |
2318 |
atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F |
2319 |
ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F |
2320 |
To fix: global_sum of var in common block is wrong (multi-threaded) in: |
2321 |
dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F |
2322 |
To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops) |
2323 |
o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd |
2324 |
"nlfs" mpi test is going to stop when checking for unconnected tile egdes. |
2325 |
o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error |
2326 |
o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile |
2327 |
edges are closed (zero depth); might happen with "blank tiles"; |
2328 |
for now, disabled if using OBCS. |
2329 |
o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi": |
2330 |
link *_mpi files from "MODS" dir) to return to a strait-forward behavior. |
2331 |
o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D) |
2332 |
to reduce length of 1.D array print in STDOUT. |
2333 |
o adjustment.cs-32x32x1: changed to oceanic test with 1 continent |
2334 |
+ use 48 tiles (16x8): this will allow to test "blank tiles". |
2335 |
o start to test MPI + multi-threaded (change testreport to skip tests |
2336 |
where number of tiles do not match). |
2337 |
o genmake2: add option "-omp" to turn on Open-MP ; |
2338 |
passed to testreport (if using -mth) ; merge few (*+mth) optfiles. |
2339 |
o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them) |
2340 |
and keep the original tile numbering. Note: compatible with old |
2341 |
W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files. |
2342 |
|
2343 |
checkpoint61l (2009/04/07) |
2344 |
o Overlaps had been forgotten in calculating ijk keys : fixed |
2345 |
o fix cyrus makedepend for gcc 4.4 |
2346 |
o experiment fizhi-cs-aqualev20: |
2347 |
switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE) |
2348 |
and generate new output. Note: new output is much closer to the old |
2349 |
one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from |
2350 |
the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007. |
2351 |
o pkg/fizhi: |
2352 |
- change to avoid indices going deliberately over array-bounds |
2353 |
- remove unnecessary MPI stuff |
2354 |
- perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY" |
2355 |
- new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE: |
2356 |
does not go over array-bounds and therefore returns reliable output. |
2357 |
- in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls: |
2358 |
this S/R has 4 output arguments, which are used inside "get_alarm"; |
2359 |
when it is called with the same variable "ndum" in place of several |
2360 |
output arguments, this produces weird side effect inside "get_alarm" |
2361 |
(e.g., datein=dates(n) is overwritten by timein=times(n) since both |
2362 |
datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum" |
2363 |
address) and produces error. |
2364 |
o tools/gemake2: (March 27-29 2009) |
2365 |
with option "-mpi": link *_mpi files from "MODS" dir (this is what |
2366 |
testreport does). |
2367 |
o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output |
2368 |
o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F: |
2369 |
update lab_sea.lsr & lab_sea.salt_plume results |
2370 |
o pkg/seaice: |
2371 |
Major overhaul of the LSOR solver: change discretization from original |
2372 |
finite differences to finite volume. The old routine is still in the |
2373 |
file seaice_lsr.F and can be turned on with the CPP-flag |
2374 |
SEAICE_OLD_AND_BAD_DISCRETIZATION |
2375 |
Along with this change, the discretization of the strain rates is changed. |
2376 |
The same flag turns on the old discretization in seaice_calc_strainrates.F |
2377 |
All verification experiments with seaice are affected (except for |
2378 |
seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old |
2379 |
results by setting the above flag. |
2380 |
Further changes involve changes in defaults: |
2381 |
- ALLOW_FLOODING is defined and turned on by default |
2382 |
- SEAICEadvSnow = .true. is now the default |
2383 |
- SEAICEadvSalt = .true. is now the default |
2384 |
- SEAICEadvAge = .true. is now the default |
2385 |
- SEAICE_clipVelocities = .false. is now the default |
2386 |
(as per J. Zhang's recommendation) |
2387 |
- B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE |
2388 |
is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS |
2389 |
- seaice_growth: replace computation of UG by a simple copy from wspeed |
2390 |
|
2391 |
checkpoint61k (2009/03/18) |
2392 |
o pkg/seaice: a few bug fixes mostly concerning the metric terms: |
2393 |
seaice_lsr: fixed a few metric terms, |
2394 |
affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs |
2395 |
add more debugging diagnostics |
2396 |
seaice_evp: removed superfluous many metric terms of FV discretization |
2397 |
of stress divergence |
2398 |
affects lab_sea, lab_sea.hb87 |
2399 |
seaice_ocean_stress: removed superfluous many metric terms of FV discretization |
2400 |
of stress divergence for non-evp solver |
2401 |
(this part is not tested anywhere) |
2402 |
seaice_calc_strainrates: fixed a bug in no-slip boundary conditions, |
2403 |
they were effectively only half slip |
2404 |
affects lab_sea.hb87 |
2405 |
updated all relevant verification experiments (except lab_sea//output_adm.txt |
2406 |
which was left over, but fails at level 7 & 6) |
2407 |
|
2408 |
checkpoint61j (2009/03/17) |
2409 |
o pkg/seaice: turn a few hard wired parameters into run time parameters |
2410 |
o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model |
2411 |
time in seconds as promised by the usints in seaice_monitor and exf_monitor |
2412 |
o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids |
2413 |
that are not cubed-sphere grids |
2414 |
o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR |
2415 |
o pkg/ctrl: |
2416 |
fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low) |
2417 |
o non-hydrostatic (calc_gw.F): |
2418 |
fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec |
2419 |
update output of exp. global_ocean.cs32x15.viscA4 |
2420 |
o remove backward compatibility for thetaMin,phiMin |
2421 |
(replaced by xgOrigin,ygOrigin on Jan 27, 2009) |
2422 |
o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the |
2423 |
interpolated wind field not only for curvilineargrid=.true., but also |
2424 |
for a rotated grid (rotateGrid=.true.) |
2425 |
o pkg/exf: add capability to bypass interpolation for runoff |
2426 |
by setting yet another CPP-flag |
2427 |
o eesupp/src, B-grid exchange: |
2428 |
add simple (6 tiles, non MPI) CS exch + standard interface S/R. |
2429 |
o autodiff |
2430 |
new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV |
2431 |
allows to switch to single-prec common blocks; |
2432 |
corresponding switch occurs in tamc.h, integer isbyte |
2433 |
TAF store directivs "byte" and "kind" seem equivalent; |
2434 |
Most tamc.h have been updated correspondingly. |
2435 |
|
2436 |
checkpoint61i (2009/02/13) |
2437 |
o autodiff: |
2438 |
fix autodiff_sore/_restore indices for obcs |
2439 |
(spotted by I. Hoteit, M. Mazloff) |
2440 |
o pkg/autodiff, pkg/ctrl: |
2441 |
Add flag to reduce all tapelev I/O to single-prec. |
2442 |
In data.ctrl set |
2443 |
doSinglePrecTapelev = .TRUE. |
2444 |
o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2: |
2445 |
check in hack for SX8 compiler (for dxV, dyU); remove it afterwards. |
2446 |
o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for |
2447 |
real fresh water flux (not yet) |
2448 |
o pkg/mdsio & rw: |
2449 |
- add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta) |
2450 |
- add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX. |
2451 |
o pkg/flt: |
2452 |
- replace FLT_INIT by 3-steps standard initialization S/R: readparms, |
2453 |
init_fixed & ini_varia. |
2454 |
- clean-up & simplify linear interpolation S/R: |
2455 |
move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid. |
2456 |
- fix some indices (mainly vertical index) ; add IMPLICIT NONE. |
2457 |
- more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R. |
2458 |
- add vert. coordinate & horiz. indices to output files. |
2459 |
- change vertical position in initial condition, from index to depth [m]. |
2460 |
- store horizontal (decimal) indices i,j in common block (instead of coord. x,y) |
2461 |
(easier to get to a curvilinear grid) ; delX,delY no longer used. |
2462 |
o pkg/ggl90: a few modifications: |
2463 |
- fix bottom boundary condition, and interpolation of KappaE |
2464 |
near top and bottom |
2465 |
- use same set of viscosity/diffusivity for TKE/momnetum/tracer |
2466 |
- add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH) |
2467 |
- add a few options for mixing-length upper limit (--> mxlMaxFlag) |
2468 |
o rename thetaMin,phiMin -> xgOrigin,ygOrigin |
2469 |
(maintain temporary backward compatibility, until next checkpoint) |
2470 |
|
2471 |
checkpoint61h (2009/01/27) |
2472 |
o pkg/diagnostics with "periodic averaging diagnostics": |
2473 |
fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. |
2474 |
o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82 |
2475 |
o pkg/obcs: fix loop ranges for balancing code |
2476 |
o pkg/flt: |
2477 |
- improve criteria for finding which tile owns a float. |
2478 |
- fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case. |
2479 |
o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg |
2480 |
aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling |
2481 |
with ocean biogeo) |
2482 |
o pkg/flt: |
2483 |
- do some cleaning and fix the restart ; |
2484 |
- add output.txt in flt_example/results to get this pkg tested. |
2485 |
o genmake2: add an EXTENDED_SRC option and flag. |
2486 |
for now, cannot be turned on on command line (only through genmake_local) |
2487 |
o pkg/mdsio: read/write vector: |
2488 |
- singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS |
2489 |
- singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR |
2490 |
& MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. |
2491 |
- affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) |
2492 |
(drop to 4 digits matching for grad). But this test does not look very |
2493 |
reliable (was already failling on eddy, fc5, at 6.digits). Update output. |
2494 |
|
2495 |
checkpoint61g (2008/12/29) |
2496 |
o pkg/flt: |
2497 |
- move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) |
2498 |
+ make OPTIONS file more standard. |
2499 |
- rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) |
2500 |
- fix _BYTESWAPIO CPP-Flag |
2501 |
- standard reading of file-parameter "data.flt" |
2502 |
- fix argument list of S/R FLT_RESTART |
2503 |
still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F |
2504 |
o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell |
2505 |
o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to |
2506 |
a still unfixed compiler/optimization bug |
2507 |
|
2508 |
checkpoint61f (2008/11/21) |
2509 |
o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; |
2510 |
update results of global_ocean.cs32x15.icedyn test. |
2511 |
o move getcon.F from model/src to pkg/fizhi. |
2512 |
o pkg/exf: add parameter for extrapolation of temp up to the surface |
2513 |
and option to prevent negative evap (in bulk_largeyeager04 only). |
2514 |
o Prather Advection scheme: fix tracer conservation for divergent flow |
2515 |
(e.g., when using NonLin Free-Surface). |
2516 |
o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead |
2517 |
o gmredi (Visbeck-variable-K): |
2518 |
- add more parameters to Visbeck-variable-K. |
2519 |
- use a 5 points average for dSigmaR in Visbeck-K calculation |
2520 |
(more "homogenous": same stencil and same weights as in dSigmaH) |
2521 |
- update output of ideal_2D_oce experiment. |
2522 |
o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 |
2523 |
(#undef REAL4_IS_SLOW) |
2524 |
- pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 |
2525 |
coordinate variable |
2526 |
- pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables |
2527 |
(surface forcing fields), removes some of the functionality |
2528 |
- model/src/write_grid.F: write _RS variables as RS-netcdf variables |
2529 |
- model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but |
2530 |
probably not all: copy _RS surface flux fields to RL field before |
2531 |
calling DIAGNOSTICS_FILL |
2532 |
- model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into |
2533 |
real*4 (CALL EXCH_*_RS) versions. |
2534 |
- tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 |
2535 |
(generate new output). |
2536 |
|
2537 |
checkpoint61e (2008/10/23) |
2538 |
o gmredi (Visbeck-variable-K): |
2539 |
- fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h |
2540 |
- change computation of Visbeck-K where Slope > Smax : |
2541 |
now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct) |
2542 |
previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output. |
2543 |
o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic |
2544 |
to be the same as with Z-coord. (i.e., m/s & no-units respectively). |
2545 |
o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc) |
2546 |
o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz |
2547 |
does not become too large (to avoid precision problems in implicit-diffusion |
2548 |
solver); update ideal_2D_oce output. |
2549 |
o pkg ggl90: |
2550 |
- in ggl90_cal.F: compute only one set of visc/diff, used to |
2551 |
step forward TKE/T/S/momentum |
2552 |
- default value of GGL90viscMax/GGL90diffMax larger and equal (to |
2553 |
have Prandlt =1) |
2554 |
o gmredi (fm07): |
2555 |
- add lower limit on Transition layer thickness + lower limit on 1/lambda |
2556 |
- allow to set few more params from data.gmredi |
2557 |
o pkg ggl90: |
2558 |
- add missing sqrt(2) factor in computation of mixing length |
2559 |
scale in ggl90_calc.F |
2560 |
(see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) |
2561 |
|
2562 |
checkpoint61d (2008/09/25) |
2563 |
o adjoint modifs |
2564 |
- adapt to new field rhoInSitu |
2565 |
- allow to revert from StoreDynVars2D, StoreDynVars3D |
2566 |
to individual fields |
2567 |
(switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) |
2568 |
o store 3-D (in-situ) density in commom block (DYNVARS.h) |
2569 |
- save 1 rho computation. |
2570 |
- no longer modify T & S inland when using down_slope pkg. |
2571 |
o gad_som : allow to switch to SOM advection for T & S without corresponding |
2572 |
pickup files (using new S/R: MDS_CHECK4FILE). |
2573 |
o keep removing _BEGIN/_END_MASTER between MDSIO S/R call |
2574 |
(for useSingleCpuIO to work in multi-threaded) |
2575 |
o pkg/shelfice: |
2576 |
- disentangle parameters: retire shelfIceFile in data/PARM05 and substitute |
2577 |
with SHELFICEtopoFile in data.shelfice |
2578 |
- move code for reading ice shelf topography and modifying hFacC into separate |
2579 |
subroutines of the shelfice package |
2580 |
- separate initialisation of "fixed" and "variable" variables |
2581 |
- kTopC is not (yet) replaced by kSurfC, although this is possible |
2582 |
o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
2583 |
o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
2584 |
and rename: |
2585 |
ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
2586 |
ini_reference_state.F --> load_ref_files.F (- set anelastic factors) |
2587 |
o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) |
2588 |
|
2589 |
checkpoint61c (2008/08/30) |
2590 |
o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" |
2591 |
to add mass source/sink of fluid in the interior (3-D generalisation |
2592 |
of oceanic real-fresh water flux). |
2593 |
o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) |
2594 |
o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) |
2595 |
o new pkg: down_slope |
2596 |
density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). |
2597 |
- presently, modify T & S inland (dwnslp_calc_rho.F). |
2598 |
can be avoided if rho was stored in common bloc and used in calc_phi_hyd. |
2599 |
- implementation for ocean in P-coords not tested. |
2600 |
- add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. |
2601 |
o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) |
2602 |
(to facilitate conversion of oceanic pkg to p-coordinate). |
2603 |
o change FIND_RHO to FIND_RHO_2D : |
2604 |
pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. |
2605 |
o new pkg: cheapaml |
2606 |
|
2607 |
checkpoint61b (2008/08/05) |
2608 |
o exch2: |
2609 |
change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) |
2610 |
- no longer depend on the order sequence (N,S,E,W). |
2611 |
- 3rd exchange no longer needed (tested with 24 tiles). |
2612 |
- same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) |
2613 |
- exch_UV_A-grid readily available (but not yet tested). |
2614 |
comment out 3rd exch call and remove copy of V to U at SE & NE face-corners |
2615 |
(both are no longer needed) in exch_uv: no effect in forward run; but |
2616 |
get truncation error differences with adjoint exch. |
2617 |
o exch2: |
2618 |
- change index-bounds storage (moved from target to local tile, |
2619 |
more intuitive this way) ; rename/remove some variables. |
2620 |
- change utils/exch2/matlab-topology-generator & code_mods accordingly. |
2621 |
|
2622 |
checkpoint61a (2008/07/29) |
2623 |
o exch2/matlab-topology-generator: |
2624 |
fix bug in index bounds for N-S internal exchange (hard to tell if this |
2625 |
had any effect on the solution). |
2626 |
o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf |
2627 |
is exceeded |
2628 |
o testreport: modify syntax of awk, so that it works also with |
2629 |
awk, and not only with nawk and gawk |
2630 |
|
2631 |
checkpoint61 (2008/06/24) |
2632 |
o autodiff |
2633 |
Change default for TAF usage by removing argument '-nonew_arg' |
2634 |
This changes TAF subroutine argument list (ordering of active var.) |
2635 |
Omission of this flag leads to incompatibility w.r.t. TAMC |
2636 |
To restore TAMC-compatibility, need following modifs: |
2637 |
* use adoptfile tools/adjoint_options/adjoint_tamc_compatibility |
2638 |
* use CPP option #define AUTODIFF_TAMC_COMPATIBILITY |
2639 |
Tested TAF version is 1.9.22 |
2640 |
N.B.: exch2 hand-written adjoint code currently not TAMC compatible |
2641 |
|
2642 |
checkpoint60 (2008/06/19) |
2643 |
--->>> This is the last checkpoint for which generating the adjoint |
2644 |
--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" |
2645 |
--->>> by default. |
2646 |
--->>> Future checkpoints will ommit this flag by default. |
2647 |
o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. |
2648 |
o pkg/grdchk: Add gradient check to etan0 perturbations. |
2649 |
o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). |
2650 |
o pkg/autodiff: more flexibility in zeroadj. |
2651 |
model/src: modifying do_oceanic_phys.F accordingly. |
2652 |
o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. |
2653 |
o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option |
2654 |
special setup of gmredi for which the adjoint is stable |
2655 |
enough for parameter optimization. |
2656 |
o bridging the gap between eddy stress and GM. |
2657 |
-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) |
2658 |
along with a change in CPP option (now ALLOW_EDDYPSI). |
2659 |
-> when using GM w/ GM_AdvForm: |
2660 |
The total eddy streamfunction (Psi = eddyPsi + K x Slope) |
2661 |
is applied either in the tracer Eq. or in momentum Eq. |
2662 |
depending on data.gmredi (intro. GM_InMomAsStress). |
2663 |
-> ALLOW_EDDYPSI_CONTROL for estimation purpose. |
2664 |
The key modifications are in model/src/taueddy_external_forcing.F |
2665 |
pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F |
2666 |
|
2667 |
checkpoint59r (2008/05/29) |
2668 |
o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array |
2669 |
from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); |
2670 |
fix option to read coriolis(@ cell-corner) from files with CS-grid. |
2671 |
o pkg/mnc: add some attributes to standard 1D-coordinate variables |
2672 |
o pkg/diagnostics: enforce missing_value attribute for scalar variables at |
2673 |
mass points, when using mnc for output |
2674 |
- add runtime parameter (missing_value, missing_value_int) to override |
2675 |
default (which is the value of getcon('UNDEF')) |
2676 |
o pkg/mnc: prepare mnc for the actual use of missing values with the |
2677 |
diagnostics package: small fix in mnc_cw_readwrite.template and more |
2678 |
initialisation of never used fields |
2679 |
- replace mnc_common.h and mnc_id_header.h with corresponding upper case |
2680 |
versions |
2681 |
o pkg/thsice/thsice_ini_vars.F added default initial values so that |
2682 |
thermodynamics sea ice solver does not blow up when some initial fields |
2683 |
are missing. |
2684 |
o move from external_forcing_surf.F to ini_forcing.F |
2685 |
the p-coord. hack consisting in using pLoad to set phi0surf ; |
2686 |
update output of tutorial_global_oce_in_p (affected @ truncation level). |
2687 |
o Freshen up a bit hs94.1x64x5, notably: |
2688 |
remove rotationPeriod and tRef=5*0. (adjoint only), and add |
2689 |
exactConserv=.TRUE. |
2690 |
o pkg/generic_advdiff: |
2691 |
change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
2692 |
applies to files where Temperature & Salinity 2nd Order moments are used. |
2693 |
o pkg/ptracers: add second-order moment advection schemes (80 and 81); |
2694 |
this uses a dynamically allocated internal state data structure |
2695 |
(#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) |
2696 |
and requires a fortran 90 compiler |
2697 |
|
2698 |
checkpoint59q (2008/05/06) |
2699 |
o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) |
2700 |
(from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) |
2701 |
o Refresh tutorial_global_oce_biogeo, notably: |
2702 |
- change bathymetry (put back seamounts in ACC, use hFacs) |
2703 |
- change EOS (POLY3 --> JMD95Z) |
2704 |
- use Bryan-Lewis vertical diffusivity |
2705 |
- use multidimensional advection |
2706 |
- remove old virtual virtual in dic pkg, now done through ptracer pkg |
2707 |
- change a couple of parameters in dic pkg |
2708 |
o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F |
2709 |
o pkg/obcs: change default to OBCSfixTopo = .true., |
2710 |
- set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result |
2711 |
- replace "debugMode" with "debugLevel .GE. debLevB" |
2712 |
o implementation of TAF directives for gchem,cfc,dic |
2713 |
o remove "exp5" (replaced by tutorial_deep_convection). |
2714 |
o pkg/obcs: add code to fix topography gradients normal to open boundaries; |
2715 |
this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; |
2716 |
the code can be turned on by setting OBCSfixTopo = .true. in data.obcs |
2717 |
--> changes results in exp4, seaice_obcs |
2718 |
o tutorial_deep_convection : |
2719 |
update the set-up and increase resolution and domain size ; start |
2720 |
from pseudo initial conditions = output at t=120mn in order to see |
2721 |
something happening when running testreport. |
2722 |
o pkg/seaice: add os7mp as an advection scheme |
2723 |
add check for advection schemes |
2724 |
add a flag for restoring T and S underneath sea ice |
2725 |
o pkg/my82: add netcdf-support and diagnostics |
2726 |
o thsice pkg: |
2727 |
- Now hsMax limits snow height by turning it into ice following |
2728 |
flooding scheme (and now conserving energy) |
2729 |
- Slight rewriting of the formula in thsice_calc_thick.F |
2730 |
- Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos |
2731 |
--> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice |
2732 |
|
2733 |
checkpoint59p (2008/04/10) |
2734 |
o gchem / dic / cfc : |
2735 |
- add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); |
2736 |
- add new parameter files: "data.dic" & "data.cfc" ; |
2737 |
- various re-arrangement in initialisation & header file ; |
2738 |
- fix tutorial_global_oce_biogeo for multi-threaded test. |
2739 |
o pkg/dic: test for "pickup_dic" file when restarting ; |
2740 |
if no pickup-file, can restart with a re-initialised pH (same as it did |
2741 |
before) providing pickupStrictlyMatch is set to False. |
2742 |
o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP |
2743 |
+ fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP |
2744 |
o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2 |
2745 |
and staggerTimeStep is off (needed for stability of Internal-wave dynamics). |
2746 |
o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax, |
2747 |
& lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers |
2748 |
(note: not clear to me what lambdaTr1ClimRelax is still used for ...) |
2749 |
o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which |
2750 |
scheme to use for vorticty-term ; |
2751 |
- compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F |
2752 |
(with default selectVortScheme, return to original discretisation) |
2753 |
- remove weird combination (e.g.: upwindVorticity & highOrderVorticity) |
2754 |
o pkg/seaice: add a line to the summary to indicate grid type (B/C) |
2755 |
o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the |
2756 |
bottom ; only used with variable horizontal viscosity and non-hydrostatic. |
2757 |
also fix diagnostics VISCAHW & VISCA4W. |
2758 |
|
2759 |
checkpoint59o (2008/03/07) |
2760 |
o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). |
2761 |
o change the loop ordering in most gad_*_adv_x.F to improve vectorization: |
2762 |
move a few statemens out the main loop into separate loops |
2763 |
o pkg/shelfice: |
2764 |
- sort out freshwater flux; convert freshwater fluxes to mass fluxes |
2765 |
(kg/m^2/s), does not break tests, because in verification/isomip, |
2766 |
rhoConstFresh=rhoConst (by accident) |
2767 |
- rearrange computation of tLoc, sLoc, pLoc to make code more efficient |
2768 |
- move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into |
2769 |
new file model/src/seawater.F, so that they are available for all pkgs. |
2770 |
- convert potential temperature into in-situ temperature. This changes the |
2771 |
isomip tests => update tests |
2772 |
o add a flag writePickupAtEnd (default=true) to be able to suppress |
2773 |
writing a pickup at the last timestep |
2774 |
o tools/mpack-1.6 : |
2775 |
- disable automake (not working) and autoconf (not needed). |
2776 |
- update to version 1.6.4 which fix MD5 code on some 64 bits platforms |
2777 |
also cleaner with much less compilation warnings. |
2778 |
o pkg/profiles: |
2779 |
rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg |
2780 |
(for "less than 32 characters name" compiler requirement) |
2781 |
o pkg/obcs and pkg/exf: added capability to specify seaice open boundary |
2782 |
conditions that have a different sampling frequency than S/T/U/V obcs |
2783 |
o pkg/diagnostics (stats-diags): |
2784 |
- fix global Min/Max in case 1 processor get only empty tiles |
2785 |
o genmake2: replace (4 times) |
2786 |
make genmake_tc_1.o >> genmake_warnings 2>&1 |
2787 |
with |
2788 |
COMM="$CC $CFLAGS -c genmake_tc_1.c" |
2789 |
echo $COMM >> genmake_warnings |
2790 |
$COMM >> genmake_warnings 2>&1 |
2791 |
to make genmake2 always see the value of CC as specified in the optfile. |
2792 |
o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid. |
2793 |
- add diagnostics for 1srt & 2nd Order moments and sub-grid variance. |
2794 |
- modify verification advect_cs test to test SOM-advection on CS-grid. |
2795 |
o pkg/ctrl: |
2796 |
- Rewrite of ctrl_map_ini_ecco.F, |
2797 |
introducing a generic routine (ctrl_map_ini_gen.F). |
2798 |
- Modification of ctrl_bound/adctrl_bound handling control vector bounds. |
2799 |
|
2800 |
checkpoint59n (2008/02/09) |
2801 |
o pkg/diagnostics: for large number of diagnostics, store diagnostic mate |
2802 |
number in dedicate array "hdiag": |
2803 |
- new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST |
2804 |
with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST. |
2805 |
- many small changes (integer format) for large number of diagnostics |
2806 |
- start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with |
2807 |
a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23. |
2808 |
o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For |
2809 |
usingSphericalGrid, this allows to define the rotated grid coordinates |
2810 |
via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the |
2811 |
geographical coordinates according to the inverse of the rotation defined |
2812 |
by the Euler angles, so that Coriolis parameter and online-interpolation by |
2813 |
exf works with the geographical coordinates on XC/YC/XG/YG. |
2814 |
Naturally, this feature does not work with all packages, so some |
2815 |
combinations are prohibited in config_summary (flt, flt_zonal, ecco, |
2816 |
profiles), because there the coordinates are assumed to be regular |
2817 |
spherical grid coordinates. |
2818 |
o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc: |
2819 |
- introduce isopycnal diffusion coefficient control. |
2820 |
o tools/adjoint_options: |
2821 |
- additional control vector components. |
2822 |
o pkg/mnc: have mnc create marginally meaning full coordinate variables |
2823 |
(that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 |
2824 |
o pkg/mypackage: |
2825 |
- add example of read/write pickup for state-var ; |
2826 |
- add entry points to the main code for state-vars diags & write-pickup. |
2827 |
o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year |
2828 |
transitions for useExfYearlyFields |
2829 |
- add new subroutine that determines the file to read from for |
2830 |
use*YearlyFields = .TRUE. and .FALSE. |
2831 |
- add a verification experiment to global_with_exf that tests |
2832 |
useExfYearlyFields with USE_EXF_INTERPOLATION defined |
2833 |
o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in |
2834 |
analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new |
2835 |
subroutines (which could be generated from a template, because they are |
2836 |
almost identical), for now they are included in obcs_prescribe_read.F for |
2837 |
simplicity |
2838 |
o pkg/exf: |
2839 |
- add a little more diagnostic to exf_interp_read (in analogy to |
2840 |
mds_read_field, can be turned off with debugLevel < debugLevA=1) |
2841 |
- improve vectorizability of exf_interp for TARGET_NEC_SX, makes code |
2842 |
ugly but fast by unrolling short inner loops, inserting a unroll=8 |
2843 |
directive in routine lagran, and splitting a loop and making do while the |
2844 |
outermost loop (the latter requires the intoduction of index arrays) |
2845 |
o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice |
2846 |
o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver |
2847 |
http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html |
2848 |
o verification/seaice_obcs: updated for restart test and latest options |
2849 |
o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different |
2850 |
ice rheology (so-called truncated ellipse, that gets rid of tensile stress); |
2851 |
for now this is only available for the C-grid code and also within |
2852 |
#ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code |
2853 |
|
2854 |
checkpoint59m (2008/01/14) |
2855 |
o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) |
2856 |
and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature |
2857 |
o gad_som : fix flux output (& diagnostics) to have same units as other |
2858 |
advection scheme fluxes (was previously multiplied by deltaT). |
2859 |
o added verification/seaice_obcs both to test seaice open boundaries |
2860 |
and to provide an example matlab scrpt for generating them |
2861 |
o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume |
2862 |
o pkg/salt_plume: clean up salt_plume_frac.F to |
2863 |
remove redundancy in PlumeMethod 1 and 4 |
2864 |
o pkg/kpp: added saltplume diagnostics |
2865 |
o pkg/obcs and pkg/seaice: |
2866 |
- do not set uice and vice to zero when OB*icefile are unspecified |
2867 |
- OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default |
2868 |
- moved seaice tracer obcs after call to seaice_growth |
2869 |
o pkg/salt_plume: added various options for salt plume depth |
2870 |
criterion and for vertical distribution of the salt |
2871 |
|
2872 |
checkpoint59l (2007/12/18) |
2873 |
o pkg/ptracers: new version of ptracers pickup: |
2874 |
read meta file and write only fields which are needed to restart. |
2875 |
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
2876 |
o pkg/seaice: |
2877 |
- add timescale for melting due to warm mixed layer as a means of |
2878 |
setting SEAICE_availHeatFrac more conveniently |
2879 |
- add a CPP-flag/runtime parameter check for flooding algorithm |
2880 |
- reformulated availHeat in seaice_growth.F to be independent of AREA |
2881 |
o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent |
2882 |
unit changes |
2883 |
o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint |
2884 |
o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC |
2885 |
SX vector computer. |
2886 |
o pkg/seaice: |
2887 |
- removed SEAICE_FFIELDS.h and seaice_get_forcing.F |
2888 |
seaice forcing fields can now be read only through pkg/exf |
2889 |
- removed some unused halos |
2890 |
o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP |
2891 |
o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL |
2892 |
or U/VICE from U/VWIND before computing U/VSTRESS |
2893 |
|
2894 |
checkpoint59k (2007/11/30) |
2895 |
o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between |
2896 |
dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. |
2897 |
o fix un-initialised variable problem (in mom_vecinv & shap_filt): |
2898 |
all experiments pass when compile with un-initialised var. checking option. |
2899 |
o added pkg/salt_plume |
2900 |
o script to test restart (for now, in MITgcm_contrib/jmc_script) |
2901 |
o pkg/seaice: new read/write pickup version. |
2902 |
read meta file and write only fields which are needed to restart. |
2903 |
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
2904 |
o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) |
2905 |
o lab_sea.hb87: modify the domain & update output.hb87.txt : |
2906 |
lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 |
2907 |
at j=1 & j=Ny+1 : this case is not treated correctly in the restart |
2908 |
process. Fixed here by closing the domain at the Northern boundary. |
2909 |
o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. |
2910 |
o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing |
2911 |
a set of consecutive levels in/from a 3-D array. |
2912 |
o pkg/ptracers: |
2913 |
use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). |
2914 |
to-do: fix pkg/diagnostics when large number of diagnostics are defined. |
2915 |
|
2916 |
checkpoint59j (2007/11/09) |
2917 |
o in pkgs: dic, obcs, offline, rbcs: |
2918 |
standard way to compute coeff. for time interpolation between 2 time reccords |
2919 |
which retains full precision (& make results less dependent on compiler). |
2920 |
update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. |
2921 |
o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those |
2922 |
packages instead of reading ice cover and wind speed separately |
2923 |
o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h |
2924 |
(keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad |
2925 |
to allow to compile customized code before the update) |
2926 |
o cleaning-up: |
2927 |
- fix CPP instruction syntax in pkg/obcs |
2928 |
- replace (some) call to MDSIO S/R with call to RW interface S/R ; and |
2929 |
add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio) |
2930 |
- fix some threads issue in IO parts. |
2931 |
o pkg/dic: |
2932 |
- add tons of "_d 0" (--> much better testreports !) |
2933 |
and then update outputs of tutorial_global_oce_biogeo |
2934 |
o pkg/mom_fluxform: |
2935 |
add a special version of momentum advection intended to conserve momentum |
2936 |
next to a bathymetry step or a coastline edge. (default = off = #undef) |
2937 |
o new read/write pickup version: |
2938 |
- for now, only implemented for main (mdsio) pickup file. |
2939 |
- write out only what is needed to restart; merge pickup_nh , pickup_ph |
2940 |
and main pickup together. |
2941 |
- read meta file; read only what is needed to restart; stop if a field |
2942 |
is missing (if pickupStrictlyMatch=T, = the default) or try to restart |
2943 |
if it make sense (even if the restart is not perfect). |
2944 |
- if no meta file, assume that pickup to read corresponds exactly to |
2945 |
a pickup that would currently be written. |
2946 |
- read pickup written in the old format (until checkpoint59i) if it |
2947 |
recognizes an old meta file (no field-list). |
2948 |
- add a meta file in exp. which starts from a pickup: 2 cases: |
2949 |
a) minimal meta file (with just file precision) + pickupStrictlyMatch=F |
2950 |
e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta |
2951 |
b) a meta file describing the content of the associated pickup file |
2952 |
e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta |
2953 |
o pkg/mdsio & pkg/rw: |
2954 |
- new routine to read a meta file ; new set of routine to read |
2955 |
Multiple-fields file (with meta file). |
2956 |
o added open boundary conditions capability for seaice |
2957 |
HSNOW, HSALT, UICE, and VICE |
2958 |
|
2959 |
checkpoint59i (2007/10/21) |
2960 |
o adjoint: |
2961 |
* fix multiDimAdvection adjoint |
2962 |
(partial recomputation problem by TAF for fVerT(:,:,kDown) |
2963 |
and comlev1 size definition (maxpass vs. max. number of tracers) |
2964 |
* verification/global_ocean.90x45x15 adjoint now tests |
2965 |
NLFS and multiDimAdvection using DST3 (=30) |
2966 |
* verification/lab_sea now tests multiDimAdvection using DST3 (=30) |
2967 |
o pkg/kpp: add "_d 0" to real constant (if missing); |
2968 |
update output of exp: natl_box (10.digits); vermix (std, 7.digits) |
2969 |
and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). |
2970 |
o prepare for "clever pickup" implementation: add new header file "RESTART.h" |
2971 |
for internal parameters related to restart process (formerly from PARAMS.h) |
2972 |
and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. |
2973 |
o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed |
2974 |
as argument. (only atm2d & obcs write_pickup have not yet been updated) |
2975 |
o pkg/monitor: |
2976 |
- use GLOBAL_SUM_TILE instead of _GLOBAL_SUM |
2977 |
- fix mon_stats_rs (statistics over the full domain, even where field is zero) |
2978 |
- account for deep Atmosphere factor and density factor (anelastic) |
2979 |
o added open boundary conditions capability for seaice HEFF and AREA |
2980 |
o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) |
2981 |
thermodynamics |
2982 |
- requires a little reorganization, which affects the testreport results |
2983 |
of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, |
2984 |
so that now the conservative form is tested |
2985 |
- add a few comments |
2986 |
o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* |
2987 |
o add a little bit of code to gad_os7mp_adv_?.F to help vectorization |
2988 |
o add new diagnostics to seaice: advective, diffusive fluxes (only for |
2989 |
multidim-advection, for scheme 2 they are not filled) and transports, |
2990 |
thermodynamic growth rates |
2991 |
o change units of EmPmR (inside the code, + within coupling interface) |
2992 |
from m/s to kg/m2/s (mass flux) but leave input file unchanged. |
2993 |
Affects results @ truncation level (cg2d match) and update output of |
2994 |
experiments: lab_sea(6), global_ocean.90x40x15(10), |
2995 |
global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) |
2996 |
+ adjoint results: global_ocean_ebm(11) and lab_sea (12). |
2997 |
Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). |
2998 |
Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). |
2999 |
|
3000 |
checkpoint59h (2007/09/29) |
3001 |
o pkg/exf: |
3002 |
- improve vectorization by moving if-statement out of loops in |
3003 |
exf_mapfields, exf_radiation |
3004 |
- exf_bulkformulae.F: introduce 2D fields and vectorize code |
3005 |
o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package |
3006 |
o testreport: |
3007 |
- allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE |
3008 |
monitor & update offline_exf_seaice exp. output. |
3009 |
- AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) |
3010 |
o pkg/seaice: |
3011 |
- bug fix in the evp solver: boundary conditions were affected be |
3012 |
masking of zMax/zMin (changes results) |
3013 |
- minor bug fix in boundary conditions in seaice_calc_strainrates |
3014 |
(changes results for no_slip) |
3015 |
- seaice_lsr.F: make interpolation of eta dependent on boundaries |
3016 |
- replace hardcoded lower limit for zeta (zMin) by runtime parameter |
3017 |
- add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean |
3018 |
stress formulation and no-slip boundary conditions |
3019 |
o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP |
3020 |
in gad_calc_rhs.F ; add few safety stops in initialisation phase. |
3021 |
o pkg/seaice: a first HSALT time stepping equation has been checked in |
3022 |
o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV |
3023 |
in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem |
3024 |
without requiring DO-IF statements |
3025 |
o pkg/thsice: |
3026 |
use continuous power-law function for partition of energy between lateral |
3027 |
melting/freezing and thinning/thickening ; old code using step function |
3028 |
still available with #undef THSICE_FRACEN_POWERLAW |
3029 |
update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice |
3030 |
o testreport: change AD testing : check against results/output_adm.txt |
3031 |
using same scripts as for forward test. |
3032 |
|
3033 |
checkpoint59g (2007/09/17) |
3034 |
o adjoint testing: in preparation for changing testreport: |
3035 |
- output format: cost and grad written on separated lines |
3036 |
- ad output results in directory "results" (instead of "results_ad") |
3037 |
o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
3038 |
o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
3039 |
o pkg/ecco: allow user defined cost function contributions |
3040 |
o testreport: |
3041 |
Allow to choose (per experiment) the list of tested output variables |
3042 |
and the main variable (used to issue a pass/FAIL ) ; |
3043 |
- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
3044 |
- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
3045 |
Also modify printing of summary: |
3046 |
a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
3047 |
b) echo the list of tested variables in the individual summary.txt of |
3048 |
each experiment. |
3049 |
o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
3050 |
threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
3051 |
(but still depend on the tile decompostion of the domain). |
3052 |
o pkg/seaice: change a discretization detail to make the B-grid code |
3053 |
"more symmetric". This change is likely to remove all "ridges/leads" that |
3054 |
where quasi-aligned with the grid in B-grid solutions. It may also be |
3055 |
the solution to the stress coupling issues with the B-grid. |
3056 |
o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
3057 |
remove .cvsignore from input dir. (since testreport no longer run here). |
3058 |
o pkg/thsice: |
3059 |
- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
3060 |
- fix reshaping of sea-ice just after advection: |
3061 |
melt all the ice only if ice-volume is too small. |
3062 |
- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
3063 |
prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
3064 |
and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
3065 |
o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
3066 |
tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
3067 |
o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
3068 |
forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
3069 |
(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
3070 |
and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
3071 |
of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
3072 |
-> update output.txt |
3073 |
o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
3074 |
this affects truncation error: -> update output.txt of exp: |
3075 |
global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
3076 |
ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
3077 |
|
3078 |
checkpoint59f (2007/08/21) |
3079 |
o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
3080 |
o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
3081 |
a bounded range (in forward mode) |
3082 |
o pkg/ecco, ctrl, autodiff and mom_common: |
3083 |
internal parameter controls, completements of implementations |
3084 |
o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
3085 |
o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
3086 |
(not seem any difference in testing results). |
3087 |
o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
3088 |
at face corners. |
3089 |
o pkg/generic_advdiff: |
3090 |
- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
3091 |
loop range indices for computing vertical advection tendency |
3092 |
and do the calculation in the interior only (no overlap) ; |
3093 |
for now, only implemented for SOM advection (to save CPU time). |
3094 |
- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
3095 |
o exch2 adjoint |
3096 |
First set of changes: |
3097 |
- add exch2 hand-written adjoint templates |
3098 |
- exch2 hand-written no longer use TAF-flag 'nownew_arg' |
3099 |
This will require cleanup in pkg/autodiff/*.F |
3100 |
(changed routines currently kept separate in verif. code/) |
3101 |
- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
3102 |
that used to hide exch2 or cubed-sphere specific code |
3103 |
(commented via 'cph-exch2') |
3104 |
o pkg/seaice |
3105 |
- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
3106 |
o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
3107 |
output of global_ocean.cs32x15.thsice . |
3108 |
|
3109 |
checkpoint59e (2007/07/26) |
3110 |
o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
3111 |
for B-grid vector (not yet tested) and C-grid vector (<- only used |
3112 |
when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). |
3113 |
o starting implementation of Duffy et al. (GRL 1999) salt plume scheme |
3114 |
(#ifdef ALLOW_SALT_PLUME) |
3115 |
o gather_2d/scatter_2d: removed halo regions |
3116 |
o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
3117 |
scheme and the corresponding test case (under front_relax dir). For now, |
3118 |
only available with Skew-flux form and not yet tested in realistic set-up. |
3119 |
adjoint: store directives updated, but gradient checks deteriorated, |
3120 |
so maybe GM/Redi adjoint is now broken. |
3121 |
o seaice adjoint |
3122 |
* add AREA, HEFF, HSNOW as control variable |
3123 |
(should not change lab_sea results) |
3124 |
* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
3125 |
o pkg/seaice: |
3126 |
* added computation of saltFlux in seaice_growth; |
3127 |
For time being, sea ice salinity is assumed constant |
3128 |
contribution of snow flooding to freshening of sea ice is neglected. |
3129 |
SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
3130 |
defaults to 0.0 in order to maintain backward compatibility. |
3131 |
Typical values for SEAICE_salinity are 4 to 10 g/kg. |
3132 |
* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
3133 |
* added SEAICE_availHeatFrac, which specifies fraction of surface level |
3134 |
heat content used to melt or grow ice |
3135 |
* commented out cap of HICE: it helps keep ice thinner |
3136 |
* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
3137 |
* applied OBCS T/S mask to HEFFM sea ice mask |
3138 |
|
3139 |
checkpoint59d (2007/06/21) |
3140 |
o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
3141 |
for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
3142 |
(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
3143 |
o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
3144 |
and change default value of parameter "GM_Small_Number"; |
3145 |
update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
3146 |
global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
3147 |
tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
3148 |
o pkg/ecco: cost function when applying pkg/smooth to controls |
3149 |
o pkg/ctrl: add forcingPrecond run time parameter |
3150 |
o pkg/seaice: |
3151 |
- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
3152 |
- fix bug in metric terms of u-equation in LSR solver (implicit part), |
3153 |
changes verification/lab_sea |
3154 |
- rearrange implicit part of u-equation in LSR solver to make it easier to |
3155 |
read, understand, and debug. This causes changes at the truncation level. |
3156 |
- fix (serious) bug in the boundary conditions (sign error in the implicit |
3157 |
part) of the LSR solver. Changes all LSR results. |
3158 |
- fixed problem with HSNOW initialization to avoid thick snow when AREA |
3159 |
is initilized with small values - does not change lab_sea results. |
3160 |
- added HsnowFile initialization capability |
3161 |
o pkg/smooth: addition to model/src and pkg/ctrl so allow |
3162 |
initialization of pkg/smooth and application to control vector |
3163 |
o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
3164 |
o dependencies: pkg/profiles requires pkg/cal |
3165 |
o pkg/profiles: |
3166 |
- added option ALLOW_PROFILES_GENERICGRID |
3167 |
-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
3168 |
that interpolation information (grid points and coefficients) is provided |
3169 |
within the netcdf input files. |
3170 |
-> sample matlab scripts can be found in MITgcm_contrib/gael |
3171 |
that allow you to prepare netcdf input files. |
3172 |
- also modified: cleaner include statements, cleaner error print statements, |
3173 |
cleaner stops when error, and more tests of the netcdf input files consistency. |
3174 |
o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
3175 |
o pkg/seaice: |
3176 |
- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
3177 |
requires a new routine: seaice_diagnostics_fill.F |
3178 |
- make sure that seaice does not move if not forced (pressure replacement |
3179 |
method, Hibler and Ip, 1995), changes results |
3180 |
- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
3181 |
- SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). |
3182 |
It is turned off by default (=-1.), because it changes the results. |
3183 |
- make it possible to read AREA from a file, too. |
3184 |
|
3185 |
checkpoint59c (2007/06/04) |
3186 |
o add S/R and diagnostics for oceanic mixed-layer depth |
3187 |
o move GMRedi call after all vertical mixing schemes (including KPP) |
3188 |
o pkg/thsice: |
3189 |
- ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs |
3190 |
(melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice |
3191 |
o pkg/obcs: |
3192 |
- bug fix for balance code |
3193 |
o pkg/seaice: |
3194 |
- allow values of SEAICE_elasticParm > 1 |
3195 |
- add new parameter SEAICE_evpTauRelax as an alternative |
3196 |
to SEAICE_elasticParm |
3197 |
- make lsr boundary conditions free slip (by default), changes result |
3198 |
- add code for no slip boundary conditions for lsr |
3199 |
- set minimum of zeta to zero (and not 4e8) (changes results) |
3200 |
- add a cap on AREA after advecting AREA if seaice_growth is not called |
3201 |
o change calculation of Visbeck K: |
3202 |
- no longer depend on tapering scheme; instead, compute slope (limited |
3203 |
by GM_maxSlope). this is equivalent to what was comuted before with |
3204 |
clipping or linear tappering. |
3205 |
- fix vertical averaging (wrong by 1/2 level) |
3206 |
- leave the old version (but will not be maintained) within |
3207 |
#ifdef OLD_VISBECK_CALC / #endif |
3208 |
- update output of exp. ideal_2D_oce |
3209 |
o change error catch in calc_r_star to improve vectorization |
3210 |
o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
3211 |
add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
3212 |
o adjoint: |
3213 |
Re-organized adjoint checkpointing according to Matt Mazloff |
3214 |
(but with modifs/completions/cleanups) |
3215 |
Storing is now bundled into large arrays to optimized I/O |
3216 |
(and second step in cleanup of the_main_loop) |
3217 |
|
3218 |
checkpoint59b (2007/05/16) |
3219 |
o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
3220 |
- export/import (between ocean & coupler) fields needed for ocean DIC. |
3221 |
o pkg/seaice: |
3222 |
- get rid of three more exchanges seaice_calc_viscosities (required |
3223 |
different loop boundaries in seaice_lsr and seaice_ocean_stress) |
3224 |
- bug fix in seaice_ocean_stress (update of lab_sea required) |
3225 |
- reduce loop boundaries to necessary minimum also in seaice_evp |
3226 |
- go back to the old way of computing deltaC/Z as the adjoint likes that |
3227 |
better |
3228 |
o Refresh of tutorial_global_oce_latlon (includes changing salinity-like |
3229 |
passive tracer to an Age Tracer) + update output.txt |
3230 |
o pkg/exf: |
3231 |
- implement A-grid / C-grid selection for wind-stress input files. |
3232 |
- clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) |
3233 |
for now, in exf_bulk_largeyeager04.F only : |
3234 |
- change implementation for case where windspeed + 2. components wind-stress |
3235 |
are read-in. AND use rhoConstFresh to convert evap. |
3236 |
o pkg/seaice: |
3237 |
- use correct EXCH_UV for wind-forcing (on A-grid). |
3238 |
- change SEAICE_OPTIONS.h to limit the number of option combinations (regarding |
3239 |
SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops. |
3240 |
o pkg/exf: |
3241 |
- default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC) |
3242 |
EXF_INTERPOLATION: |
3243 |
- merge global_with_exf/code version of exf_interp_read.F |
3244 |
to the main code ; |
3245 |
- Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when |
3246 |
reading the file ; Important: This options needs to be defined to recover |
3247 |
previous code. |
3248 |
otherwise, use fixed size array to read in (size=exf_interp_bufferSize). |
3249 |
- no longer loose real*8 precision along the way when using exf_iprec=64. |
3250 |
o pkg/seaice: rearrangement of common blocks (really needs more cleaning up) |
3251 |
- change discretisation of evp-solver in order to avoid another exchange |
3252 |
(changes lab_sea) and clean up a little |
3253 |
- replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS) |
3254 |
help the adjoint (this also changes the results slightly) |
3255 |
- add a few "_d 0" where they had been missing in seaice_evp.F |
3256 |
- cleaning up: remove unused seaice_calc_rhs.F |
3257 |
o pkg/exf: some cleaning-up: |
3258 |
- change various "constants" into runtime parameters |
3259 |
- cleaned-up Large&Yeager04 routine which should eventually |
3260 |
replace exf_bulkformulae.F (changed names of S/R and CPP) |
3261 |
and merged various ALLOW_ATM_WIND options |
3262 |
only used with thsice pkg (in thsice_get_exf.F): |
3263 |
- implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04) |
3264 |
which are used when useStabilityFct_overIce=TRUE (= the default) |
3265 |
- change default values of ice & snow emissivity and scale downward LW |
3266 |
by ice & snow emissivity. |
3267 |
o pkg/thsice: |
3268 |
fix few little problems, in thsice_calc_thickn.F: |
3269 |
- growth vertically (and not laterally) if iceFrac == iceMaskMax |
3270 |
- melt only laterally if hIce < hThinIce (as the comments say) |
3271 |
and in thsice_extend.F: |
3272 |
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
3273 |
- start to form ice as soon as the minimum ice-volume is reachable. |
3274 |
update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice), |
3275 |
and cpl_aim+ocn |
3276 |
o pkg/kpp |
3277 |
- move computation of surface related input fields to KPP into a new |
3278 |
subroutine kpp_forcing_surf.F |
3279 |
- remove wrong (within bi,bj loops) EXCH calls. |
3280 |
- little cleaning (add argument myThid in last position, cvs header ...) |
3281 |
- for now, fix conservation problem by exchanging KPPviscAz (may not |
3282 |
be the best fix) |
3283 |
o pkg/seaice |
3284 |
- check for inconsistent evp parameter/cpp-flag combination |
3285 |
- remove leftover errIO flat for obsolete name list error handling |
3286 |
o OpenAD |
3287 |
- changed verification/OpenAD to full baroclinic setup (including GM/Redi) |
3288 |
|
3289 |
checkpoint59a (2007/05/01) |
3290 |
o pkg/seaice: some parameter clarifications and a little bit of clean up |
3291 |
o pkg/thsice: rename run-time parameters: |
3292 |
himin -> hIceMin |
3293 |
himin0 -> hThinIce |
3294 |
hihig -> hThickIce |
3295 |
i0 -> i0swFrac |
3296 |
transCoef -> bMeltCoef |
3297 |
frac_energy -> fracMelting |
3298 |
add new parameters: hNewIceMax, fracFreezing, dhSnowLin |
3299 |
with default values (for now) that do not change the results. |
3300 |
remove old version of thsice vars advection in pkg/seaice. |
3301 |
o in FFIELDS.h: |
3302 |
- replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD |
3303 |
- make pLoad & sIceLoad always available (but still only used if |
3304 |
ATMOSPHERIC_LOADING is #define). |
3305 |
o pkg/kpp: replaced _KPP_RL with _RL |
3306 |
o bug fixes for vertical diffusivity computations when both KPP and |
3307 |
3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F |
3308 |
are no longer updating the vertical diffusivity array |
3309 |
(passed as argument) but are (re-) setting those arrays. |
3310 |
o pkg/seaice: fix bug in evp solver, while doing that |
3311 |
- change (improve?) discretization of stress computations for both |
3312 |
cgrid-lsr and evp solver |
3313 |
- add a new routine to compute strain rates |
3314 |
- the above changes lab_sea results |
3315 |
- add no slip conditions for evp solver (off by default), lsr-version |
3316 |
may follow |
3317 |
- fix exchange for shear at Z-points (does not change lab_sea) |
3318 |
- retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp |
3319 |
(to force the user to pick a time step since there is not "safe" way |
3320 |
of choosing it) |
3321 |
- add principal stress diagnostics |
3322 |
- rearrange fields for evp a little to avoid having to call a: too many |
3323 |
exchanges and b: exchanges for stress trensor components which we do |
3324 |
not have. |
3325 |
- modify Hibler+Bryan (1987) stress coupling so that it reuses information |
3326 |
of evp, complete rewrite for lsr case (latter is does not yet work |
3327 |
in all cases) |
3328 |
o pkg/kpp: add code to have mixing in shelf ice caverns |
3329 |
- add myThid to all kpp routines (long overdue) |
3330 |
|
3331 |
checkpoint59 (2007/04/19) |
3332 |
o pkg/exf: |
3333 |
- fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND & |
3334 |
ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid |
3335 |
- move exf header files from lower_case.h to UPPER_CASE.h ; |
3336 |
add missing cvs Header & Name |
3337 |
- add adjoint routines and flow dirs for newly used exch_uv_agrid routines |
3338 |
- add namelist param. selectStressGridPosition, exf_monFreq |
3339 |
- retire many _CLIM routines, and remove data.exf_clim |
3340 |
+ params moved to data.exf |
3341 |
+ climsst, climsss now handled by exf_set_gen, i.e. |
3342 |
climss?period=0 refers to constant field, |
3343 |
climss?period=-12 to monthly forcing |
3344 |
- split up namelists in data.exf |
3345 |
o pkg/seaice: |
3346 |
- remove seaice_exch and seaice_exch_uv |
3347 |
- remove superfluous exchange of theta |
3348 |
- add myThid to seaice_budget_ocean/ice |
3349 |
- add new interface for atmospheric wind forcing (C-grid only) |
3350 |
+ new routine |
3351 |
+ two new field (taux, tauy for stress over ice) |
3352 |
+ removed one global field (DAIRN) for C-grid case only |
3353 |
o pkg/thsise |
3354 |
- 2nd set of modifs for thsice adjoint in conjunction with exf |
3355 |
o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.) |
3356 |
|
3357 |
checkpoint58y_post (2007/04/15) |
3358 |
o Added capability for latitudinal dependence of Bryan and Lewis, 1979 |
3359 |
vertical diffusivity, similar to that in MOM4; turned on using |
3360 |
#define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using |
3361 |
diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file. |
3362 |
o Added capability for 3D specification of background vertical diffusion |
3363 |
coefficient. This is done by (i) #define ALLOW_3D_DIFFKR |
3364 |
in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime |
3365 |
"data" file that contains the 3D vertical diffusivity coefficients. |
3366 |
o ice dynamics (pkg/seaice) with thsice thermodynamics: |
3367 |
- add code within pkg thsice to advect & diffuse sea-ice fields |
3368 |
similar to (and will replace) what has been added in seaice_advdiff.F, |
3369 |
but: - conserving Mass, Heat & Salt. |
3370 |
- better when using non-linear advection scheme (not yet fully tested) |
3371 |
- can also be used in atmospheric set-up (for now, only the diffusion). |
3372 |
|
3373 |
checkpoint58x_post (2007/04/04) |
3374 |
o IO option for global-file compact format: |
3375 |
- add options when generating topology (utils/exch2/matlab-topology-generator) |
3376 |
- add I/O capability (pkg/mdsio). |
3377 |
- adapt utils/matlab/rdmds.m to read this format. |
3378 |
for now long-line format not yet supported by pkg/mdsio (& exch2). |
3379 |
o shelfice: add a few diagnostics |
3380 |
|
3381 |
checkpoint58w_post (2007/03/13) |
3382 |
o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: |
3383 |
rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref |
3384 |
(and replace horiVertRatio in NH code). |
3385 |
Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) |
3386 |
and tutorial_plume_on_slope (sensitive to truncation) |
3387 |
o seaice: if ALLOW_ATM_WIND is undefined use wind stress |
3388 |
directly to drive seaice model (C-grid only) |
3389 |
o exf: when input wind-stress (#undef ALLOW_ATM_WIND): |
3390 |
- reintroduce computation of wind from stress, |
3391 |
- compute tau (in exf_bulkformulae.F) from windstress averaged to |
3392 |
mass points to avoid tau = 0 |
3393 |
- fix serious bug: (1/3) in Fortran is not the same as (1./3.) |
3394 |
o rdmnc.m: make it work with "global" files created with gluemnc |
3395 |
o rdmnc.m : some improvements in dealing with singleton dimension |
3396 |
(tested on all testreport mnc output files). |
3397 |
o genmake2: disable pkg/profiles if netcdf test fails. |
3398 |
o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output. |
3399 |
o move call to cal_readparms up to make calendar parameters/variable available |
3400 |
to all packages |
3401 |
|
3402 |
checkpoint58v_post (2007/02/08) |
3403 |
o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get |
3404 |
useDynP_inEos_Zc tested. |
3405 |
o pkg/exf: changes to properly interpolate/mask/scale initial fields |
3406 |
o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields |
3407 |
and portions thereof. See read_cs.txt for description and examples. |
3408 |
o utils/matlab/cs_grid/bk_line: to compute transport through passages, |
3409 |
add a script (grt_circ_bkl.m) to generate broken-line between 2 points, |
3410 |
following the great-circle arc between those 2 points. |
3411 |
o trap un-initialized variable with pathscale compiler on weddell.mit.edu |
3412 |
(thanks to Constantinos): fix few problems and get (almost) all exp to pass. |
3413 |
o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in |
3414 |
- enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) |
3415 |
- used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81) |
3416 |
- still needs work (not working with some options ; efficiency to improve) |
3417 |
and serious testing. |
3418 |
- use this scheme for temperature & salinity in 2 advection test exp.: |
3419 |
advect_xy & advect_xz, respectively. |
3420 |
|
3421 |
checkpoint58u_post (2007/01/12) |
3422 |
o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. |
3423 |
o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. |
3424 |
o testreport: add option "-skipdir" to skip some test. |
3425 |
o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent |
3426 |
momentum calculation. |
3427 |
o gad_advection: fix vertAdvecScheme (if different from advectionScheme) |
3428 |
o some cleaning: usePickupBeforeC35 no longer supported ; remove this option. |
3429 |
remove checkpoint.F and the_correction_step.F (no longer used); |
3430 |
do the k loop inside CYCLE_TRACER (supposed to be more efficient). |
3431 |
o add option (linFSConserveTr) to correct for tracer source/sink due to |
3432 |
Linear Free surface |
3433 |
o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine |
3434 |
o pkg/thsice: fix reading mnc-pickups |
3435 |
|
3436 |
checkpoint58t_post (2006/12/30) |
3437 |
o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) |
3438 |
o pkg/mdsio: |
3439 |
- clean-up mdsio_readfield.F & mdsio_writefield_new.F and |
3440 |
move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & |
3441 |
mdsio_write_field.F (S/R MDS_WRITE_FIELD); |
3442 |
- fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD |
3443 |
- collect old S/R in one file: mdsio_rw_field.F (now just a call to |
3444 |
either MDS_READ_FIELD or MDS_WRITE_FIELD ) |
3445 |
- new S/R (to replace MDSWRITEMETA), which allows to write more |
3446 |
informations (variable names, time ...) to meta files. |
3447 |
- modify rdmds.m to give back the meta file content. |
3448 |
o pkg/diagnostics: change vertical interpolation to be safer, and more |
3449 |
flexible (define p-levels to interpolate to in data.diagnostics); |
3450 |
add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right |
3451 |
diagnostic pointer. |
3452 |
o pkg/seaice: more cleaning up of seaice_growth, added many comments |
3453 |
o pkg/exf: put runoff0 and runoff1 into the appropriate common block |
3454 |
o fix multi-category seaice: |
3455 |
- change cpp flag SEAICE_MULTILEVEL to more meaningful name: |
3456 |
SEAICE_MULTICATEGORY |
3457 |
- fix short wave heat flux |
3458 |
o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics |
3459 |
and allow to use EVP solver. Change forward lab_sea: test both EVP |
3460 |
solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) |
3461 |
o Initial check-in of lab_sea adjoint |
3462 |
(very similar to natl_box_adjoint/code_seaice) |
3463 |
* used C-grid and EVP solver |
3464 |
* used KPP, GM/Redi |
3465 |
* uses inAdExact=.TRUE. |
3466 |
* gradient checks fail for both ADM and TLM |
3467 |
due to sensitive snow melt code in seaice_grwoth (look for "JZ") |
3468 |
f.d. gradients actually seem more problematic than ADM, TLM gradients; |
3469 |
issue is related to forward mismatch between g77 an ifort |
3470 |
o pkg/seaice: overhaul of thermodynamics |
3471 |
- growth.F and groatb.F are replaced by new routine seaice_growth.F |
3472 |
- budget.F is replaced by two new routines seaice_budget_ocean/ice.F |
3473 |
- move a few global fields out of SEAICE.h into seaice_growth.F and |
3474 |
make them 2D (FICE/QNETO/ ...) |
3475 |
- remove FO (it is the same as QNETO) |
3476 |
- introduce a few local fields to avoid modifying external fields such |
3477 |
as atemp, etc. |
3478 |
|
3479 |
checkpoint58s_post (2006/12/11) |
3480 |
o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F |
3481 |
changed exf_set_gen.F so that |
3482 |
genperiod=0 means input file is one time-constant field and |
3483 |
genperiod=-12 means input file contains 12 monthly means |
3484 |
o CG2D: use pre-computed solver main-diagonal (stored in common block); |
3485 |
this affects truncation error ; generate new output file for exp. which |
3486 |
fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), |
3487 |
global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), |
3488 |
ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), |
3489 |
MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), |
3490 |
tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), |
3491 |
vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) |
3492 |
o start implementation of deep-atmosphere and anelastic formulation |
3493 |
o verification: remove 2nd copy of input files and use script "prepare_run" |
3494 |
to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) |
3495 |
o mom_common/vecinv/fluxform: fix a few initialisation isssues |
3496 |
o profiles: fix for multithreaded case |
3497 |
|
3498 |
o diagnostics: rename few diags: |
3499 |
s/'PRESSURE'/'RCENTER '/g |
3500 |
s/'TICE '/'oceFreez'/g |
3501 |
s/'TAUX '/'oceTAUX '/g |
3502 |
s/'TAUY '/'oceTAUY '/g |
3503 |
s/'SWFLUX '/'oceQsw '/g |
3504 |
s/DIFx/DFxE/g |
3505 |
s/DIFy/DFyE/g |
3506 |
and add few ocean-forcing diagnostics: |
3507 |
atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS |
3508 |
o modifications to pkg/seaice/growth.F and budget.F, which change results of |
3509 |
lab_sea experiment: HSNOW was sometimes treated as effective and sometimes |
3510 |
as actual snow thickness. It now refers everywhere to effective snow |
3511 |
thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. |
3512 |
|
3513 |
checkpoint58r_post (2006/11/17) |
3514 |
o modifications to pkg/seaice/growth.F, which change results of |
3515 |
lab_sea experiment: fixes pertain to melting snow over open water, to |
3516 |
masking EVAP under sea ice, and to using the correct AREA variable for |
3517 |
computations of EVAP, PRECIP, HSNOW, and GHEFF |
3518 |
o add ability to read bathy, salt, and theta using MNC (off by def) |
3519 |
o add flooding algorithm and advection of HSNOW for pkg/seaice; |
3520 |
both are turned off by default and do no change any results |
3521 |
o seaice advection with pkg/thsice: a step toward the use of non-linear |
3522 |
advection scheme, but #ifdef or commented out for now (requires more EXCH). |
3523 |
o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens |
3524 |
(identical results) and the standard version of EXTERNAL_FIELDS_LOAD |
3525 |
in natl_box (affects results @ truncation level: update output.txt) |
3526 |
o multi-threading and IO: |
3527 |
- replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. |
3528 |
- remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls |
3529 |
(needed to work with SingleCpuIO): tested in all verif. exp. |
3530 |
o GAD: use simpler DST3 formulation as default (old version left within #ifdef) |
3531 |
affects the results (but none of the verification test uses this scheme). |
3532 |
o Adding some pkg/diagnostics capability to pkg/seaice |
3533 |
(will certainly be subject to changes) |
3534 |
o ctrl: adding new control variables: |
3535 |
lwflux, lwdown, evap, snowprecip, apressure, runoff |
3536 |
|
3537 |
checkpoint58q_post (2006/10/20) |
3538 |
o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up |
3539 |
1/6-deg Southern Ocean configuration by 8% on IBM Datastar and |
3540 |
high_res_cube configuration by 4% on Columbia. |
3541 |
o clean-up multi-threaded problems (reported by debugger tcheck on ACES); |
3542 |
add (in global_with_exf/code) a version of EXF_INTERP_READ without |
3543 |
dynamical allocation (seems to work in multi-threaded). |
3544 |
o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using |
3545 |
single CPU io) so that TAF does not have to see EESUPPORT.h |
3546 |
o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
3547 |
|
3548 |
checkpoint58p_post (2006/09/08) |
3549 |
o obcs: stop if obcs is used with useCDscheme = .true. |
3550 |
o shelfice: |
3551 |
- fix a sign error so that no slip at shelfice interface works |
3552 |
- remove stop for combination non-hydrostatic code and shelfice. That does |
3553 |
not mean, that the results are correct, but at least they are numerically |
3554 |
stable |
3555 |
o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) |
3556 |
o added adjoint exch routined for all exch*3d* routines |
3557 |
and updated flow directives |
3558 |
|
3559 |
checkpoint58o_post (2006/08/28) |
3560 |
o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; |
3561 |
remove old subroutines (_XY_ & _XYZ_); update the adjoint version. |
3562 |
o change controling S/R for writing pickup file (new S/R do_write_pickup) |
3563 |
and clean-up reading/writing of pickup files. |
3564 |
o fix local version of read/write pickup (NH part) in rotating_tank/code |
3565 |
o simplify EXCH interface: |
3566 |
- change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) |
3567 |
- not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version |
3568 |
o added the regrid package |
3569 |
o shelfice: |
3570 |
- add a simple boundary layer scheme to reduce noise |
3571 |
- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
3572 |
|
3573 |
checkpoint58n_post (2006/08/14) |
3574 |
o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
3575 |
local variable (not in common block). |
3576 |
o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
3577 |
- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
3578 |
- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
3579 |
to work with SingleCpuIO. |
3580 |
o add "_d 0" to real constant of pkg/cfc subroutines ; |
3581 |
update exp. cfc_exemple & tutorial_cfc_offline output files. |
3582 |
o multi-threading and IO: |
3583 |
- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
3584 |
(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
3585 |
- barrier before and after reading. |
3586 |
- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
3587 |
- avoid using MDS_WRITELOCAL for LAND pkg output. |
3588 |
- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
3589 |
common-block variables ; Allows multi-threading with master-thread IO. |
3590 |
o change default MAX_NO_THREADS from 32 to 4 ; |
3591 |
and stop cleanly when MAX_NO_THREADS is too small. |
3592 |
o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
3593 |
|
3594 |
checkpoint58m_post (2006/07/17) |
3595 |
o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
3596 |
and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
3597 |
o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
3598 |
keep global_ocean.90x40x15 (for AD testing) with former secondary test |
3599 |
(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
3600 |
o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
3601 |
add MITgcm_tutorials (= code + all the tutorials) |
3602 |
o ecco, option to compute cost for total ssh (mean+anom) |
3603 |
o consistent with addition of ptracer and ssh in pkg/profiles |
3604 |
o profiles: adding ptracer and ssh |
3605 |
o testreport: change multi-test output-file name |
3606 |
(from output.txt.{name} to output.{name}.txt) |
3607 |
o profiles: now ok for mutli-tiles case |
3608 |
o seaice: add 4 parameters for different advection schemes for area, |
3609 |
(effective) seaice thickness, enthalphy, and snow height. Their default |
3610 |
is the standard parameter SEAICEadvScheme |
3611 |
o calc_gw: |
3612 |
- add cosFacU in zonal viscous flux (harmonic.visc.). |
3613 |
- put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. |
3614 |
of tutorial_plume_on_slope. |
3615 |
o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). |
3616 |
o calc_gw: true flux-form, account for horizontal grid spacing. |
3617 |
update rotating_tank results, but not plume_on_slope (affected at |
3618 |
truncation level, 11 digits). |
3619 |
|
3620 |
checkpoint58l_post (2006/07/12) |
3621 |
o calc_gw: |
3622 |
- take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V |
3623 |
- remove side-drag for now (need to fix it); update plume_on_slope results. |
3624 |
- fix for partial-cell & non-uniform dz; update plume_on_slope results. |
3625 |
o commit code to make SST/SSS weights spatially variable |
3626 |
(based on either variable in-situ or variable initial T/S weights) |
3627 |
o pkg/ecco: |
3628 |
* commit code to relax deviations of xx_theta, xx_salt to 5*sigma, |
3629 |
now based on horizontally varying weights wthetaLev, wsaltLev |
3630 |
* cost_averagesflags now returns year indices in addition to day, month |
3631 |
* sflux balance is performed on annual basis |
3632 |
(sflxumm, sfluxmm2, bal_sfluxmm) |
3633 |
* for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, |
3634 |
including separate counting and multipliers |
3635 |
o pkg/rbcs |
3636 |
* add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing |
3637 |
|
3638 |
checkpoint58k_post (2006/07/06) |
3639 |
o testreport: |
3640 |
- always build in dir. "build" (if not there, mkdir build instead of building |
3641 |
& running in input) |
3642 |
- run in dir run (if it exists), in build otherwise. |
3643 |
- call prepare_run (if input/prepare_run exists) |
3644 |
- run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. |
3645 |
o pkg/exf modifications to interpolation and rotation routines for more |
3646 |
reasonable treatment of North Pole singularity: for tracers North Pole |
3647 |
value is set to northernmost zonal-mean value, for zonal velocity it is |
3648 |
set to zero, and for meridional velocity it is set to northernmost value. |
3649 |
o pkg/exf/exf_check_range.F |
3650 |
- add tile index to diagnostics and move stop statement to the very |
3651 |
end of the routine. |
3652 |
o pkg/diagnostics: (diagnostics_main_init.F) |
3653 |
define title of isomorphic variables according to the current config. |
3654 |
o pkg/thsice with pkg/seaice dynamics: |
3655 |
- fix domain of computation (interior only, required for exf) and do exchanges |
3656 |
- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient |
3657 |
o towards a standard way of dealing with multi-threading in MONITOR |
3658 |
and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. |
3659 |
o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) |
3660 |
to W momentum equation in nonhydrostatic and quasihydrostatic runs. |
3661 |
o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. |
3662 |
o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) |
3663 |
o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL |
3664 |
(problems ? with gradient check in bottom_ctrl_5x5 adjoint test) |
3665 |
o tracer advection: |
3666 |
- clean-up and simplify calc_common_factors.F |
3667 |
- make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer |
3668 |
advection subroutine (but still not used within DST advection S/R) |
3669 |
o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
3670 |
|
3671 |
checkpoint58j_post (2006/06/15) |
3672 |
o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
3673 |
from file (collects calls previously in FORWARD_STEP) |
3674 |
o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS |
3675 |
o adjoint store dir. adjusted accordingly |
3676 |
o genmake2 |
3677 |
replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. |
3678 |
|
3679 |
checkpoint58i_post (2006/06/14) |
3680 |
o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
3681 |
on wind stress (SEAICEstressFactor defaults to 1.) |
3682 |
o Total number of Timers is finite (<=40): comment out 2 non-essential one |
3683 |
in the_main_loop.F to avoid Pb (e.g., when running fizhi test) |
3684 |
o vector_invariant: fix highOrderVorticity(=4.th.Order) advection |
3685 |
on CS-grid: no longer loosing mass. |
3686 |
o exf & curvilinear-grid: no longer modify longitude xC & xG. |
3687 |
o pkg/ggl90: fix sloppy output and fix a bug |
3688 |
o pkg/seaice: added SEAICEuseEVPpickup parameter |
3689 |
- Set to false in order to start EVP solver with |
3690 |
non-EVP pickup files when using SEAICEuseEVP |
3691 |
- fix sign error in diffusion in seaice_calc_rhs |
3692 |
|
3693 |
checkpoint58h_post (2006/06/07) |
3694 |
* Modifications for bottom topography control |
3695 |
o replace hFacC by _hFacC at various places |
3696 |
o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL |
3697 |
o add non-self-adjoint cg2d_nsa |
3698 |
o update autodiff support routines |
3699 |
o re-initialise hfac after ctrl_depth_ini |
3700 |
o works for 5x5 box, doesnt work for global_ocean.90x40x15 |
3701 |
* Adding verification for 5x5 box (4-layer) bottom topography control |
3702 |
|
3703 |
checkpoint58g_post (2006/06/07) |
3704 |
o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., |
3705 |
used for mean seasonal cycle, mean diurnal cycle); add an example |
3706 |
in verification/global_ocean.cs32x15/input.thsice/data.diagnostics |
3707 |
o pkg/ggl90: |
3708 |
- add parameter (minimum surface kinetic energy) |
3709 |
- fix bug (avoiding division by zero) |
3710 |
o couple pkg/thsice to pkg/seaice: |
3711 |
- modify advection in seaice to accomodate new scalar fields to be advected |
3712 |
- only muliDimAdection scheme work with seaice/thsice |
3713 |
- mapping of thsice-variables to seaice-variables, back and forth |
3714 |
- does not break the verification experiments, but does not give the |
3715 |
desired results either |
3716 |
o pkg/seaice |
3717 |
- make (default) second order advection a bit less confusing? |
3718 |
|
3719 |
checkpoint58f_post (2006/06/05) |
3720 |
o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice |
3721 |
to pkg/seaice): |
3722 |
- new routines thsice_map_exf and thsice_get_exf provide the interface |
3723 |
- add an additional formal parameter to thsice_solve4temp |
3724 |
o pkg/exf: |
3725 |
- add new fields wspeed, snowprecip (to be able to couple to thsice) |
3726 |
- correct Stefan-Boltzmann constant |
3727 |
- new parameter for longwave surface emittance |
3728 |
- separate some stuff from exf_bulkformulae into new routines |
3729 |
exf_radiation, exf_wind |
3730 |
- add new parameters and constants: longwave emissivity for ocean, ice |
3731 |
and snow, evaporation parameters over ice |
3732 |
- decouple wind/stress computation from ALLOW_BULKFORMULA: always compute |
3733 |
either wind from stress or stress from wind |
3734 |
o pkg/thSIce: |
3735 |
- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F |
3736 |
- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND |
3737 |
and THSICE_CALC_THICKN |
3738 |
- for now, call to THSICE_GET_BULKF remains inside i,j loops. |
3739 |
- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h |
3740 |
to make debugging easier. |
3741 |
- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output |
3742 |
o pkg/bulk_force: |
3743 |
- clean-up comments and parameters ; |
3744 |
- add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; |
3745 |
o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; |
3746 |
generate new output for test-experiment: aim.5l_cs.thSI |
3747 |
o results_ad : rename "output.txt_adm" to "output_adm.txt" and change |
3748 |
testreport accordingly |
3749 |
|
3750 |
checkpoint58e_post (2006/05/17) |
3751 |
o SEAICE_CGRID adjoint done |
3752 |
o R_STAR adjoint implemented. |
3753 |
* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
3754 |
* need to sort out init. of h0facc, etc. |
3755 |
o Make pkg/profile fully independent of ecco,cost, etc. stuff |
3756 |
to be able to use it in pure forward. |
3757 |
|
3758 |
checkpoint58d_post (2006/04/21) |
3759 |
o upgrade simple test-experiment to tutorial example: |
3760 |
step.1: duplicate the experiment and (step.2) will remove the old copy. |
3761 |
tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
3762 |
tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) |
3763 |
tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
3764 |
tutorial_global_oce_biogeo <- copy of dic_example |
3765 |
tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
3766 |
tutorial_plume_on_slope <- copy of plume_on_slope |
3767 |
tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) |
3768 |
tutorial_global_oce_optim <- empty for now (David ?) |
3769 |
tutorial_global_oce_in_p <- copy of global_ocean_pressure |
3770 |
some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
3771 |
o correct a sign problem in cost_scat.F |
3772 |
o obcs and ptracers: fix boundary conditions for advections schemes |
3773 |
with larger stencil |
3774 |
o thsice adjoint: start |
3775 |
o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for |
3776 |
completeness |
3777 |
o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING |
3778 |
and COSINEMETH_III, add comments in default CPP_OPTIONS.h |
3779 |
o ptracers adjoint: |
3780 |
* avoid extensive recomputatations |
3781 |
* fix missing re-init. of gptr (missed by TAF) |
3782 |
o obcs: add a flag (OBCSprintDiags, defaults is true) that allows |
3783 |
me to turn off the excessive output to STDOUT that this package produces |
3784 |
o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common |
3785 |
and add those terms in Vector-Invariant formulation. |
3786 |
o in ctrl pkg, if ALLOW_CAL, use monthly mean controls |
3787 |
if the control period (xx_hfluxperiod etc) is 0 |
3788 |
o in profiles pkg, clean routines and fix details |
3789 |
o in ecco pkg, reading ssh data: |
3790 |
fix problem in case the model does not start at iter0=0 |
3791 |
o fix mnc-pickup/restart for ptracers |
3792 |
o new package prifiles: |
3793 |
code to compute profile-based cost by Gael Forget |
3794 |
(modifs in ecco, ctrl, autodiff) |
3795 |
o Benign bug fix in initialization (spotted by M. Mazloff) of |
3796 |
ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F |
3797 |
|
3798 |
checkpoint58c_post (2006/03/23) |
3799 |
o adjoint: finish NLFS adjoint and provide reference output in |
3800 |
verification/global_ocean.90x40x15/results_ad_nlfs |
3801 |
o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the |
3802 |
documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in |
3803 |
SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only |
3804 |
with SEAICE_CGRID defined. |
3805 |
o move calendarDumps from "data" to "data.cal" and clean-up the code |
3806 |
with a simple call to pkg/cal S/R: CAL_TIME2WRITE |
3807 |
o add useEXF & useCAL flags (for now, set in hard-coded way) |
3808 |
o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum |
3809 |
(were missing in NH mode, and wrong in quasihydrostatic mode). |
3810 |
waiting for Chris updated version of calc_gw to add those CALLs. |
3811 |
o fix bug in quasihydrostatic S/R ; |
3812 |
add a test for this option: global_ocean.90x40x15.qshyd |
3813 |
o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs. |
3814 |
(called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS) |
3815 |
o add on/off flag useOffLine for package OFFLINE |
3816 |
o seaice: |
3817 |
- modify advection so that it works also on the C-grid |
3818 |
- extend loop ranges in seaice_lsr and seaice_dynsolver; fixes |
3819 |
problem in multi-tile runs with C-grid |
3820 |
- add flags for clipping ice velocities and/or masking solver forcing |
3821 |
- fix drag (ocean on ice) formulation and a bug that caused noise in the |
3822 |
C-grid solver |
3823 |
- added a few comments to seaice_diffusion.F |
3824 |
- separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V |
3825 |
are now exclusive) |
3826 |
- add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which |
3827 |
required re-ordering the code a little: |
3828 |
+ make DAIRN global variable (defined in SEAICE) |
3829 |
+ move computation of the viscosities eta and zeta into a new separate |
3830 |
routine (because I need to recompute them in seaice_ocean_stress.F) |
3831 |
|
3832 |
checkpoint58b_post (2006/03/13) |
3833 |
o AIM+thSIce: fix sign of Short-Wave through the Ice ; |
3834 |
update output.txt of exp. aim.5l_cs.thSI |
3835 |
o various mnc cleanups and improvements: |
3836 |
+ shrink lookup tables by factor of ~4 |
3837 |
+ better error reporting when running out of lookup space |
3838 |
+ able to handle longer path/file names (up to 500 chars) |
3839 |
o adjoint: |
3840 |
- Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. |
3841 |
- TBD: "hidden" mom_vecinv recomp. in dynamics |
3842 |
o change forcing_In_AB to affects both T,S forcing and Momentum forcing |
3843 |
(allow to differentiate between forcing components using new integer flags: |
3844 |
momForcingOutAB=1/0 & tracForcingOutAB=1/0) |
3845 |
and add new flag to put Dissipation tendency out of Adams-Bashforth. |
3846 |
o ecco |
3847 |
- enable trend removal from SSH anomaly obs. |
3848 |
o adjoint |
3849 |
- a fix for PmEpR when #undef EXACT_CONSERV |
3850 |
- fix of "hidden" recomp. in thermodynamics (no TAF warnings) |
3851 |
- try to fix "hidden" recomp. in forward_step for NLFS |
3852 |
(NLFS seems broken sometimes after I checked it in) |
3853 |
o seaice: |
3854 |
- add c-grid version of the dynamic solver: |
3855 |
+ three new routines that are the c-grid substitute lsr, dynsolver |
3856 |
and ostres |
3857 |
+ put a few fields that were local to dynsolver into global common |
3858 |
blocks, so that I can move the computation of stresses etc into |
3859 |
seaice_lsr (saves coding but may break the adjoint). |
3860 |
- replace more hardwired parameters by runtime parameters |
3861 |
- add ice masks that mask the rhs of the implicit solvers where there |
3862 |
is no ice (commented out in seaice_dynsolver, because i am not sure |
3863 |
if this works properly), eventually this should replace the clipping |
3864 |
of ice velocities in seaice_dynsolver to +/-40cm/s. |
3865 |
o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly |
3866 |
include it only where its needed |
3867 |
o move balancing of fluxes before the call of external_forcing_surf |
3868 |
o seaice: |
3869 |
- correct units of turning angles (now they are really in degrees) |
3870 |
- move computation of GWATX/Y out of main routine into dynsolver |
3871 |
- initialize GWATX/Y in seaice_init |
3872 |
o Apply mask on Fresh-Water flux (needed for SSH forcing). |
3873 |
update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) |
3874 |
o seaice: add runtime flags for turning angles (default to zero) |
3875 |
o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean |
3876 |
and trend from exf forcing and ctrl control adjustments |
3877 |
o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF |
3878 |
(since checkpoint57x_post) |
3879 |
o change the default rotation period to 86164.s = the Earth rotation |
3880 |
o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) |
3881 |
and based on a reference stratification. Tested within hs94.cs-32x32x5. |
3882 |
o seaice advection: add code for choosing between the default (2nd order |
3883 |
central differences) and multiDim advection schemes provided by |
3884 |
pkg/generic_advdiff |
3885 |
o seaice: |
3886 |
- removed all references to SEAICE_GRID.h fields from |
3887 |
dynsolver, advect, diffus, lsr, without changing the results of lab_sea |
3888 |
(cubed-sphere configuration will change a little) |
3889 |
- grid computations in seaice_init are obsolete now. |
3890 |
- cleaned up code a little so that is easier to read (hopefully). |
3891 |
- added new (better?) discretizations of default advection and diffusion |
3892 |
(turn on with SEAICEuseFluxForm) |
3893 |
- replace 1 in 3d global fields by kSurface in growth.F |
3894 |
|
3895 |
checkpoint58a_post (2006/02/13) |
3896 |
o seaice: |
3897 |
- bug fix in advect.F |
3898 |
o shelfice: |
3899 |
- separate shelfice load anomaly from pload (breaks with time |
3900 |
dependent forcing), => introduce constant field shelficeLoadAnomaly. |
3901 |
Its default is 0., but it may be computed more cleverly from (unknown) |
3902 |
t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be |
3903 |
done offline. A good approximation of the pressure load anomaly is |
3904 |
necessary to avoid large initial adjustment processes underneath |
3905 |
deep-reaching shelfice. |
3906 |
- small fix in ISOMIP shelfice_thermodynamics |
3907 |
- add more sophisticated thermodynamics of Hellmer (1989), this is |
3908 |
now the default |
3909 |
- give a few constants more intuitive names |
3910 |
o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful |
3911 |
if bulk formulae are used in long integration (especially EmPmR). Turn |
3912 |
on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01 |
3913 |
if balancePrintMean, the imbalance that is substracted is printed to |
3914 |
STDOUT. |
3915 |
o fix bug (typo) in obcs_apply_eta.F |
3916 |
o add a new package shelfice which enables us to model the circulation |
3917 |
underneath shelf-ice with draughts of hundreds of meters. |
3918 |
- works |
3919 |
- to do: + include improved thermodynamics |
3920 |
+ check whether kSurfC (from model/inc/SURFACE.h) can be used |
3921 |
instead of new field kTopC |
3922 |
+ can we use topoFile, Ro_surf and existing code in ini_depth.F |
3923 |
instead of new field R_shelfIce and new code in ini_depth.F |
3924 |
and ini_mask_etc.F? |
3925 |
+ adjust vertical mixing schemes? |
3926 |
o seaice pkg: |
3927 |
- add a cpp-flag to include a simple formula for a salinity dependent |
3928 |
freezing point of sea water at the surface |
3929 |
- change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and |
3930 |
meridional stresses are now different (and hopefully correct) |
3931 |
o AIM pkg: change threshold on large-scale condensation to conserve Heat. |
3932 |
update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics |
3933 |
and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG) |
3934 |
o pkg/diagnostics: add options and parameters for regional-statistics |
3935 |
diagnostics ; define regions by reading a region-mask from a file |
3936 |
(might add other options later) |
3937 |
o pkg/bulk_force: |
3938 |
- add option and parameters to use AIM surface-flux formulae. |
3939 |
- Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ; |
3940 |
others forcing fields (defined in PARM05, parameter file "data") are loaded |
3941 |
from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F). |
3942 |
- initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F |
3943 |
- use the right EXCH call for uwind,vwind (to work on CS-grid). |
3944 |
- re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h) |
3945 |
and parameters (note: calcWindStress replaces .NOT.readwindstress). |
3946 |
- cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). |
3947 |
|
3948 |
checkpoint58 (2006/01/12) |
3949 |
o add "--embed-source" option to genmake2 which, when the supporting |
3950 |
tools can be compiled (as determined by genmake2) will turn on the |
3951 |
embed_files package which then embeds the entire MITgcm source code |
3952 |
(*.[fFhc] + Makefile) used for the build within the executable |
3953 |
- requested by CNH but off by default |
3954 |
- adds a paltry <9MB to the mitgcmuv executable in most cases |
3955 |
- only writes the output when useEMBEDSRC in eedata is true |
3956 |
o clean up 3-dim. relaxation codes: |
3957 |
* Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec |
3958 |
* Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) |
3959 |
* Thanks to Tom Haine for testing! |
3960 |
|
3961 |
checkpoint57z_post (2005/12/31) |
3962 |
o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): |
3963 |
affects output (@ truncation level) of exp. plume_on_slope ; updated. |
3964 |
o fix the pickup behavior for obcs in combination with ptracers |
3965 |
o fix a bug in ptracers_external_fields_load |
3966 |
o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...) |
3967 |
affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) |
3968 |
o transfered surface NH pressure to eta field (if exactConserv). |
3969 |
o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign) |
3970 |
and update lab_sea output.txt file. |
3971 |
o completing 3-dim. relaxation code: additional term |
3972 |
1/tau*( theta(i,j,k) - thetaStar(i,j,k) ) |
3973 |
in S/R EXTERNAL_FORCING_T (file external_forcing.F) |
3974 |
* At compile time, in "EXF_OPTIONS.h" set |
3975 |
#define ALLOW_CLIMTEMP_RELAXATION |
3976 |
#define ALLOW_CLIMSALT_RELAXATION |
3977 |
* At runtime in "data", under &PARM03 set (e.g., units in seconds) |
3978 |
tauThetaClimRelax3Dim = 15552000.0, |
3979 |
tauSaltClimRelax3Dim = 15552000.0, |
3980 |
* 3 cases: |
3981 |
1) Use a constant-in-time 3-dim. field |
3982 |
2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec. |
3983 |
3) Real-time relax. to time-evolving prescribed field |
3984 |
o Adding Laplacian-type smoothness constraint on |
3985 |
initial and boundary (forcing) controls (ic, bc) |
3986 |
* enable at compile-time via |
3987 |
ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION |
3988 |
* enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1 |
3989 |
* Absolute scale somewhat unclear so far |
3990 |
* no area weighting was included since no other cost term does so far |
3991 |
|
3992 |
checkpoint57y_post (2005/12/08) |
3993 |
First step for a NLFS adjoint |
3994 |
o initially suppress rStar (new flag DISABLE_RSTAR_CODE) |
3995 |
o new init. routines for calc_r_star, calc_surf_dr |
3996 |
o still need to deal with ini_masks_etc |
3997 |
o testreport seemed happy |
3998 |
checkpoint57y_pre (2005/12/08) |
3999 |
|
4000 |
o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
4001 |
o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) |
4002 |
o add new offset feature to offline pkg (plus minor cleanup) |
4003 |
o cfc fixes for final year of integration |
4004 |
o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should |
4005 |
be in GCHEM_OPTIONS). |
4006 |
|
4007 |
checkpoint57x_post (2005/12/04) |
4008 |
o fix testreport Pb in multiple test experiment. |
4009 |
o cleanup our namelist syntax in verification: |
4010 |
- make it more F95 standards compliant (some work still needed) |
4011 |
- allows the vast majority of our tests to work with gfortran |
4012 |
o Non-Hydrostatic: |
4013 |
- put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h |
4014 |
- fix exchange calls for CS-grid using the new EXCH_S3D_RL. |
4015 |
o Allow to apply AB on T,S rather than on AB(gT,gS): |
4016 |
- implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 |
4017 |
- use the same arrays (gtNm,gsNm) to hold tracer field at previous |
4018 |
time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). |
4019 |
- need a "clever" read_pickup to restart from the other AB formulation |
4020 |
o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h |
4021 |
o remove some unused variables (reduces number of compiler warnings) |
4022 |
o adjoint |
4023 |
* Disable useVariableViscosity for adjoint for time being |
4024 |
(there are a number of extensive recomputations) |
4025 |
* Initialize certain variables needed for adjoint |
4026 |
|
4027 |
checkpoint57w_post (2005/11/03) |
4028 |
o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names |
4029 |
fix the singleCpuIO RS version of MDSWRITEFIELD |
4030 |
and add a WARNING if using globalFiles=T with multi-processors. |
4031 |
o write grid-file(s) in only one format (MDS or MNC): default=MNC (if |
4032 |
using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc |
4033 |
o tracer advection scheme: |
4034 |
add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get |
4035 |
those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, |
4036 |
was not very convenient). |
4037 |
add implicit version for DST-3 & DST3_Flux_Limit vertical advection; |
4038 |
(further tests needed for the implicit DST & Flux-Limiter schemes). |
4039 |
o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef |
4040 |
and sRef for convenience, handy, when you want to initialize |
4041 |
ptracers in a large domain with a constant non-zero value. Also, |
4042 |
untangle ptracers_init.F a little. |
4043 |
|
4044 |
checkpoint57v_post (2005/10/13) |
4045 |
o change dome exp. to use variable viscosity in side-drag terms. |
4046 |
o remove all the files from the cfc_offline test since they are now |
4047 |
incorporated into tutorial_cfc_offline which has been producing |
4048 |
identical results for a few days of testing |
4049 |
o add new parameter: sideDragFactor to enable half-slip-side BC |
4050 |
and change side-drag S/R to use viscosity from mom_calc_visc |
4051 |
(can switch back by setting sideDragFactor=0.); affects results at |
4052 |
truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), |
4053 |
global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). |
4054 |
o vorticity & strain are now computed without masking, to account for |
4055 |
no-slip-side BC in variable viscosity calculation ; mask is applied |
4056 |
anyway later on, before computing advection/coriolis terms. |
4057 |
o modify exp4 to test new obcs support for reading from external files |
4058 |
and for passive tracers |
4059 |
o fix behavior of ptracers_monitor when monitor output is written to a |
4060 |
netcdf-file; still not independent of monitor.F (writes in the same |
4061 |
file). |
4062 |
o change default value of tRef (put a uniform, meaningful value for ocean |
4063 |
& atmos) and initialize sRef (was missing, as Martin mentioned). |
4064 |
o Redefine viscC?Leith*. Change the coefficients of Leith viscosity |
4065 |
to be proportional to enstrophy dissipation length. Thus, |
4066 |
viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) |
4067 |
This is now consistent with Smagorinsky and with the manual. |
4068 |
|
4069 |
checkpoint57u_post |
4070 |
o OBCS and PTRACERS: add open boundary support for passive tracers |
4071 |
- either use homogenous (pseudo) v.Neumann conditions or prescribe |
4072 |
OB-values from file; this is not different from the way theta and salinity |
4073 |
are treated |
4074 |
- however, Orlanski-radiation conditions are not supported, and the model |
4075 |
will stop if you use pTracers and Orlanski at the same time. |
4076 |
- beefed up the rountine obcs_external_fields_load: now only those open |
4077 |
boundary values are overwritten with values from files for which there |
4078 |
are really files, otherwise the OB-fields remain untouched. This makes |
4079 |
it possible to use different OBs at different ends of the domain (as |
4080 |
with EXF) |
4081 |
o reduce number of exch calls in shap_filt (s2). |
4082 |
o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ |
4083 |
truncation level) 4/5 MLAdjust test results (11&12 digits match). |
4084 |
|
4085 |
checkpoint57t_post (2005/10/03) |
4086 |
o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
4087 |
o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
4088 |
same truncation, independent of the face number: affects affects several |
4089 |
test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). |
4090 |
o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); |
4091 |
note that biharmonic viscosity + no-slip was not tested in any experiment. |
4092 |
o fix bug in non-linear free-surf side-drag ; generate new output for |
4093 |
global_ocean.cs32x15(+.thsice) & global_ocean_pressure. |
4094 |
o make mnc honor the writeBinaryPrec flag for most kinds of output |
4095 |
o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
4096 |
o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
4097 |
error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
4098 |
o add brackets in multi-terms sum to get same truncation, independent of |
4099 |
the face number (manage to get exactly same value of gU,gV at the cs-edge) |
4100 |
affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
4101 |
o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
4102 |
and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
4103 |
a maximum grid-scale Reynolds number. Also, changes all length calculations |
4104 |
in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
4105 |
Suggested values of viscosity parameters found in mom_calc_visc. |
4106 |
Many new viscosity diagnostics available. |
4107 |
|
4108 |
checkpoint57s_post (2005/09/20) |
4109 |
o Add clearing-house for viscosity calculations, mom_calc_visc and |
4110 |
correct numerous bugs in LeithD and Smagorinsky discretizations. |
4111 |
mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
4112 |
used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
4113 |
Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
4114 |
and with Strain-Tension viscous term calculation (mom_hdissip.F). |
4115 |
The Strain-Tension form is now called with useStrainTensonVisc=.true. |
4116 |
ViscAhStrain and viscAhTension are now retired. |
4117 |
o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
4118 |
o In response to JMC's bug report, genmake2 now ignores any soft-links |
4119 |
that it finds in the *current* directory when searching for files. |
4120 |
Soft-links found in any other source directories will still work as |
4121 |
they did before. |
4122 |
o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
4123 |
a C routine to unlimit the stack size |
4124 |
o mnc-ify pkg/aim snapshot vars |
4125 |
o mnc-ify pkg/land as requested by Daniel |
4126 |
o various changes to mnc including: |
4127 |
- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
4128 |
- output can now be grouped so that all files within a group |
4129 |
change the ITER portion of their names in lock-step together |
4130 |
- can now read ("global") PER-FACE (in addition to PER-TILE) files |
4131 |
and works with both EXCH1 and EXCH2 (but needs more testing) |
4132 |
- writing works for all verification test cases w/ g77 on Linux |
4133 |
|
4134 |
checkpoint57r_post (2005/09/07) |
4135 |
o make MNC variable initialization happen earlier |
4136 |
o add diagnostics for (almost) each term of the momentum Eq. |
4137 |
o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
4138 |
o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
4139 |
o remove MINIMAL_TAVE_OUTPUT option ; |
4140 |
add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
4141 |
o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
4142 |
allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
4143 |
o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
4144 |
o add time-dependent SST, SSS control |
4145 |
o cost terms in ecco/ modularized (new cost_generic.F) |
4146 |
o cost_averages routines are modularized (new cost_averagesgeneric.F) |
4147 |
o new infrastructure for seaice model vs. obs misfits in seaice/ |
4148 |
* driver from the_main_loop.F is seaice_cost_driver.F |
4149 |
* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
4150 |
* gradient check in Exp. 6a of natl_box_adjoint/ |
4151 |
o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
4152 |
(see README file) |
4153 |
|
4154 |
checkpoint57q_post (2005/08/19) |
4155 |
o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
4156 |
o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
4157 |
- bug was reported by Jean-Michel and Ian Fenty |
4158 |
o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
4159 |
update exp. cpl_aim+ocn output. |
4160 |
o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
4161 |
Needed for high-res. runs with large global files |
4162 |
to be able to limit tapelev size |
4163 |
o Changed some tests for adjoint: |
4164 |
* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
4165 |
* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
4166 |
* global_ocean.90x40x15/ back to default 3-level checkpointing |
4167 |
o Modifications to enable scripted COMMON to MODULE conversion |
4168 |
* verification/OpenAD/code/ has necessary scripts and description; |
4169 |
* converts, compiles and runs successfully; |
4170 |
|
4171 |
checkpoint57p_post (2005/08/01) |
4172 |
o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
4173 |
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
4174 |
(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
4175 |
o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
4176 |
o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
4177 |
(was already the case for dissipation with mom_vecinv, |
4178 |
and also the case for grad.PhiHyd when staggered-timeStep) |
4179 |
This will allow to put dissipation out-off the AB time-stepping. |
4180 |
Unfortunately, affects truncation error. Update output of exp. that "fails" |
4181 |
(cg2d matching number) and leave the others for later: front_relax(10), |
4182 |
global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
4183 |
matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
4184 |
|
4185 |
checkpoint57o_post (2005/07/30) |
4186 |
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
4187 |
(2) its ready to be documented during the 20050801 DocFest |
4188 |
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
4189 |
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
4190 |
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
4191 |
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
4192 |
(worth another tag) |
4193 |
|
4194 |
checkpoint57n_post (2005/07/29) |
4195 |
o adding precip control xx_precip 32 |
4196 |
o adding swflux control xx_swflux 33 |
4197 |
o Replacing 10 forcing penalty cost routines by 1 generic. |
4198 |
o Implementing partitioning in time-mean and variable adjustment |
4199 |
for atmos. state. |
4200 |
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
4201 |
o in natl_box_adjoint: |
4202 |
* updated exp 1 to 10 |
4203 |
(but does not have time-mean vs. variable split results yet) |
4204 |
o updated global1x1/*_seaice_adj/ |
4205 |
to incorporate latest changes |
4206 |
o enable useSingleCpuIO for mdsio vector routines |
4207 |
(applies in particular to tapelev I/O) |
4208 |
o removed inefficient K-loop in all active_file*control*.F |
4209 |
|
4210 |
checkpoint57m_post (2005/07/28) |
4211 |
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
4212 |
and advect_cs (use EXCH-2 and standard cs-32 grid files). |
4213 |
o pkg/exch2: filling of face-corner halo regions is optional |
4214 |
(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
4215 |
|
4216 |
checkpoint57l_post (2005/07/14) |
4217 |
tag before updating tutorials (pre-release-2) |
4218 |
o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
4219 |
for output and interpolation of input fields onto model grid) |
4220 |
o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
4221 |
Affects results of exp. rotating_tank ; update output.txt. |
4222 |
o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
4223 |
and taking the square quantity and/or using a fraction-weight field. |
4224 |
o fix aim_diagnostics_init.F mate numbers. |
4225 |
o add mnc output capability to diagnostics/diagstat and update |
4226 |
our cvsignore files for the ACSII output generated |
4227 |
|
4228 |
checkpoint57k_post (2005/07/02) |
4229 |
o lab_sea now uses diagnostics package and provides a suite of |
4230 |
new EXF diagnostics output. |
4231 |
|
4232 |
checkpoint57j_post (2005/06/30) |
4233 |
o exf |
4234 |
* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
4235 |
Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
4236 |
terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
4237 |
* extended diagnostics output |
4238 |
- now includes all EXF variables |
4239 |
- hs, hl moved to common block |
4240 |
- separate S/R for diagnostics, called after ctrl vector is added |
4241 |
- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
4242 |
- EXFqnet contains true Qnet (i.e. includes qsw) |
4243 |
* updated verif. lab_sea, global_with_exf |
4244 |
* Rearranging hflux (exf_mapfields -> exf_getforcing) |
4245 |
to ensure that diagnostics sees a true EXFqnet |
4246 |
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
4247 |
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
4248 |
several times with different frequencies. |
4249 |
o mnc-ify the thsice package as requested by Daniel Enderton |
4250 |
- the monitor--MNC output needs work |
4251 |
- many attributes need to be added (most are currently blank) |
4252 |
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
4253 |
- many attributes need to be added (most are currently blank) |
4254 |
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
4255 |
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
4256 |
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
4257 |
update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
4258 |
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
4259 |
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
4260 |
(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
4261 |
|
4262 |
checkpoint57i_post (2005/06/19) |
4263 |
o Diagnostics package was changed: diagnostic allocation is now deactivated |
4264 |
by setting an empty file name in the namelist (used to be by setting 0 frequency) |
4265 |
o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
4266 |
add 1rst Order upwind vertical Shear. |
4267 |
o add a quick fix for A/B checkpointing in OFFLINE mode |
4268 |
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
4269 |
end-run around the C/Fortran linking horror in eesup/src/timers.F |
4270 |
o added pkg/runclock: allows user to terminate run based on wall clock |
4271 |
o added non-hydrostatic scaling parameter: nh_am2 |
4272 |
o pkg/my82: futile attempt to make results compiler-independent by adding |
4273 |
some "_d 0", etc. no effect. |
4274 |
o for mnc output, fill the 'T' coordinate var with myTime and create a |
4275 |
separate 'iter' variable for iteration count |
4276 |
o pkg/diagnostics: |
4277 |
add new capability: output of Global/Regional & per-level statistics ; |
4278 |
tested against monitor output (including land & thSIce) on various exp. |
4279 |
o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
4280 |
|
4281 |
checkpoint57h_done (2005/05/19) |
4282 |
tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
4283 |
data.diagnostics, data.gchem, data.ptracers) is done. |
4284 |
|
4285 |
o pkg/diagnostics: prepare for Global/Regional statistics. |
4286 |
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
4287 |
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
4288 |
and rename it: DIFFERENT_MULTIPLE |
4289 |
|
4290 |
checkpoint57h_post (2005/05/14) |
4291 |
o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
4292 |
o pkg/diagnostics: change output frequency, now in seconds (instead |
4293 |
of Nb of iterations). This requires to change data.diagnostics. |
4294 |
checkpoint57h_pre (2005/05/12) |
4295 |
|
4296 |
o in mnc, let the user create the output dir if both mnc_outdir_date |
4297 |
and mnc_outdir_num are false |
4298 |
o add fflags() to pkg/diagnostics which allows one to specify, on a |
4299 |
per-file basis, the file precision [default behavior is unchanged] |
4300 |
o added diagnostics to pkg/kpp, including computation of mixed layer |
4301 |
depth based on a temperature/density criterion |
4302 |
o updated verification/natl_box to test the new pkg/kpp diagnostics |
4303 |
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
4304 |
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
4305 |
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
4306 |
not mnc -- this mistake was found by JMC and is now corrected |
4307 |
|
4308 |
checkpoint57g_post (2005/04/15) |
4309 |
o add Adams-Bashforth 3rd Order time stepping: |
4310 |
- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
4311 |
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
4312 |
checkpoint57g_pre (2005/04/15) |
4313 |
|
4314 |
o make lambda[Theta,Salt]ClimRelax spatially varying |
4315 |
(default remains spatially uniform constant based on tau) |
4316 |
o added new control variables |
4317 |
* init. uVel, vVel, etanN |
4318 |
* lambda[Theta,Salt]ClimRelax |
4319 |
o separate masks used for ctrl_pack/unpack 'from write_grid' output |
4320 |
(suggested by G. Forget) |
4321 |
|
4322 |
checkpoint57f_post (2005/04/06) |
4323 |
o add parameter "baseTime" = model base time = time at iteration zero |
4324 |
new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
4325 |
account for baseTime shift |
4326 |
o move Coriolis arrays from PARAMS.h to GRID.h |
4327 |
checkpoint57f_pre (2005/04/06) |
4328 |
|
4329 |
o mnc-ifying the seaice package |
4330 |
o introduced an alternative length scale calculation for use in the limiting |
4331 |
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
4332 |
o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
4333 |
o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
4334 |
as well as grad(vort3). Made it compatible with both approximate form |
4335 |
for the cubed sphere and full form of these gradients. Added flag |
4336 |
useFullLeith to select between approximate and full form. |
4337 |
o add "d0" in getcon.F to reduce differences between compilers/platforms |
4338 |
update output.txt of exp. fizhi-gridalt-hs |
4339 |
o change port_rand funtion to allow to set the seed. |
4340 |
o fix obscure MNC bug involving conversion between reals and integers |
4341 |
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
4342 |
new version is now more standards-compliant |
4343 |
o adjoint-related modifications |
4344 |
* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
4345 |
* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
4346 |
* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
4347 |
|
4348 |
checkpoint57e_post (2005/02/28) |
4349 |
o Adding eddy stress controls a la Ferreira et al. |
4350 |
checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
4351 |
|
4352 |
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
4353 |
update output.txt of exp. fizhi-gridalt-hs |
4354 |
o add more "Z" dimensions and associated coordinate vars to MNC |
4355 |
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
4356 |
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
4357 |
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
4358 |
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
4359 |
months and years. Requires pkg/cal. |
4360 |
o diagnostics: add pickup functionality |
4361 |
- off by default for backwards compatibility |
4362 |
- current version only uses MDSIO -- MNC will be added |
4363 |
o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
4364 |
o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
4365 |
|
4366 |
checkpoint57d_post (2005/02/11) |
4367 |
o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
4368 |
o modify verification/ideal_2D_oce so that it tests the creation of mnc |
4369 |
output from the diagnostics package |
4370 |
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
4371 |
o make genmake2 more portable by using ".$FS" instead of ".f" for more |
4372 |
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
4373 |
o add coordinate variables to the MNC output from the diagnostics package |
4374 |
o change MNC-flags default value: true when useMNC=TRUE |
4375 |
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
4376 |
the ability (off by default) to read the grid information using MNC |
4377 |
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
4378 |
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
4379 |
o do snap-shot diagnostics at the middle of the time-interval (instead of |
4380 |
at the end). |
4381 |
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
4382 |
new test for AIM with thSIce + slab-ocean |
4383 |
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
4384 |
o move state variable diagnostics to the beginning of the time step ; |
4385 |
(note: still needs some work specially for snap-shot diagnostics) |
4386 |
duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
4387 |
|
4388 |
checkpoint57c_post (2005/01/27) |
4389 |
o Change testing option (-ieee) to get closer agreement between g77 & ifort |
4390 |
o generate new output.txt files on faulks with g77 & the new -ieee option |
4391 |
checkpoint57c_pre (2005/01/27) |
4392 |
|
4393 |
o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
4394 |
update output.txt of exp. global_ocean.90x40x15 |
4395 |
o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
4396 |
results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
4397 |
o add saltFlux(+File) forcing capability with periodicExternalForcing |
4398 |
o allow to use pkg diagnostics for GM-Redi & ThSIce output |
4399 |
o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
4400 |
o improvements for the MNC output from DIAGNOSTICS: |
4401 |
- correct handling of the unlimitied dimension |
4402 |
- all dims now have associated coordinate variables |
4403 |
- variables located at U, V, and Corner ("Z") points are now written |
4404 |
with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
4405 |
*all* data points are output |
4406 |
o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
4407 |
o added pkg/seaice/seaice_monitor.F |
4408 |
o mdsio_readfield.F can now read files visible only to master MPI process. |
4409 |
o pkg/seaice: some test code for ice-modified ocean stress |
4410 |
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
4411 |
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
4412 |
spurious negative numbers for precipitation and humidity. Will cause |
4413 |
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
4414 |
o pkg/ctrl/ |
4415 |
* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
4416 |
May be enabled via doPackDiag |
4417 |
* introduce z-scaling of |
4418 |
+ gradient (doZscalePack) and |
4419 |
+ control (doZscaleUnpack) |
4420 |
o pkg/mdsio/ |
4421 |
* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
4422 |
* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
4423 |
|
4424 |
checkpoint57b_post (2004/12/20) |
4425 |
o simplify options in diagnostics_fill arguments (remove weird combinations) |
4426 |
o fix MNC coordinate variables so that they now contain per-face index |
4427 |
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
4428 |
general, EXCH2 grids are only aligned to a "local" coordinate system |
4429 |
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
4430 |
o Implement instantaneous output within pkg diagnostics: |
4431 |
setting a negative frequency in data.diagnostics produces |
4432 |
"snap-shot" output (as opposed to time-average if freq > 0) |
4433 |
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
4434 |
NOTE: change ptracer diagnostics name: use 2 characters to work with |
4435 |
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
4436 |
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
4437 |
becomes the coordinate variable for the 'T' dimension |
4438 |
o add CF-style coordinate variables to MNC |
4439 |
- just a first cut: numbers are meaningless on the cubesphere and |
4440 |
missing along the T axis but otherwise it works! |
4441 |
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
4442 |
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
4443 |
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
4444 |
this is based directly on what the model compute, so that the content of |
4445 |
each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
4446 |
o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
4447 |
o clean up build options files for SunOS, in particular |
4448 |
- remove -traditional from xmakedepend |
4449 |
- change -xarch=v9 to -xarch=native for f77 |
4450 |
- restore use of make (not gmake) |
4451 |
- add CC=gcc if using g77 |
4452 |
o changes per discussion of AM, JMC, & EH3 today: |
4453 |
- move redundant "grid" variables out of "state" -- in preparation of |
4454 |
creating proper CF-style coordinate variables and in recognition |
4455 |
that any/all grid variables can be easily copied (eg. w/NCO) from |
4456 |
the grid files into any of the other NetCDF files |
4457 |
- *always* output grid variables with MDSIO (this will eventually be |
4458 |
changed) |
4459 |
- output MNC grid file if useMNC is true |
4460 |
o every instance of _END_MASTER() has been found and replaced with |
4461 |
_END_MASTER( myThid ) in order to satisfy certain picky Sun |
4462 |
preprocessors |
4463 |
o re-arrange diagnostics pkg initialisation: |
4464 |
- allow each package to extend the available diagnostics list |
4465 |
- add some checking and fix small problems (multi-threaded, ...) |
4466 |
- new S/R diagnostics_fill (replace fill_diagnostics): |
4467 |
look through the short list of active diag. (instead of the long list) |
4468 |
create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
4469 |
|
4470 |
checkpoint57a_post (2004/12/10) |
4471 |
o this set of changes restores TAMC compatibility |
4472 |
tested for global_ocean.90x40x15 adjoint on trough |
4473 |
(what a pain) |
4474 |
|
4475 |
checkpoint57a_pre (2004/12/10) |
4476 |
o some modifs in tools/build_options for sunos |
4477 |
o call ctrl_pack for ctrl at end for optimcycle=0 |
4478 |
|
4479 |
checkpoint57 (2004/12/09) |
4480 |
o add horizontal bi-harmonic viscosity for vertical velocity |
4481 |
- new parameter viscA4W (defaults to viscA4) |
4482 |
- affects only non-hydrostatic code |
4483 |
- to be done: no-slip lateral boundary conditions |
4484 |
o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
4485 |
o implement Implicit Vertical advection for pTracers |
4486 |
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
4487 |
(implemented also for implicit vertical diffusion & advection) |
4488 |
o OBCS: extend application of tracer open boundary conditions |
4489 |
to a strip beyond the boundary of width Olx/Oly |
4490 |
o add call monitor to TAF set of required calls (flow directives) |
4491 |
and include in natl_box_adjoint |
4492 |
o untangle a few ifdefs related to cost, ctrl, autodiff |
4493 |
untangel a few ALLOW_ECCO_OPTIMIZATION |
4494 |
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
4495 |
(theta2, salt2 in ecco_cost_weights) |
4496 |
|
4497 |
checkpoint56c_post (2004/12/03) |
4498 |
o OBCS as control variables |
4499 |
- update ctrl_ad_diff.list, obcs_ad_diff.list |
4500 |
- remove balance of obcs controls from default |
4501 |
- fix index bug nobcs in ctrl_init |
4502 |
- fix dummy fields filen in ctrl_pack |
4503 |
- add dummy weights for obcs |
4504 |
o lsopt: comment out fort.94 output |
4505 |
o optim: |
4506 |
- remove unnecessary header files |
4507 |
- adjusted namelists |
4508 |
- add xerbla.F to Makefile |
4509 |
o exf: |
4510 |
- multiple modifications of exf_check_range |
4511 |
- unit change in exf_init_runoff from [m/year] to [m/s] |
4512 |
o mdsio: |
4513 |
- i/o-vector change debugLevel from debLevA to debLevB |
4514 |
|
4515 |
checkpoint56b_post (2004/12/01) |
4516 |
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
4517 |
is called from DO_THE_MODEL_IO |
4518 |
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
4519 |
- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
4520 |
- clean up PTRACERS_WRITE_TIMEAVE a little |
4521 |
o add another verification experiment that tests both the cfc-pkg and |
4522 |
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
4523 |
reactive tendencies treated inline with regular timestepping |
4524 |
o testreport previously did a lousy job of comparing small numbers, so |
4525 |
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
4526 |
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
4527 |
testreport. |
4528 |
o ptracers_monitor: bug fix for MPI |
4529 |
|
4530 |
checkpoint56a_post (2004/11/28) |
4531 |
o GCHEM: finish reorganizating the package |
4532 |
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
4533 |
(introduces another 3D-array for each passive tracer, but only if |
4534 |
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
4535 |
gchemTendency is not needed because the timestep is done separately) |
4536 |
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
4537 |
- GCHEM is now---more or less cleanly---separate from PTRACERS |
4538 |
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
4539 |
so clear to me how that should be done in a general way. |
4540 |
o CFC: improve formatting of output in CFC_ATMOS |
4541 |
o PTRACERS: |
4542 |
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
4543 |
that ALL experiments with ptracers enable can be checked. This makes |
4544 |
GCHEM_MONITOR obsolete. |
4545 |
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
4546 |
monitorFreq |
4547 |
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
4548 |
o add PTRACERS (PTR0[1-5]) to testreport output |
4549 |
o exf_check_range: |
4550 |
* default changed to .TRUE. |
4551 |
* will check values for niter0 if debLevA, every timestep if debLevB |
4552 |
* STOP in exf_check_range if 'out of range' |
4553 |
* range chosen generous to allow for potential extema |
4554 |
TBD: a version with stricter range |
4555 |
permitted range would be runtime parameters |
4556 |
o GMredi: |
4557 |
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
4558 |
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
4559 |
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
4560 |
o GCHEM: |
4561 |
- move call to GCHEM_FORCING_SEP, so that it is now called before |
4562 |
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
4563 |
- introduced a useGCHEM runtime flag and applied it everywhere. |
4564 |
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
4565 |
this flag is now only visible within GCHEM-pkg routines. |
4566 |
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
4567 |
be replaced by a 3D array that is computed before thermodynamics; for |
4568 |
this, the tracer ID iTracer had to be included into the parameter list |
4569 |
of ptracers_forcing |
4570 |
- set up forward_step to call gchem_forcing, that will replace |
4571 |
gchem_forcing_int in ptracers_forcing |
4572 |
- cleaning up |
4573 |
o small cleaning of exch2: remove files that are also in eesupp/src |
4574 |
|
4575 |
checkpoint56 (2004/11/17) |
4576 |
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
4577 |
o mnc: cleanup "full" files--fixes out-of-memory problem |
4578 |
o ECCO-GODAE |
4579 |
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
4580 |
* fully merged and updated from SIO code |
4581 |
windstress sign change affects |
4582 |
- exf_inscal_[u/v]stress |
4583 |
- sign of xx_tau[u/v] adjustments |
4584 |
- signs in cost_scat |
4585 |
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
4586 |
* natl_box_adjoint updated and compressed |
4587 |
* 2-level checkpoint switch added |
4588 |
(tested in EXP. 1 of natl_box_adjoint) |
4589 |
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
4590 |
o SVD |
4591 |
* first complete, non-hacked version for SVD calculations |
4592 |
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
4593 |
performed via direct access files admtlm_vector.it???? |
4594 |
(via ctrl_[un]pack) |
4595 |
* optimcycle is used for ARPACK iteration counter |
4596 |
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
4597 |
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
4598 |
and add linear transforms where necessary |
4599 |
* controls are initial/final SST, SSS (can be extended; need to check |
4600 |
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
4601 |
o mdsio: filename info to both stderr, stdout |
4602 |
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
4603 |
from sign change |
4604 |
|
4605 |
checkpoint55j_post (2004/11/10) |
4606 |
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
4607 |
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
4608 |
o add consistent build directories and .cvsignore files to verification |
4609 |
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
4610 |
o make all subroutines 30 or less characters in length for certain older |
4611 |
compilers to work (a thorough search only turns up two routines in |
4612 |
pkg/ptracers) |
4613 |
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
4614 |
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
4615 |
|
4616 |
checkpoint55i_post (2004/10/28) |
4617 |
o change arrays for total vertical diffusivity (2.D if explicit, |
4618 |
3.D if implicit) ; each ptracer uses its own background value. |
4619 |
o added mnc/NetCDF output capability to ocn_compon_interf |
4620 |
- added bits to verification/cpl_aim+ocn so that it can run on |
4621 |
ITRDA and other clusters without the mpirun "-wd" option |
4622 |
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
4623 |
configuration |
4624 |
o give MNC the ability to create additional files rather than |
4625 |
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
4626 |
- the default is just less than 2GB which is a practical limit |
4627 |
on many systems |
4628 |
o Compute the non-local term using either KPP vertical diffusivity (=default) |
4629 |
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
4630 |
|
4631 |
checkpoint55h_post (2004/10/20) |
4632 |
o add verification test "vermix" |
4633 |
o remove all the *_ioinc flags and replace with the single global |
4634 |
outputTypesInclusive flag |
4635 |
o allow to set a vertical profile of vertical diffusivity for T & S |
4636 |
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
4637 |
o useMNC moved from data.mnc to data.pkg |
4638 |
|
4639 |
checkpoint55g_post (2004/10/14) |
4640 |
o Renaming carbon AD experiments to comply with testreport conventions |
4641 |
o Updating adjoint of Held-Suarez hs94.1x64x5 |
4642 |
o Fixing directives for non-ECCO forward_step, after ECCO directives |
4643 |
have been fixed to avoid recomp. of do_oceanic_phys |
4644 |
Works well for global_ocean.90x40x15, |
4645 |
but recomp. issue remains for carbon |
4646 |
o Updating adjoint output for natl_box_adjoint after |
4647 |
pkg/ecco has been modified (see taga c55d_post) |
4648 |
|
4649 |
checkpoint55f_post (2004/10/13) |
4650 |
o rename to timeave_init_fixed |
4651 |
|
4652 |
checkpoint55e_post (2004/10/13) |
4653 |
o some delicate re-shuffle of store directives to avoid one |
4654 |
extra call of do_oceanic_physics |
4655 |
affects ecco_the_main_loop.F, do_oceanic_physics.F |
4656 |
checkpoint_lev1_directives.h |
4657 |
o NB: this may break global_ocean adjoint temporarily, |
4658 |
but it is clear how to fix it. Will do later, need this now. |
4659 |
|
4660 |
checkpoint55d_post (2004/10/11) |
4661 |
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
4662 |
o ecco_cost_weights is modified to 1x1 runs |
4663 |
o modifs to allow observations to be read in as |
4664 |
single file or yearly files |
4665 |
o enable to read exf forcing fields as either |
4666 |
single file or yearly files (flag useExfYearlyFields) |
4667 |
checkpoint55d_pre (2004/10/08) |
4668 |
|
4669 |
o switch between 2-level and 3-level checkpointing |
4670 |
o add ability of MNC to write local and "partial" (eg. 2D slices where |
4671 |
the full 3D field is never actually stored) arrays to NetCDF files |
4672 |
with the correct (that is, the complete multi-dimensional) set of |
4673 |
array indicies |
4674 |
- used in mom_vecinv() to write the diagFreq output |
4675 |
- tested (demonstrated) in verification/aim.5l_cs |
4676 |
o further mnc-ification |
4677 |
- add verification/lab_sea to the list with mnc setups |
4678 |
- fix undefined mnc v-names in cd_code |
4679 |
- add kpp to mnc output (both snapshot and timeave) |
4680 |
o non-hydrostatic code |
4681 |
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
4682 |
in calc_gw.F |
4683 |
- defaults to viscAh |
4684 |
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
4685 |
friction or Leith) in non-hydrostatic mode, as long as there is |
4686 |
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
4687 |
o pkg/cost |
4688 |
extend simple cost functions to treat time mean quantities |
4689 |
(T,U,V) via cost_accumulate_state from cost_tile |
4690 |
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
4691 |
be 2 times larger than the minimum size the advection scheme requires. |
4692 |
now get a perfect conservation of salt in advect_cs test-exp (updated) |
4693 |
o GGL90 (Gaspar's TKE mixed layer) |
4694 |
- add horizontal diffusion of TKE, requires exchanges in |
4695 |
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
4696 |
default. In OPA there is no horizontal diffusion of TKE but the |
4697 |
mixing coefficients are computed from a horizontal average of TKE of |
4698 |
6 points or so. I think that diffusion has a little more physical |
4699 |
justification. |
4700 |
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
4701 |
was in vain) |
4702 |
- mask tke-variable in ggl90_init |
4703 |
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
4704 |
o fix biharmonic diffusion on CS-grid. |
4705 |
o more obcs stuff |
4706 |
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
4707 |
for reading boundary values. This routine is called from |
4708 |
obcs_prescribe_read |
4709 |
- updated obcs_check |
4710 |
- changed sponge layer relaxation parameter units for days to seconds |
4711 |
- turned off sponge layer by default |
4712 |
- changed argument list of OBCS_CALC to myTime+deltaTclock |
4713 |
- fixed about 35 bugs in obcs_external_fields_load |
4714 |
|
4715 |
checkpoint55c_post (2004/09/23) |
4716 |
o obcs stuff |
4717 |
- new runtime flags useOBCSprescribe, useOBCSbalance |
4718 |
- re-arranged obcs_calc |
4719 |
- moved exf_getobcs to obcs_prescibe_read |
4720 |
obcs_prescibe_read is called after ORLANSKI stuff |
4721 |
and independent of it (executable can contain all). |
4722 |
- updated obcs_check |
4723 |
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
4724 |
These may be necessary only if tangential velocities are |
4725 |
prescribed at OB, not sure, needs testing. |
4726 |
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
4727 |
which simplifies the calls and passes the ifc check-bounds test |
4728 |
|
4729 |
checkpoint55b_post (2004/09/22) |
4730 |
o add a 2D scalar, Z location, exchange_2 routine. |
4731 |
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
4732 |
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
4733 |
affects advect_cs results (for the wrong reason): update output.txt |
4734 |
o use a more standard discretization for biharmonic viscosity ; |
4735 |
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
4736 |
affects results of dome set-up: update output.txt |
4737 |
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
4738 |
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
4739 |
|
4740 |
checkpoint55a_post (2004/09/20) |
4741 |
o merged code to |
4742 |
* prescribe/read time-dependent open boundaries |
4743 |
(works in conjunction with exf, cal) |
4744 |
* sponge layer code for open boundaries |
4745 |
* each boundary N/S/E/W now has its own CPP option |
4746 |
(healthy for the adjoint) |
4747 |
|
4748 |
checkpoint55 (2004/09/17) |
4749 |
o up-to-date adjoint of previous breaks |
4750 |
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
4751 |
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
4752 |
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
4753 |
- carbon: * remove tr1-related adjoint verification |
4754 |
* add ptracer as control variable |
4755 |
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
4756 |
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
4757 |
|
4758 |
checkpoint54f_post (2004/09/16) |
4759 |
o in verification/carbin/ remove experiment related to |
4760 |
ALLOW_PASSIVE_TRACER (array tr1 etc) |
4761 |
code_ad/ input_ad/ results_ad |
4762 |
|
4763 |
o add two new packages |
4764 |
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
4765 |
+ subject to optimization (memory) |
4766 |
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
4767 |
+ subject to reordering (many GOTOs in the original code) |
4768 |
+ so far opps is called for every (i,j) point, and then operates in |
4769 |
the vertical; one may want to reorder the scheme in order operate in |
4770 |
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
4771 |
fields) |
4772 |
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
4773 |
- all verification tests compile and run with linux_ia32_g77 |
4774 |
- defaults are compatible with current input files--nothing |
4775 |
should change if you were not previously using MNC |
4776 |
- MNC output has been added in numerous places (eg. timeave) |
4777 |
but there are still a few writes not yet do-able with MNC |
4778 |
(this is in progress) |
4779 |
- flags now allow for either/or/both use of MDSIO and MNC and |
4780 |
documentation will soon follow |
4781 |
- numerous small formatting cleanups for ProTeX |
4782 |
o add version info (via BUILD_INFO.h) to MNC and stdout |
4783 |
|
4784 |
checkpoint54e_post (2004/09/02) |
4785 |
o add two new packages |
4786 |
- pp81 (Packanowski and Philander, 1981), Richardson number and |
4787 |
stratification dependent mixing |
4788 |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
4789 |
- these scheme operate in a similar manner as KPP (without ghat, of |
4790 |
course), however there is only one diffusivity that is used for both |
4791 |
temperature and salinity (and passive tracers) |
4792 |
o add offline package |
4793 |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
4794 |
provided by Stephanie Dutkiewicz |
4795 |
o genmake2: add ability to search for C compilers and cleanup test output |
4796 |
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
4797 |
|
4798 |
checkpoint54d_post (2004/07/27) |
4799 |
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
4800 |
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
4801 |
leading to additional shift by 5 days each year of integration |
4802 |
(i.e. leading to considerable offset over the years) |
4803 |
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
4804 |
o start with no AB and no initial filtering (staggerTimeStep): |
4805 |
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
4806 |
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
4807 |
(external loading & cpl import/export stay in forward_step.F) |
4808 |
o update coupling interface to work with new staggerTimeStep |
4809 |
o change MDSIO ptracers_pickup. |
4810 |
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
4811 |
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
4812 |
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
4813 |
|
4814 |
checkpoint54c_post (2004/07/18) |
4815 |
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
4816 |
this affects (truncation error) output.txt of test-exp: |
4817 |
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
4818 |
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
4819 |
o change Qnet to always be the net heat flux, (+upward). |
4820 |
affects (truncation error) output of natl_box exp.: updated |
4821 |
o define the max number of passive tracers in PTRACERS_SIZE.h |
4822 |
o start to test mnc routinely in exp0 |
4823 |
o add sea-ice loading (sIceLoad) as a new forcing field. |
4824 |
|
4825 |
checkpoint54b_post (2004/07/08) |
4826 |
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
4827 |
impressive on Altix and Opteron systems) |
4828 |
o diagnostics can now write NetCDF files through the mnc package |
4829 |
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
4830 |
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
4831 |
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
4832 |
affects (truncation error) output of lab_sea & natl_box exp.: updated |
4833 |
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
4834 |
|
4835 |
checkpoint54a_post (2004/07/06) |
4836 |
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
4837 |
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
4838 |
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
4839 |
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
4840 |
+ internal_wave (shift in writing cg2d_ini_res) |
4841 |
checkpoint54a_pre (2004/07/05) |
4842 |
|
4843 |
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
4844 |
- modified verification/lab_sea and natl_box_adjoint accordingly |
4845 |
|
4846 |
checkpoint54 (2004/07/02) |
4847 |
checkpoint53g_post (2004/07/02) |
4848 |
o prepare splitting of thermodynamics: store convect.counter in common block |
4849 |
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
4850 |
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
4851 |
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
4852 |
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
4853 |
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
4854 |
o restore adjointability |
4855 |
|
4856 |
checkpoint53f_post (2004/06/25) |
4857 |
o modifications that affect AIM experiment results (update output.txt): |
4858 |
- no advection of S at top interface Nr (pkg/generic_advdiff) |
4859 |
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
4860 |
o AIM pkg: |
4861 |
- include stability function into surf.Flux derivative relative to Tsurf |
4862 |
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
4863 |
|
4864 |
checkpoint53e_post |
4865 |
o merged cylindrical coord configuration |
4866 |
o added rotating_tank experiment |
4867 |
checkpoint53e_pre |
4868 |
|
4869 |
checkpoint53d_post (2004/06/14) |
4870 |
o faulks upgraded: re-generate output.txt that have changed: |
4871 |
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
4872 |
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
4873 |
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
4874 |
o added Sadourny discretization of Coriolis |
4875 |
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
4876 |
- re-enabled use of omega3 (useAbsVorticity) |
4877 |
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
4878 |
vector-invariant equations |
4879 |
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
4880 |
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
4881 |
hopefully without new bugs |
4882 |
- still to do: biharmonic friction for non-hydrostatic w |
4883 |
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
4884 |
o regenerated output for global_ocean_ebm (using -ieee) |
4885 |
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
4886 |
of mom_common/ |
4887 |
- simple re-arrangement of instructions within computing loop |
4888 |
checkpoint53d_pre (2004/05/21) |
4889 |
|
4890 |
checkpoint53c_post (2004/05/21) |
4891 |
o new version of coupler for AIM+thSIce and Ocean models |
4892 |
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
4893 |
- land: change Evaporation of snow |
4894 |
- aim with thSIce: fix bug in snow-precip. |
4895 |
o changes to calc_gw.F |
4896 |
- bug fix for w^2 term near the bottom boundary |
4897 |
- (hopefully) improve the lateral slip boundary condtions for use with |
4898 |
partial/looped cells |
4899 |
- because the bug fix changes two verification experiments anyway (exp5 |
4900 |
and plume on slope), change the lateral boundary condition from half slip |
4901 |
to the value of no_slip_sides |
4902 |
o ebm package wasnt quite up to the parallel task. Fixed that. |
4903 |
o Adjoint of EBM package + verification |
4904 |
* TLM OK |
4905 |
* ADM not sufficient accuracy yet (needs further testing) |
4906 |
|
4907 |
checkpoint53b_post (2004/05/14) |
4908 |
o Commiting new energy balance model to repository |
4909 |
* package is pkg/ebm |
4910 |
* verif. is verification/global_ocean_ebm |
4911 |
* references are in ebm_driver.F |
4912 |
C * X. Wang, P. Stone and J. Marotzke, 1999: |
4913 |
C Global thermohaline circulation. Part I: |
4914 |
C Sensitivity to atmospheric moisture transport. |
4915 |
C J. Climate 12(1), 71-82 |
4916 |
C * X. Wang, P. Stone and J. Marotzke, 1999: |
4917 |
C Global thermohaline circulation. Part II: |
4918 |
C Sensitivity with interactive transport. |
4919 |
C J. Climate 12(1), 83-91 |
4920 |
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
4921 |
C Destabilization of the thermohaline circulation |
4922 |
C by atmospheric eddy transports. |
4923 |
C J. Climate 7(12), 1870-1882 |
4924 |
o Will need long integration testing. |
4925 |
checkpoint53b_pre (2004/05/14) |
4926 |
|
4927 |
o created pkg/mom_common in preparation for variable viscosity code |
4928 |
o renamed and split ini_mnc_io |
4929 |
o pkg/land: only liquid water can diffuse or run-off |
4930 |
o AIM using land: soil wetness availability account for snow |
4931 |
o added printMapIncludesZeros to EEPARMS namelist |
4932 |
|
4933 |
checkpoint53a_post (2004/05/11) |
4934 |
o restore TAMC compatiility for exf_constants.h |
4935 |
(no usage of _d in .h) |
4936 |
o Additional storing in KPP in an attempt to fix |
4937 |
TAMC problem with adjoint of KPP code. |
4938 |
(no success...) |
4939 |
Identical code works fine with TAF. |
4940 |
o Fixed verification/natl_box_adjoint experiments. |
4941 |
Initial conditions for Experiments 4 and 5 are now |
4942 |
set to "SEAICE_initialHEFF=0", which is more reasonable, |
4943 |
and hence gives results closer to that of Experiment 2. |
4944 |
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
4945 |
|
4946 |
checkpoint53 (2004/05/06) |
4947 |
o stable checkpoint with up to date adjoint |
4948 |
TLM tests only run for 1st grdchk at the moment. Its unclear if |
4949 |
this is a code problem or a problem with resetting code for g_ |
4950 |
variables that is being autogenerated wrong. |
4951 |
Otherwise: |
4952 |
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
4953 |
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
4954 |
are both still in chaos following their security messes. |
4955 |
|
4956 |
checkpoint52n_post (2004/05/06) |
4957 |
o various build (mostly genmake2) changes including: |
4958 |
- ability to build/run more easily within Cygwin and MacOS X |
4959 |
- more complicated Makefiles with a stronger dependence on Gnu Make |
4960 |
o pkg/seaice modifications |
4961 |
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
4962 |
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
4963 |
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
4964 |
- changed proxy for geostrophic velocity and updated |
4965 |
verification/lab_sea/results/* accordingly |
4966 |
- removed ADI dynamic solver from pkg/seaice |
4967 |
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
4968 |
they caused a segmentation fault under certain circumstances |
4969 |
- removed unused field WATR |
4970 |
o bug fix in exf-package: |
4971 |
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
4972 |
now reflect that. |
4973 |
o small fixes in the cal-package: |
4974 |
- set reference date to first of January for the 'model'-calendar |
4975 |
- failing of cal_CheckDate in cal_FullDate now actually results in a |
4976 |
warning |
4977 |
o small modifications in exf-package to increase flexibility: |
4978 |
- change climtempfreeze from a constant to a runtime parameter that |
4979 |
is specified in data.exf_clim (default = -1.9) |
4980 |
- introduce runtime parameter windstressmax (default = 2.0) that is |
4981 |
specified in data.exf |
4982 |
o fix in pkg/thsice: |
4983 |
- update Evap (Tsf changes) to be consistent with Latent heat flux |
4984 |
- maintain snow precipitation unchanged (even if Tsf >=0). |
4985 |
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
4986 |
|
4987 |
checkpoint52m_post (2004/04/18) |
4988 |
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
4989 |
this does not change any of the results, because myIter=0 in swfrac always |
4990 |
lead to jwtype=2 (the default anyway), but the call makes little sense |
4991 |
as a default |
4992 |
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
4993 |
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
4994 |
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
4995 |
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
4996 |
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
4997 |
o extending useSingleCpuIO option to work with new exch2 I/O format |
4998 |
- old-style, missing-tile I/O is still accessible by defining CPP |
4999 |
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
5000 |
o monitor package can write to NetCDF files and/or STDOUT |
5001 |
o fix re-definition bug in MNC_GRID_INIT_ALL() |
5002 |
o doc/api_reference added |
5003 |
- a framework for building an API Reference Manual using all |
5004 |
the "protex" comments embedded in the code |
5005 |
- see pkg/generic_advdiff, pkg/mnc for examples |
5006 |
o MNC: |
5007 |
- make myThid the last argument for all subroutines |
5008 |
- new default for the grid files: NO halos |
5009 |
- add useMNC and other run-time flags |
5010 |
- separate per-file-group handling of the unlimited dimension |
5011 |
- early initialization of MNC w/ flags read at the eeboot stage |
5012 |
and lookup tables set in initialize_fixed |
5013 |
- write all MNC output to a freshly-created directory |
5014 |
o thermodynamics sea-ice (thsice) is now tested with testreport. |
5015 |
o test exp. advect_cs: use the standard cs32 grid ; update output. |
5016 |
o Added functionality to grdchk: |
5017 |
pick global i,j,k position (or nearest wet) where to perform check. |
5018 |
|
5019 |
checkpoint52l_post (2004/03/11) |
5020 |
o new land formulation: |
5021 |
a) use ground enthalpy as prognostic variable to ensure exact |
5022 |
energy conservation. |
5023 |
b) account for water temperature and for latent heat of freezing |
5024 |
in all processes (rain, run-off, ground storage) |
5025 |
c) compute surface and ground temperature implicitly. |
5026 |
o aim_v23 modification for new land model: |
5027 |
a) Treat separately land / ocean / sea-ice surface fluxes |
5028 |
to allow implicit computation of land & sea-ice surface temp. |
5029 |
b) add snow precipitation. |
5030 |
checkpoint52l_pre (2004/03/11) |
5031 |
|
5032 |
o fix problem (when 1 tile is empty) in min/max monitor. |
5033 |
o fix bug in timeAve (u,vZetatave in common block) |
5034 |
o no restoring terms under ice for pkg/seaice |
5035 |
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
5036 |
o bug fix for pkg/seaice pickups |
5037 |
o change MNC call locations and add coordinate attributes |
5038 |
o mask vorticity at the corner ; affects global_ocean.cs output |
5039 |
o fix ini_curvilinear_grid ; test CS experiments with mpi |
5040 |
o aim.5l_cs: modify sea-ice fraction input file ; update output |
5041 |
o exf: Adding simple range check routine for exf fields after read |
5042 |
|
5043 |
checkpoint52k_post (2004/02/23) |
5044 |
o removed top-level directory "diags" |
5045 |
- we migrated these functions to pkg/timeave a long time ago |
5046 |
o fixed bug introduced in pkg/monitor |
5047 |
o accuracy ctrlprec = 32 insuffient for gradient checks using |
5048 |
averaged fields (I/O via cost_averages) |
5049 |
-> use ctrl.h in active_file*.F to control I/O precision. |
5050 |
o paramter list of CALL ADTHE_MAIN_LOOP |
5051 |
o added initial do_the_model_io to ecco |
5052 |
o set all ...Freq to zero after cost_final |
5053 |
taveFreq, dumpFreq, pChkptFreq |
5054 |
o MAIN and ECCO differentiability restored |
5055 |
|
5056 |
checkpoint52j_post (2004/02/18) |
5057 |
o fix nchklev in tamc.h for global_ocean... |
5058 |
o Bringing flow and store directives up-to-date |
5059 |
o Really weird thing! |
5060 |
call do_the_model_io from the_main_loop with parameters |
5061 |
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
5062 |
TAF places a faulty re-call of initialise_varia |
5063 |
after cost_final call which should not be there! |
5064 |
checkpoint52j_pre (2004/02/03) |
5065 |
|
5066 |
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
5067 |
error messages |
5068 |
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
5069 |
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
5070 |
debug output |
5071 |
o modfied mdsio_writefield.F to handle non-global files under exch2 |
5072 |
o update AIM Cubed-Sphere exp (aim.5l_cs): |
5073 |
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
5074 |
o update AIM Equatorial Channel exp: |
5075 |
use standard aim_v23 pkg and change the SST fields to be more realistic. |
5076 |
o globalFile now works with exch2 |
5077 |
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
5078 |
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
5079 |
o limit timeave output for hi-res integrations |
5080 |
|
5081 |
checkpoint52i_post (2004/01/21) |
5082 |
o removed CPP_EEOPTIONS.h from verification/*/code |
5083 |
o updated the tiling for global_ocean_pressure |
5084 |
checkpoint52i_pre (2004/01/20) |
5085 |
|
5086 |
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
5087 |
the old pkg/aim). |
5088 |
|
5089 |
checkpoint52h_pre (2004/01/20) |
5090 |
o shortened offending lines in exch2_send_rx?.template |
5091 |
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
5092 |
o genmake2: add build & execute test for NetCDF code |
5093 |
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
5094 |
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
5095 |
o added useSingleCPUIO flag to monitor.F and mon_out.F |
5096 |
o added temporary hack for sea-ice dynamics on the cube: |
5097 |
metric terms are ignored and it is assumed that |
5098 |
there is no sea-ice on cube faces 1, 2, 4, and 5. |
5099 |
|
5100 |
checkpoint52f_post (2004/01/09) |
5101 |
o added exch2 cube routines to pkg/exch2 |
5102 |
o modified hs94.cs-32x32x5 to use it |
5103 |
o added new grid files to hs94.cs-32x32x5 |
5104 |
checkpoint52f_pre (2004/01/07) |
5105 |
|
5106 |
checkpoint52e_post (2004/01/07) |
5107 |
o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
5108 |
for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
5109 |
o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
5110 |
to work with implicit vertical advection and AB ; |
5111 |
o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
5112 |
o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
5113 |
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
5114 |
checkpoint52e_pre (2004/01/02) |
5115 |
|
5116 |
o fix bug in impldiff when Nr=1 or Nr=2. |
5117 |
o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
5118 |
o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
5119 |
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
5120 |
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
5121 |
o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
5122 |
o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
5123 |
o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
5124 |
|
5125 |
checkpoint52d_post (2003/12/16) |
5126 |
o re-tiled many expts to allow comparison in multi-processor mode |
5127 |
- updated output accordingly |
5128 |
- changed hs94.128x64x5 to use intial T from file rather than use the |
5129 |
random number generator |
5130 |
o add infrastructure in model routines for fizhi and gridalt packages |
5131 |
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
5132 |
o changes to permit hi-res, cubed-sphere, configuration |
5133 |
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
5134 |
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
5135 |
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
5136 |
of surface winds for the cube |
5137 |
(A verification experiment, based on global_ocean.cs32x15, but with |
5138 |
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
5139 |
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
5140 |
complete with example surface forcing files and matlab scripts to look |
5141 |
at the output and compare it with that of global_ocean.cs32x15.) |
5142 |
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
5143 |
but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
5144 |
to conform to the common rule. |
5145 |
o check-in the first version of the coupler + interfaces for multi-components |
5146 |
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
5147 |
- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
5148 |
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
5149 |
- ocean and atmos. share the same horizontal grid (no interpolation). |
5150 |
- exchanges between component and coupler is done in forward_step |
5151 |
o new verification experiment, cpl_aim+ocn: |
5152 |
coupled ocean - AIM atmosphere on cs32 grid. |
5153 |
|
5154 |
checkpoint52d_pre (2003/12/06) |
5155 |
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
5156 |
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
5157 |
|
5158 |
checkpoint52c_post (2003/11/25) |
5159 |
o Fixing OPTIONS files for use of exf: |
5160 |
- ALLOW_ECCO not needed |
5161 |
- ECCO_CPPOPTIONS.h should not be included from |
5162 |
EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
5163 |
as has been the case in the past |
5164 |
- All cal/exf related options are currently set in |
5165 |
single header file. Should remain so until we |
5166 |
agree on a consistent new policy. |
5167 |
o Removed all CPP options for cal package. |
5168 |
cal has no more CPP options. |
5169 |
o modified STOREs in GAD_ADVECTION |
5170 |
o corrected key comp. for passkey |
5171 |
|
5172 |
checkpoint52b_post (2003/11/23) |
5173 |
o new version: "thsice" of thermodynamic sea-ice pkg: |
5174 |
- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
5175 |
- modify fluxes but do not change theta directly; |
5176 |
- light cleaning of bulk_force pkg (still needed with thsice). |
5177 |
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
5178 |
+ output_thsice.txt to test thsice & bulk_force pkgs. |
5179 |
o put back grid & coriolis monitor output. |
5180 |
checkpoint52b_pre (2003/11/23) |
5181 |
|
5182 |
o call "do_the_model_io" at the beginning (=> dump initial state) |
5183 |
o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
5184 |
o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
5185 |
(need info on NUMBER_OF_PTRACERS) |
5186 |
o missing PTRACERS headers in some routines |
5187 |
o default tamc.h in pkg/autodiff supposed to crash |
5188 |
to ensure proper customization |
5189 |
|
5190 |
checkpoint52a_post (2003/11/17) |
5191 |
o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
5192 |
- moved surfaceTendencyTice from pkg/seaice to main code |
5193 |
- subroutine FREEZE_SURFACE now limits only surface temperature |
5194 |
and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
5195 |
=> new output.txt for global_ocean.cs32x15 & global_with_exf |
5196 |
- keep the old version of FREEZE for backward compatibility; |
5197 |
global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
5198 |
- corresponding modifs for TAF directives |
5199 |
o added surface flux output variables to TIMEAVE_STATVARS |
5200 |
o time-averaged output for pkg/ptracers |
5201 |
o fix problem with ECCO-related divided adjoint |
5202 |
snapshot file was missing some ad-variables, |
5203 |
but no warning issued by TAF |
5204 |
|
5205 |
checkpoint52a_pre (2003/11/12) |
5206 |
o some bug fixes for #undef REAL4_IS_SLOW |
5207 |
|
5208 |
checkpoint52 = ecco_c52_e35 |
5209 |
o after testing adjoints of checkpoint51u_post |
5210 |
|
5211 |
checkpoint51u_post (2003/11/06) |
5212 |
o this is the post-merge tag of the ecco-branch |
5213 |
(needs another clean checkout and re-testing) |
5214 |
o various natl_box_adjoint configs and results |
5215 |
but no input fields |
5216 |
o obcs adjoint not yet merged! |
5217 |
o adding ECCO global 1x1 and 2x2 degree configs |
5218 |
o updated/extended some store directives for seaice |
5219 |
o pkg/ecco now containes ecco-specific part of cost function |
5220 |
o top level routines the_main_loop, forward_step |
5221 |
supersede those in model/src/ |
5222 |
previous input data.cost now in data.ecco |
5223 |
(new namelist ecco_cost_nml) |
5224 |
o in ctrl/ cleaned some cross-dependencies and updated CPP options |
5225 |
|
5226 |
checkpoint51t_post (2003/11/04) |
5227 |
o this is the pre-merge tag of the ecco-branch |
5228 |
|
5229 |
checkpoint51s_post (2003/11/04) |
5230 |
o cleanup: removed various obsolete #define-s |
5231 |
o pkg/grdchk |
5232 |
- renamed 'ph-grd 3' to 'grad-res' |
5233 |
- merged from ecco-branch |
5234 |
(remaining bug fixes for obcs gradient checks) |
5235 |
- additional high-precision output for testreport |
5236 |
(grep for 'precision_grdchk_result') |
5237 |
|
5238 |
checkpoint51r_post (2003/11/03) |
5239 |
o cleaned up or removed CPP_OPTIONS.h files |
5240 |
o updated results for some of the tests to reflect the new |
5241 |
optfiles (-ieee: -O0 instead of -O3) |
5242 |
|
5243 |
checkpoint51q_post (2003/10/30) |
5244 |
o cd_code: |
5245 |
- moved cd_scheme.F -> cd_code_scheme.F |
5246 |
- separate read_checkpoint from cd_code_ini_vars.F |
5247 |
- separated cd_code part from write_checkpoint |
5248 |
- updated AD_SOURCE, generated .flow |
5249 |
- added CD_CODE_VARS.h to the_main_loop |
5250 |
- Moving cd_code specific store dir.s to pkg/cd_code |
5251 |
o ctrl package totally restructured |
5252 |
- pack/unpack now optional and decoupled from |
5253 |
xx_/adxx_ I/O |
5254 |
- ctrl_pack/unpack cleaned |
5255 |
(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
5256 |
- confined inclusion of AD_CONFIG.h to where necessary. |
5257 |
o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
5258 |
|
5259 |
checkpoint51p_post (2003/10/30) |
5260 |
o create initial cd_code package |
5261 |
- WARNING: the initialization of fields within packages |
5262 |
is broken because INI_FIELDS (where READ_CHECKPOINT is |
5263 |
called) is called *before* PACKAGES_INIT_VARIABLES. |
5264 |
This seems to be backwards since |
5265 |
1) its important to initially zero the entire field including |
5266 |
the "halo" region |
5267 |
2) zeroing needs to be done *before* reading pickup info |
5268 |
and the pickup call might or might not happen in any |
5269 |
particular run |
5270 |
- this needs an overhaul for R2 |
5271 |
o cleanup verification/*/code/GMREDI_OPTIONS.h |
5272 |
o cleanup testreport |
5273 |
|
5274 |
checkpoint51o_post (2003/10/27) |
5275 |
o bringing AD-related verif's up to date with genmake2 |
5276 |
- carbon/ |
5277 |
- global_ocean.90x40x15/ |
5278 |
- hs.94.1x64x5/ |
5279 |
- (front_relax/ ) |
5280 |
o (more) consistent directory structure for AD-related verif.'s |
5281 |
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
5282 |
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
5283 |
o bug fix in find_alpha.F for MDJWF: |
5284 |
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
5285 |
change rho -> rho-rhoConst |
5286 |
- replace call find_rho to find_rhonum |
5287 |
o initialisation of rFlx extended to full array (required by TAF) |
5288 |
and shifted to thermodynamics |
5289 |
o removed PTRACERS.h in ptracers routine |
5290 |
o added surfacetendencyPtr to S/R parameter list pracers_forcing |
5291 |
o Correcting initialisations for fVerU, fVerV. |
5292 |
o helping TAF to recognize dependency on kUp for |
5293 |
fVerU, fVerV |
5294 |
o Replacing delZ by delR in pkg/ctrl/ |
5295 |
checkpoint51o_pre (2003/10/24) |
5296 |
|
5297 |
o undid all of cp51 pending some cleanups and discussion |
5298 |
o added the [#include "AD_CONFIG.h"] statement to all files that need |
5299 |
it for adjoint/tl #defines |
5300 |
o re-worked the build logic in genmake2 to support AD_CONFIG.h |
5301 |
o removed tools/genmake since it no longer works |
5302 |
|
5303 |
checkpoint51n_post (2003/10/23) |
5304 |
o modifications to make FREEZE flux visible to pkg/kpp |
5305 |
- moved surfaceTendencyTice from pkg/seaice to main code |
5306 |
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
5307 |
- subroutine FREEZE now limits only surface temperature |
5308 |
(this means new output.txt for global_ocean.90x40x15, |
5309 |
global_ocean.cs32x15, and global_with_exf) |
5310 |
o added surface flux output variables to TIMEAVE_STATVARS |
5311 |
|
5312 |
checkpoint51n_pre (2003/10/23) |
5313 |
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
5314 |
o added [#include "AD_CONFIG.h"] to all files that use the following |
5315 |
defines: |
5316 |
- ALLOW_ADJOINT_RUN |
5317 |
- ALLOW_TANGENTLINEAR_RUN |
5318 |
- ALLOW_ECCO_OPTIMIZATION |
5319 |
|
5320 |
checkpoint51m_post (2003/10/21) |
5321 |
o incorporating changes to get TAMC/TAF working in genmake2 |
5322 |
- added new TAMC/TAF targets to the Makefile |
5323 |
- various cleanups related to package handling |
5324 |
- these changes should have no impact on the forward model |
5325 |
|
5326 |
checkpoint51l_post (2003/10/20) |
5327 |
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
5328 |
- faster algorithm for cal_addtime.F |
5329 |
- higher precision arithmetic, where needed |
5330 |
- pkg/exf *startdate variables changed from calendar date to |
5331 |
model integration time |
5332 |
|
5333 |
checkpoint51l_pre (2003/10/17) |
5334 |
o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
5335 |
o enable to apply restoring on S & T only in a latitude band. |
5336 |
o update output (external_forcing_surf modif. change truncation errors) |
5337 |
global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
5338 |
|
5339 |
checkpoint51k_post (2003/10/16) |
5340 |
o change default to: useNHMTerms=.FALSE. |
5341 |
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
5342 |
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
5343 |
- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
5344 |
exp1, ideal_2D_oce |
5345 |
- change data file of oceanic exp (leave the results unchanged for now) |
5346 |
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
5347 |
o set gravitySign automatically according to the vertical coordinate used |
5348 |
(and change sign: back to "logical" value: +1 when R increases downward) |
5349 |
o added an include barrier to the default CPP_OPTIONS.h and |
5350 |
removed the #include "PACKAGES_CONFIG.h" from it |
5351 |
o fix a bug in mom_fluxform (from chk51j_post) |
5352 |
|
5353 |
checkpoint51j_post (2003/10/10) |
5354 |
o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
5355 |
o adjusted some flow directives (dynamics, thermodynamics) |
5356 |
o added cubed-sphere case to test cost function |
5357 |
o heckpoint_lev?_directives.h now include |
5358 |
pkg-specific directives, whenever those are enabled. |
5359 |
o Moving pkg-specific flow directives to corresponding pkg |
5360 |
Moving pkg-specific differentiation list to corresponding pkg |
5361 |
Moving pkg-specific checkpoint-lev storing to corresponding pkg |
5362 |
---> conventions are |
5363 |
- pkg_ad.flow |
5364 |
- pkg_ad_diff.list |
5365 |
- pkg_ad_check_lev?_dir.h |
5366 |
|
5367 |
checkpoint51i_post (2003/10/09) |
5368 |
o merge of the branch-genmake2 |
5369 |
- knowingly breaks the older genmake |
5370 |
- automatic generation of all ALLOW_${PKG_NAME} defines |
5371 |
- new testreport supersedes older testscript |
5372 |
o large number of package inclusion and header cleanups |
5373 |
checkpoint51i_pre (2003/10/08) |
5374 |
|
5375 |
o new output for adjoin of global ocean vector invariant |
5376 |
o fix for checkpoint of thermodynamic seaice and bulk_force |
5377 |
o Steph gchem various cleanups |
5378 |
|
5379 |
checkpoint 51h_pre |
5380 |
o fixed some single quotes |
5381 |
o modify gchem pkg to be more versatile |
5382 |
o modifications to clean up dic pkg |
5383 |
o add pkg/cfc |
5384 |
|
5385 |
checkpoint51g_post (2003/10/02) |
5386 |
o provide links for ARPACK and ADM*TLM |
5387 |
o start removing verification/vero/ |
5388 |
o update AD-related stuff |
5389 |
(in particular some IF-statements in model/src/ routines) |
5390 |
o adding to verification/global_ocean.90x40x15/ adjoint of |
5391 |
vector invariant setup |
5392 |
|
5393 |
checkpoint51f_post (2003/10/02) |
5394 |
o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
5395 |
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
5396 |
of tracer Green's fucntions for ocean inversion project. |
5397 |
|
5398 |
checkpoint51f_pre (2003/08/07) |
5399 |
o Added on-the-fly spatial interpolation capability |
5400 |
"USE_EXF_INTERPOLATION" to pkg/exf. |
5401 |
- This is a temporary Cartesian-grid hack until |
5402 |
the super-duper ESMF coupler becomes available. |
5403 |
- See verification/global_with_exf/README for usage example. |
5404 |
- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
5405 |
flags and modified pkg/seaice accordingly. |
5406 |
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
5407 |
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
5408 |
non-local transport term. |
5409 |
|
5410 |
checkpoint51e_post (2003/08/03) |
5411 |
o pkg/mom_vecinv: |
5412 |
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
5413 |
- add time-ave diagnostic of vorticity advection. |
5414 |
o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. |
5415 |
o atmospheric geopotential: - include water vapor effect; |
5416 |
- use p^kappa in p* scaling. |
5417 |
o land pkg: read initial state from files. |
5418 |
o AIM : add stratospheric drag in the upper level |
5419 |
|
5420 |
checkpoint51d_post (2003/07/18) |
5421 |
o change function ILNBLNK (=> last non-blank char.) to return zero |
5422 |
(instead of the string length) when the string. char is empty |
5423 |
o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) |
5424 |
o modif's to restore TAMC compatibility |
5425 |
- avoid "_d" constructs in PARAMETER declarations |
5426 |
- avoid interrupting lines by comment lines |
5427 |
o Use cluster local disks for purely local I/O |
5428 |
vs. globally visible disks needed for ctrl stuff |
5429 |
(merged from ecco-branch) |
5430 |
- new active_file_loc... and mdsio_..._loc routines |
5431 |
- affected packages: autodiff, ctrl, grdchk, mdsio |
5432 |
|
5433 |
checkpoint51c_post (2003/07/08) |
5434 |
o introducing integer flag debugLevel |
5435 |
- debLevZero: suppress all output |
5436 |
- debLevA: standard |
5437 |
- debLevB: equivalent to current debugMode=.TRUE. |
5438 |
o introducing pathname variable mdsioLocalDir for mdsio |
5439 |
that can be specified at runtime |
5440 |
(relevant for cluster I/O to local disk) |
5441 |
` |
5442 |
>>>checkpoint51b_post |
5443 |
adjoint of ptracers |
5444 |
o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
5445 |
o extended state in checkpoint_lev?, etc. |
5446 |
o alternative ctrl/cost with tr1 or ptracer |
5447 |
o new comlev1_bibj_ptracers |
5448 |
o new ptracers.flow |
5449 |
o made ptracers_forcing same as external_forcing_s |
5450 |
o added verification for adjoint with ptracers |
5451 |
- adm. grdchk fail so far |
5452 |
- tlm. grdchk OK |
5453 |
- checked tapelev/comlev recomputations: OK |
5454 |
<<<checkpoint51b_pre |
5455 |
|
5456 |
checkpoint51a_post (2003/06/25) |
5457 |
o added code for biogeochemistry package |
5458 |
- new pkgs: dic, gchem |
5459 |
- new subroutine in ptracers |
5460 |
o modify code for biogeo packages |
5461 |
- in model/src and pkg/ptracers |
5462 |
|
5463 |
checkpoint51 (2003/06/24) |
5464 |
o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN |
5465 |
- autodiff, ctrl, exf, grdchk, seaice |
5466 |
kept separate packages |
5467 |
- cost, ecco, obcs |
5468 |
o updating verification/internal_wave, verification/lab_sea |
5469 |
(all verif's pass on faulks.lcs.mit.edu RH7.3, g77) |
5470 |
|
5471 |
checkpoint50i_post (2003/06/23) |
5472 |
o Preparing next differentiable checkpoint and sync |
5473 |
of MAIN vs. ecco-branch |
5474 |
- 1st step: this one is differentiable |
5475 |
- 2nd step: next(! not this) checkpoint will have updated packages |
5476 |
from ecco-branch) |
5477 |
|
5478 |
checkpoint50h_post (2003/06/20) |
5479 |
o new package "land": provide surface BC for AIM. |
5480 |
o pkg/ptracers: apply exchange to all tracers after reading a pickup. |
5481 |
o AIM: use true log-P extrapolation for near surface temp (= as in |
5482 |
F.Molteni paper) ; update aim.5l_cs output. |
5483 |
o New variable in PARM03 for more flexible pickups |
5484 |
o somewhat cleaned package initialisation sequence for |
5485 |
ctrl/ cost/ ecco/ in packages_... routines |
5486 |
|
5487 |
checkpoint50g_post (2003/05/23) |
5488 |
o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
5489 |
- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
5490 |
- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
5491 |
made the default because of faster convergence than ADI |
5492 |
|
5493 |
checkpoint50f_post (2003/05/23) |
5494 |
o exf totally restructured |
5495 |
- replaced all exf_set_ routines by one generic exf_set_gen.F |
5496 |
and made sure it's still differentiable |
5497 |
- split exf_getffields.F into new exf_bulkformulae.F |
5498 |
- exf_inscal_/exf_outscal_ suffixes consistent with field names |
5499 |
- updated adjoint/makefile and relevant verif. accordingly |
5500 |
|
5501 |
checkpoint50f_pre (2003/05/23) |
5502 |
o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; |
5503 |
+ change Evap over land. (update aim.5l_cs output) |
5504 |
o added missing .cvsignores and made uniform across expts |
5505 |
o changed configuration of tidal_basin_2d expt |
5506 |
o added pkg/debug functions for tracing code in fatal crashes |
5507 |
o tidied pkg/monitor to use MONITOR_OPTIONS.h |
5508 |
o new fn in pkg/monitor to stop model if solution grows too big |
5509 |
o removed lots of single quotes from comments |
5510 |
|
5511 |
checkpoint50e_post (2003/05/14) |
5512 |
o make KPP work with PTRACERS |
5513 |
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
5514 |
nearly a copy of kpp_transport_s |
5515 |
- there is no analogue to SurfaceTendencyS, so I have to use |
5516 |
gPtr(of the surface layer) instead |
5517 |
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
5518 |
checkpoint50e_pre (2003/05/13) |
5519 |
|
5520 |
checkpoint50d_post (2003/05/13) |
5521 |
o change kpp output from multiple-record state files to single-record state |
5522 |
files analogous to write_state.F |
5523 |
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
5524 |
analogous to the cg2d-related output. |
5525 |
o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
5526 |
so that writing to internal file fn (with length 512) fails. |
5527 |
checkpoint50d_pre (2003/05/12) |
5528 |
|
5529 |
checkpoint50c_post (2003/05/12) |
5530 |
o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) |
5531 |
o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. |
5532 |
o add time-average diagnostic of U*V and vertical diffusive flux for theta. |
5533 |
o bug fixed in convective adjustment diagnostic (multi-tile set-up). |
5534 |
o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. |
5535 |
|
5536 |
checkpoint50c_pre (2003/04/30) |
5537 |
Merging from release1_p13: |
5538 |
o bug fix for pkg/seaice dynamic solver |
5539 |
o Added SEAICE_initialHEFF to pkg/seaice |
5540 |
|
5541 |
checkpoint50b_post (2003/04/17) |
5542 |
o store u*,v* in gU,V instead of in guNm1,gvNm1 |
5543 |
o in order to put the momForcing out of the Adams-Bashforth: |
5544 |
move forcing & CD-scheme calls from mom_fluxform & mom_vecinv |
5545 |
to timestep.F |
5546 |
o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays |
5547 |
o re-generate output for highly sensitive test-exp: |
5548 |
global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box |
5549 |
|
5550 |
checkpoint50b_pre (2003/04/17) |
5551 |
o restore the use of momAdvection & useCoriolis flags (mom_vecinv) |
5552 |
o corrected CPP option mismatch in exf_Bulk... functions for case |
5553 |
#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
5554 |
|
5555 |
checkpoint50a_post (2003/03/21) |
5556 |
o Bug fix for merging between c50 and KPP. |
5557 |
ikey was passed from thermodynamics to kpp_calc via |
5558 |
common block rather than being recomputed in kpp_calc, |
5559 |
in contradiction with new key itdkey. |
5560 |
New key ikppkey created, and tamc.h headers updated. |
5561 |
|
5562 |
checkpoint50 (2003/03/08) |
5563 |
- 2nd step of merge with ecco-branch: |
5564 |
merge changes in ecco-branch back into main trunk |
5565 |
- bug fix in find_alpha |
5566 |
- more storing in gmredi_calc_tensor.F, kpp_routines.F |
5567 |
- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
5568 |
- merged some sliced AD support routines |
5569 |
|
5570 |
checkpoint49 (2003/03/06) |
5571 |
merged from ecco-branch: |
5572 |
o exf: |
5573 |
- Enable initialisation of forcing fields to constant |
5574 |
(runtime) values. |
5575 |
- in exf_getffields.F |
5576 |
Reduce i-/j-loop to interior domain, discarding overlaps. |
5577 |
That also fixes wrong TAF-key computations for key_1, key_2 |
5578 |
with bulf formulae. |
5579 |
- exf_init.F modify #ifdef for exf_init_evap |
5580 |
- exf_getffieldrec.F, ctrl_getrec.F |
5581 |
The following INT-usages are not safe: |
5582 |
fldsecs = int(fldsecs/fldperiod)*fldperiod |
5583 |
fldcount = int(fldsecs/fldperiod) + 1 |
5584 |
and were modified. |
5585 |
o autodiff: checkpoint_lev... |
5586 |
- updated storing for bulk formulae (some arrays were missing) |
5587 |
- added state for seaice package |
5588 |
- synchronized with main branch |
5589 |
o DIVA: |
5590 |
Modif.s in |
5591 |
- the_main_loop.F |
5592 |
- the_model_main.F |
5593 |
and added cost_final_restore.F cost_final_store.F |
5594 |
o With these changes, it is possible to fully separate |
5595 |
the first forward run to compute the cost function (mdthe_main_loop) |
5596 |
and adjoint runs over individual DIVA intervals (adthe_main_loop) |
5597 |
into separate model executions. |
5598 |
This enables better tuning of DIVA to given queue sizes. |
5599 |
o Loss of cost function value in consecutive DIVA runs is |
5600 |
fixed by storing to 'costfinal' file. |
5601 |
o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
5602 |
beginning/end of adjoint integration is accounted for. |
5603 |
The current changes apply to TAF-1.4.26. |
5604 |
TAF has one remaining bug, requiring one manual change |
5605 |
(see MITgcm manual). |
5606 |
o cal: synchronized between MAIN and ecco-branch |
5607 |
|
5608 |
checkpoint48i_post (2003/03/05) |
5609 |
o Changes to restore differentiability of code w.r.t. previous tag |
5610 |
(mostly adding new routines to make list and replacing |
5611 |
pressure by totPhiHyd). |
5612 |
o Updated and merged grdchk package |
5613 |
- has both ADM and TLM checks |
5614 |
- works for single- and multi-proc. |
5615 |
- output cleaned |
5616 |
- worked successfully for parallel DIVA |
5617 |
o genmake: |
5618 |
- Adding -platform=SP4 |
5619 |
- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
5620 |
o Modif. for DIVA: |
5621 |
ctrl_unpack should not be called in intermediate DIVA interval. |
5622 |
(similar thing would apply for active files such as |
5623 |
tbar, sbar, psbar, which should not be reinitialised; |
5624 |
only relevant for ecco-branch) |
5625 |
|
5626 |
checkpoint48h_post (2003/02/28) |
5627 |
o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
5628 |
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
5629 |
o Added SEAICE_initialHEFF to pkg/seaice |
5630 |
o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
5631 |
|
5632 |
checkpoint48g_post (2003/02/18) |
5633 |
--- EOS: |
5634 |
o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
5635 |
store total Potential in totPhyHyd for diagnostics & EOS. |
5636 |
o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
5637 |
--- Pressure/geopotential gradient: |
5638 |
o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
5639 |
o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
5640 |
( changes results of global_ocean_pressure ) |
5641 |
o NLFS + z-coord.: add eta*Rho' contribution. |
5642 |
o accurate phiHyd when using interface-W at the middle between 2 centers |
5643 |
( changes results of ideal_2D_oce ) |
5644 |
o includes r* 2nd term in potential gradient. |
5645 |
|
5646 |
checkpoint48f_post (2003/02/18) |
5647 |
Merging from release1_p12: |
5648 |
o Modifications for using pkg/exf with pkg/seaice |
5649 |
- improved description of the various forcing configurations |
5650 |
- added basic radiation bulk formulae to pkg/exf |
5651 |
- units/sign fix for evap computation in exf_getffields.F |
5652 |
- updated verification/global_with_exf/results/output.txt |
5653 |
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
5654 |
(SBO) core products, including oceanic mass, center-of-mass, |
5655 |
angular, and bottom pressure (see pkg/sbo/README.sbo). |
5656 |
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
5657 |
to avoid negative values in shallow regions. |
5658 |
- updated verification/natl_box/results/output.txt |
5659 |
- updated verification/lab_sea/results/output.txt |
5660 |
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
5661 |
o Added useSingleCpuIO option (see PARAMS.h). |
5662 |
o Updated useSingleCpuIO option in mdsio_writefield.F to |
5663 |
work with multi-field files, e.g., for single-file pickup. |
5664 |
o pkg/seaice: |
5665 |
- bug fix in growth.F: QNET for no shortwave case |
5666 |
- added HeffFile for specifying initial sea-ice thickness |
5667 |
- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
5668 |
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
5669 |
kpp_transport_t.F, forward_step.F, and the_main_loop.F |
5670 |
o pkg/seaice: |
5671 |
- adjoint-friendly modifications |
5672 |
- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
5673 |
|
5674 |
checkpoint48e_post (2003/02/12) |
5675 |
o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) |
5676 |
o dynamics: change definition of computational domain & adapt mom_fluxform |
5677 |
accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. |
5678 |
o following exp works with Olx=Oly=2 (and pass through checkbounds option): |
5679 |
adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 |
5680 |
exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 |
5681 |
global_ocean.90x40x15 global_with_exf global_ocean_pressure |
5682 |
inverted_barometer solid-body.cs-32x32x1 |
5683 |
(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) |
5684 |
|
5685 |
checkpoint48d_post (2003/02/09) |
5686 |
o in preparation for r*: |
5687 |
a) use pre-computed gradient of hydrostatic potential: |
5688 |
changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce |
5689 |
b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: |
5690 |
=> affects results of glob_oce_pressure (different truncation error) |
5691 |
update output.txt of ideal_2D_oce & global_ocean_pressure |
5692 |
|
5693 |
checkpoint48d_pre (2003/02/08) |
5694 |
o in preparation for r*: |
5695 |
new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
5696 |
pass the 2 comp. of the grad. as arguments to momentum S/R. |
5697 |
but for the moment, only used if it does not change the results. |
5698 |
o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP |
5699 |
|
5700 |
checkpoint48c_post (2003/02/06) |
5701 |
Modifications in treatment of initial flux forcing controls |
5702 |
to avoid extra storing of flux fields. |
5703 |
|
5704 |
checkpoint48c_pre (2003/01/21) |
5705 |
o Added tidal_basin_2d experiment (currently 1D!) |
5706 |
o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) |
5707 |
|
5708 |
checkpoint48b_post (2003/01/27) |
5709 |
o r* coordinate added in #ifdef NONLIN_FRSURF block. |
5710 |
(modification to pressure gradient not yet implemented) |
5711 |
o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports |
5712 |
(for U & V) that are used for vertical advection of momentum. |
5713 |
|
5714 |
checkpoint48a_post (2003/01/24) |
5715 |
o In preparation for r*, use temp. array to compute vertical transport |
5716 |
in flux-form momentum pkg. => change results of few test-exp. |
5717 |
Update output of: exp4, exp5, front_relax, global_ocean_pressure, |
5718 |
lab_sea, natl_box & plume_on_slope |
5719 |
|
5720 |
checkpoint48 (2003/01/23) |
5721 |
o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') |
5722 |
|
5723 |
checkpoint47j_post (2003/01/21) |
5724 |
o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. |
5725 |
o moved adexch from forward_step to addummy_in_stepping |
5726 |
o added exch in ctrl_map_... |
5727 |
o aveFreq.=0. at end of cost_final to avoid overwrite in |
5728 |
reverse checkpointing loop |
5729 |
o Yet more changes in gmredi: |
5730 |
* adgmredi_calc_tensor |
5731 |
avoiding all recomputation of gmredi_slope_limit |
5732 |
* adgmredi_x/y/rtransport |
5733 |
added flag for excessive storing to avoid recomp. of |
5734 |
u/v/rtans, dTdx/y/z |
5735 |
-> this is not really necessary and very memory-consuming |
5736 |
* adgmredi_slope_psi: |
5737 |
consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff |
5738 |
* gmredi_slope_limit |
5739 |
re-activated full calculation of taperfct for case 'ac02' |
5740 |
o updating verification/ adjoints of carbon, global_ocean.90x40x15 |
5741 |
|
5742 |
checkpoint47i_post (2003/01/13) |
5743 |
o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. |
5744 |
o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) |
5745 |
default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) |
5746 |
o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) |
5747 |
o gmredi: fix few bugs. |
5748 |
|
5749 |
checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) |
5750 |
This will be a good checkpoint to plug into the ecco-branch. |
5751 |
o few modif.'s to get latest version adjointed |
5752 |
(mainly kick out code in ini_linear_phisurf) |
5753 |
o modif's to run adjoint with exactConserv |
5754 |
o case GM_BOLUS_ADVEC should be cleaned |
5755 |
S/R gmredi_slope_psi should be cleaned |
5756 |
o verification/carbon now has exactConserv=.TRUE. |
5757 |
|
5758 |
checkpoint47g_post (2003/01/10) |
5759 |
o time-average AIM output: becomes independent from statvars time-average |
5760 |
(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
5761 |
o After TAF bug fix: |
5762 |
Tested adjoint of gmredi package. |
5763 |
Tests were done with checkpoint47 rather than with latest |
5764 |
checkpoint47f_post since the latter is broken for the adjoint |
5765 |
verification/carbon/ contains both ADM and TLM gradient checks. |
5766 |
Here they are, before they get changed/lost/stolen. |
5767 |
Mostly modif.'s to fix numerical sensitivities. |
5768 |
Gradient checks OK for |
5769 |
- GM_taper_scheme: |
5770 |
* clipping |
5771 |
* ac02 |
5772 |
* linear |
5773 |
* glw91 |
5774 |
* dm95 |
5775 |
* ldd97 |
5776 |
- GMREDI_OPTIONS: |
5777 |
* GM_VISBECK_VARIABLE_K |
5778 |
* GM_NON_UNITY_DIAGONAL |
5779 |
* GM_EXTRA_DIAGONAL |
5780 |
* GM_BOLUS_ADVEC |
5781 |
in conjunction with data.gmredi parameters to be checked in |
5782 |
in a few minutes under verification/carbon/code/ |
5783 |
|
5784 |
checkpoint47f_post (2002/12/28) |
5785 |
Merging from release1_p10: |
5786 |
o modifications for using pkg/exf with pkg/seaice |
5787 |
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
5788 |
and SEAICE_EXTERNAL_FLUXES |
5789 |
- pkg/exf CPP options EXF_READ_EVAP and |
5790 |
EXF_NO_BULK_COMPUTATIONS |
5791 |
- usage examples are Experiments 8 and 9 in |
5792 |
verification/lab_sea/README |
5793 |
- verification/lab_sea default experiment now uses |
5794 |
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf |
5795 |
|
5796 |
checkpoint47e_post (2002/12/27) |
5797 |
o created a tag prior to creating a branch |
5798 |
|
5799 |
checkpoint47d_post (2002/12/16) |
5800 |
o fixed bug in the oceanic pressure coordinates code: vertical viscosity |
5801 |
at the bottom boundary had an erroneous half slip boundary condition |
5802 |
o added bottom drag and no slip boundary condition capabilities to |
5803 |
oceanic pressure coordinates code |
5804 |
o added new verification experiment global_ocean_pressure, this experiment is |
5805 |
also described in the tutorial section of the manual |
5806 |
checkpoint47d_pre (2002/12/16) |
5807 |
|
5808 |
checkpoint47c_post (2002/12/16) |
5809 |
o Added a verification experiment for a global cubed-sphere ocean run |
5810 |
- verification/global_ocean.cubed32x32x30 |
5811 |
- uses pkg/therm_seaice and pkg/bulk_forcing |
5812 |
|
5813 |
o allow to run AIM physics with SPEEDY input files (from Franco Molteni) |
5814 |
o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) |
5815 |
when using P-coordinate; only implemented for atmospheric config. |
5816 |
o OCEANICP & realFreshWater: include P-E direct effect on wVel ; |
5817 |
NOTES: requires option NONLIN_FRSURF to be "#define". |
5818 |
o update advect_xz/results/output.txt (left from checkpoint44g_post) |
5819 |
|
5820 |
checkpoint47b_post (2002/12/05) |
5821 |
Merging from release1_p9: |
5822 |
o pkg/seaice |
5823 |
- removed GOTO's and added taf directives |
5824 |
- double precision constants to reduce the g77 (Linux) |
5825 |
to F77 (SGI) differences reported in release1_p8 |
5826 |
o tools/genmake |
5827 |
- added SGI options |
5828 |
o verification/testscript |
5829 |
- updated to that of checkpoint47a_post |
5830 |
o verification/global_ocean.90x40x15/input/eedata |
5831 |
- modified for SGI f77 compatibility |
5832 |
o verification/lab_sea |
5833 |
- added description of sea-ice model |
5834 |
- added missing matlab routines |
5835 |
- added test of thermodynamics parallelization |
5836 |
|
5837 |
checkpoint47a_post (2002/11/23) |
5838 |
o new pkg: aim_v23 |
5839 |
= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
5840 |
for now, keep the same surface forcing as before. |
5841 |
- Part-Cell implemented into AIM; check that Heat & Water are conserved |
5842 |
- aim.5l_cs: use new aim pkg (run 10yr & get better results than before) |
5843 |
- aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg |
5844 |
o add diagnostic of surface correction term in monitor output |
5845 |
|
5846 |
o bulk_force and therm_seaice |
5847 |
- Two packages: bulk_force (Bulk forcing) |
5848 |
and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 |
5849 |
- Earlier integration from Stephaine Dutkiewicz |
5850 |
and Patrick Heimbach. |
5851 |
- Two ifdef statements for compile time, |
5852 |
ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE |
5853 |
|
5854 |
checkpoint47 (2002/11/15) |
5855 |
differentiable version of checkpoint46n_post |
5856 |
o bug fix in quasihydrostaticterms |
5857 |
o * "clean" adjoint code (in terms of extensive recomputations) |
5858 |
can now be obtained for all GMREDI options (i.e. for |
5859 |
- GM_VISBECK_VARIABLE_K |
5860 |
- GM_NON_UNITY_DIAGONAL |
5861 |
- GM_EXTRA_DIAGONAL |
5862 |
- GM_BOLUS_ADVEC ) |
5863 |
* However, wrong gradient check problem remains unsolved. |
5864 |
* New CPP options have been introduced for different |
5865 |
tapering schemes |
5866 |
o external_fields_load now part of differentiation list |
5867 |
o pressure needs multiple storing; |
5868 |
would be nice to have store_pressure at beginning or |
5869 |
end of forward_step, e.g. by having phiHyd global (5-dim.) |
5870 |
(NB: pressure is needed for certain cases in find_rho, |
5871 |
which is also invoked through convective_adjustment). |
5872 |
o recomputations in find_rho for cases |
5873 |
'JMD95'/'UNESCO' or 'MDJWF' are OK. |
5874 |
o #define ATMOSPHERIC_LOADING should be differentiable |
5875 |
o ini_forcing shifted to begining of initialise_varia |
5876 |
o Incorporating QNVS line search routines into MITgcm |
5877 |
(this is separate code, and therefore not under pkg) |
5878 |
lsopt/, optim/ |
5879 |
o Updated verification/carbon/ |
5880 |
- #define GM_VISBECK_VARIABLE_K |
5881 |
- GM_taper_scheme = 'ldd97' |
5882 |
|
5883 |
checkpoint46n_post (2002/11/12) |
5884 |
Merging from release1_p8: |
5885 |
o verification/natl_box: |
5886 |
updating new external_fields_load routine |
5887 |
o New package: pkg/seaice |
5888 |
Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). |
5889 |
The sea-ice code is based on Hibler (1979-1980). |
5890 |
Two sea-ice dynamic solvers, ADI and LSR, are included. |
5891 |
In addition to computing prognostic sea-ice variables and diagnosing |
5892 |
the forcing/external data fields that drive the ocean model, |
5893 |
SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
5894 |
The implied surface heat flux is then stored in variable |
5895 |
surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and |
5896 |
kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the |
5897 |
non-local transport term. Because this call precedes model |
5898 |
thermodynamics, temperature under sea-ice may not be "exactly" at |
5899 |
the freezing point by the time theta is dumped or time-averaged. |
5900 |
N.B.: fairly large differences in accuracy occur across |
5901 |
different platforms/compilers; comparison between |
5902 |
g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) |
5903 |
generated output gives: |
5904 |
T S U V |
5905 |
C D M c m s m s m s m s |
5906 |
n p a R g m m e . m m e . m m e . m m e . |
5907 |
f n k u 2 i a a d i a a d i a a d i a a d |
5908 |
g d e n d n x n . n x n . n x n . n x n . |
5909 |
|
5910 |
Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea |
5911 |
o GAD: |
5912 |
- generated new common blocks to account for call of |
5913 |
same gad routines with differing traceridentities |
5914 |
(needed to modify tracerIdentity indices in GAD.h) |
5915 |
- generated separate common blocks for case useCubedSphereExchange |
5916 |
(Department of Futurology) |
5917 |
- parameter lists to gmredi_?transport: added tracerIdentity |
5918 |
- added new key indices to tamc.h |
5919 |
o external_fields_load: |
5920 |
- added this routine to TAF list |
5921 |
- needed to make some common blocks global and additional storing |
5922 |
along the same lines as exf package (checkpoint_lev?_directives.h) |
5923 |
o exf: |
5924 |
updated external forcing package |
5925 |
- bug fixes carried over from ecco-branch |
5926 |
(missing OBCS_OPTIONS.h in two routines) |
5927 |
- enable easy to use "no forcing". |
5928 |
- added exf I/O for atmospheric loading |
5929 |
- added exf I/O for runoff data |
5930 |
- transfered scaling between exf <-> MITgcm to exf namelist |
5931 |
o Adding new verification experiment global_with_exf. |
5932 |
This verification experiment is almost identical to the |
5933 |
global_ocean.90x40x15 experiment, except that it uses |
5934 |
the exf (and cal) package instead of the |
5935 |
external_fields_load routine (cf README file). |
5936 |
|
5937 |
checkpoint46m_post (2002/11/07) |
5938 |
o modified testscript to return -- when there are no lines of "%MON" output |
5939 |
o added new flag "quasiHydrostatic" for QH mode |
5940 |
and new routine quasihydrostaticterms() |
5941 |
o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
5942 |
New routine: mom_u_coriolis_nh() |
5943 |
o fixed sign of non-hydrostatic metric terms in u and v equations. |
5944 |
Depend on correct sign of gravitySign. |
5945 |
o added work.pc* to .cvsignore in aim directories using ifc |
5946 |
o introduced flag for controllin non-hydrostatic metric terms |
5947 |
o removed gravitySign from PARM04 |
5948 |
o switched to g77/ifc from pgf77 in aim experiments |
5949 |
|
5950 |
checkpoint46l_post (2002/11/01) |
5951 |
o made convective adjustment work with pressure coordinates: |
5952 |
- changed the direction of k-loop in convective_adjustment.F for the |
5953 |
case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
5954 |
- adjusted the reference pressure k-index in convective_adjustment.F |
5955 |
- adjusted the convection condition in convect.F (in analogy to |
5956 |
calc_ivdc.F) |
5957 |
- convective_adjustment no longer computes anything on the halos |
5958 |
- removed the warnings about negative salinity from find_rho.F and |
5959 |
find_alpha.F; instead the new routine look_for_neg_salinity, called |
5960 |
at the beginning of find_rho, find_alpha, and find_beta, does a |
5961 |
check of the entire slice, if CPP-option |
5962 |
CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined |
5963 |
checkpoint46l_pre (2002/10/23) |
5964 |
|
5965 |
checkpoint46k_post (2002/10/23) |
5966 |
o fixed the verification/global_ocean.90x40x15 experiment: |
5967 |
- new bathymetry (the world according to A., JMC, and M.) |
5968 |
- new initial fields and forcing fields (*.bin files) |
5969 |
- new POLY3.COEFFS (for the next release one should switch to a full |
5970 |
equation of state: JMD95P or MDJWF) |
5971 |
- fixed several errors and redundancies in the data file |
5972 |
- experiment uses looped cells |
5973 |
- added matlab directory with diagnostic scripts for plotting of output |
5974 |
|
5975 |
o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
5976 |
- read AIM physics parameters from a file (data.aimphys) |
5977 |
- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
5978 |
|
5979 |
checkpoint46j_post (2002/10/07) |
5980 |
o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
5981 |
o move wVel computation at the end of the time step, in S/R integr_continuity |
5982 |
o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
5983 |
o update timeave pkg for wVel diagnostic. |
5984 |
checkpoint46j_pre (2002/09/27) |
5985 |
|
5986 |
checkpoint46i_post (2002/09/25) |
5987 |
o Clean up AIM package (and keep the results unchanged): |
5988 |
include CPP_OPTION and use IMPLICT NONE in all routines ; |
5989 |
declare all the variables _RL ; use _d 0 for all numerical constants. |
5990 |
use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
5991 |
|
5992 |
checkpoint46h_post (2002/09/25) |
5993 |
o cleaned up the use of rhoNil and rhoConst. |
5994 |
- rhoNil should only appear in the LINEAR equation of state, everywhere |
5995 |
else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
5996 |
and the dynamical equations are all divided by rhoConst |
5997 |
o introduced new parameter rhoConstFresh, a reference density of fresh |
5998 |
water, to remove the fresh water flux's dependence on rhoNil. The default |
5999 |
value is 999.8 kg/m^3 |
6000 |
o cleanup up external_forcing.F and external_forcing_surf.F |
6001 |
- can now be used by both OCEANIC and OCEANICP |
6002 |
checkpoint46h_pre (2002/09/18) |
6003 |
|
6004 |
Added code to convert surface volume flux (fresh water) into |
6005 |
a mass flux when using P coordinates in the ocean (OCEANICP). |
6006 |
Note: It assumes you have set rho0=rhoConst=density of fresh water. |
6007 |
|
6008 |
checkpoint46g_post (2002/09/18) |
6009 |
o Include a new diagnostic variable phiHydLow for the ocean model |
6010 |
- in z-coordinates, it is the bottom pressure anomaly |
6011 |
- in p-coordinates, it is the sea surface elevation |
6012 |
- in both cases, these variable have global drift, reflecting the mass |
6013 |
drift in z-coordinates and the volume drift in p-coordinates |
6014 |
- included time averaging for phiHydLow, be aware of the drift! |
6015 |
o depth-dependent computation of Bo_surf for pressure coordinates |
6016 |
in the ocean (buoyancyRelation='OCEANICP') |
6017 |
- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
6018 |
Theta, Salinity, and Pressure in the parameter list. This routine is |
6019 |
presently contained in find_rho.F. This routine does not give the |
6020 |
correct density for 'POLY3', which would be a z-dependent reference |
6021 |
density. |
6022 |
o cleaned up find_rho |
6023 |
- removed obsolete 'eqn' from the parameter list. |
6024 |
o added two new verification experiments: gop and goz |
6025 |
(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
6026 |
checkpoint46g_pre (2002/09/16) |
6027 |
|
6028 |
checkpoint46f_post (2002/09/16) |
6029 |
o Enable tangent linear (forward mode) gradient checks: |
6030 |
- extended active file handling to g_... files |
6031 |
- added TANGENT_SIMULATION to theSimulationMode |
6032 |
- extended grdchk package accordingly |
6033 |
o added tangent linear setup in verification/carbon/code_ftl |
6034 |
o added adjoint setup in verification/front_relax/code_ad |
6035 |
|
6036 |
checkpoint46e_post (2002/09/05) |
6037 |
o Added new equation of state -> MDJWF |
6038 |
- EOS of McDougall et al., 2002, JAOT, submitted |
6039 |
- caveat: the equation of state is only valid for a smaller (more |
6040 |
realistic?) range of values than JMD95P/Z and UNESCO |
6041 |
- added masks to the calculation of pressure in store_pressure |
6042 |
- added more check values for density in check_eos (ini_eos.F), some of |
6043 |
the old check values are out of the range of the MDJWF-eos, so don't |
6044 |
expect perfect matches for those |
6045 |
checkpoint46e_pre (2002/08/19) |
6046 |
|
6047 |
checkpoint46d_post (2002/08/19) |
6048 |
o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
6049 |
'OCEANICP', also initialised field pressure correctly in ini_eos in the |
6050 |
case of pressure coordinates. eosType='JMD95Z' in |
6051 |
combination with buoyancyRelation='OCEANICP' now causes an error. |
6052 |
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
6053 |
in find_alpha/beta. |
6054 |
checkpoint46d_pre (2002/08/15) |
6055 |
|
6056 |
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
6057 |
so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
6058 |
|
6059 |
checkpoint46c_post (2002/08/15) |
6060 |
o Changes necessary for ocean in p-coordinates |
6061 |
- Added new buoyancy relation = 'OCEANICP' |
6062 |
- Added new parameters = gravitySign (this used to be contained inside |
6063 |
the factor dRdZ which I added when we first switched to R coordinates). |
6064 |
X GM/Redi is not compatible (yet) |
6065 |
X bottom drag and no-slip need to be debugged. |
6066 |
checkpoint46c_pre (2002/08/07) |
6067 |
|
6068 |
checkpoint46b_post (2002/08/07) |
6069 |
o Added new equation of state -> JMD95Z and JMD95P |
6070 |
- EOS of Jackett and McDougall, 1995, JAOT |
6071 |
- moved all EOS parameters into EOS.h |
6072 |
- new routines ini_eos.F, store_pressure.F |
6073 |
o Added UNESCO EOS, but not recommended because it requires |
6074 |
in-situ temperature (see JMD95) |
6075 |
o Modified formatting for knudsen2.f in utils/knudsen2 and added |
6076 |
unesco.f to be used with POLY3 |
6077 |
checkpoint46b_pre (2002/07/31) |
6078 |
|
6079 |
checkpoint46a_post (2002/07/31) |
6080 |
o Added (atmospheric) pressure loading |
6081 |
- new field in FFIELDS.h, etc... |
6082 |
- new cpp flag ATMOSPHERIC_LOADING |
6083 |
o Changed hFacC to _hFacC in calc_phi_hyd.F |
6084 |
o Added SHORTWAVE_HEATING to some files for consistency |
6085 |
checkpoint46a_pre (2002/07/13) |
6086 |
|
6087 |
checkpoint46 (2002/07/13) |
6088 |
further merges from release1_p5 |
6089 |
o new ctrl package |
6090 |
- adopted from ECCO environment to enable optimization |
6091 |
- added Eliassen Palm fluxes to controls |
6092 |
o added Eliassen Palm flux controls to gradient check package |
6093 |
o cost package |
6094 |
- Compatible with new ctrl package |
6095 |
- added Eliassen Palm cost hooks |
6096 |
- modif's of existing cost functions |
6097 |
o Adjoint-related bug fixes in kpp: |
6098 |
- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
6099 |
- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
6100 |
o autodiff package |
6101 |
- flow directives: |
6102 |
+ new for S/R do_the_model_io |
6103 |
+ enhanced for S/R checkpoint |
6104 |
+ new gmredi.flow |
6105 |
- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
6106 |
disable adcommon.h/g_common.h by default. |
6107 |
- fixed problem for adjoint of global_max |
6108 |
o modified verification/carbon/ |
6109 |
o New setup for adjoint of global_ocean |
6110 |
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
6111 |
o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
6112 |
o incorporated hooks for sponge layer code (external_forcing.F) |
6113 |
|
6114 |
checkpoint45d_post (2002/07/12) |
6115 |
o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
6116 |
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
6117 |
(affects plume_on_slope "cg2d" output) |
6118 |
o add new parameter deltaTfreesurf for free-surface time stepping |
6119 |
o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
6120 |
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
6121 |
o change phiMin in exp1 (to agree with documentation) |
6122 |
o add new flags: |
6123 |
- T,S forcing inside/outside Adams-Bashforth |
6124 |
- turn off temp,salt advection and/or forcing |
6125 |
- for each tracer, define internal flag for multiDimAdvection & A-B |
6126 |
o monitor: change definition of KE to check conservation of Energy |
6127 |
|
6128 |
checkpoint45c_post (2002/05/30) |
6129 |
o Removed f90 comments ("!") |
6130 |
o Modified initialisations to enable exf package for MITgcm |
6131 |
(without invoking ECCO_PACKAGE). |
6132 |
o modifications to gradient check package (Martin Losch) |
6133 |
- enable centered differences |
6134 |
- modified format of standard output |
6135 |
|
6136 |
checkpoint45b_post (2002/05/30) |
6137 |
o cleaned exchange calls in cg2d |
6138 |
o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
6139 |
o included CPP option SINGLE_LAYER_MODE in thermodynamics |
6140 |
to configure barotropic setup (Martin Losch) |
6141 |
o moved some initialisations within bi,bj loop in dynamics |
6142 |
(TAF flow dependency) |
6143 |
o in initialise_varia, moved call packages_init_variables |
6144 |
before convective_adjustment_init |
6145 |
(corresponding adjustment of TAF tape initialisation). |
6146 |
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
6147 |
|
6148 |
checkpoint45a_post (2002/05/01) |
6149 |
o compute Rho over the whole domain (extend iMin,jMin indices) |
6150 |
o specific exchange for X-slice domain (case Ny=1) |
6151 |
o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
6152 |
o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
6153 |
|
6154 |
checkpoint44h_post = checkpoint45 |
6155 |
o Fix to restore differentiability: |
6156 |
place at which packages_init_variables is called in |
6157 |
initialise_varia is crucial for reverse control flow. |
6158 |
o modifications in GMRedi to enable stable adjoint |
6159 |
(corresponding modif's in thermodynamics, dynamics) |
6160 |
o added missing hook for sponge layer code in external_forcing |
6161 |
o modified test cost functions |
6162 |
o storing in gad_advection (plus removal of write(0,*)! |
6163 |
o missing headers TR1.h added in convective_adjustment routines |
6164 |
o errorMessageUnit set non-equal zero in eeboot |
6165 |
(conflict on some platforms, e.g. IBM SP3) |
6166 |
o modified carbon verif. |
6167 |
|
6168 |
checkpoint44h_pre (2002/03/14) |
6169 |
o vertical grid option: allow to put the Interface at the middle between |
6170 |
2 cell-centers ; replace delZ in pkg/kpp by drF. |
6171 |
o GM Advective form: Tracers are advected using the residual transport (= |
6172 |
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
6173 |
|
6174 |
checkpoint44g_post (2002/03/05) |
6175 |
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
6176 |
results) ; ifdef missing in thermodynamics.F |
6177 |
|
6178 |
checkpoint44f_pre,checkpoint44f_post |
6179 |
o added PTRACERS package |
6180 |
This allows an arbitrary number of passive tracers to be integrated |
6181 |
forward simultaneously with the dynamicaly model. |
6182 |
+ Implemented so far: |
6183 |
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
6184 |
- I/O and checkpointing |
6185 |
- GM/Redi *but* using the GM/Redi coefficient of Salt |
6186 |
+ Not implemented so far: |
6187 |
- KPP |
6188 |
- OBCS |
6189 |
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
6190 |
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
6191 |
line in data.pkg. |
6192 |
+ This package is disabled by default since it increases storage. |
6193 |
|
6194 |
|
6195 |
o testscript: added -cleanup option |
6196 |
o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
6197 |
b) enable to filter 2D fields. |
6198 |
|
6199 |
checkpoint44e_pre,post |
6200 |
o re-wrote convective adjustment to use pre-calculated weights |
6201 |
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
6202 |
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
6203 |
Original calls to convect() still in place. |
6204 |
|
6205 |
chkpt44d_pre,post |
6206 |
o added missing EXCLUDE_MONITOR flags |
6207 |
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
6208 |
(incompatible typ in MIN/MAX expressions caused problems |
6209 |
on IBM SP3) |
6210 |
o in genmake added variable MAKEDEPEND |
6211 |
plus resetting for case SunOS |
6212 |
o added timer_stats.c routine for IBM SP3 |
6213 |
o removed variables in dynamics |
6214 |
!!! I forgot to create tag chkpt44d_pre !!! |
6215 |
!!! But chkpt44d_pre = chkpt44c_post !!! |
6216 |
|
6217 |
o real fresh water flux implemented with non-linear free-surface. |
6218 |
|
6219 |
chkpt44c_pre,post |
6220 |
o few fix (mask in shap_s2, EmPmR in external_field_load, |
6221 |
USE_NATURAL_BCS in solve_for_P); |
6222 |
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
6223 |
|
6224 |
checkpoint44b_pre/_post |
6225 |
o merge of relevant stuff from the ecco-branch: |
6226 |
- genmake: removed $S64 overwrite for case SunOS |
6227 |
- pkg/exf: update and corrections for field swapping and obcs |
6228 |
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
6229 |
harmonized between ECCO and MITgcm |
6230 |
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
6231 |
updated checkpointing_lev... lists for obcs |
6232 |
- model/src: minor changes in forward_step, plot_field |
6233 |
added directive for divided adjoint in the_main_loop |
6234 |
- pkg/mdsio: added mdsio_gl_slice |
6235 |
|
6236 |
o check parameters & config (chkpt44a_pre,post) |
6237 |
o OBC and NonLin_FrSurf. |
6238 |
|
6239 |
checkpoint44 (2002/01/18) |
6240 |
o fix bug in mom_vi_del2uv |
6241 |
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
6242 |
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
6243 |
o update AIM experiments (NCEP input files) |
6244 |
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
6245 |
o added some stuff for AD |
6246 |
|
6247 |
checkpoint43 (2001/09/28) |
6248 |
o added two new advection tests |
6249 |
o added global 4x4 degree ocean test |
6250 |
o added test of H&S94 with free surface on cube |
6251 |
o some final mods for gradient check, adjoint,... |
6252 |
|
6253 |
checkpoint42 (2001/09/27) |
6254 |
Fixed AD-related problems: |
6255 |
o Store directives up-to-date with re-arranged Adams-Bashforth |
6256 |
(mainly thermodynamics.F) |
6257 |
o New store directives for multi-dim. advection schemes |
6258 |
* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
6259 |
* new common block and key passkey |
6260 |
(mainly gad_advection.F) |
6261 |
o Modified store directives for split of dynamics/thermodynamics |
6262 |
for the case ALLOW_KPP |
6263 |
o Cleaned argument list for timestep_tracer.F |
6264 |
|
6265 |
checkpoint41 (2001/09/27) |
6266 |
o re-formatted/added comments in prologues of key subroutines |
6267 |
to work with protex |
6268 |
|
6269 |
checkpoint40 (2001/09/27) |
6270 |
o moved calc_gs, calc_gt and calc_tr1 back to model/src |
6271 |
o added FLT (floats) package from Arne along with demo. experiment |
6272 |
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
6273 |
implementation of forward-in-time forcing terms |
6274 |
o more mods for non-linear free-surface including new variable |
6275 |
o modified multi-dim method to work on cube |
6276 |
o bug fix in KPP (from DM) |
6277 |
|
6278 |
checkpoint40pre9 (2001/09/27) |
6279 |
o added DST advection schemes |
6280 |
o fix MPI bug on SGI's |
6281 |
o modifications for non-linear free-surface |
6282 |
o fixed conditionals for fixed flow/passive tracer only mode |
6283 |
o added tension/strain form of stress tensor |
6284 |
o changes to commenting of arguments for TAF/TAMC |
6285 |
o added/updated many matlab scripts |
6286 |
o added multi-dimensional advection method for tracers |
6287 |
|
6288 |
checkpoint40pre8 (2001/09/05) |
6289 |
o new package rw/ |
6290 |
Added method for dumping intermediate local arrays: |
6291 |
mdsio_writetile - same as mdsio_writefield except works from inside |
6292 |
bi,bj loop |
6293 |
mdsio_writelocal - same as mdsio_writetile except works for local |
6294 |
arrays |
6295 |
write_local_r? - higher-level wrapper for mdsio_writelocal |
6296 |
Controlled by diagFreq. Defaults to zero (ie. no dumps) |
6297 |
Example given at end of mom_vecinv.F that dumps some local arrays. |
6298 |
o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
6299 |
control flux-form versus vector invariant code. |
6300 |
Switch is runtime flag vectorInvariantMomentum (defaults to false) |
6301 |
or genmake -DISABLE ... |
6302 |
o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
6303 |
(additional storing is now needed for case vecinv; |
6304 |
currently nothing implemented to switch this storing off |
6305 |
in case fluxform is used since no CPP flag available). |
6306 |
|
6307 |
checkpoint40pre7 (2001/08/14) |
6308 |
o bug fix in dynamics.F |
6309 |
calc_viscosity called before k=1,Nr loop. |
6310 |
o added some #ifdef's ALLOW_PASSIVE_TRACER |
6311 |
o cleaned initialisations in ctrl_map_ini |
6312 |
related to TAF |
6313 |
|
6314 |
checkpoint40pre6 (2001/08/13) |
6315 |
o split dynamics into thermodynamics & dynamics |
6316 |
o corresponding split of calc_diffusivity into |
6317 |
calc_diffusivity, calc_viscosity |
6318 |
(kpp_calc_diff, kpp_calc_visc). |
6319 |
o Added diffkr, kapgm to control variables |
6320 |
o bug fix in gmredi_slope_limit for ldd97 |
6321 |
|
6322 |
checkpoint40pre5 (2001/07/31) |
6323 |
o proper initialization of Adams-Bashforth time stepping |
6324 |
+ uses forward step for very first step of model (iter=0) |
6325 |
o re-generated *all* output since almost all output is modified by this |
6326 |
change (sorry but we've been putting this one off for about 2 years) |
6327 |
+ natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were |
6328 |
*not* regenerated since they are already out of date and I don't |
6329 |
want to create the impression that they are suddenly working. |
6330 |
o removed KAP stuff for DEC's |
6331 |
o modified/added many .cvsignore files in */code and */input |
6332 |
o added new expt "solid-body.cs-32x32x1" |
6333 |
+ this uses an alternative form of ini_curvilinear_grid.F which |
6334 |
is not necessarily any better than the current one... |
6335 |
|
6336 |
checkpoint40pre4 (2001/07/30) |
6337 |
o added re-initialisations of utrans,vtrans,rtrans in |
6338 |
calc_common_factors which are crucial for TAF. |
6339 |
o extended iMin,jMin range for calc_common_factors, |
6340 |
calc_diffusivity |
6341 |
o added option ALLOW_PASSIVE_TRACER |
6342 |
o a few minor updates and fixes |
6343 |
|
6344 |
checkpoint40pre3 (2001/07/13) |
6345 |
o created calc_gtr1.F for gad package |
6346 |
o split the_main_loop and re-introduced forward_step |
6347 |
o some recomputations of nIter0 for TAMC |
6348 |
|
6349 |
checkpoint40pre2 (2001/07/13) |
6350 |
o Updated to latest branch of AJA, JMC |
6351 |
o Added gradient check package |
6352 |
o Added routines for passive tracer handling |
6353 |
o Added carbon sequestration sensitivity experiment |
6354 |
|
6355 |
checkpoint39 (2001/05/14) |
6356 |
o Modifications and fixes to support TAMC |
6357 |
(mainly missing or wrong directives) |
6358 |
o Corrected common blocks when fooling TAMC to produce adjoint I/O |
6359 |
in addummy_in_stepping |
6360 |
o Updated verification/vero/ (bug fixes in code/, correct pickups in input/) |
6361 |
o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs. |
6362 |
o Included following packages: |
6363 |
cal: calendar |
6364 |
exf: external forcing |
6365 |
ecco: essential routines to control use of cal, exf |
6366 |
(NB: this is not the full ECCO environment) |
6367 |
o disabled some packages by default in genmake |
6368 |
|
6369 |
checkpoint38 (2001/04/10) |
6370 |
o see notes_c37_adj.txt |
6371 |
o corrected wrong layer index in external_forcing_t |
6372 |
o replaced the_main_loop/forward_step by the_main_loop |
6373 |
o removed forceoutput from write_state |
6374 |
(replaced criteria for initial/final state) |
6375 |
o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
6376 |
|
6377 |
checkpoint37 (2001/03/13) |
6378 |
o mdsio.F routine split and packaged in pkg/mdsio |
6379 |
(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
6380 |
used unless genmake -disable=mdsio) |
6381 |
o allow a more precise surface-geopotential gradient for the atmosphere |
6382 |
taking into account the change in space of Alpha (=1/rho) at the surface. |
6383 |
o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit] |
6384 |
(ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa]) |
6385 |
o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and |
6386 |
Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential |
6387 |
[m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere). |
6388 |
o Time-Average diagnostics defined as a pseudo package "timeave". |
6389 |
o pickup files : old pickup (before c35) did not work with new code (c35 |
6390 |
and after) unless activating 2 commented lines in initialise-varia. |
6391 |
o Non-Hydrostatic pickup file Pb fixed. |
6392 |
o bug with Rigid-lid version (since c35) fixed. |
6393 |
|
6394 |
checkpoint36 (2001/02/20) |
6395 |
o implement Crank-Nickelson barotropic time-stepping |
6396 |
o recover Time-Average diagnostics |
6397 |
o fix Pb in checkpoint (PR#19) |
6398 |
o AIM become a standard package ; clean unused CPP_kees |
6399 |
|
6400 |
checkpoint35 (2001/02/08) |
6401 |
o subtantial rewrite of dynamics.f |
6402 |
o allows staggered time-stepping |
6403 |
o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
6404 |
o added bottom drag (linear + quadratic) |
6405 |
|
6406 |
checkpoint34 (2001/01/30) |
6407 |
o Modified exchange routines for correct reverse simulation. |
6408 |
o Added verification output to comply with bug fix in impldiff.F |
6409 |
as of c33 (exp2, natl_box). |
6410 |
o Corrected store directives in dynamics.F |
6411 |
o Corrected array boundaries in impldiff.F |
6412 |
o Corrected array dimensions in gmredi. |
6413 |
Added temporary scalars to avoid storage by TAMC (gmredi, kpp). |
6414 |
o Added routine GLOBAL_SUM_INT to global_sum.F |
6415 |
o Added mdsio_gl.F for ECCO purposes. |
6416 |
|
6417 |
checkpoint33 (2000/11/30) |
6418 |
o Fixed bug in lower BC in impldiff.F |
6419 |
o Fixed confusion about units of forcing arrays in FFIELDS.h |
6420 |
namely Fu,Fv,Qnet,Qsw,EmPmR: |
6421 |
- Removed verification/natl_box/code/external_fields_scale.F |
6422 |
(did not differ from that in model/src) |
6423 |
- Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units |
6424 |
(see FFIELDS.h for description) |
6425 |
- Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F, |
6426 |
kpp_calc.F and kpp_transport_t.F |
6427 |
- Removed model/src/external_fields_scale.F and calls to it |
6428 |
- verification/natl_box uses flux data with "atmospheric" sign so |
6429 |
a special version of external_fields_load.F is used to |
6430 |
change the data as it's read in. This way, the arrays |
6431 |
have the right units and signs at all times tha a user could |
6432 |
possibly use them. |
6433 |
o Corrected genmake to delete a temporary file during configuration |
6434 |
|
6435 |
checkpoint32 (2000/11/13) |
6436 |
o Scaling of forcing fields moved from external_forcing.F to |
6437 |
external_fields_scale.F, called directly after loading fields. |
6438 |
o Surface relaxation terms added to surface tendency fields in |
6439 |
extra subroutine. |
6440 |
o impldiff.F changed to avoid storing by TAMC of huge intermediate |
6441 |
fields. |
6442 |
o Changes in GMRedi to comply with packaging structure. |
6443 |
o Modifications and bug fixes in KPP package. |
6444 |
o Verification experiment for KPP added (verification/nat_box/) |
6445 |
|
6446 |
checkpoint31 (2000/09/11) |
6447 |
o Packages interface brought in line with defined standard |
6448 |
-> new routines packages_...F |
6449 |
-> changes in initialise_fixed.F, initialise_varia.F |
6450 |
-> enables initialisation interface for ECCO package |
6451 |
o Rescaling of external forcing fields immediately after read |
6452 |
(removed from external_forcing.F) |
6453 |
-> new: surface_fields_scale.F |
6454 |
-> affects ini_foorcing.F, external_fields_load.F |
6455 |
o Computation of surface tendencies before tendency updates. |
6456 |
-> new: external_forcing_surf.F |
6457 |
o Change of variable names useGMRedi, useKPP, useECCO |
6458 |
o Further changes in dynamics.F, impldiff.F for TAMC |
6459 |
o Tested for experiments 0, 2, 4. |
6460 |
- not yet tested for GMRedi. |
6461 |
- not yet tested for KPP. |
6462 |
|
6463 |
checkpoint30 (2000/07/13) |
6464 |
o Updates for OBCs |
6465 |
o New experiment for test OBCs (internal_wave) |
6466 |
o New output.txt in verification/exp4/results/ |
6467 |
o Updates for KPP: calculation of viscosity corrected, new variables |
6468 |
kpp_dumpFreq and kpp_taveFreq |
6469 |
o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) |
6470 |
and entry for T90 in genmake |
6471 |
|
6472 |
checkpoint29 (2000/06/21) |
6473 |
o packaged KPP and GM/Redi |
6474 |
|
6475 |
checkpoint28 (2000/06/09) |
6476 |
o Corrected initialization of hFacMin for difference vertical coordinates |
6477 |
o Modified calculation of partial cell thickness to more robust algorithm |
6478 |
o config_summary.F: replaced write_1D_... by write_0D_... |
6479 |
read_write.F: added subroutines write_0D_... |
6480 |
o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho: |
6481 |
included some initialisations required for TAMC. |
6482 |
o routine calc_isoslopes: modified sqrt computation to make it |
6483 |
differentiable for zero argument. |
6484 |
o routines dynamics, impldiff: |
6485 |
included store directives and tape key computations required for TAMC. |
6486 |
o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC |
6487 |
|
6488 |
checkpoint27 (2000/04/10) |
6489 |
o fixed calc_isoslopes() to so that cancellation of terms in tensor |
6490 |
formulation works properly with variable resolution. |
6491 |
o restructured the calling tree between the_model_main() and dynamics() |
6492 |
o split initialise() into initialise_fixed() and initialise_varia() |
6493 |
o introduced initialization file pSurfInitFile for free surface (cg2d_x) |
6494 |
in new routine ini_psurf() |
6495 |
|
6496 |
checkpoint26 (2000/04/05) |
6497 |
o moved some #ifdef in optional routines to encompass everything |
6498 |
except the argument declarations. This was using up some memory. |
6499 |
o fixed macros like _ADT to work with both versions of Linux cpp |
6500 |
o cleaned up some unused and uninitialized variables |
6501 |
(helps when debugging with strict compile options) |
6502 |
o split up CPP_EEOPTIONS.h into options and macros |
6503 |
(macros are now in eesupp/inc/CPP_EEMACROS.h) |
6504 |
o patch for 2 processor JAM mode |
6505 |
|
6506 |
checkpoint25 (2000/03/15) |
6507 |
o updates for OBCs and NH |
6508 |
o dramatically reduced memory usage |
6509 |
o added "JAM" routines for use on Artic network |
6510 |
o parameterization of convection by implicit vertical diffusion |
6511 |
o added a diagnostic of convective index |
6512 |
o moved call to calc_divg_hat() from dynamics() to solve_for_pressure() |
6513 |
(this is was partly for OBCs and NH but also in anticipation of |
6514 |
an explicit free-surface option) |
6515 |
o initial state input files for U and V |
6516 |
|
6517 |
checkpoint24 (1999/08/02) |
6518 |
o Removed some spurious "REAL"s |
6519 |
o Updated KPP to latest version from JPL |
6520 |
o Added a COS(latitude) in horizontal viscosity |
6521 |
|
6522 |
checkpoint23 (1999/05/26) |
6523 |
o Added del^4 diffusion for salt and temperature |
6524 |
o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) |
6525 |
|
6526 |
checkpoint22 (1999/05/18) |
6527 |
o Made many small changes: implicit none, format(i5), etc... |
6528 |
o Introduced KPP mixing scheme (compiles and runs but *not* tested) |
6529 |
|
6530 |
checkpoint21 (1999/05/18) |
6531 |
o Introduced new I/O package that supports direct-access records (mdsio.F) |
6532 |
o Split-up mid-level I/O routines |
6533 |
o Updated input data for experiments 0,1,2,4 and 5 |
6534 |
o Finally removed the genmake.* scripts (everyone seems happy with genmake) |
6535 |
|
6536 |
checkpoint20 (1999/03/22) |
6537 |
o Tidied up open-boundaries some more |
6538 |
o Added non-hydrostatic code |
6539 |
o Fixed some input data |
6540 |
o Modified MPI start-up to work in "coupled" context. |
6541 |
|
6542 |
checkpoint19 (1998/12/15) |
6543 |
o Tidied up directory structure for verification experiments. |
6544 |
o Added new code for open boundaries. |
6545 |
o Corrected advective terms near boundaries. |
6546 |
o Added CPP flag for "old UV" geometry and corrected spherical geometry. |
6547 |
o Implemented free-slip/no-slip BCs and del^4 dissipation. |
6548 |
o Split default parameters out of ini_parms.F into set_defaults.F. |
6549 |
|
6550 |
checkpoint18 (1998/11/30) |
6551 |
o Further changes for optional code generation with |
6552 |
CPP - ugh! |
6553 |
|
6554 |
checkpoint17 (1998/11/03) |
6555 |
o Beginning to incorporating modularity |
6556 |
for supporting atmos. and ocean configs. |
6557 |
o Small changes for TAMC complinace |
6558 |
o New ultra simple test case. Barotropic box |
6559 |
configuration "exp0". |
6560 |
|
6561 |
checkpoint16 (1998/10/28) |
6562 |
o Minor changes to exchange routines to support |
6563 |
accumulation in reverse mode. Adjoint of an |
6564 |
assignment is an addition. |
6565 |
o Changes to support compilation by TAMC (LR(1) |
6566 |
syntax) and by g77 under Linux ( 72 character |
6567 |
limit ). |
6568 |
|
6569 |
checkpoint15 (1998/09/29) |
6570 |
Rewrote exchange routines to allow |
6571 |
o General tile <-> tile connectivity. |
6572 |
o TAMC reverse mode flag ( is this really needed? ) |
6573 |
o Variable width overlap and exchange region widths. |
6574 |
o Hooks for sharing data via DMA, Arctic, Memory Channel, |
6575 |
shmput/shmget, VIA, SYSV shmem and every other cool |
6576 |
communication method. |
6577 |
|
6578 |
checkpoint14 (1998/09/09) |
6579 |
Consistent isomorphism chages made. These allow dynamical core |
6580 |
to support both pressure and meters as a vertical coordinate. |
6581 |
|
6582 |
checkpoint13 (1998/07/17) |
6583 |
Release which corrects global_max problem and a couple |
6584 |
of KGM time-averaging diagnostic errors. Also contains |
6585 |
a double-gyre experiment setup as well as the baseline |
6586 |
4 degree global template. The double gyre template is |
6587 |
organised to allow it to be applied automatically to |
6588 |
the baseline configuration. |
6589 |
|
6590 |
branch-point-rdot |
6591 |
A few tidy-ups have been made bt the real point of this |
6592 |
check-point (excuse the pun) is to allow a branch to be |
6593 |
made for the purposes of adding the rDot alterations. |
6594 |
I don't want to commit the rDot to the main-trunk until |
6595 |
we've actually tested it... |
6596 |
|
6597 |
checkpoint12 (1998/07/08) |
6598 |
Tidy up and added generic genmake script (formerly |
6599 |
configure script). |
6600 |
Released to testers. |
6601 |
|
6602 |
checkpoint11 (1998/07/02) |
6603 |
Re-arranged initialise() and introduced ini_vertical_grid() |
6604 |
and ini_masks_etc(). |
6605 |
|
6606 |
checkpoint10 (1998/07/01) |
6607 |
Introduced the configure script. |
6608 |
Separated out the diags package. |
6609 |
Added template for writing time-averages of tile/intermediate quantities. |
6610 |
Updated SIZE.h in exp2 and made the data big-endian. |
6611 |
|
6612 |
checkpoint9 (1998/06/22) |
6613 |
MPI fix. Filename changes (meta/data). salbin*y stuff. |
6614 |
General tidy-up. |
6615 |
SST.bin SSS.bin added to verification/exp2 |
6616 |
|
6617 |
checkpoint8 (1998/06/22) |
6618 |
Inludes time-dependant forcing and time-averaging. |
6619 |
Works at 4x4 and 2.8125x2.8125 global |
6620 |
|
6621 |
checkpoint7-4degree-ref |
6622 |
Branch from checkpoint7. Released for application to |
6623 |
global modeling and general modeling - process studies, regional |
6624 |
model etc.. |
6625 |
Configured for verification/exp2 - 4 degree global, two process. |
6626 |
|
6627 |
checkpoint7 (1998/06/15) |
6628 |
Created by cnh |
6629 |
Simple 4 degree global simulation |
6630 |
configuration. |
6631 |
Includes climatological wind, |
6632 |
hydrography, bathymetry etc |
6633 |
Does not include Heat Flux and E-P |
6634 |
|
6635 |
checkpoint6 (1998/06/08) |
6636 |
Created by cnh |
6637 |
merged checkpoint5 with CD and |
6638 |
spherical polar code. |
6639 |
Still some problems with GM Redi |
6640 |
abd full topography. |
6641 |
|
6642 |
checkpoint5 (1998/06/08) |
6643 |
Created by AJA |
6644 |
contains updates to GM Redi |
6645 |
and reordered timestepping loop |
6646 |
for Implicit Diffusion. |
6647 |
|
6648 |
checkpoint4 (1998/05/30) |
6649 |
Created by cnh |
6650 |
Contains memory saving macros ( _rdxc etc..) for when |
6651 |
grid variations are limited. |
6652 |
Contains polynomial coeffs for EOS and knudsen program |
6653 |
for generation. |
6654 |
|
6655 |
checkpoint3 (1998/05/26) |
6656 |
Created by cnh |
6657 |
Added extra flags for runtime options |
6658 |
Added this file |
6659 |
Added implicit free-surface |
6660 |
Added pre-conditioner |
6661 |
Put compare01 into repository ( compare01/... ) |
6662 |
Put data and eedata into repository ( verification/exp1 ) |
6663 |
|
6664 |
checkpoint2 |
6665 |
Created by AJA |
6666 |
Added GM/Redi |
6667 |
|
6668 |
checkpoint1 |
6669 |
Created by AJA |
6670 |
Restructured kloop in dynamics.F |
6671 |
Added non-linear EOS |
6672 |
|
6673 |
baseline |
6674 |
Original checked in code |