--- MITgcm/doc/tag-index 2009/05/11 12:36:41 1.1095 +++ MITgcm/doc/tag-index 2012/07/11 21:51:27 1.1687 @@ -1,9 +1,2826 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1095 2009/05/11 12:36:41 jmc Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1687 2012/07/11 21:51:27 gforget Exp $ $Name: $ Notes on tags used in MITgcmUV ============================== +o verification/global_ocean.cs32x15/input.seaice : + - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget. + - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces). + - update results (output.seaice.txt) accordingly. +o verification/lab_sea/input/data.seaice : + - remove SEAICEheatConsFix, which is now be tested + in global_ocean.cs32x15. The presently coded fix + is only consistent with real fresh water + nlfs. + - update results (output.txt) accordingly. +o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd). +o AD_CONFIG.h file: + - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h; + - remove #include "AD_CONFIG.h" from all included OPTIONS files and + add it explicitly in each fortran src file where it is needed. + motivation: header file AD_CONFIG.h is generated/modified after "make depend" + thus introducing potentially wrong dependency; therefore, better to include + it only where it's really needed, and after any other included OPTIONS file + (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN + or ALLOW_TANGENTLINEAR_RUN). + +checkpoint63p (2012/07/06) +o pkg/autodiff: + - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ; + - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters + which are now read from new parameter file "data.autodiff" (inAdExact + previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg) + - add file "data.autodiff" in all verification/*/input_ad/ directories. + - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward + mode (used in global_ocean.cs32x15.seaice_dynmix test exp.) +o verification/tutorial_tracer_adjsens/ + - add extra sub-verification which uses "SOM" advection scheme + (2nd Order-Moment Advection Scheme, Prather Limiter) with + #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h + and in data: + multiDimAdvection=.TRUE., + tempAdvScheme=81, + saltAdvScheme=81, +o model/src: + - introduce ALLOW_BALANCE_RELAX which allow the removal + of the global mean of relaxation terms by setting + balanceThetaClimRelax and balanceSaltClimRelax + - disable balanceEmPmR and balanceQnet in the case when useSeaice. + This case is now treated appropriately in seaice_growth.F +o pkg/seaice: + - do balanceEmPmR and balanceQnet based on the net fluxes + (SItflux) that enter the ocean+ice system rather than QNET + and EMPMR. Works best in real fresh water. + - SIatmFW, SIatmQnet, and SItflux computations had to be moved + out of the diagnotics bloc, and stored in global arrays. + +checkpoint63o (2012/06/29) +o vertical mixing schemes: + - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging) + - replace computation of density (in Function STATE1, opps_calc.F) by a call + to S/R FIND_RHO_SCALAR + - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC + and use it for N^2 calculation in ggl90_calc.F (save 2 density computations); + affects output (vermix.ggl90) at truncation level. +o testreport: + - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles + (nSx,nSy) for the number of threads (from eedata.mth) +o model/src: + - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part) + related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary). +o verification/tutorial_tracer_adjsens/ + - compile with ALLOW_CG2D_NSA + - run with nonlinFreeSurf=3 + - update reference output_adm.txt +o tools/genmake2: + - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ; + refine usePROFILES switching off (only when NetCDF is not available). +o verification (atmospheric set-up): + - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration +o pkg/profiles : refine profiles and files handling. +o model/src and pkg/ecco : introduce run-time switch usePROFILES. +o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h : + - changes to use model/src/the_main_loop.F rather than the ecco version + in ecco type adjoint runs. +o model/src: + - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID + - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC + - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL) +o model/src: + - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before); + update output of test experiment bottom_ctrl_5x5. +o pkg/generic_advdiff: + - implement vertical bi-harmonic diffusion (for now, only for T & S and + only explicitly). +o verification/bottom_ctrl_5x5/ + update reference output (results changed quite some time ago, + not sure when; but new reference results look ok in terms of grdchk) +o verification/1D_ocean_ice_column/ + For verification purposes, the exact adjoint rather than an approx. + should be used (e.g., to comare against F.D. or TLM). + removed autodiff_inadmode*_ad.F routines in code_ad/ + Update results/ accordingly. +o pkg/cal: + - change cal_getdate.F so that output date is function of input time only + (less ambiguous, not mixed up with input iteration number). + - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP). +o pkg/diagnostics: + - implement calendarDumps also for stats-diags + - implement calendarDumps also for snap-shot output (negative freq) + - for now, ignores calendarDumps if non-zero phase-lag. + +checkpoint63n (2012/06/04) +o model/src: + - recompute rSurfW & S to ensure consistent column thickness (needed for rStar) + between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice; + - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more + similar to calc_r_star.F); update results of experiment internal_wave and + tutorial_global_oce_in_p (affected @ truncation level). +o pkg/shelfice: + - add parameterisation of advective-diffusive flux into the ice shelf + according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd + - simply eps3/3a computation +o eesupp: + - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange + between tiles, just fill-in edges assuming locally periodic subdomain) and + add corresponding exchange subroutines (EXCH0); + - new CG-solver version (_EX0) for disconnected-tiles special case. +o model/src (CG-solvers): + - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached + (similar final residual output and max-Iter number as with standard version); + - allows to store and use lowest-residual solution (standard & _SR versions); + - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...). + - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h) +o eesup/src: + - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef + ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012) +o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn + +checkpoint63m (2012/04/27) +o pkg/shelfice: + - account for partical cells in surface level below ice-shelf for hydrostatic + pressure calculion (set uniformFreeSurfLev to F); update isomip experiments. +o ad test experiments: + - update and rename to "ad_optfile.local" local AD-optfile specific to a + particular adjoint verification experiment (in verification/*/code_ad/) +o pkg/seaice & pkg/exf: + - Part two of ECCO-CLIVAR code merges. + Completes merge of seaice area relax. code. + Requires unified CPP option EXF_ALLOW_SEAICE_RELAX + to be set in EXF_OPTIONS.h since this pkg controls its I/O + (and avoids second CPP option in SEAICE_OPTIONS.h) + - change default value of costIceStart & costIceEnd to a valid date. + - add snowPrecip to HSNOW in seaice_growth +o pkg/ptracers: + - move ptracers summary and setup check into separated S/R ; add a check for + valid PTRACERS_Iter0 value (error+stop or just warning). +o pkg/cal (+ pkg/ecco): + - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used + as input; and for AD, unless both are not differentiable (e.g., k index)). +o model/src: + - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index + is everywhere k=1) to speed-up some calculations (by pass kSurf reference); + temporary set to usingZCoords value (to be changed to F when using shelfice). + - hydrostatic pressure: implement partial cell near the surface also for + Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on + usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code). +o pkg/ctrl/ctrl_init.F: + - add a formal parameter to s/r ctrl_init_rec to print + xx_$(ctrl_valiable)_file for easier debugging + - move call of cal_* routines into the if-block where they are really + needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having + to specify a startdate +o pkg/seaice: + - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and + global_ocean.cs32x15/code versions). + - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for + verification experiment global_ocean.cs32x15.seaice and update results. +o pkg/exf: + - new S/R EXF_GETFIELD_START to return starting-time of a forcing field + (according to useExfYearlyFields). +o pkg/cal: + - move calendar setting & summary (previously in cal_readparams.F) into new + S/R CAL_INIT_FIXED to be called later in the initialisation process, once + length of the simulation is set (after SET_PARMS call); This is an attempt + to fix Pb when, e.g.: pkg/longstep, modifies the length of the run. + - For safety: keep a record of pkg/cal parameter settings status + to allow to STOP if one pkg/cal S/R is called too early. + - add a stop in all basic pkg/cal subroutines if called before setting is done. + - modify cal_getdate.F: stop when nothing was returned; + if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2); + this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F. + +checkpoint63l (2012/04/04) +o pkg/bbl: + - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc); + update global_with_exf output.yearly.txt file. +o pkg/cal: + - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero. + - remove 2 unsused and very short (1 line only) functions ; + - remove unsused subroutines from AD-Diff list. +o model/src: + - start to implement clean wait to stop in initialization S/R (config_check.F, + packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage) +o folowing PRINT_MESSAGE changes: + - remove reminder multiple print to the same file (STDOUT) when multi-threads. +o pkg/bbl: + - modification so it can work with z* + - replace deltaT with dTtracerLev(k) for asynchronous time stepping + - global_with_exf/input.yearly verification; changes output.yearly.txt +o eesupp/src: + - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR); + writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1 + - CHECK_THREADS: specific code if using OpenMP threading: improve checking of + # of threads across processors (e.g., different env OMP_NUM_THREADS setting) + - improve special preliminary call to EESET_PARMS (if eedata is read 2 times). + - when using MPI, always set usingMPI=T ; set default accordingly and stop + if not consistent. + - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread + argument is zero (in case called within single-thread section). +o pkg/fizhi: + clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored + in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO. +o pkg/exch2: + - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to + activate EXCH_IGNORE_CORNERS in vector EXCH S/R). + - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS) + but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data + with bad ones coming from a not-yet-updated halo. + This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx. +o pkg/frazil: + move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F + http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html +o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy +o verification/lab_sea + * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING + * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL + * nTimeSteps 3 -> 4 + * changed reference output accordingly +o pkg/ctrl: + * fix ctrl_get_gen for xx_sst, xx_sss +o pkg/fizhi: + - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F + update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d) + - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE); + fix few out-of-bounds indices in referencing vars (initialise igrd to 1); + clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array). +o pkg/gmredi: + - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp +o pkg/fizhi: + - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the + (old)aces open64 tuv test. +o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F +o pkg/mom_vecinv: + - fix 1 loop range in mom_vecinv.F to be like all the other loops which + set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv + with non-lin free-surf). +o model/src: move k-loop outside of i/j-loops when (re-)computing R_low + in ini/update_masks_etc.F in order to avoid -O3 optimization problems with + some compilers (gfortran 4.6.0 on MacOS) +o momentum: + - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM + & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised + fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control. + +checkpoint63k (2012/03/17) +o model/src: + - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum + flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations. + - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version + (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp. +o model/src: solve_*diagonal.F + - replace division with multiplication by inverse (similar to original version) + update output of AD exp. global_ocean.90x40x15. + - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F + to enable the use of the vectorized & differentiable solve_tridiagonal.F + - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for + vertical advection (to get solve_tridiagonal tested in AD mode). +o pkg/seaice: ECCO-CLIVAR merge: + 1. seaice AREA relaxation + * CPP option: SEAICE_ALLOW_AREA_RELAXATION + * runtime flag: SEAICE_tauAreaObsRelax + 2. modified global mean cost imbalance code: CPP option + ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION +o another iteration on solve_*diagonal.F + Make choices independent of AUTODIFF + Default will be the adjoinable vectorized version. + Alternative choices are: + * non-adjoinable original version with low memory footprint: + #define SOLVE_DIAGONAL_LOWMEMORY + * still adjoinable but does not vectorize (k as inner-most loop): + #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef) +o testreport + - add option to use a home made wrapper around "make" + - remove MITGCM_IEEE env. variable (no longer active) +o pkg/shelfice + - improve computation of friction velocity for velocity dependent + exchange coefficients: include velocities into SHELFICEBoundaryLayer + block to average velocities vertically + - add TAF store directives for SHI_ALLOW_GAMMAFRICT +o Modify diagonal solvers, now three versions (upon request): + #ifndef SOLVE_DIAGONAL_AUTODIFF + 1. default version (dating back a while ago) + #else /* def SOLVE_DIAGONAL_AUTODIFF */ + # ifdef SOLVE_DIAGONAL_KINNER + 2. adjoinable version with k-innermost loop (G. Forget) + # else + 3. adjoinable vectorized version of 2. + # endif + #endif /* SOLVE_DIAGONAL_AUTODIFF */ + All flags are currently set within routines, but could/should be moved to CPP-options. + Array bounds for 1. are as before, for 2.,3. cover the entire domain + (could be changed for 1. too). +o verification/lab_sea (fwd): + - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY, + use 7 categories (except hb87), new solve4temp params (except salt_plume), + constant salinity (=4) or variable salinity (salt_plume) done through + SItracer. +o pkg/seaice: + - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0; + - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t, + SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz) + from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when + SEAICE_freeze got retired) but already better than previously with + SEAICE_freeze=123456.7 deg.C; + - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS + (safer multi-threaded setting); always set SEAICEuseEVP; + - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to + SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report); + stop if multiple specifications for the same coeff; make sure default + SEAICE_mcPheePiston is compatible with drF(1) & deltaT. +o pkg/obcs: + - allow to switch to upwind 1rst order advection scheme for the advective + flux computation at the open-boundary; disabled for adjoint built. +o pkg/ptracers: + - rename PTRACERS_RESTART.h -> PTRACERS_START.h + - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F + - add parameter to decide when to start a tracer; use internal flag to + know which tracer to step-forward; switch this internal flag at the top + of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled + for adjoint built. +o pkg/seaice: + - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ; + - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ; + - keep experiment offline_exf_seaice truly single category (set MULTDIM=1). +o pkg/ecco: + - fix writing of output file DiagnosCost_ClimSalt/Theta + and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc). +o pkg/seaice: + - add missing initialisation of COR_ICE array in dynsolver.F + - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is + compiled either way, and is tested in all exps (multidim was only tested + in lab_sea ad before). + - cosmetic change to prepare for future addition of ITD. no change to results. + no defaults change. + - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise). + - by lack of adequate verification experiments, I further used custom versions + of global_ocean.cs32x15 to test multicat or not, with pickup or not. All + should be correct. + - avoid recomputations in ad. +o array initialisation in adjoint mode: + 1) pkg/mom_common/mom_calc_ke.F: + add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC): + The S/R which calls MOM_CALC_KE initialises KE but in some recomputation + part this initialisation is gone, resulting in Floating Point Exception + (caught by open64 compiler with debug option). + 2) model/src/convective_weights.F + set output convectCount over the full array range (instead of doing + an update): this fix a similar issue when called within recomputation (adjoint) + which could by-pass the initialisation (normally done in the caller S/R). +o pkg/seaice: + - final version of turbulent flux params, as agreed at MIT ice meet: + SEAICE_mcPheePiston (default is ~ 0.000875) + SEAICE_mcPheeTaper (default is 0.) + SEAICE_frazilFrac (defualt is 1.) + SEAICE_mcPheeStepFunc (default is false) + - changes results at trunction error level + - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo +o added pkg/frazil: + - see frazil_description.tex for details + - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt +o pkg/shelfice/shelfice_thermodynamics.F + - fix exponents for velocity dependent exchange coefficients: change + from 2/3(=0) to 0.66666666666666667 + - move computation of velocity dependent exchange coefficients into + separate loop, so that it applies to both thermodynamics + - move some divisions by constants out of loops + +checkpoint63j (2012/02/16) +o pkg/seaice: + - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc. + - SItracer: added run time params, and allow coupling to ocn salinity. +o pkg/seaice: remove (almost) all divisions by constants within loops + in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d + results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only + those, caused by 1/QI -> recip_QI) -> update output.seaice.txt, + output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt +o pkg/seaice : + - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula + = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper. + - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148. + - add permanent SItflux diag that corresponds to TFLUX but includes + ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget. + - allow activation/testing of a fix for suspected missing term in + ocn-ice heat budget (to be confirmed). To test this, you want to + undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param + SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic. + - no change in results, fwd or ad. +o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below: + - switch to variable freezing point. + Results change : cg2d -> 1 digits; ad -> 3-6-6 digits. + - bug fix : the sublimation term that was missing is now activated. + Results change : cg2d -> 2 digits; ad -> 8-6-6 digits. + - bug fix : flooding sign term for SIsal0.NE.0. + Result change : cg2d -> 8 digits; ad -> 11-12-9 digits. +o pkg/seaice: + - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT + is now the default, and the old default constant freezing point is recovered + with SEAICE_tempFrz0 = -1.96, + SEAICE_dTempFrz_dS = 0., + - retire SEAICE_freeze (= the old way of specifycing the constant freezing point) + - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there. + - bug fix (thanks to M. Losch) : the sublimation term that was missing is now + activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM. + - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211) + was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail). + - bug fix (thanks to O. Jahn) : area loss for melting got messed up in + seaice_growth r149 for legacy branch (no results change). + - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code + from I. Fenty). + - results did not change except for global_ocean.cs32x15, mostly due to the + switch to variable freezing point (see above item for detail). +o pkg/thsice: + - fix and simplify interface to salt_plume pkg ; diagnose directly amount of + seawater freezing in thsice_calc_thickn (not used). +o pkg/seaice: turbulent flux term specification via run time params. + - replace CPP switches with run time switches to facilitate testing + - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, + GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR + - added runtime parameter : SEAICEturbFluxFormula + - move Mcphee constants to SEAICE_PARAMS.h + - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula; + SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); + remove seaice_summary call (moved to seaice_init_fixed) + - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on + SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms) + - seaice_summary.F : add missing report of read turbulent flux term set up + and SITRACER. + - seaice_check.F : check range; inform and stop if retired CPPs are used + (incl. SEAICE_AGE). + - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without + CPP switch, same computation as before for the different options. + - change results at the truncation level. +o pkg/seaice: + - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters: + useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and + SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY. + - update verification/*/input*/data.seaice: + to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY + code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ; + and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code, + set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0. +o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY): + - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same + algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0); + difference in results only due to machine truncation. + - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using + MaykutPolySatVap; keep MIN_LWDOWN. + - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation. + - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87, + + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits). +o pkg/salt_plume: + - isolate saltPlumeFlux array exch into a specific S/R called from + do_oceanic_phys.F + - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice. +o verification: + - move untested set-up to MITgcm_contrib/verification_other. +o pkg/seaice: + - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER. +o pkg/seaice: + - seaice_solve4temp.F (keeping results unchanged): + * add 2 future run-time params to select which saturation vapor pressure + formula is used and how post-iteration fluxes are set. + Temporary set these 2 params according to option SOLVE4TEMP_LEGACY; + * New piece of code (not used) to update surf. atmos. heat flux F_ia using + the linearized expression to stay consistent with tsurf finding. + - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x + can be < 0. +o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef): + - remove from F_ia (and from it's derivative dFiDTs1) the contribution of + conductive heat flux F_c , and add it explicitly when updating tsurf as + solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf + so that now F_ia has a consistent meaning through the entire routine. + This causes differences at truncation level: update output of fwd exp. + global_ocean.cs32x15.seaice. +o pkg/seaice: + - lots of editing/cleaning in seaice_solve4temp.F + better documentation + of arrays, sign/direction of fluxes; no effect on results. + - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K + in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part); + note: this should have been done before changing celsius2K default. + - to keep results unchanged, add back old value of celsius2K in verification + exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs + - replace hard coded seawater freezing temp in seaice_solve4temp.F (part + SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default + value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater + freezing temp is consistent with value in seaice_growth.F ; this causes + differences at machine truncation level: update lab_sea AD output (3/4). +o pkg/seaice: + - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask + and climsst/sss even when using seaice (to prevent calculation that might + use SST on land); does not affect any verification exp. + - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output + of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix. +o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness + over land (non-legacy code) +o vectorize salt_plume package: + - add extra code to salt_plume_frac and salt_plume_tendency_apply_s + - this code computes plumebk everywhere (also over land), thus requires + code to avoid divisions by zero and catch the case of kLev=Nr. + - efficiency of salt_plume_frac is still sub-optimal +o tools (genmake2): + - fix makefile NAME specification (option: -makefile NAME) by adding + "-f $MAKEFILE" in few places where it was missing including makedepend + command (contribution from Paul). + +checkpoint63i (2012/01/24) +o model/src: + - add factorized versions of some EOS code to find_rho.F, + define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX) +o model/src: + - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h; + - change default celsius2K from 273.16 to 273.15 + - to keep results unchanged, add back old value of celsius2K in verification + exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd), + global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm). +o model/src: add a little initialisation trick to find_rho.F and find_alpha.F + to make TAF generate vectorizable code +o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows. + Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers + have flags that do this more efficiently. +o pkg/diagnostics/diagstats_calc.F + - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact +o pkg/obcs (with exch2): + - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F) + and remove code (in obcs_readparms.F) which was based on EXCH of indices + (through buffer) and did not account for exch2 (e.g., CS-grid) topology. +o pkg/exf and seaice exp: + - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0) + so that switching off area & heff advection flags does not affect results. + - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h + - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef + EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update + results of verification experiments: 1D_ocean_ice_column(fwd), + global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8) + and offline_exf_seaice (all 4). +o pkg/seaice: + - remove array YNEG, RIVER, TMIX (replaced by local var) from common block; + remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef. + - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY) + but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and + not multi-dim advection; + - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and + SHORTWAVE_HEATING #undef. +o optim: make Makefile more robust (?) +o pkg/obcs: + * fix treatment of obcs_read_pickup for TAF +o pkg/shelfice: + * add missing initialisation of num_shifwflx + * new adjoint verification exp. for isomip + * change Prandtl and Schmidt numbers from generic formulations + (in terms of model diffus. and visc.) to separate runtime + parameters, with Holland and Jenkins (1999) default values. +o pkg/exf (interpolation): + - extended input field (2 rows) near the N & S poles: + * fill in with the symetric value (when even Nb of data in longitude) + * add average value at the poles only for scalar quantities ; for vector + component interpolation, skip the averaging and keep duplicated values, + unless the 2 components have same location (uvInterp=T) in which case + interpolate the 2 components together using S/R EXF_INTERP_UV. + - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field + together: this allows to account properly for local orientation when + averaging at N & S pole. + - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding + exf-interpolation near N & S poles. Undef by default. + - add debug check/print on 1rst iter if debugLevel >=2. +o pkg/exf: + - change masking flags definition (no longer "parameter"), put them in + common block and set them in S/R EXF_INIT_FIXED. + - change recognized masking flag from s,u,v to c,w,s since the mask + to use (maskC,W,S) depends on position on model grid and has little to + do with scalar/vector difference; fix masking if using P-coordinates. + - fix masking of wind-stress (was wrong if interpolated or read on A-grid) + and update results of exp. global_with_exf (x2). + - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef. +o pkg/obcs + - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate) +o pkg/exf (interpolation): + - assume periodicity in X only if input field cover full longitude range. + - improve search for lat. index (supposed to be faster, in ~log2(ny) steps, + and should vectorise). + - fix input lat of the 2 added row (in case we provide N.pole data). + +checkpoint63h (2011/12/30) +o pkg/seaice: + - change declaration of UVM from _RL to _RS in order to get B-grid + uIce,vIce monitor when _RS = real*4 +o pkg/offline: + - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags); + - compute vertical velocity if not read from file (switch on exactConserv + & staggerTimeStep); + - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq. +o verification: + - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input) + with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m": + fix Pb in yG definition @ 2 missing corners (previously yG was averaged); + - update output of exp. global_ocean.cs32x15.viscA4 after changing + grid-file angles (used here for coriolis-3d); + - remove (or gzip) few files not needed to run fizhi-cs experiments. +o pkg/exf (vector interpolation): + - rotate vector component toward local grid-axis orientation using grid-angles + (stored in GRID.h) instead of locally computed rotation angle; keep old code + available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default). +o pkg/seaice: + - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION + undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined. +o pkg/PKG_OPTIONS.h files: + - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h", + outside of the #ifdef ALLOW_THISPKG / #endif block. + - update verification/*/code/PKG_OPTIONS.h files. +o add a verification experiment (offline_exf_seaice/input.seaice) that test + the B-grid LSOR solver +o pkg/seaice: sort out emissivity and long wave radiation step 2: + - add emissivity for snow and ice as new run-time parameters + (unfortunately) that default to the corresponding exf values; this + changes results in most verification experiments so that for backward + compatibility these parameter have to be set explicitly to inconsistent + values (ugly); + - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired + emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp + until we agree how to handle this bug properly +o pkg/exf (interpolation): + - add a set of run-time param ({inputfield}_interpMethod), one for + each interpolated input field, to select the interpolation method + with a value of zero switching off the interpolation; + - print interpolation parameters to standard output; + - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined + (to use instead runoff_interpMethod=0 in data.exf). + - simplify default setting of interpolation parameters (for all fields, + set position to match model grid cell-center position, leading to trivial + interpolation in case of regular Lat-Lon grid) and fix for the case of + non-uniform delY. +o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for + within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1. + this factor is absolutely required, because the lw exitance (= out-going + long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown, + where the reflectivity rho = 1-emissivity for conservation reasons. Once + this is established, we can remove the CPP-Flag (if we want to). +o pkg/seaice: + - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and + ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined + - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity + what the name implies (and not emissivity*BoltzmannConstant), this means + the old default value of 5.5e-8 now means + 5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in + S/R exf_readparms + - FV-discretization of the B-grid LSOR solver, turn on with + SEAICE_LSRBNEW. This new solver also involves a slight re-organization + of the calling routine dynsolver, so that B and C-grid code look a + little more alike. + - fix index bugs in ostres.F (B-grid code) +o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better +o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the + default for SEAICE_emissivity, if useEXF; requires setting a wrong + parameter value in global_ocean.cs32x15/input.seaice/data.seaice for + backward compatiblity +o model/src: use sigmaR in calc_ivdc + +checkpoint63g (2011/12/16) +o pkg/seaice/seaice_growth.F: + fix heat conservation of the coupled ocean-seaice system. + when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of + solid vs liquid water treatment is resolved via QNET. +o pkg/seaice/seaice_growth.F: + add missing term for sublimation in saltFlux, which was breaking conservation. +o pkg/seaice/seaice_model.F: + Remove this patholigical case treatment in evolution branch, + where it is un-necessary and breaks conservation. + Update global_ocean.cs32x15/results accordingly for + output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt +o model/src: + useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in + external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE. +o pkg/obcs: + modify Stevens boundary conditions so that S/R obcs_calc_stevens computes + tendency for temperature and salinity that is then applied to update + theta and salt in S/R obcs_apply_ts; this requires proper masking of all + horizontal advection and diffusion contributions on the boundary (in + S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and + removing the mask in S/R timestep_tracer. The advantage of this approach is + that the updated tracer values include contributions from the surface + forcing and vertical diffusion. + This modification changes exp4.stevens because of vertical diffusion. +o model/src: + change non-curvilinear grid setting to also work with exch2 + blank tiles: + - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst + face dimensions. + - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units + as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID + and INI_SPHERICAL_POLAR_GRID. + change test-experiment global_ocean.90x40x15: + - split the domain in many more tiles (9x4 tiles of 10x10 each); + - switch to exch2 and remove 1 blank-tile (but only for MPI test). + - update results of both test (std & dwnslp). +o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in + tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation +o model/src: + - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS + and fix initialisation when using sigma-coords. +o model/src: + - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc. + to their current value at the beginning of forward_step.F": add a new run-time + switch "doResetHFactors" (default=false) and use it to do (or not) the resetting. + - set doResetHFactors=T in the following test exp: + global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS), + global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS) + and tutorial_global_oce_in_p (nonLinFS in p) +o pkg/ecco + - added IES cost term +o verification/advect_xz + - scale down the depth by 1/100 (from 200 km to just 2.km) + - add secondary test using divergent flow, r-star and implicit vertical advection. + - add note (check_conserve_TS.txt) and matlab script to check global + conservation of T & S with NonLin-FreeSurf and Adams-Bashforth. +o pkg/rbcs: + - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F). +o pkg/obcs (Stevens BCs): + - fix various problems in the phase speed computations of the Stevens + boundary conditions: + - sign error for western and southern boundaries, + - time tendencies were underestimated by factor of dTracerLev and some just + zero (for multidim advection schemes) -> now estimate time tendencies + from difference between previous (n) time level and the one before (n-1); + this requires storing a field per tracer per boundary, also in the pickup + files. + - replace deltaTmom in cflMer/Zon computation with dTracerLev + - set default phase velocity to cflMer/Zon + - update verification experiment exp4.stevens +o pkg/generic_advdiff (implicit_r): + - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf + (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F); + - fix implicit vertical diffusion or advection with NonLin FreeSurf + (was using current recip_hFacC instead of future recip_hFacC): set future + recip_hFac in thermodynamics.F and pass & use it in all vertical implicit + solver S/R ; + - fill diagnostics of vertical advective fluxes (computed from tendency) + when using implicit vert. advection; + - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion: + global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD), + tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD) + and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5. +o pkg/diagnostics: + - add diags for T & S tendency which goes through Adams-Bashforth. + +checkpoint63f (2011/11/30) +o pkg/obcs/obcs_calc_stevens.F: + - join some loops to reduce number of if-statements + - fix a bug in code for northern and southern boundaries. +o pkg/seaice/seaice_init_varia.F + - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and + caused zero ice-velocities for the B-grid code +o pkg/seaice/seaice_init_fixed.F + - fix a bug in the initialisation of the second metric terms + k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0. + - this affects all seaice configurations with useCurviLinearGrid = .true. + and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms + = .true. (default) + - the only verification experiment affected is global_ocean.cs32x15: + icedyn, seaice, and seaice_dynmix (AD) +o pkg/thsice/thsice_diagnostics_state.F + - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does + not contain garbage that can lead to surprises in diagstats_calc.F +o model/src: + - move bi,bj loops inside INTEGR_CONTINUITY ; + - call INTEGR_CONTINUITY directly from forward_step.F + (previously called from momentum_correction_step.F) + - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F, + forward_step.F and pkg/ecco/the_main_loop.F +o model/src/do_oceanic_phys.F: + - reset addMass to zero only if useICEFRONT ; + - separated k-loop for rhoInSitu calculation ; + - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P) + and at constant T,S (= WdRHOdP); + NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport + of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical + transport of locally-referenced potential density); + to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP) +o gluemnc: + - replace ncrcat with ncks when adding variables to *.glob.nc + - change the way variables without record dimensions are handled so that + files that have variables with and without record variables can be glued: + add a record dimension with a new unique name to be able to differentiate + between variable with and without a-prior record dimensions. Remove + this record dimension before adding the variable to the *.glob.nc file. + This procedure automatically works also for grid.*.nc files that do not + have any record dimension. +o verification/cpl_aim+ocn: + - generate new reference output on baudelaire (gfortran, mpich2) (previously + from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script. +o pkg/obcs/obcs_calc_stevens.F: + - add code for northern and southern boundaries. + - reorder some loops to save some operations and so that drFBar can be scalar +o model/src: + - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine + truncation) and add diagnostics for Adams-Bashforth tendency increment. + - update test-exp. AD output: + 1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl; + and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20, + front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5), + global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4), + matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre, + tutorial_global_oce_in_p, tutorial_global_oce_latlon and + tutorial_plume_on_slope. +o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX + that vectorises. This code uses 3 extra 2D fields, F90 array assignments + and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX + does not even come with an F77 compiler anymore, this should not be + a limitation + +checkpoint63e (2011/11/06) +o pkg/seaice adjoint of LSR: + - substantially rework STORE dirs. + - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED + this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields + and only perform SOLV_MAX_FIXED adjoint iters. + If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration + always goes to same record, meaning that the last forward field will be + the one used in the adjoint - an approximation. + - now produces non-zero LSR-related gradients, and acceptable gradients for + An's zonal (x-z) test case (to be checked in) + - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR + (but these are screwed up by the thermodynamics in the first place); + reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution; + output_adm.txt also reflects changes to seaice_lsr + - global_ocean.cs32x15: + * the "default" input_ad.seaice has been re-defined to always exclude dynamics + (output_adm.seaice.txt was updated) + * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift + (output_adm.seaice_dynmix.txt) +o test-exp. exp4+stevens: + - switch off pTracers and nonHydrostatic (restart problems with NH); update output +o pkg/seaice (lsr solver): + - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only); + update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15 + - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD) + - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution + into initial guess for linearised solver; use weight ~ (1/err)^2,4. + - compute (with new S/R) and print initial (+ free-driff sol. if available) + and final residual of linearised system. +o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity + (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F) +o pkg/obcs: Stevens BCs (still only for east and west) + - fix Stevens BCs by using intermediate velocities of previous + time step as "baroclinic" contribution rather velocity of one grid cell + inside the boundaries; more consistent but makes the entire treatment + more complicated, requires new pickup files and two new S/Rs: + obcs_copy_uv_n and obcs_save_uv_n + keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY + (undefined by default) + - silently move computation of some grid factors into separate loops to + save some recomputations + - add a hack for non-linear free surface + - add a verification experiment to exp4 that tests this code +o make gluemnc/xplodemnc work with (moron) non-GNU shell tools + +checkpoint63d (2011/10/25) +o pkg/obcs + seaice-dynamics: + - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before + solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB + values (consistent with an implicit method). + - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to + return to older implementation (same results as before); note that none of + the "experimental" OBCS_SEAICE options are implemented in the new version. + - switch test exp. seaice_obcs to use new version (update output). +o pkg/seaice: + - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS) + - add parenthesis in Water-Ice drag calculations (evp & lsr); + - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1; + and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice) + - update output of test exp lab_sea that uses evp or lsr (fwd+ad) + and global_ocean.cs32x15 (icedyn & seaice fwd+ad). +o pkg/layers: + - Include potential density as new coordinate (Thanks to David Munday) +o pkg/dic: + - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add + carbonate computation/output to CALC_PCO2_APPROX +o pkg/generic_advdiff + - make TAF generate code that vectorizes: + gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F +o model/src: + - improve vectorization also for adjoint code of + solve_tridiagonal and solve_pentadiagonal. As this requires up to + 5 new 3D-fields, this code is only turned on for the combination of + ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message + for singular matrix check (only for TARGET_NEC_SX). + - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to + ALLOW_AUTODIFF. This flag now needs to be set outside of + solve_tri/pentadiagonal.F +o pkg/exf: + - fix previous modif in exf_readparms.F (revision 1.66: treatment of + optional namelist EXF_NML_OBCS). + - add many debug-print (to trace down where pkg/cal error msg comes from) +o pkg/mom_vecinv/mom_vi_hdissip.F + - rearrange loops so that vectorization is improved and in particular + the adjoint routine vectorizes. The code is a little longer now, but I + think easier to read. + Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested. +o pkg/seaice: + - allow to specify initial seaice velocity from files (uIceFile,vIceFile) +o pkg/exch2: + - alternative code (without tile x tile matrix) for cumulated (global) sum; + used as default; keep using matrix version in adjustment.cs-32x32x1. +o tools/build_options: + - after merging some MPI and/or multi-threads specific optfiles so that + the modified default optfile support both built (using genmake2 -mpi + for the MPI built, using genmake2 -omp for OpenMP built), + move now obsolete optfiles to tools/build_options/unsupported/ + (add copy of email sent to support list in doc/optfiles_changes.txt) + +checkpoint63c (2011/09/28) +o pkg/ebm: + - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of + test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d) +o pkg/seaice (SItracer pickup) +* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER) + To be done: + - thorough testing of missing fields in S/R seaice_read_pickup + - thorough matching between generic tracers and specific fields used + (e.g. volume-weighted age, area-weighted age, salinity, ...) +o pkg/grdchk: + - all procs calculate and print finite-difference gradient (for testreport) + - change description output used by testreport; + - AD testing: also compare and report Finite-difference gradient; + => update all output_adm*.txt +o test exp. global_ocean_ebm: + - switch back useRealFreshWaterFlux (no problem anymore with run-off); + and turn on exactConserve; update (fwd) output. +o pkg/seaice (LSR): + - print to STDOUT number of solver iterations at SEAICE_monFreq interval. + - modify solver to deal cleanly with u/v switch at face edges (CS-grid): + * identical results with non-CS topology (but save up to half of EXCH calls) + * no much changes in cs-32 verification tests since no ice at face edges + (differences due to convergence criteria, since nb of iterations changed) + * expect some differences on lat-lon-cap grid. + update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice) +o pkg/exch2: + - add new CPP option to disable Cumul-Sum matrix (to save storage when using + many tiles); until alternative coding is added, just add a stop. +o pkg/kpp: + - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F + to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list). +o optfiles: + - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles + into corresponding standard one, which now support different build: + (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built) + - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael) +o pkg/obcs (seaice): + - add missing EXCH for uIce,vIce after applying OBCS; + - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding + argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R + EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F; + - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared) + - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi + and eedata.mth for MPI and mutlti-threaded testing. +o pkg/flt: + - make FLT EXCH working with multi-threads (and MPI + multi-threads); + - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h; + - fix pickup and trajectories + profiles output with multi-threads; + - add parameter to select group of fields to write along trajectory and + profile (default unchanged); + - only call PORT_RAND* function when flt_noise <> 0; + - add multi-threaded test for verification exp. flt_example. +o eesupp/src: + - fix S/R ALL_PROC_DIE for MPI+multi-threads. + - USE_OMP_THREADING: check that number of threads (from eedata) matches + actual number (from env.var. setting). +o pkg/ebm: + - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file. + - add multi-threaded test for verification exp. global_ocean_ebm + +checkpoint63b (2011/08/29) +o pkg/ebm: + - fix sign of runoff; + - update directly forcing fields (Qnet,EmPmR) to use standard + external_forcing_surf.F (remove ebm_forcing_surf.F); + - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F); + - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm) + and apply relaxation towards corresponding SST field (2-D map or ZonAver). + - update global_ocean_ebm parameters file data and update output (fwd+ad). +o verification/matrix_example: + - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for + MPI and mutlti-threaded testing. +o pkg/matrix: + - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ; + - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter); + - fix for multi-threaded (remove DATA statement); + - use standard DIFFERENT_MULTIPLE function; + - add MATRIX_OPTIONS.h +o verification/matrix_example: + To allow to split the domain in several tiles, change the domain size + from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on + Western side) of land points. +o (*_)write_pickup: + - fix few bugs in mypackage_read/write_pickup.F + - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into + array of length 1 (was caught by compiler syntax-check). +o pkg/diagnostics (velocity potential solver): + - fix initialisation of main diagonal matrix (for overlap values) +o tools/build_options: + - towards single optfile for MPI and non-MPI built: merge few +mpi optfile + into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11) + - linux_amd64_gfortran: merge +mpi_generic version into standard optfile: + * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ; + * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list; + and use "-devel" testreport option for standard testing on baudelaire. +o pkg/grdchk: + - Assume that all gradient-check position are within the same tile + corresponding to global indices (iGloTile,jGloTile) and that + positions (i,j indices or nbeg) are local to this tile; + - set tile local-indices and proc. number according to tile global-indices; + - remove grdchkwhichproc from namelist (retired param); + - send adjoint gradient to all procs so that all procs print it to STDOUT; + - switch on MPI test for global_ocean.90x40x15 AD test experiment. +o adding package bbl (Bottom Boundary Layer) + description in MITgcm/pkg/bbl/bbl_description.tex + example/test experiment in MITgcm_contrib/bbl +o adjoint verifications + - changed 5 experiments to multi-tiles + * global_ocean.90x40x15 + * obcs_ctrl + * offline_exf_seaice + * tutorial_dic_adjoffline + * tutorial_tracer_adjsens + changed reference output for those that crossed tile boundaries + (changed choices of gradient check positions) + - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi) + - temporary bug fix in grdchk_loc.F for obcs +o genmake2 & testreport + - add target "obj" (just for OBJFILES files) to Makefile; + - add option to specify FEXTRAFLAGS on command line. +o pkg/mypackage: + - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS + +checkpoint63a (2011/08/02) +o pkg/diagnostics (velocity potential): + - fix velocity-potential calculation when using OBCS: balance net inflow + at each level (new S/R OBCS_DIAG_BALANCE). + - fix some of the problems with OBCS in stream-function calculation. +o pkg/exf/exf_readparms.F + - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF, + EXF_NML_OBCS) more consistent, so that you need not have these lists + in data.exf when they are not used. +o optim/optim_readdata.F: + - add some output about obcs variables that might help debugging + - add a check about nvarlength +o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec +o pkg/diagnostics (velocity potential): + - fix mask for OBCS (still problems in stream-function with OBCS); + - add specific parameter (default = main code CG2D params) for solver; + - in case of poor convergence, use solution corresponding to lowest residual. +o pkg/seaice/seaice_growth.F: small changes that permit vectorizable + adjoint code. In general statements like tmpscal=fld(i,j) are problematic + and should be avoided where possible. +o model/src (rStar): + - include r* effect on reference-state (PhiRef) in totPhiHyd + (so that it's really the potential anomaly at the cell center); + affect solution only if z* with full pressure in EOS. + - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and + update output (because of z* in totPhiHyd and viscA4 changes); + - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly + @ constant r) until interpolation at constant r is implemented. +o pkg/diagnostics + - fix RCENTER diagnostics in case cell center is not at interface middle +o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use + this eos with eosType = 'TEOS10', in data (PARM01). This eos implies + that THETA and SALT are "conservative temperature" and "absolute + salinity" +o pkg/ctrl + - fix computation of endrec in s/r ctrl_init_rec + - ctrl_pack/unpack_*: remove unused variables and some obsolete code +o pkg/seaice/seaice_growth.F + - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code, + remove then obsolete STORE directives + - fix STORE directives for tice and tices, so that only the + appropriate part of the fields are stored (and not the entire + field); update global_ocean.cs32x15.seaice AD output. + - cosmetic changes: adjust CPP flags and indentation for better + legibilty +o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by + Chris Wilson) +o pkg/gmredi: + Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF), + and test it in verification exp. "front_relax.bvp" (update output.bvp.txt) + +checkpoint63 (2011/07/11) +o pkg/exch2: + - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h + - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the + (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y + increments, calculates Cumul-Sum @ tile origin and sends results to each tile. +o pkg/diagnostics: + - deal with pairs of post-processed diags which are computed together; in + particular, re-order list of diags within 1 file to save 2nd computation. + - add S/R to compute velocity stream-function (called after velocity-potential + calculation) from divergence free transport -> new diagnostics "PsiVEL". + - add parameter to select grid-point location where PsiVEL == 0. +o eesupp/src: + new S/R to calculate cumulated sum on tiled array, corner grid-cell location + (specific S/R needed with exch2 topology - for now, just print an error msg) +o pkg/shelfice + - Implement friction velocity-dependent transfer coefficients following + Holland and Jenkins, JPO, 1999 + Original code by M. Losch with small modifs. + Enable with CPP option SHI_ALLOW_GAMMAFRICT + and runtime flag SHELFICEuseGammaFrict +o verification lab_sea & global_ocean.cs32x15: + - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local): + does not miss some dependencies (but is slower) and also works with many files + (default makedepend limitation for AD built). + - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested). +o pkg/diagnostics: + - add run-time parameter "useMissingValue" (def=False) to fill land-point + (i.e., where mask=0) with MissingValue ; used only in MNC output file. + This replaces CPP-option DIAGNOSTICS_MISSING_VALUE. + - Extend the use of "missing_value" setting from data.diagnostics for the case + of counter-diagnostics (where fraction-weight is zero). This applies both to + MNC and MDS output files. +o pkg/seaice/seaice_growth.F: + - add 'a priori' cap of latent heat flux based on actual mass considerations + when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the + non-legacy seaice_solve4temp. + - add diagnostic of the residual sublimation freshwater flux (the freshwater + flux taken from the ocean if the total actual latent heat fluxes exceed + the maximum) + - remove the CPP switch around the *_FWbySublim unit change and move diagnostic + fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F. + - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef + SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim). + - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET. + - bug fix : missing part to Martin's r_FWbySublim pathological case fix. +o verification 1D_ocean_ice_column: + made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet + update results +o pkg/diagnostics: + - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P') + which are not filled-up but computed from other diags ; In this case, the mate + diag points to the primary (filled-up) diag to used for post processing. + - Update Velocity-potential computation using post-processed diag framework. + ==> Change the ordering of fields and time-periods in MDS output file + when using periodic averaging: now writes one time record with the full set + of fields for this time period, then the next time reccord (it used to be + one field with the full set of time records then the next field). + Note: this is now similar to NetCDF (MNC) output file. <== + +checkpoint62z (2011/06/21) +o adjoint monitor: + - Add adjoint monitor output for packages exf, seaice + and update relevant testreport output +o pkg/seaice: + - re-order diags inits so that they appear in order in available_diagnostics.log + - added diags: hsnow thermo. rates of change, area preceeding ridiging process, + area/heff/hsnow preceeding thermodynamic growth/melt. + - modified diag: SIdA; output actual effect, as the description states. + - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. + - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. + (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; + and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) + - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. + - added diagnostics for seaice generic tracers (SItr*). + - added SItrUnit and SItrNameLong run time param (for SItr* diags). + - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. + I. Fenty: 18-Jun-2011: + Minor changes to seaice package: + 1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and + added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) + - Differentiated "regularization variables" from "floor variables" + * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor + * hiceMin became SEAICE_hice_reg (old hiceMin) + (with _reg meaning regularization variable) + - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion + so as to ensure energy conservation when going between phases + - A22 was not used anywhere + 2) Changed regularization procedure for heffActual and hsnowActual to ensure + well-boundedness and smooth adjoint in seaice_growth.F + 3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells + because the old regularization always set heffActual >= 0.05 cm + 4) Changed the model so that the default behavior is to put a small (10^-5) "floor" + on AREA when HEFF > 0. + - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to + requiring that DISABLE_AREA_FLOOR *not* be defined + Affected verifications: + - 1D_ocean_ice_column (output.txt output_adm.txt) + - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) +o pkg/diagnostics: + - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). + - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument + (was _RL, now integer) with option = 0 to retrieve all levels. + - add pieces of code to compute velocity potential at each level (new diagnostics + PhiVEL, works only when UVELMASS & VVELMASS are also turned on); + for now, using same params as CG2D (target-resisual, max Nb of iter ...). + - fix few issues with counter diagnostics in diagnostics_setdiag.F & + diagstats_setdiag.F (if diagnostic counter is itself a counter diag) + and in diagnostics_fract_fill.F (do not need a valid pointer for the + diagnostics counter-mate); check that definition of counter-diagnostic + includes a valid counter-mate (in diagnostics_set_levels.F). +o model/src (rStar): + - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); + affect solution only if z* with full pressure in EOS; + update output of test-exp global_ocean.90x40x15. +o pkg/seaice: + - introduce siEps=1e-5 parameter + - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5). + - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code. + - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer. + For now it covers, and was tested for, ice salinity and age (attached to HEFF), + as well as ice cover age and ridging index (attached to AREA). + For now the run time parameters (in data.seaice/SEAICE_PARM03) are + SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA'). + Up to SItrMaxNum=3 tracers can be used simultaneously. +o pkg/salt_plume: + -introduce SPsalFRAC run time parameter that sets the fraction of the + salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically) + that gets vertically redistributed (fluxed down) by pkg/salt_plume. +o model debug options: + - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored + in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h). + - Refine debug-msg printing selection (3 new levels): + debugMode : controls printing of debug messages (sequence of S/R calls). + debugLevel : controls printing of algorithm-relevant auxiliary/debug messages + debLevZero = 0 ; /* level of disabled aux. msg printing */ + debLevA = 1 ; /* level of minimum aux. msg printing */ + debLevB = 2 ; /* level of low aux. print (report read-file opening)*/ + debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */ + debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */ + debLevE = 5 ; /* level of extensive debug printing */ + New debugLevel default: with default debugMode value (=F), + = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.; + and if debugMode=T, default debugLevel = 4 (debLevD). + Relation with previous settings: + debLevB (=2) corresponds to former debLevA (=1) + debLevD (=4) corresponds to former debLevB (=2) + Note: + a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before); + b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs); + to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5) + - Add new parameter (printResidualFreq, read from PARM02 namelist) to print + detailed CG solvers convergence; off (=0) by default, except if debugLevel=5. +o pkg/obcs: + - change OBCSfixTopo default from True to False (should not change the results); + keep OBCSfixTopo=T in verification-exp. seaice_obcs. +o pkg/thsice: + - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in + 2nd layer seaice sublimation (unlikely to happen) + - use Interior mask for OBCS in thsice_advection.F (similar to what is + done in gad_advection & seaice_advection). +o adjoint: + bug fix spotted by Gael Forget: + seaice_advection and thsice_advection still had + legacy CPP options to avoid CS corner updates for adjoint +o pkg/seaice: + => Change some of the defaults (2011/05/29): + - change SEAICEuseFluxForm default (from False to True) + - change DIFF1 default (from 0.004 m/s to 0. m/s) + And print warnings if DIFF1 is not set in data.seaice and centered + avection scheme is used without any diffusion. + also: + - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F; + - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[] + - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any + other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with + #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE. + update results of test exp.: + lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20) + output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200) + output_adm.noseaicedyn (SEAICEuseFluxForm=T) + offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T) + seaice_obcs: output (SEAICEuseFluxForm=T) + and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004) + for standard fwd & AD lab_sea tests (to keep the same output). +o pkg/seaice/seaice_growth.F: + - use Ian Fenty's capping formulas for actual ice + thickness thoughout EVOLUTION branch. + - put treatment pathological case #2) in CPP brackets + (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). + - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. +o pkg/seaice: + - seaice_diffusion.F : remove the min(DX,DY) factor permanently; + pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter; + also pass fac as a param, which can be 1. (to update the tendency + field) or the time step (to update the field itself). + - seaice_advdiff.F: for multidim, call seaice_diffusion with + e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call + seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. + - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : + hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. +o pkg/seaice: + diffusion with centered advection scheme (diffus.F & advect.F): + - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) + to just compute the laplacian of input-field. + - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call. + - fix flux-form version in diffus.F to conserve tracer. + update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects + machine truncation) and lab_sea.salt_plume (conservative flux-form modif) + +checkpoint62y (2011/05/26) +o pkg/seaice: + - seaice_growth.F : in EVOLUTION branch, always include + a_QSWbyATM_cover in qnet (as it should be). + - verification/global_ocean.cs32x15 : update results accordingly + (output.seaice.txt output_adm.seaice.txt). +o pkg/seaice + obcs: + - use maskInW & maskInS in multi-dim advection and biharmonic diffusion: + equivalent of assuming no tracer gradient outside the OB region. + update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion) + - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed + after changes above); + - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field + only at OB location (instead of over a band of OLx width). +o pkg/seaice: + - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F + (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid) +o pkg/obcs: + - split header file "OBCS.h" into 4 separated files: + OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h + Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h + (contain no conditional statement which depends on OBCS options). + - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h) + to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h). +o ctrl, cost, grdchk & autodiff pkgs: + - make options file more standard (like other {PKG}_OPTIONS.h file but + with AD_CONFIG.h); clean-up some of the included header files. +o pkg/obcs: + - do not mask tracer when applying OB (tracer == 0 could generate problems) + - apply tracer OB values to tracer field only at OB location (instead of + over a band of OLx width) + - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R) + - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove + obcs_apply_tloc.F & obcs_apply_sloc.F +o obcs in model/src: + - call OBCS_APPLY_W only if NonHydrostatic. + - call OBCS_APPLY_ETA only if NonLinFreeSurf. + - reset dEtaHdt and wVel to zero outside OB interior region ; + - leave tracer unchanged outside OB interior region: This has no effect + on the solution but just to prevent unrealistic tracer value outside OB. + - zero out velocity outside OB interior region: This has no effect on + the solution but just to prevent unrealistic velocity outside OB. +o obcs and non-lin free-surf: + move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F + and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F + + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR: + this fixes missing EXCH + get consistent eta OB value (+ fix restart). + update results of test-exp. exp4(nlfs). +o exp4 (nlfs) test-exp: + use OBC for Eta at Western & Eastern OB (to test prescribing Eta + with NonLin-FreeSurf); update output.nlfs.txt +o obcs and 2d/3d solver norm: + use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB + and outside OB interior region (will allow to place OB further inside the + domain). Depending on the domain, can affects cg2d-Norm (previous + cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl, + and cg3d-Norm (previous Norm was computed before canceling OB terms), + e.g. in tutorial_plume_on_slope. + - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope. +o pkg rbcs: + - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h + - add capability to apply relaxation to horizontal velocity uVel & vVel. +o pkg/grdchk: add gradient check for control variable xx_shifwflx +o pkg/shelfice/shelfice_init_fixed.F + fix CPP-flag combinations +o pkg/seaice: Merge iceage code of Pierre Rampal + * update/change/correct ice age calculations + * add age updates for pathological cases + Probably needs more testing... + +checkpoint62x (2011/05/13) +o pkg/mom_vecinv: + high-order vorticity scheme: use interior masks (maskInW & S) + to zero-out (outside OB) gradient of vorticity. +o verification exp.: + turn on "useEnergyConservingCoriolis" (better discretisation) in exp. + hs94.128x64x5 and seaice_obcs ; update results. +o pkg/obcs: + fix bug in OBeta for YZ sections in obcs_exf_load.F +o pkg/ctrl, pkg/shelfice, and optim: + - add new control variable xx_shifwflx (fresh water flux underneath ice + shelves). This is almost as tedious as obcs-ctrl, because the + variables needs its own mask. + - add a cost function term that penalizes the deviation of xx_shifwflx + from the first guess (zero) in analogy to other control variables +o pkg/shelfice: + - start basic adjoint +o pkg/ctrl: + - remove extra 2D field "for good measure" when initializing in + ctrl_set_globfld_[xy/xz/yz].F + - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec + - improve error messages in ctrl_set_unpack_* +o OBC implementation in momentum: + use interior masks (maskInC,W & S) in momentum S/R: + - multiply divergence, tension and some del^i.u or del^j.v by maskInC + - multiply del2u,del2v by maskInW/S (biharmonic viscosity) + - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) + - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) + Motivation: fix/clean implementation of OBC with biharmonic-viscosity + (and also with Leith/Smagorinsky harmonic-viscosity). + Update output of experiment dome and exp4 (+nlfs). +o exp4 test-exp: + - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) + and prescribe time-varying OB (without pkg/exf) for zonal-velocity + at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe + time-varying OB at Western-side for wVel (NonHyd); update output. + - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv + and biharmonic-viscosity ; also use prescribed time varying OB. +o pkg/obcs: + fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F +o model/src: + - fix startTime setting when baseTime<>0 & nIter0=0 are specified ; + - initialise startTime & nIter0 with unlikely values: allows to set one + from the other without ambiguity. +o seaice_obcs test-exp.: + add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output. +o pkg/obcs: + - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: + no longer needed with maskInC,W,S in pkg/generic_advdiff. +o pkg/seaice: + - retired SEAICE_SALINITY and SEAICE_salinity in favor of + SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively. + - fixed bug in the initialization of sea ice salinity variable HSALT + in seaice_init_varia.F (removed dependence on ICE2WATR) +o fizhi-cs test exp.: + switch reference output convention for these 2 non-standard test-exp, + from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5) + to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11) + reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran +o model/inc: + - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4") + of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS) +o pkg/seaice: + - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY +o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15 + - updated output*.txt files due to bug fixes in salt, saltPlumeFlux, + and initial HSALT + +checkpoint62w (2011/04/26) +o pkg/mom_fluxform: + - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf. + - use parameter "sideDragFactor" in no-slip BC side-drag part. + - update output of exp. global_ocean.90x40x15 +o pkg/mom_vecinv: + mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform) +o update seaice exp.: + use more consistent parameter values (remove "backward compatability only": + ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh) + related to thermodynamics seaice. Update output (fwd+AD) of exp.: + 1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs +o update test-exp global_ocean.90x40x15: + o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis). + o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.) + o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params) + o turn on zStar & viscA4 in standard set-up (dir input/) + and update output files: output.txt & output.dwnslp.txt +o new AD-test experiment: obcs_ctrl + (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector. +o pkg/dic: + fix two bugs in handling water vapour pressure in carbonate chemistry + and air-sea fluxes. Found by Val Bennington and Galen McKinley + (add DIC Option = WATERVAP_BUG to recover old results) + update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline +o adding allowInteriorFreezing option to check for water below freezing point + at depth and bring the negative heat anomaly to the surface level +o pkgs _fields_load: + - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs) + - use new S/R GET_PERIODIC_INTERVAL in pkgs: + bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and + rbcs to get interpolation weights and time reccord number. + - fix multi-threading in aim_fields_load.F + - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F +o external_fields_load: + new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear + interpolation weights) to use in a periodic time-series ; do not divide by + time-step to convert to integer: + - this fixes case where externForcingPeriod is not multiple of time-step + (Thanks to Christopher L. Wolfe) + - this fixes case where externForcingPeriod is an odd multiple of time-step + (was wrong by half of time-step); update results of tutorial_global_oce_in_p. + store index of time-record which is currently loaded: + - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ; + - needed for the adjoint but not yet used because of extensive recomputations; + (to be fixed soon) + +checkpoint62v (2011/04/02) +o verification/1D_ocean_ice_column added to test Ian Fenty's + pkg/seaice_growth.F modifications for improving sea ice code differentiability +o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope + (new velocity statistics after changing maskInW & maskInS definition) +o pkg/generic_advdiff with OBCS: + use maksInW & maskInS in advective flux and in biharmonic diffusion calculation: + equivalent to assumption of no tracer gradient outside the OB region. + This will affect the results if using obcs+biharmonic diffusion. + update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc) +o pkg/obcs: + change definition of maskInW & maskInS: leave OB edges inside (maskIn=1) + (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still + in Interior region. No impact on solution but affects Velocity monitor stats. +o pkg/ptracers (adjoint) + New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate + tape file for each tracer +o model/inc/src and pkg/autodiff: add parameters that allow to turn + of parts of the adjoint code at run time. For now, there are only + useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These + parameters are set in data.pkg. + This is the lazy coward's version of doing this, but still useful for + debugging. In order to do it right, everything needs to be moved to + pkg/autodiff. +o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at + the end; this fixes the adjoint balancing code for open boundaries. +o pkg/ctrl: + - change behavior of xx_${varname}period to be analogous to exf-conventions: + xx_${varname}period = 0., means time-independent control part + xx_${varname}period = -12., means one-year-periodic monthly control part + - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to + clean up ctrl_init a little, remove unused variables + - ctrl_init: fixed the handling of the start/endrec for obcs-variables + - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec + +checkpoint62u (2011/03/15) +o model/src: + - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in + h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ; + - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to + INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF. +o pkg/ctrl/obcs/ecco: + - remove obsolete, unused, and partially broken code: + ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within + ALLOW_CTRL_OBCS_BALANCE + - put a stop statement into ecco/cost_obcsvol.F, but also add + cost_obcsvol to ecco_ad_diff.list +o pkg/ecco: fix counting cost function contributions for obcs (code + by Matt M.) and diffkr for diagnostics +o pkg/ecco, pkg/ctrl, pkg/grdchk: + add cost penalty terms for initial uvel, vvel, eta controls + and I/O for prior error files +o pkg/mdsio: + move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option + (new argument) to check for tiled file in mdsioLocalDir : this fix the + restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir. +o pkg/ctrl: + - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by + ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove + unused and superfluous variables + - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0. +o pkg/ecco + - enable adjoint of Stevens OB +o pkg/ctrl/ecco/grdchk: + - remove global declaration of tmpfldx/yz and tmpfldx/yz2. + Fortunately, we do not have any tests for the numerous cpp-flagged + option of "obcs as control parameters" so we will never know + if this is an improvement (but at least now things compile). + - remove an obsolete initialization from ecco_cost_init_barfiles.F + - fix some problems within never used ifdefs to make the code compile +o pkg/obcs: + - Refine Interior mask definition to work with more complex OB (e.g. + if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to + read in Interior mask from file. Check if Interior mask is consistent + with OB list of indices. +o pkg/seaice + - beginning code for a seaice tracer package, + but currently only used for seaice age: SEAICE_AGE + SEAICE_num = 4 + iTracer = 1: area-weighted ice age + = 2: volume-weighted ice age + = 3, 4: template for one-year vs. multi-year ice + data.seaice has new namelist SEAICE_PARM03 for arrays related to + SEAICE_num + +checkpoint62t (2011/03/05) +o pkg/obcs: + - obcs_apply_uv.F: change to a 2 steps method, first tangential component; + then normal component. This ensures that the normal component is set + correctly even when it conficts with tangential setting from an other OB. + Affects results of test-experiment seaice_obcs: update the output.txt +o pkg/obcs: + - add code to monitor statistics of dynamical fields at OB. + - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW : + - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection). + - change default: balance the Net inflow through all OB (instead of balancing + each OB separately); keep the old method if setting OBC_balanceFacX < 0. + - switch on useOBCSbalance in dome experiment: only correct Western OB outflow + to match Nortern OB inflow (OBCS_balanceFacN=0). +o pkg/seaice: + - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL +o pkg/seaice (seaice_growth v 1.113): + - reverting seaice_growth to v 1.111 in order to have code with exact bit + compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge + CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced + runtime flag SEAICEareaFormula is kept but is inactive +o model/src: + - add new param to scale curvilinear grid distance and area when using + a different sphere radius from the grid-files. + - test/check multi-threads EXCH applied to local variable (cg2d_x) +o adjoint: + - enable adjoint of Stevens OB + - add dummy_in_dynamics to enable extraction of ADJrhoinsitu + (a bit delicate because of potentially modified adj. common block structure; + current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later) + +checkpoint62s (2011/02/15) +o pkg/seaice (seaice_growth v 1.112): + - introduce SEAICEareaFormula run time parameter, which selects the recipe for + computing the ice cover tendency from effective thickness tendencies. Include + Ian Fenty's formula. + - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using + SEAICEareaFormula. + - simplify notations for the various d_HEFF/d_AREA terms. +o pkg/gmredi: + - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code + from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative; + add a verification test-run (front_relax.bvp) to test GM_useBVP. +o pkg/seaice (seaice_growth v 1.111): + - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's. + - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to + also melt ice. +o pkg/seaice: + - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty). + - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h +o pkg/cheapaml: + - from Nico Wienders: New version of this package. +o pkg/flt: + - add CPP options to prevent floats to re-enter the opposite side of + a periodic domain (default: keep periodicity) +o pkg/gmredi: + - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners + (needed for multi-dim advection). + - switch on GM Advective form in global_ocean.cs32x15 and update output.txt +o model/src: + - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run. +o tutorial_tracer_adjsens + - extend to NLFS and replace maskC by hFacC + (change reference output accordingly) + +checkpoint62r (2011/01/24) +o testreport: + - add option -deloutp (-do) to remove output file after successful run + - add option -mfile (-mf) for MPI machile-file and for each test-exp, + extract exact list of procs from this file ; adjust COMMAND by + replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs. +o pkg/ecco: replace old ineffective way of penalizing deviations from + first guess (of obcs) with code by Matt Mazloff +o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without + exf/cal + - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl + and handle case of obcs?period == 0 + Not affected by these changes: There is still an inconsistency in + the computation of start/endrec for the obcs variables for ALLOW_CAL + defined (see comment by Menemenlis, 7-Mar-2003) + - make S/R ctrl_get_gen_rec return something meaningful even if + ALLOW_CAL is not defined + - ctrl_getobcs?: simplify code so that it does not need to use + S/R exf_swapfields +o testreport: + allow to test MPI with different number of processors for each experiment: + create file "SIZE.h.mpi" in each build dir. + Note: update of "-command" argument not yet implemented. +o model/src, pkg/autodiff, pkg/ecco, pkg/seaice: + alleviate the need for additional 3D tapes when using + the non-inear free surface in the adjoint. This is done + by adding an 'update' of hfacc etc. to their current + value at the beginning of forward_step.F. +o pkg/seaice + seaice_lsr: move stress-divergence computations out of outer pseudo- + timestepping loop +o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD' + up, so that the calls of the ctrl_* subroutines are really at the end + of the routine. +o pkg/gmredi: + allow to specify a 2-D horizontal map and a 1-D vertical profil + as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity. +o pkg/seaice: + move lsr iterations from seaice_dynsolver to seaice_lsr. +o pkg/seaice: + reduce memory footprint of seaice mutldim advection tapes, + by using a 2D tape independent of the generic_advdiff ones, + and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc. + +checkpoint62q (2010/12/29) +o model/src: + - check horizontal grid-spacing for unset or zero/negative values. + - change AD test hs94.1x64x5 to be truly a 2-D set-up. +o pkg/flt: + - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR + - precision of input and output files set according to readBinaryPrec + and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits. + - initial float position from tiled file was not converted to index space + (looks like a bug): fixed to make it similar to initial pos. global file. +o global_ocean.cs32x15: + change SIZE.h of AD set-up to get same tiling as with MPI. + Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11) +o model/src: + add flag to control printing of domain fields (bathymetry, hFac ...) in + ini_mask_etc (call to plot_fieds_xy*). +o pkg/thsice: + if useEXF, some forcing fields are not valid in overlap: fixed by computing + over the interior only + apply EXCH at the end (like with SEAICE advection). +o pkg/mdsio: + - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer + to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS. + - change barrier call for safe multi-threads access to 3-D shared buffer. + - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones) + - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and + remove the 4 S/R MDS_PASS_WH_R4/8toRL/S. +o pkg/flt: + - add fourth-order Runge-Kutta integration + - add basic exch2 support (only 1 facet supported so far!) +o pkg/mdsio+rw: + new S/R to read local (or tile independent) vector (read counterpart of + mds_writevec_loc, and front-end write_glvec_rl/rs). +o global_ocean.cs32x15: additional input_ad.seaice experiment + that uses pkg/seaice rather than pkg/thsice. + (using multidim advection for seaice) +o towards more F95 syntax for array specification in namelist: + - change "data.diagnostics" (data.ptracers was changed before checkpoint62p) + of all verification experiments. + e.g.: line: fields(1,3)='ETAN ','ETANSQ ', + was changed to: fields(1:2,3)='ETAN ','ETANSQ ', + - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles +o global_ocean.cs32x15: additional input.seaice experiment + that uses pkg/seaice rather than pkg/thsice. + +checkpoint62p (2010/12/17) +o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it + to THSICE_SIZE.h to avoid conflict with pkg/seaice. +o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint. + allow for use of multim. advection in seaice adjoint. +o pkg/seaice: add diagnostics for snow precipitation and sublimation flux + - first attempt to close budgets by taking into account the freshwater + flux implied by the sublimation of snow and ice. So far only the + volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag + SEAICE_ADD_SUBLIMATION_TO_FWBUDGET +o eesupp/src: + new S/R with new option (NML_EXTENDED_F77) to change array specification + from F95 standard to commonly accepted extended F77 form. + This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5) + and to revert back to the original syntax (with -DNML_EXTENDED_F77) + for less tolerant f77 compiler (e.g., pgf77, g77). +o globalFiles: + commented out in parameter file "data" since it's not safe with MPI + (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much + in this case); no longer commented out in restart test (tst_2+2). +o add adTapeDir to specify a special directory where adjoint tapes are + written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05 + and cannot be used together with mdsioLocalDir. +o nesting pkgs: + - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position + - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) + - add parameter files + utils dir + output from short run on beagle. +o pkg/seaice: + fix seaice_growth.F store directives; update results of exp. lab_sea.ad +o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid + unnecessary copying in adjoint code, requires new parameter NMAX_ITER + +checkpoint62o (2010/11/25) +o pkg/exf: + - change CPP option EXF_VERBOSE to run-time logical param exf_verbose. +o pkg/seaice: + - seaice_ocean_stress: split a loop for better vectorization of the + adjoint code + - seaice_growth.F: fix bug in conservation of freshwater connected to + capping of heff, put contribution into d_HEFFbyNEG + - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat + by something more sensible (parameters that are what their name implies) + - change some defaults, so that by default exf-parameters are used for + things like rhoAir, cpAir,latent/sensible heat parameters, in order + to reproduce the old results, many data.seaice now contain funny values + for cpAir and latent heat of sublimation +o packages_readparms.F: move exf_readparms up in line so that + exf-parameters are visible for other packages (e.g. seaice) +o debugMode & debugLevel=2: + - differentiate between debugMode & debugLevel=2: + debugMode: controls printing of debug messages (sequence of S/R calls). + debugLevel: controls printing of algorithm intermediate results and stats. + - remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2"; + => allows to print debug-stats without all sequence of call messages. + - switch control of debug print from debugLevel to debugMode in many S/R. +o pkg/obcs (obcs-sponge): + fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the + call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge) +o pkg/generic_advdiff: + - record overlap minimum size for each advection scheme; + - refine criteria on overlap minimum size; + - check and stop (in gad_check) if overlap size is too small. +o pkg/obcs: + - with ptracers: remove multiple calls to obcs_apply_ptracer (only done + once, in ptracers_implicit.F) + - with seaice: remove test on empty file name in obcs_apply_seaice (always + apply OB values when tile has OB) +o model/src, coriolis setting: + - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical + useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from + files (selectCoriMap=3) with any grid. + - add parameter "fPrime" for constant second Coriolis coeff (default=0). +o pkg/seaice/seaice_growth.F: + a few cosmetic changes that reduce the number of lines of code +o pkg/obcs: add boundary conditions following Stevens (1990) + - the code follows old MOM/NAOSIM code + - so far it is only implemented for the eastern and western boundaries + and NOT for pTracers +o pkg/rbcs: + - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the + beginning of the first rbcs forcing period. + - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the + offline package, i.e., one file per time, labeled by iteration number; + deltaTrbcs sets the timestep with which the data was generated; + rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset. + - rbcsForcingCycle=0 makes forcing non-cyclic. + - make arithmetic safe for negative times and odd forcing periods. + +checkpoint62n (2010/11/09) +o pkg/seaice: + fix masking in free-drift S/R ; update results of exp. lab_sea.fd +o pkg/obcs: + New S/R to copy tracer value from the OB location to narrow band region + (width = same as overlap) beyond the OB: preserve OB value (needed for + high-order scheme) which were overwritten by EXCH call if in overlap + region. Applied to theta, salt, ptracer and advected seaice variables. + With seaice: use maskInC in similar way as in gad_advection.F, + in seaice_advection.F and advect.F. + Update output of experiment seaice_obcs and change exp4 to test OBCS with + 4th order Adv.Scheme. for pasive salt and ptracer. +o tools/genmake2: + - when looking for an optfile (not specified), only search for Fortran compiler + (remove sym-link test + setting of CPP + makedepend check + C-compiler check) + - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm + (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong) + - set default for CPP to "cpp -traditional -P" (was the case without specifying + an optfile, but otherwise default was just "cpp". + - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from) + - when "CC" is not set in the optfile, look for possible C compiler + (instead of just setting CC=cc) + - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes: + => add a ".F" to ".o" rule for source files with no "#include" (such as + port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS. + - move gfortran before g77 in list of possible Fortran compiler (consistent + with reference compiler switch from g77 to gfortran) +o pkg/seaice: + o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to + seaice_check that stops the model, when the CPP flag is used. + o seaice_growth.F: make capping of ice volume conserving by returning the + capped ice as freshwater to EmPmR. This does not change the verification + experiments but will change runs where the capping is acutally active +o change reference platform+compiler from faulks+g77 to baudelaire+gfortran + (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5, + global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD), + lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd) +o tools/genmake2: + - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log") + - change DUMPSTATE default to false (can use "-ds" option to switch it to T) + - clean previous genmake log files before anything else. + - change Makefile to remove testreport log files (*.tr_log) and genmake log + files only with "CLEAN" target (instead of "Clean"); +o pkg/generic_advdiff: + Change OBCS in multiDim advection (gad_advection.F): + Use maskInC to prevent intermediate update of tracer-field in OB regions, + thus keeping current-time-step OB values; and remove the call to OBCS_APPLY + which were applying future time-step OB values. + This way, all explicit calculations use current-time-step OB values + (simpler and more consistent). + Affects results when set-up uses time-varying OBC and multi-dim advection; + update output of experiment seaice_obcs. +o pkg/seaice: + move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h: + this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH & + SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY. + Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY + but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp + unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h) +o pkg aim (2010/10/26): + - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation + formulation with obliquity, eccentricity, ... as run-time parameters, + - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and + upward shortwave radition at the surface (all-sky and clear-sky). +o pkg/obcs: + - writing sections with globalFiles=T does not work: switch to tiled-files + when writing sections for OBCS (change pkg/rw/write_rec.F accordingly). + - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F + - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs + +checkpoint62m (2010/10/21) +o pkg/seaice: vectorize seaice_solve4temp.F + - move iterations loops outside of i/j-loops + - requires 2D arrays for TB and effConduct + - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is + modified in this routine + - a little bit of clean up, adjusting indentation, etc. + - replaced a few TEN**a by exp(a*log(10.)) in new code for better + performance and '**TWO' by '**2' (because TWO is a float), + replaced ONE, ZERO +o eesupp/src: + fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube +o pkg/seaice/seaice_growth.F + Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and + merging process. The merged routine has two branches, and one activates the 'evolution' + branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now). + In summary, here is what the '10/10 revision' did consist of + part 1: seaice_growth.F revisions 1.71 to 1.75 + - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged. + The emphasis here was on improving readability (e.g. by trying to use meaningful + variable names) and modularity (e.g. by adding arrays to store heff etc. updates). + part 1.5: + - revising the lab_sea experiment to make it a more useful (i.e. stable + and representative of an actual model run). This was done by generating a + (winter) pickup to start from, switching back the main experiment dynamic + solver from evp to lsr, having one of the experiments use the free drift solution. + part 2: seaice_growth.F revisions 1.76 to 1.85 + - Sorting out hard-coded constants that prevented heat and fresh water conservation. + - Sorting out the various fields units and sign (set early on and reset at the end) + to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and + fresh water stock is 'effective ice meters', and >0 implies more ice/snow. + - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks, + and simplifying logical expressions to further improve readibility. + part 3: seaice_growth.F revisions 1.86 to 1.89 + - Re-organize the blocks of code more logically. + - Merging the '_if.F' pieces that add something new. +o pkg/thsice: + - vectorize thsice_solve4temp and thsice_get_exf. + Problem: thsice_solve4temp has an unvectorizable statement that + might also be problematic for TAF + - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This + does not change the verifcation experiment, but will change all + experiments that have this flag undefined (not tested in verification); + a little reorganization to save a few 2D fields and recomputations + - 1st step of revisiting thsice adjoint (major recomp. sorted out) + - 2nd step: fix some store dirs + o seems to work somewhat, i.e. using ifort but not g77 + o likely cause are incomplete init. or recomputation + o start verification/global_ocean.cs32x15/input_ad.thsice +o pkg/obcs: add support for exch2 + - the position of the boundary and prescribed values are specified using + a global domain with exch2 facets stacked + - in x for N,S boundaries (like W2_mapIO=-1) + - in y for E,W boundaries (so E,W boundaries do not overlap) +o pkg/mdsio: add support for writing global sections with exch2 + file layout is as for obcs described above: + - for x-z sections, facets are stacked in x (like W2_mapIO=-1) + - for y-z sections, facets are stacked in y +o pkg/thsice: + - change a few routines for better vectorization: thsice_albedo.F, + thsice_step_temp.F, and in thsice_calc_thickn.F. Results are + not affected, but in particular the latter routine has changed + dramatically (not necessarily easier to read now). + - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops + iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF. +o verification/lab_sea: + - overhaul of the forward model experiments. The main motivation + for this revision is that lab_sea has proven quite fragile (when + changing the sea-ice code, and switching platforms) to a point + when failures were very hard to attribute to specific code problems. + - the suspected reason for this fragility is noise amplification by evp so, + to start with, we decided to replace evp with lsr in the main experiment. + - the input.lsr experiment thus became obsolete and was removed. + - it was replaced with the input.fd experiment that uses an + analytical "free drift" solution as the ice velocity field. + - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp) + will hopefully allow us to discriminate problems due to dynamic solvers + from problems due to the thermodynamic code. input.salt_plume (lsr) allows + us to test additional options, along with the salt plume package. + - Finally a pickup was generated (at the end of a one year run) to + make the tests more representative of an actual model run. Previously + the tests starting point was a 1m thickness of ice everywhere. +o pkg/seaice: + - introducing S\R seaice_freedrift.F that compute the + analytical solution to an approximate ice momentum + equation (i.e. the simple stress/coriolis balance). + - define SEAICE_ALLOW_FREEDRIFT to trigger the computation + of the free drift velocity field, and enable its use. + To actually use the free drift solution as the model ice + velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice. +o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata" + +checkpoint62l (2010/10/04) +o pkg/seaice: + -fix the USE_ORIGINAL_SBI version (for variable freezing point); + -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new + version (with USE_ORIGINAL_SBI undef); +o add hooks for new packages OASIS, the package will follow + (hooks exclude the seaice pkg for now) +o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO + Option to use mdsio_read_whalos.F/mdsio_write_whalos.F, + rather than mdsio_readvector.F/mdsio_writevector.F, within + adread_adwrite.F to read/write adjoint-related tapes to disk. +o eesupp and pkg/mdsio: ALLOW_WHIO + Option to write/read 2D fields to files including tiles halos. + The main purpose is for adjoint related "tape I/O". + The secondary purpose is for debugging phases. + A word on those rather specifically intended purposes. + The code was meant to be stripped down to the bare minimum. + Typically, there is a unique and basic mapping to the global + buffer (tile by tile, then proc by proc, then level by level), and + byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not + meant to generate user friendly outputs of various shapes and forms. + Rather it is intended, for the knowledgeabale developers, + to be largely independent of the many mdsio options, to allow + outputs of tiles+halos in debugging phases and in adjoint runs, + and to allow some flexibility in tuning (adoint) I/O depending on each + file system behavior. With regard to tuning, most of the potential knobs + (to leave files open, to allocate the I/O indep. of usesinglecpuio, + to specify directories, to specify the typical size of I/O calls, etc.) + are not yet included, and will be added if they prove useful. +o pkg/seaice: + fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F +o pkg/seaice: + new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty + code (seaice_budget_ice_if.F) which enable to recover old standard + code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined. + temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F. +o model/src (rStar): + use simple average (not area weighted) of rStarFac at U,V point when using + vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection) + update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20. + +checkpoint62k (2010/09/17) +o adjoint + * changed verification/global_ocean.cs32x15 ; adjoint now tests + Adams-Bashforth 3 + NLFS + RSTAR + * some more modifs required for ECCO-GODAE v4 +o pkg/seaice + add SEAICE_AGE_VOL option to use volume instead of area for + integrating SEAICE_AGE +o model/src: + first check-in of sigma & hybrid-sigma coordinate code ; also includes + non-linear free-surface parts ; but pressure-gradient not yet coded. +o pkg/ptracers: + option for ptracer to convert Salt Relax into additional EmP. + tested in exp. global_ocean.90x40x15.dwnslp (update output) + +checkpoint62j (2010/08/25) +o pkg/ggl90: + other minor changes: remove 3-D temp array gTKE (+ add argument myIter) +o pkg/dic: car_flux.F, phos_flux.F + - reduce number of exp-calls in order to improve performance + - clean up a little (replace fields by their macros, etc., fix + typo in CPP-flag) +o pkg/ggl90: minor changes + - GGL90diffKrS was removed --> always use GGL90diffKr + - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV + - hack of mxlMaxFlag=2 --> ensure mixing between first and second level + (commented out for now) + - change in max/min operations to ensure that smoothing is ok + - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr) + - always use diffKrNrT as background profile (i.e. never use diffKr field) +o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj) +o pkg/dic: + - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better + vectorization + - small bug fix in insol for the unlikely case of a cartesian grid + - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F + + now vectorize, which also removes adjoint recomputations; + + replace integer maksp1 by _RL maskp1 + + replace a**x by exp(x*log(a)) in phos_flux.F for speed + +checkpoint62i (2010/07/21) +o pkg/flt: + - with OBCS: stop floats which enter the OB region +o model/src: + - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones) + for implicit vertical advection. +o pkg/seaice: + - account for melting in seaice age evolution. + - remove double counting of seaice ridging effect on seaice age. + +checkpoint62h (2010/06/18) +o pkg/exch2: + - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1). +o tools/genmake2 + - remove "-pdefault" option: redundant with the use of "packages.conf"; + - remove file pkg/pkg_default : set the default as a pkg group + ("default_pkg_list") defined in pkg/pkg_groups; + - fix for case pkg/pkg_depend is missing (was hanging before); + - add option "-pgroups" to specify a different pkg_groups than the default. +o verification/adjustment.cs-32x32x1: + add a "minimal" set-up test (code_min & input_min) which only compiles + eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc. +o tools/genmake2 + - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg])) + - fix details of checking for mnc & profile pkg when NetCDF is unavailable. +o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these + files are nearly the same anyway. + Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04: + - redefinition of tau(i,i) (by a factor of ustar) + - 1./exf(Const/T) -> exf(-Const/T) (big change in the results) + - replace rhonil by rhoConstFresh in computation of evap (bug fix) + - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results) + - replace + rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh ) + shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j) + by + shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh ) + (changes results) + -> exf_bulkformulae v1.22, + update verification experiments lab_sea, offline_exf_seaice, seaice_obcs + (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13, + output.txt 1.63 + offline_exf_seaice: output.seaicetd.txt 1.7 + seaice_obcs: output.txt 1.10) + Step 2: do the actual merge and remove exf_bulk_largeyeager04.F + -> exf_bulkformulae v1.23, + unfortunately requires updating lab_sea.salt_plume (6 matching digits), + and global_ocean.cs32x15.icedyn (only 11 matching digits) + Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice. +o adjoint of exch-1: + - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list) + (note: was already like this when using EXCH-2) and remove flow dir + and hand-written AD version of high-level EXCH S/R (pkg/autodiff); + - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow); + - update pkg/exch2 diff list. + +checkpoint62g (2010/05/19) +o eesupp/src (exch-1): + - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F) + and remove argument "simulationMode"; same thing for all exch_*rx_cube.F + (renamed to exch1_*rx_cube.F). + - change accordingly exch_*_rx.template and AD version in pkg/autodiff + to call new exch1 S/R ; update Makefile and .cvsignore. + - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove + exch2_xy_rx later) + Note: after updating your code, need to run "make clean" in eesupp/src +o test experiment bottom_ctrl_5x5: + new output_adm.txt with fewer grdchk & less monitor output. +o model/src: + remove the call to ini_cori in initialise_varia.F (just keep the usual one + in initialise_fixed.F). More consistent with coriolis & horizontal grid + beeing treated in the same way (ini_grid is not called a 2nd time). +o pkg/exf: + - rewrite exf_bulk_largeyeager04.F for better vectorization, changes + global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated + - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now) + - cosmetic changes to exf_bulkformulae.F to make it look more like + exf_bulk_largeyeager04.F +o eesupp/src (exch-1): + - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1). + - Separate buffer filling and MPI sending: allow EXCH-1 to work for local + array (non-shared) when using MPI+MTH. Also reduces number of BARRIER + (even without using MPI). + - Message mode: move RecvAck setting (indicator of buffer being ready) + from send_put to recv_get S/R (was useless before, but not sure if + it's much more useful now); + - Switch the order of sync: MPI-proc 1rst and then threads; + - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead. + - fix AD code for communication mode ='get' (but not used). +o model/src: + initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does + not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp). +o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API +o pkg/ctrl: require a specific set of control variables and exf-flags for + adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied) +o model/src: + a) 1rst version of a new driver S/R to turn-off output freq and flags after the + 1rst forward sweep, to avoid over-writing output files during recomputations + recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?) + b) 2nd version: + - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO); + - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast, + writePickupAtEnd) + seaice & ptracers output; + - do not switch off MNC flags (otherwise, won't get admonitor netcdf file) +o model/src: + - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields. +o pkg/exch2: + - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ; + - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch). +o pkg/autodiff & exch2: + process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF + (for now, only if ALLOW_EXCH2 is defined). +o pkg/autodiff: + - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F + (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly. + + clean-up comments (_RS is not always real*4) + - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R) + - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2: + was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs. +o testreport (AD-tests): + no longer link files from dir "../input" (1rst link files from + "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad") + +checkpoint62f (2010/04/29) +o model/src/the_main_loop.F: + adjust store directives for seaice evp and multicategory according to + pkg/ecco/the_main_loop.F +o adjoint: + global_sum_ad was incomplete (noted many times by many people ;) + nice description by Jean U. as follows: + * allreduce(var) in global_sum.F can be interpreted as + reduce(sum) followed by broadcast of sum. + * The adjoint of that is + sum(adjoint) followed by broadcast(summed adjoint value) + or in other words, allreduce(sum, adjoint vars) + We were missing the sum(adjoint)! + Benign, except(!) for "global" scalars appearing in tile loops (bi,bj) + (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset). + The fix should produce 16-digit accuracy between + single-CPU multi-tile (e.g. nSx=2, nPx=1) and + multi-CPU single-tile (e.g. nSx=1, nPx-2) + We'll probably change this yet again shortly +o eesupp/src: + - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?) +o pkg/icefront + - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving + specification of addmass array based on a 2D field, which is added + at bottommost wet level at each horizontal location. +o model/src: + horizontal grid initialisation (other than curvilinear): add code for Exch2 IO + layout; (not always compatible with delX,delY setting; commented out for now). +o pkg/exch2: + change tile to processor setting (case nSy*nPy > 1): allows default model mapping + (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config. + +checkpoint62e (2010/04/15) +o pkg/obcs: + - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert). +o pkg/dic: + -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up; + (note: not presently tested in any forward verification exp.) + update tutorial_global_oce_biogeo AD output file. +o pkg/exf: + - account for the variation of albedo as a function of zenith angle + by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h +o build_options: + - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas" +o pkg/dic: + change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart: + - use binary pickup file for restart; + - initialise atmos-CO2 box from dic_pCO2 parameter; + - fix multi-threaded. +o pkg/rbcs: + - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ; + change (+ fix IO calls) type of array RBC_mask from _RL to _RS. + - add RBCS to exp4 passive tracer 01 (rbcs was previously untested) + and update output.txt +o pkg/kpp: + - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers; + - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS + (= ratio of KPP non-local (salt) flux relative to surface-flux) when + using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat '); + - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file + KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile). +o pkg/offline: + fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor + (bug was added in version 1.10 on 2007-08-23). +o pkg/offline: + - no need to specify periodicExternalForcing, etc ... to use offline pack + - offline input files no longer just single prec --> parameter offlineLoadPrec +o verification/lab_sea: + change AD test to multi-tile setup and update all 4 AD output. + NOTE: while cost function values remain very similar, + gradients are very different, although gradient checks are self-consistent + Should try to get to the bottom of this (cost function summation order?) +o pkg/dic: + in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid + a weakness of TAF that drops part of double precision in log10 derivative. + <= changes removed since problem has been fixed in current TAF version 1.9.71 + update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo. +o pkg/ecco: + add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F + update all 4 lab_sea AD output. + +checkpoint62d (2010/03/22) +o build_options: + remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles. +o remove unbalanced quote (single or double) in commented line of source code + (may cause some warning with some preprocessor/makedepend versions). +o pkg/seaice: + fix seaice_model.F for adjoint (gael) and update AD results of experiments + lab_sea (std + evp + noseaicedyn) and offline_exf_seaice. +o testreport: + add option '-runonly' (short: '-ro') to just do the run part (without make). +o eesupp: remove JAM communication code (obsolete). +o add option to genmake2 & testreport to switch "_RS" type to "real*4" + (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return + to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1 + (update also the output). + +checkpoint62c (2010/03/02) +o tools/build_options : + move (some) old optfiles from build_options/ to build_options/unsupported/ +o model/src and pkg/exf + surface relaxation -- separating data and data.exf options + The point is to ensure that we specify the surface relaxation + either in data or in data.exf (but not half and half) and to + avoid an accidental relaxation to 0 (which happened if a time + scale was specified but the file name was left empty) +o model/src model/inc and pkg/mom_common + ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity + => addition to the viscosity field as computed by others schemes +o tools/build_options: + - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile) + but keep the former optfile for few weeks for smooth transition +o pkg/ecco + - allow user defined cost function contributions + CPP: ALLOW_USERCOST_CONTRIBUTION + USAGE: compute contributions in cost_usercost_all.F + - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. + the two options are complementary. +o pkg/smooth + - migration from contrib to the main repository + +checkpoint62b (2010/01/26) +o pkg/monitor: + - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop + (in case someone forgot to update customized pieces of code) +o nonHydrostatic: + - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested); + - add a simple 2-D experiment (short_surf_wave) to test it. +o pkg/icefront: + adding the shell of, and the hooks to, a new package that + will model melting and freezing of vertical glacier ice fronts +o momentum: + add diagnostics of momentum tendency from Hydrostatic pressure gradient + (without surf.pressure term: would need a 2nd filling since implicit term). +o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace + two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR + cannot deal with the former +o cleaning: + - remove all (except OpenAD) old TLM output from results_ad dirs. + - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R) + - comment out maskH definition (replaced by maskInC) +o pkg/monitor: + - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl + & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs. + +checkpoint62a (2010/01/15) +o model/src: + - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4) +o pkg/diagnostics: + - add optional level number diagnostics (i.e., level number to be define + explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X". + - strictly check for valid parser-code(10) ; + - check if adding diag to the list from the right place. +o pkg/longstep: + - change parameters and fix tracer conservation with rstar/nonlinear free surface +o diagnostics: + - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer + S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics. +o pkg/diagnostics: + - Add option for writing vertical integral (sum of selected levels) of an output + field instead of writing output field levels. Activate this option on a per + output-file basis, by setting the 2nd character of fileflag to 'I'. + - Add field-specific information relative to level integral in 3rd postion + of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate + vertically (x level-thickness x hFac), "r"=same but without hFac. +o do_the_model_io: + - pass end-of-model-run flag as argument, from forward_step to diagnostics_write: + in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before + writing pickups and stopping. +o pkg/diagnostics (for now, only with mdsio): + - write time information to meta file (and modify accordingly rdmds.m) : + time-averaged diagnostics output: write starting and ending time of the + time-averaging interval ; snap-shot diagnostics output remains unchanged; +o pkg/timeave: + - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously + always Nr), now assumed to be equal to number of levels of averaged field; + only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F +o pkg/sbo: + - fix ocean bottom pressure global-average & 2-D time-ave output (was + neither initialised nor filled). + - add starting iteration in suffix of global-average output file + (to avoid over-writing the file after a restart) + - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb). +o time-average: + - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj) + (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf, + ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice) + this fix DIC_COST cumulative-time array (previously: bi,bj,k) + - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice) + - fix missing accumulation for pkg/opps. + - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0) + (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81); + - fix initialisation of time-ave vars and do only full time-step increment + (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81); +o pkg/layers: + - use standard RW pkg S/R to write the output + and remove local write_fld version (which had a problem). + - use simple cumulative-time array (no level index) to fix time-ave S/R calls. + - fix LAYERS_CALC argument list. +o pkg/timeave: + - store cumulative-time in a simple tiled array (drop the level index) + - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array. +o pkg/ocn,aim_compon_interf + - changes for multi-threaded coupled run. (tested with ifort-11 on danton) + +checkpoint62 (2009/12/23) +o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output. + (was not previously tested in any other exp.) +o pkg/monitor: + - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume: + mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one + (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics. + - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F). + - change del2 calculation. + - use interior masks (instead of maskH, <- to be remove). + - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing"). +o mask & obcs: + - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S). + - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F + (called after packages_init_fixed) +o pkg/obcs: + - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once. + Fixes bug in obcs+exf with nSx*nSy.GT.1 + - fix multi-tile handling in obcs balance code +o nonHydrostatic: + - Implement AB-3 for non-hydrostatic vertical momentum ; + (change ordering of var. stored in pickup file when using NH) + - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D. + - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x + (in prep. for new NH free surface form). +o pkg/obcs: + add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe +o model/src: + fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography + +checkpoint61z (2009/12/01) +o nonHydrostatic: + Fix missing vertical flux of vert. momentum near surface (k=1). This fixes + a spurious source of energy in simple baroclinic adjusment test case. + Update all non-hydrostatic exp output. +o model/src (3-d solver): + Change again 3-D solver free-surface RHS term when exactConserv=T: + simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1 + (which was not the case with previous formulation). + To recover previous version, just reset "oldFreeSurfTerm" to previous value. + Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW. +o nonHydrostatic: + - compatible with implicDiv2Dflow < 1 ; + implement implicit factor + for Non-Hydrostatic pressure gradient (similar to implicSurfPress). + - change 3-D solver to work with r* (for now, only with linear free-surf.) + - add few debug diagnostics (cg3d_x, residual) +o model/src: + fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b). + update output of exp. global_ocean.cs32x15.viscA4 +o update output of exp. global_ocean.cs32x15.icedyn after removing + #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h +o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) +o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output + for complex grids, for now only to "state", "adstate", "adexf", "adseaice" +o model: add Christopher Wolfe's implemetation of the single reduction cg2d + (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and + runtime flag useSRCGSolver. Modify verification experiment global_with_exf + to test this code +o pkg/cd_code: + Change defaut D-grid time-stepping to get the same for D-grid momentum as for + C-grid momentum. D-grid velocity used to be stepped forward in time with + Adams-Bashforth only on surface pressure term. Tests show that using AB on + D-grid coriolis term improves stability (as expected from CD-scheme paper). + To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h). + Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2), + lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD), + tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens. + Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2, + global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD. +o pkg/obcs: + - fix bug in initialisation (broken since Oct 1rst modification) + for useOBCSprescribe without useEXF. + +checkpoint61y (2009/11/15) +o pkg/seaice + - change (once again) the discretization for the evp solver: rather than + squaring the averages of strain rates, average the squares to give + a better approximation to VP behavior (in simple test); this breaks + verification experiments that use EVP (lab_sea and lab_sea.hb87) + --> update outputs +o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit) + to improve vectorization of adjoint code on TARGET_NEC_SX +o verification/vermix: + - change vermix to a more "classical" 1d column with high vertical + resolution, seasonal heat flux forcing and constant wind forcing + --> update outputs +o pkg/seaice + - fix diagnostics of principal stress components for EVP + - add optional diagnostics of non-linear convergence for LSOR solver + - make maximum zeta a runtime parameter +o model/src (3-d solver): + Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49), + which consisted in removing the Surf. Non-Hydrostatic pressure from the + whole column and adding it to Eta (inspired from Casualli, 1999): + Only affects 3-D solver initial guess and only if using ExactConserv, + but tests did show a degradation of solver convergence. For this reason, + decide to disable this piece of code. + to recover previous version, just set zeroPsNH = exactConserv (line 78). + Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW +o pkg/ggl90: + - fix previous modif (unfortunatly has not been documented here). +o pkg/seaice/autodiff: + - add CPP flag to include clipping of zeta in EVP code; + although clipping of zeta is not necessary for EVP and not recommended + it was done by default, now clipping is disabled by default + - modify computation and store zetaC/Z in seaice_evp for TAF + - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default) + - change seaice_calc_viscosities/strainrates for better + vectorization after AD by TAF + - rearrange common blocks in SEAICE.h once again for easier dumps of + adjoint output, adjust adcommon.h and g_common.h + - change flux form of default advection scheme for better vectorization + of adjoint code + - modify lab_sea/input.lsr to test the flux form of default advection + scheme +o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level + transition in checkpoint61r) + +checkpoint61x (2009/10/19) +o adjoint: adding two new verification experiments + * tutorial_global_biogeo: an online dic sensitivity experiment + (work with G. Forget) + * tutorial_dic_adjoffline: an offline dic sensitivity experiment + (an update of the Dutkiewicz et al., 2006 paper) + Both use the same CO2FLUX cost function, but different controls + Gradient checks look good, but some recomp. could still be traightened out + Should add xx_dic control variable to test at some point +o model/src: + add run-time parameters to check and/or mask initial Temp & Salt +o pkg/ptracers: + apply zonal filter (if used) to all passive tracers + +checkpoint61w (2009/10/12) +o adjoint: + * update and finish work on adjoint of dic package (G. Forget) + * start adjoint of offline package + * bug fix for cube-sphere TLM code (active_file_g.F) +o tutorial_global_oce_optim: + now tested with 4 tiles (change data.grdchk and update output_adm.txt) + and add SIZE.h_mpi for MPI testing +o pkg autodiff + - fix bug in autodiff_restore + - make genmake2 remove comments and empty lines from ad_input_code.f in + order to reduce file size (new script file remove_comments_sed) +o allows to specify vertical profile of vertical viscosity (viscArNr) +o pkg autodiff + autodiff_ini_model_io: comment out writing of grid information to netcdf + files, because at this time the grid fields are a bunch of zeros + (this is analogous to ini_mnc_vars.F) +o pkg seaice/autodiff: + left-over from removing the 3-time-level fields: + - small rearrangement of common blocks (SEAICE.h) + - fix field declaration in order to get meaningful output in + adseaice.*.nc (adcommon.h) +o pkg obcs: + - go through NH code only if nonHydrostatic=T + - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart) + - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields + => Update output of experiment seaice_obcs + - useOBCSbalance: code is wrong with multi-tile / proc: add a stop. + - fix NH+Orlanski restart (add wvel OBC value in pickup file) + - fix restart for useOBCSprescribe + useEXF +o pkg ctrl + - make obcs as control parameter work also with useSingleCPUio + - replace a few sny and snx by Ny and Nx to be consistent with + ctrl_set_globfld_x/yz.F +o pkg seaice + - re-introduce global field frWtrAtm for the case of + ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F) + - catch the case of an empty filename in seaice_cost_init_fixed.F +o pkg ecco: + - small bug fixes in the_main_loop + . fix order of monitor arguments + . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY + . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so + that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF + - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the + imbalance diagnostics for wmean_h/sflux = 0 + - add actual values to f_obcsn/s/w/e in ecco_cost_final.F + - catch the case of empty filenames in ecco_cost_init_fixed.F + and ecco_readparms.F + - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta) + to make this statement meaningfull in ecco_cost_weights.F +o pkg zonal_filt: + - change ZONAL_FILTER S/R interface (allows to filter 2-D fields) + - when using rStar, filter uVel*hFacW instead of uVel + (tested without topography: fix a Pb of growing instability with NLFS) +o pkg/aim/thsice: + -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F + (works as SST restoring) +o pkg/thsice: + -add specific parameter for salt restoring in slab mixed-layer + (by default equal to the temperature restoring) + +checkpoint61v (2009/09/21) +o pkg/kpp: + -add double diffusive contributions as a hack, turned off by default + for now, and the code can be excluded with a CPP-flag + EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX + -add a verification experiments to "vermix" to test this code +o pkg/mom_common: + Move computation of length scales to mom_init_fixed.F (avoid recomputation + at each time-steps*levels). +o pkg/layers: + Created a new package for computing volume fluxes in temperature or + [not yet implemented] density layers, e.g. for calculating residual + overturning circulations. +o pkg/diagnostics: + implement a RS type version for the set of DIAGNOSTICS-FILL subroutines +o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option) +o pkg/mdsio (& pkg/rw): rework high level S/R interface: + To avoid mixing type (RS/RL) of input/output array argument, + replace single mixed-type array with a pair from each type (RS/RL). +o setting pickupSuff force to start from a pickup (even if nIter0=0): this + is now implemented for all pkgs (previously only done for the main pickup) + +checkpoint61u (2009/08/25) +o pkg/obcs: + - change OB?eta from _RS to _RL and put them into a separate commen block + - add code to read OB?eta from a file via obcs_prescribe_read: the code + compiles and does not destroy any other experiments, the data is read + properly, but the code is not tested in actual applications +o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to + create a meaningful unit attribute for the time coordinate variable +o pkg/ebm: add plenty of missing "_d 0" ; + update results of experiment global_ocean_ebm (fwd + adjoint tests) + Notes: several pieces of code only works for (very) specific set up + (domain size, lat range, etc ...); should be documented & stop if one + of those assumptions is not meet. +o pkg/seaice: add missing "_d 0" in HSNOW initialisation + update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests) + and offline_exf_seaice (seaicetd + adjoint). +o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC): + update results of experiments: lab_sea (4 fwd tests + 3 adjoint), + seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2). +o few changes to pass when compiling with strick checking of arguments + across S/R (allow to find few bugs in S/R calls). +o pkg/seaice: + - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new + 2d-fields, for slightly better performance + +checkpoint61t (2009/07/22) +o pkg/seaice: + - remove unused variables in seaice_evp + - reduce number of SQRT in seaice_evp and seaice_calc_viscosities +o eeset_parms.F, open_copy_data_file.F & ini_parms.F: + named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT): + each processor opens a different file (a fix from Matt). +o cg2d: + use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F : + this reduces number of EXCH calls by 2 when using exch2. + For now, keep previous size array for gc2d_nsa.F to avoid Pb with store + directives and missing simple EXCH (exch_s3d_rx) adjoint code. +o pkg/thsice: + add code for Near Infra-Red albedo (from Jeff) + (turned on with run-time flag: thSIce_calc_albNIR, in data.ice). +o ini_model_io: + move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F + MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F + to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice. + +checkpoint61s (2009/06/30) +o pkg/exch2 (exch2_rxN_cube*): + remove last BARRIER (no need to synchronise after getting data from shared + buffer (get) as long as any change to buffer (put,recv) is between BARRIER) +o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH + and generate new output (for the 2 tests) using default rotationPeriod. +o pkg/exch2: + - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F + (was already the case with AUTODIFF_EXCH2 defined) + - add bj in exch2 arrays and S/R. + - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment + MLAdjust to exch2 (identical results except with MPI -> truncation diff); +o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep + - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY + GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT + - verification experiment natl_box.longstep +o build_options: ifort+mpi_aces optfile (following Constantinos advise): + allow different versions of ifort (8 or 9) and different versions + of mpi (mpich or mpich2) to be used with the same optfile. + requires to load a netcdf module and set MPI_INC_DIR (see comments inside + optfile). Change testing scripts (example_scripts/ACESgrid) accordingly. +o pkg/seaice: + fix previous modif (3-level field removed) for old-pickup reading + +checkpoint61r (2009/06/25) +o pkg/seaice: + - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps: + 1. introduce fields for time step (N-1) + 2. do not use levels 2 and 3 anymore (but keep them) + 3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This + includes changes to pkg/thsice/thsice_get_velocity.F, + model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and + pkg/obcs/obcs_apply_uvice.F. + - completely remove code for leap-frog time stepping for second order + advection + - adjusted adjoint accordingly; + gradient checks have improved by an order of magnitude! + +checkpoint61q (2009/06/22) +o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver + - the boundary conditions along open boundaries are unclear, because the + associated masks are set to zero and are thus treated as closed when + applying the slip-boundary conditions. + - move initialisation of grid variables from seaice_init_varia to _fixed +o adding doc/diags_changes.txt +o model/src: + do_the_model_io: rename few pkg S/R which are called from do_the_model_io, + to avoid "_diags" naming if no relation to pkg/diagnostics. + ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF + file and only call PLOT_FIELD_XYZ if debugMode=T. + remove few PLOT_FIELD_XY calls outside initialisation. + remove few unnecessary BARRIER. +o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling + of salt_plume package in Southern Ocean +o pkg/thsice: + - fix hOceMxL in overlap (needed for sea-ice advection); + update output of experiment global_ocean.cs32x15.icedyn. +o pkg/seaice: + - make the (placeholder-)tracer IceAge a little more meaningful + by avoiding ridging of age due to convergent ice flow + - add diagnostics for surface temperature, atmospheric and oceanic + heat flux, and atmospheric and oceanic ice growth + +checkpoint61p (2009/06/10) +o eesupp (global_max & global_sum): + - add one more element to buffer (start at index 0) for GL_MAX/SUM output; + - remove starting & endding barrier (no longer needed) +o pkg/mdsio, writelocal: + works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined + (remove the STOP): uses shared buffer IO to store data from all threads + and then let master-thread write nThreads tiles. +o pkg/mdsio (read/write field): + - tiled IO done in 1 piece (all levels at a time); + - new header file "MDSIO_BUFF_3D.h" with 3-D buffers. + - multi-threaded: allow to read/write local (non-shared) array + (was already working with singleCpuIO ; now works also without); + => no longer needs barrier call after reading a file (added inside + mds_read/write field). + - move barrier calls outside gather/scatter_2d to mds_read/write_field +o pkg/obcs/exf + - exf_getffieldrec.F: add a few ". _d 0" and + add code to catch the case fldperiod = 0. + - obcs_precribe_read.F: change if statements so that they match + the variable type (_RL) + - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to + exf_iprec) as part of namelist EXF_NML_01 +o pkg/mdsio: + - read/write tiled (local) files: read/write 1-level tile chunk at a time + (instead of segment of length sNx); expected to speed up tiled IO. +o pkg/exch2: + - take buffer copy from/to array out of S/R exch2_send/recv into new + S/R exch2_put/get ; Exch of local variable now works with MPI+MTH + (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h). + - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get) + - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds + (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by + including Topology header file (and common blocks). + - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1); + remove 2nd exch call in exch2_s3d_rx (no longer needed). + - document S/R arg. list (+ update some comments) +o pkg/seaice: + - added SEAICE_CLIM_AIR code, which permits modulation of surface air + temperature and humidity over sea ice based on climatological values. + - clean up computation of Hibler+Bryan (1987) stress coupling for the case + of LSR (this change is expected to change the results slightly because now + it uses slightly difference moduli from the second last LSR solution, but + that is more consistent with the stress computations; this part of the code + is not tested in the verification experiments) + - fix diagnostics for flux of ice in case of B-grid + - turn strain rates eij and press into global fields within global + common block in SEAICE.h for more straighforward diagnostics + - fix diagnostics for principal stress components, press, zeta, eta + to give something meaning full +o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate + new output (all 4 tests) using default rotationPeriod. +o pkg KPP: + - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions + - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1 + and normal grid from 1 to Nr) +o Fix computations of L4rdt in mom_calc_visc.F +o eesupp: + new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg): + should be called before a "stop" if we know that all process are going + to stop; if one Proc does call this S/R, will hang in MPI_FINALISE. + +checkpoint61o (2009/05/26) +o pkg/exch2: change check_depths to issue just a warning (instead of error+stop) +o model/src/ini_curvilinear_grid.F: + compute angleSin/CosC when they are not read from a file +o pkg/seaice: + add pseudo time stepping for LSOR +o pkg/exch2: + temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW +o pkg/seaice: + Adding separate sea ice albedo, drag coefficients, and HO in Southern + Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h +o SingleCpuIO: + fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used. +o pkg/seaice: + put exchanged variable in (local) common block for MPI+Multi-Threads + to work (necessary with exch1, and for now with exch2 too). +o verification: to get more experiments tested with mpi, mth and mpi+mth, + change tiling of: + aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15, + hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope + update output of exp: + exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5), + tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod) + + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU + (note: output.txt generated on faulks using only 1 tile) +o eesupp & mdsio (SingleCpuIO): + - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time + parameter "W2_useE2ioLayOut" (read from file "data.exch2"). + Note: was not effective for globalFile & useSingleCpuIO=F; now fixed. + - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc). + - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same + gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array). +o pkg/exch2: + - new code to set-up W2-Exch2 topology (replace matlab-topology-generator): + read parameter file "data.exch2" if it exists; otherwise try default regular + cube without blank-tile; new header file "W2_EXCH2_SIZE.h"; + - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible + with new code (not to be used, just as a backup solution). + - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2" + in utils/exch2/input. + +checkpoint61n (2009/05/12) o eesupp & mdsio (SingleCpuIO): - move mapping to global io-buffer inside gather_2d/scater_2d: this save memory (1 less 2D global RL array); skip 1 buffer copy; and only send/ @@ -16,7 +2833,7 @@ when using exch2. Add S/R to map global io-buffer to global model array. - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt. -checkpoint61m +checkpoint61m (2009/04/29) o write_utils : change WRITE_1D_R8 to WRITE_1D_RL and add 3 other S/R for other types (R4,R8,RS). Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument. @@ -52,7 +2869,7 @@ and keep the original tile numbering. Note: compatible with old W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files. -checkpoint61l +checkpoint61l (2009/04/07) o Overlaps had been forgotten in calculating ijk keys : fixed o fix cyrus makedepend for gcc 4.4 o experiment fizhi-cs-aqualev20: @@ -100,7 +2917,7 @@ is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS - seaice_growth: replace computation of UG by a simple copy from wspeed -checkpoint61k +checkpoint61k (2009/03/18) o pkg/seaice: a few bug fixes mostly concerning the metric terms: seaice_lsr: fixed a few metric terms, affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs @@ -117,7 +2934,7 @@ updated all relevant verification experiments (except lab_sea//output_adm.txt which was left over, but fails at level 7 & 6) -checkpoint61j +checkpoint61j (2009/03/17) o pkg/seaice: turn a few hard wired parameters into run time parameters o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model time in seconds as promised by the usints in seaice_monitor and exf_monitor @@ -145,7 +2962,7 @@ TAF store directivs "byte" and "kind" seem equivalent; Most tamc.h have been updated correspondingly. -checkpoint61i +checkpoint61i (2009/02/13) o autodiff: fix autodiff_sore/_restore indices for obcs (spotted by I. Hoteit, M. Mazloff) @@ -180,7 +2997,7 @@ o rename thetaMin,phiMin -> xgOrigin,ygOrigin (maintain temporary backward compatibility, until next checkpoint) -checkpoint61h +checkpoint61h (2009/01/27) o pkg/diagnostics with "periodic averaging diagnostics": fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82 @@ -204,7 +3021,7 @@ (drop to 4 digits matching for grad). But this test does not look very reliable (was already failling on eddy, fc5, at 6.digits). Update output. -checkpoint61g +checkpoint61g (2008/12/29) o pkg/flt: - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) + make OPTIONS file more standard. @@ -217,7 +3034,7 @@ o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to a still unfixed compiler/optimization bug -checkpoint61f +checkpoint61f (2008/11/21) o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; update results of global_ocean.cs32x15.icedyn test. o move getcon.F from model/src to pkg/fizhi. @@ -246,7 +3063,7 @@ - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 (generate new output). -checkpoint61e +checkpoint61e (2008/10/23) o gmredi (Visbeck-variable-K): - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h - change computation of Visbeck-K where Slope > Smax : @@ -271,7 +3088,7 @@ scale in ggl90_calc.F (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) -checkpoint61d +checkpoint61d (2008/09/25) o adjoint modifs - adapt to new field rhoInSitu - allow to revert from StoreDynVars2D, StoreDynVars3D @@ -298,7 +3115,7 @@ ini_reference_state.F --> load_ref_files.F (- set anelastic factors) o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) -checkpoint61c +checkpoint61c (2008/08/30) o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" to add mass source/sink of fluid in the interior (3-D generalisation of oceanic real-fresh water flux). @@ -316,7 +3133,7 @@ pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. o new pkg: cheapaml -checkpoint61b +checkpoint61b (2008/08/05) o exch2: change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) - no longer depend on the order sequence (N,S,E,W). @@ -331,7 +3148,7 @@ more intuitive this way) ; rename/remove some variables. - change utils/exch2/matlab-topology-generator & code_mods accordingly. -checkpoint61a +checkpoint61a (2008/07/29) o exch2/matlab-topology-generator: fix bug in index bounds for N-S internal exchange (hard to tell if this had any effect on the solution). @@ -340,7 +3157,7 @@ o testreport: modify syntax of awk, so that it works also with awk, and not only with nawk and gawk -checkpoint61 +checkpoint61 (2008/06/24) o autodiff Change default for TAF usage by removing argument '-nonew_arg' This changes TAF subroutine argument list (ordering of active var.) @@ -351,7 +3168,7 @@ Tested TAF version is 1.9.22 N.B.: exch2 hand-written adjoint code currently not TAMC compatible -checkpoint60 +checkpoint60 (2008/06/19) --->>> This is the last checkpoint for which generating the adjoint --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" --->>> by default. @@ -376,7 +3193,7 @@ The key modifications are in model/src/taueddy_external_forcing.F pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F -checkpoint59r +checkpoint59r (2008/05/29) o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); fix option to read coriolis(@ cell-corner) from files with CS-grid. @@ -407,7 +3224,7 @@ (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) and requires a fortran 90 compiler -checkpoint59q +checkpoint59q (2008/05/06) o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) o Refresh tutorial_global_oce_biogeo, notably: @@ -442,7 +3259,7 @@ - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice -checkpoint59p +checkpoint59p (2008/04/10) o gchem / dic / cfc : - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); - add new parameter files: "data.dic" & "data.cfc" ; @@ -468,7 +3285,7 @@ bottom ; only used with variable horizontal viscosity and non-hydrostatic. also fix diagnostics VISCAHW & VISCA4W. -checkpoint59o +checkpoint59o (2008/03/07) o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). o change the loop ordering in most gad_*_adv_x.F to improve vectorization: move a few statemens out the main loop into separate loops @@ -509,7 +3326,7 @@ introducing a generic routine (ctrl_map_ini_gen.F). - Modification of ctrl_bound/adctrl_bound handling control vector bounds. -checkpoint59n +checkpoint59n (2008/02/09) o pkg/diagnostics: for large number of diagnostics, store diagnostic mate number in dedicate array "hdiag": - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST @@ -563,7 +3380,7 @@ for now this is only available for the C-grid code and also within #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code -checkpoint59m +checkpoint59m (2008/01/14) o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature o gad_som : fix flux output (& diagnostics) to have same units as other @@ -581,7 +3398,7 @@ o pkg/salt_plume: added various options for salt plume depth criterion and for vertical distribution of the salt -checkpoint59l +checkpoint59l (2007/12/18) o pkg/ptracers: new version of ptracers pickup: read meta file and write only fields which are needed to restart. ( same logic as main pickup file ; also using pickupStrictlyMatch ) @@ -603,7 +3420,7 @@ o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL or U/VICE from U/VWIND before computing U/VSTRESS -checkpoint59k +checkpoint59k (2007/11/30) o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. o fix un-initialised variable problem (in mom_vecinv & shap_filt): @@ -625,7 +3442,7 @@ use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). to-do: fix pkg/diagnostics when large number of diagnostics are defined. -checkpoint59j +checkpoint59j (2007/11/09) o in pkgs: dic, obcs, offline, rbcs: standard way to compute coeff. for time interpolation between 2 time reccords which retains full precision (& make results less dependent on compiler). @@ -668,7 +3485,7 @@ o added open boundary conditions capability for seaice HSNOW, HSALT, UICE, and VICE -checkpoint59i +checkpoint59i (2007/10/21) o adjoint: * fix multiDimAdvection adjoint (partial recomputation problem by TAF for fVerT(:,:,kDown) @@ -709,7 +3526,7 @@ Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). -checkpoint59h +checkpoint59h (2007/09/29) o pkg/exf: - improve vectorization by moving if-statement out of loops in exf_mapfields, exf_radiation @@ -742,7 +3559,7 @@ o testreport: change AD testing : check against results/output_adm.txt using same scripts as for forward test. -checkpoint59g +checkpoint59g (2007/09/17) o adjoint testing: in preparation for changing testreport: - output format: cost and grad written on separated lines - ad output results in directory "results" (instead of "results_ad") @@ -787,7 +3604,7 @@ global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. -checkpoint59f +checkpoint59f (2007/08/21) o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) o pkg/ctrl: ctrl_bound forces parameter corrections to stay in a bounded range (in forward mode) @@ -818,7 +3635,7 @@ o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update output of global_ocean.cs32x15.thsice . -checkpoint59e +checkpoint59e (2007/07/26) o exch2: new S/R that only use the cube-tracer (center-position) exchange: for B-grid vector (not yet tested) and C-grid vector (<- only used when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). @@ -848,7 +3665,7 @@ * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option * applied OBCS T/S mask to HEFFM sea ice mask -checkpoint59d +checkpoint59d (2007/06/21) o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array for {PKG} state variables, and called from DO_STATEVARS_DIAGS. (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) @@ -894,7 +3711,7 @@ It is turned off by default (=-1.), because it changes the results. - make it possible to read AREA from a file, too. -checkpoint59c +checkpoint59c (2007/06/04) o add S/R and diagnostics for oceanic mixed-layer depth o move GMRedi call after all vertical mixing schemes (including KPP) o pkg/thsice: @@ -927,7 +3744,7 @@ Storing is now bundled into large arrays to optimized I/O (and second step in cleanup of the_main_loop) -checkpoint59b +checkpoint59b (2007/05/16) o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): - export/import (between ocean & coupler) fields needed for ocean DIC. o pkg/seaice: @@ -998,7 +3815,7 @@ o OpenAD - changed verification/OpenAD to full baroclinic setup (including GM/Redi) -checkpoint59a +checkpoint59a (2007/05/01) o pkg/seaice: some parameter clarifications and a little bit of clean up o pkg/thsice: rename run-time parameters: himin -> hIceMin @@ -1040,7 +3857,7 @@ o pkg/kpp: add code to have mixing in shelf ice caverns - add myThid to all kpp routines (long overdue) -checkpoint59 +checkpoint59 (2007/04/19) o pkg/exf: - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND & ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid @@ -1066,7 +3883,7 @@ - 2nd set of modifs for thsice adjoint in conjunction with exf o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.) -checkpoint58y_post +checkpoint58y_post (2007/04/15) o Added capability for latitudinal dependence of Bryan and Lewis, 1979 vertical diffusivity, similar to that in MOM4; turned on using #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using @@ -1082,7 +3899,7 @@ - better when using non-linear advection scheme (not yet fully tested) - can also be used in atmospheric set-up (for now, only the diffusion). -checkpoint58x_post +checkpoint58x_post (2007/04/04) o IO option for global-file compact format: - add options when generating topology (utils/exch2/matlab-topology-generator) - add I/O capability (pkg/mdsio). @@ -1090,7 +3907,7 @@ for now long-line format not yet supported by pkg/mdsio (& exch2). o shelfice: add a few diagnostics -checkpoint58w_post +checkpoint58w_post (2007/03/13) o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref (and replace horiVertRatio in NH code). @@ -1111,7 +3928,7 @@ o move call to cal_readparms up to make calendar parameters/variable available to all packages -checkpoint58v_post +checkpoint58v_post (2007/02/08) o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get useDynP_inEos_Zc tested. o pkg/exf: changes to properly interpolate/mask/scale initial fields @@ -1130,7 +3947,7 @@ - use this scheme for temperature & salinity in 2 advection test exp.: advect_xy & advect_xz, respectively. -checkpoint58u_post +checkpoint58u_post (2007/01/12) o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. o testreport: add option "-skipdir" to skip some test. @@ -1145,7 +3962,7 @@ o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine o pkg/thsice: fix reading mnc-pickups -checkpoint58t_post +checkpoint58t_post (2006/12/30) o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) o pkg/mdsio: - clean-up mdsio_readfield.F & mdsio_writefield_new.F and @@ -1188,7 +4005,7 @@ - introduce a few local fields to avoid modifying external fields such as atemp, etc. -checkpoint58s_post +checkpoint58s_post (2006/12/11) o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F changed exf_set_gen.F so that genperiod=0 means input file is one time-constant field and @@ -1222,7 +4039,7 @@ as actual snow thickness. It now refers everywhere to effective snow thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. -checkpoint58r_post +checkpoint58r_post (2006/11/17) o modifications to pkg/seaice/growth.F, which change results of lab_sea experiment: fixes pertain to melting snow over open water, to masking EVAP under sea ice, and to using the correct AREA variable for @@ -1246,7 +4063,7 @@ o ctrl: adding new control variables: lwflux, lwdown, evap, snowprecip, apressure, runoff -checkpoint58q_post +checkpoint58q_post (2006/10/20) o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up 1/6-deg Southern Ocean configuration by 8% on IBM Datastar and high_res_cube configuration by 4% on Columbia. @@ -1257,7 +4074,7 @@ single CPU io) so that TAF does not have to see EESUPPORT.h o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) -checkpoint58p_post +checkpoint58p_post (2006/09/08) o obcs: stop if obcs is used with useCDscheme = .true. o shelfice: - fix a sign error so that no slip at shelfice interface works @@ -1268,7 +4085,7 @@ o added adjoint exch routined for all exch*3d* routines and updated flow directives -checkpoint58o_post +checkpoint58o_post (2006/08/28) o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; remove old subroutines (_XY_ & _XYZ_); update the adjoint version. o change controling S/R for writing pickup file (new S/R do_write_pickup) @@ -1282,7 +4099,7 @@ - add a simple boundary layer scheme to reduce noise - fix the indexing in shelfice_u/v_drag so that there will be actually drag -checkpoint58n_post +checkpoint58n_post (2006/08/14) o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to local variable (not in common block). o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. @@ -1303,7 +4120,7 @@ and stop cleanly when MAX_NO_THREADS is too small. o add S/R BAR_CHECK to check multi-threaded barrier synchronization -checkpoint58m_post +checkpoint58m_post (2006/07/17) o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. @@ -1329,7 +4146,7 @@ update rotating_tank results, but not plume_on_slope (affected at truncation level, 11 digits). -checkpoint58l_post +checkpoint58l_post (2006/07/12) o calc_gw: - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V - remove side-drag for now (need to fix it); update plume_on_slope results. @@ -1347,7 +4164,7 @@ o pkg/rbcs * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing -checkpoint58k_post +checkpoint58k_post (2006/07/06) o testreport: - always build in dir. "build" (if not there, mkdir build instead of building & running in input) @@ -1380,7 +4197,7 @@ advection subroutine (but still not used within DST advection S/R) o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) -checkpoint58j_post +checkpoint58j_post (2006/06/15) o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields from file (collects calls previously in FORWARD_STEP) o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS @@ -1388,7 +4205,7 @@ o genmake2 replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. -checkpoint58i_post +checkpoint58i_post (2006/06/14) o pkg/seaice: add parameter that allows to scale/turn off effect of seaice on wind stress (SEAICEstressFactor defaults to 1.) o Total number of Timers is finite (<=40): comment out 2 non-essential one @@ -1402,7 +4219,7 @@ non-EVP pickup files when using SEAICEuseEVP - fix sign error in diffusion in seaice_calc_rhs -checkpoint58h_post +checkpoint58h_post (2006/06/07) * Modifications for bottom topography control o replace hFacC by _hFacC at various places o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL @@ -1412,7 +4229,7 @@ o works for 5x5 box, doesnt work for global_ocean.90x40x15 * Adding verification for 5x5 box (4-layer) bottom topography control -checkpoint58g_post +checkpoint58g_post (2006/06/07) o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., used for mean seasonal cycle, mean diurnal cycle); add an example in verification/global_ocean.cs32x15/input.thsice/data.diagnostics @@ -1428,7 +4245,7 @@ o pkg/seaice - make (default) second order advection a bit less confusing? -checkpoint58f_post +checkpoint58f_post (2006/06/05) o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice to pkg/seaice): - new routines thsice_map_exf and thsice_get_exf provide the interface @@ -1459,7 +4276,7 @@ o results_ad : rename "output.txt_adm" to "output_adm.txt" and change testreport accordingly -checkpoint58e_post +checkpoint58e_post (2006/05/17) o SEAICE_CGRID adjoint done o R_STAR adjoint implemented. * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) @@ -1467,7 +4284,7 @@ o Make pkg/profile fully independent of ecco,cost, etc. stuff to be able to use it in pure forward. -checkpoint58d_post +checkpoint58d_post (2006/04/21) o upgrade simple test-experiment to tutorial example: step.1: duplicate the experiment and (step.2) will remove the old copy. tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) @@ -1507,7 +4324,7 @@ o Benign bug fix in initialization (spotted by M. Mazloff) of ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F -checkpoint58c_post +checkpoint58c_post (2006/03/23) o adjoint: finish NLFS adjoint and provide reference output in verification/global_ocean.90x40x15/results_ad_nlfs o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the @@ -1541,7 +4358,7 @@ + move computation of the viscosities eta and zeta into a new separate routine (because I need to recompute them in seaice_ocean_stress.F) -checkpoint58b_post +checkpoint58b_post (2006/03/13) o AIM+thSIce: fix sign of Short-Wave through the Ice ; update output.txt of exp. aim.5l_cs.thSI o various mnc cleanups and improvements: @@ -1604,7 +4421,7 @@ (turn on with SEAICEuseFluxForm) - replace 1 in 3d global fields by kSurface in growth.F -checkpoint58a_post +checkpoint58a_post (2006/02/13) o seaice: - bug fix in advect.F o shelfice: @@ -1657,7 +4474,7 @@ and parameters (note: calcWindStress replaces .NOT.readwindstress). - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). -checkpoint58 +checkpoint58 (2006/01/12) o add "--embed-source" option to genmake2 which, when the supporting tools can be compiled (as determined by genmake2) will turn on the embed_files package which then embeds the entire MITgcm source code @@ -1670,7 +4487,7 @@ * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) * Thanks to Tom Haine for testing! -checkpoint57z_post +checkpoint57z_post (2005/12/31) o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): affects output (@ truncation level) of exp. plume_on_slope ; updated. o fix the pickup behavior for obcs in combination with ptracers @@ -1701,13 +4518,13 @@ * Absolute scale somewhat unclear so far * no area weighting was included since no other cost term does so far -checkpoint57y_post +checkpoint57y_post (2005/12/08) First step for a NLFS adjoint o initially suppress rStar (new flag DISABLE_RSTAR_CODE) o new init. routines for calc_r_star, calc_surf_dr o still need to deal with ini_masks_etc o testreport seemed happy -checkpoint57y_pre +checkpoint57y_pre (2005/12/08) o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) @@ -1716,7 +4533,7 @@ o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should be in GCHEM_OPTIONS). -checkpoint57x_post +checkpoint57x_post (2005/12/04) o fix testreport Pb in multiple test experiment. o cleanup our namelist syntax in verification: - make it more F95 standards compliant (some work still needed) @@ -1736,7 +4553,7 @@ (there are a number of extensive recomputations) * Initialize certain variables needed for adjoint -checkpoint57w_post +checkpoint57w_post (2005/11/03) o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names fix the singleCpuIO RS version of MDSWRITEFIELD and add a WARNING if using globalFiles=T with multi-processors. @@ -1753,7 +4570,7 @@ ptracers in a large domain with a constant non-zero value. Also, untangle ptracers_init.F a little. -checkpoint57v_post +checkpoint57v_post (2005/10/13) o change dome exp. to use variable viscosity in side-drag terms. o remove all the files from the cfc_offline test since they are now incorporated into tutorial_cfc_offline which has been producing @@ -1794,7 +4611,7 @@ o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ truncation level) 4/5 MLAdjust test results (11&12 digits match). -checkpoint57t_post +checkpoint57t_post (2005/10/03) o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get same truncation, independent of the face number: affects affects several @@ -1817,7 +4634,7 @@ Suggested values of viscosity parameters found in mom_calc_visc. Many new viscosity diagnostics available. -checkpoint57s_post +checkpoint57s_post (2005/09/20) o Add clearing-house for viscosity calculations, mom_calc_visc and correct numerous bugs in LeithD and Smagorinsky discretizations. mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be @@ -1843,7 +4660,7 @@ and works with both EXCH1 and EXCH2 (but needs more testing) - writing works for all verification test cases w/ g77 on Linux -checkpoint57r_post +checkpoint57r_post (2005/09/07) o make MNC variable initialization happen earlier o add diagnostics for (almost) each term of the momentum Eq. o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. @@ -1863,7 +4680,7 @@ o natl_box_adjoint input_seaice for Lab. Sea now available online via wget (see README file) -checkpoint57q_post +checkpoint57q_post (2005/08/19) o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) o fix annoying months-old bug in mnc/mdsio output for seaice pkg - bug was reported by Jean-Michel and Ian Fenty @@ -1880,7 +4697,7 @@ * verification/OpenAD/code/ has necessary scripts and description; * converts, compiles and runs successfully; -checkpoint57p_post +checkpoint57p_post (2005/08/01) o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED (already the case for some pkgs, including recent MNC_init, e.g. thsice) @@ -1894,7 +4711,7 @@ global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). -checkpoint57o_post +checkpoint57o_post (2005/07/30) o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and (2) its ready to be documented during the 20050801 DocFest o MNC-ify the gmredi package -- tested and works w/ and w/o mnc @@ -1903,7 +4720,7 @@ in global1x1_tot/code_seaice_adj to access indices 32, 33 (worth another tag) -checkpoint57n_post +checkpoint57n_post (2005/07/29) o adding precip control xx_precip 32 o adding swflux control xx_swflux 33 o Replacing 10 forcing penalty cost routines by 1 generic. @@ -1919,13 +4736,13 @@ (applies in particular to tapelev I/O) o removed inefficient K-loop in all active_file*control*.F -checkpoint57m_post +checkpoint57m_post (2005/07/28) o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) and advect_cs (use EXCH-2 and standard cs-32 grid files). o pkg/exch2: filling of face-corner halo regions is optional (ifdef W2_FILL_NULL_REGIONS) and is turned off by default. -checkpoint57l_post +checkpoint57l_post (2005/07/14) tag before updating tutorials (pre-release-2) o add cos & sin of grid-direction orientation angle (curvilinear grid only, for output and interpolation of input fields onto model grid) @@ -1937,11 +4754,11 @@ o add mnc output capability to diagnostics/diagstat and update our cvsignore files for the ACSII output generated -checkpoint57k_post +checkpoint57k_post (2005/07/02) o lab_sea now uses diagnostics package and provides a suite of new EXF diagnostics output. -checkpoint57j_post +checkpoint57j_post (2005/06/30) o exf * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); @@ -1971,7 +4788,7 @@ o fix few little things to avoid floating error with -ftrapuv (ifort v9) (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) -checkpoint57i_post +checkpoint57i_post (2005/06/19) o Diagnostics package was changed: diagnostic allocation is now deactivated by setting an empty file name in the namelist (used to be by setting 0 frequency) o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; @@ -1990,7 +4807,7 @@ tested against monitor output (including land & thSIce) on various exp. o make seaice-pkg I/O type flags (MNC/MDS) more standard. -checkpoint57h_done +checkpoint57h_done (2005/05/19) tag after changing user customized files (DIAGNOSTICS_SIZE.h, data.diagnostics, data.gchem, data.ptracers) is done. @@ -1999,11 +4816,11 @@ o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE and rename it: DIFFERENT_MULTIPLE -checkpoint57h_post +checkpoint57h_post (2005/05/14) o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers o pkg/diagnostics: change output frequency, now in seconds (instead of Nb of iterations). This requires to change data.diagnostics. -checkpoint57h_pre +checkpoint57h_pre (2005/05/12) o in mnc, let the user create the output dir if both mnc_outdir_date and mnc_outdir_num are false @@ -2017,11 +4834,11 @@ o fix mnc flags in pkg/seaice so that they are "owned" by seaice, not mnc -- this mistake was found by JMC and is now corrected -checkpoint57g_post +checkpoint57g_post (2005/04/15) o add Adams-Bashforth 3rd Order time stepping: - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... -checkpoint57g_pre +checkpoint57g_pre (2005/04/15) o make lambda[Theta,Salt]ClimRelax spatially varying (default remains spatially uniform constant based on tau) @@ -2031,12 +4848,12 @@ o separate masks used for ctrl_pack/unpack 'from write_grid' output (suggested by G. Forget) -checkpoint57f_post +checkpoint57f_post (2005/04/06) o add parameter "baseTime" = model base time = time at iteration zero new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to account for baseTime shift o move Coriolis arrays from PARAMS.h to GRID.h -checkpoint57f_pre +checkpoint57f_pre (2005/04/06) o mnc-ifying the seaice package o introduced an alternative length scale calculation for use in the limiting @@ -2057,7 +4874,7 @@ * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 * mom_vi_hdissip: to be able to use Leith scheme in adjoint -checkpoint57e_post +checkpoint57e_post (2005/02/28) o Adding eddy stress controls a la Ferreira et al. checkpoint57e_pre (actually was tagged: eckpoint57e_pre) @@ -2075,7 +4892,7 @@ o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) -checkpoint57d_post +checkpoint57d_post (2005/02/11) o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing o modify verification/ideal_2D_oce so that it tests the creation of mnc output from the diagnostics package @@ -2097,10 +4914,10 @@ (note: still needs some work specially for snap-shot diagnostics) duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z -checkpoint57c_post +checkpoint57c_post (2005/01/27) o Change testing option (-ieee) to get closer agreement between g77 & ifort o generate new output.txt files on faulks with g77 & the new -ieee option -checkpoint57c_pre +checkpoint57c_pre (2005/01/27) o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); update output.txt of exp. global_ocean.90x40x15 @@ -2133,7 +4950,7 @@ * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F * N.B.: leave tiled I/O for tapelev (i.e. mds...vector) -checkpoint57b_post +checkpoint57b_post (2004/12/20) o simplify options in diagnostics_fill arguments (remove weird combinations) o fix MNC coordinate variables so that they now contain per-face index values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in @@ -2179,16 +4996,16 @@ look through the short list of active diag. (instead of the long list) create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active -checkpoint57a_post +checkpoint57a_post (2004/12/10) o this set of changes restores TAMC compatibility tested for global_ocean.90x40x15 adjoint on trough (what a pain) -checkpoint57a_pre +checkpoint57a_pre (2004/12/10) o some modifs in tools/build_options for sunos o call ctrl_pack for ctrl at end for optimcycle=0 -checkpoint57 +checkpoint57 (2004/12/09) o add horizontal bi-harmonic viscosity for vertical velocity - new parameter viscA4W (defaults to viscA4) - affects only non-hydrostatic code @@ -2206,7 +5023,7 @@ o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) (theta2, salt2 in ecco_cost_weights) -checkpoint56c_post +checkpoint56c_post (2004/12/03) o OBCS as control variables - update ctrl_ad_diff.list, obcs_ad_diff.list - remove balance of obcs controls from default @@ -2224,7 +5041,7 @@ o mdsio: - i/o-vector change debugLevel from debLevA to debLevB -checkpoint56b_post +checkpoint56b_post (2004/12/01) o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that is called from DO_THE_MODEL_IO - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE @@ -2239,7 +5056,7 @@ testreport. o ptracers_monitor: bug fix for MPI -checkpoint56a_post +checkpoint56a_post (2004/11/28) o GCHEM: finish reorganizating the package - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency (introduces another 3D-array for each passive tracer, but only if @@ -2284,7 +5101,7 @@ - cleaning up o small cleaning of exch2: remove files that are also in eesupp/src -checkpoint56 +checkpoint56 (2004/11/17) o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 o mnc: cleanup "full" files--fixes out-of-memory problem o ECCO-GODAE @@ -2314,7 +5131,7 @@ o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] from sign change -checkpoint55j_post +checkpoint55j_post (2004/11/10) o isolate dissipation tendency (allow to keep it out off AB) in V.I form. affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) o add consistent build directories and .cvsignore files to verification @@ -2325,7 +5142,7 @@ o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) -checkpoint55i_post +checkpoint55i_post (2004/10/28) o change arrays for total vertical diffusivity (2.D if explicit, 3.D if implicit) ; each ptracer uses its own background value. o added mnc/NetCDF output capability to ocn_compon_interf @@ -2340,7 +5157,7 @@ o Compute the non-local term using either KPP vertical diffusivity (=default) or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) -checkpoint55h_post +checkpoint55h_post (2004/10/20) o add verification test "vermix" o remove all the *_ioinc flags and replace with the single global outputTypesInclusive flag @@ -2348,7 +5165,7 @@ o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS o useMNC moved from data.mnc to data.pkg -checkpoint55g_post +checkpoint55g_post (2004/10/14) o Renaming carbon AD experiments to comply with testreport conventions o Updating adjoint of Held-Suarez hs94.1x64x5 o Fixing directives for non-ECCO forward_step, after ECCO directives @@ -2358,10 +5175,10 @@ o Updating adjoint output for natl_box_adjoint after pkg/ecco has been modified (see taga c55d_post) -checkpoint55f_post +checkpoint55f_post (2004/10/13) o rename to timeave_init_fixed -checkpoint55e_post +checkpoint55e_post (2004/10/13) o some delicate re-shuffle of store directives to avoid one extra call of do_oceanic_physics affects ecco_the_main_loop.F, do_oceanic_physics.F @@ -2369,14 +5186,14 @@ o NB: this may break global_ocean adjoint temporarily, but it is clear how to fix it. Will do later, need this now. -checkpoint55d_post +checkpoint55d_post (2004/10/11) o ECCO specific cost function terms (up-to-date with 1x1 runs) o ecco_cost_weights is modified to 1x1 runs o modifs to allow observations to be read in as single file or yearly files o enable to read exf forcing fields as either single file or yearly files (flag useExfYearlyFields) -checkpoint55d_pre +checkpoint55d_pre (2004/10/08) o switch between 2-level and 3-level checkpointing o add ability of MNC to write local and "partial" (eg. 2D slices where @@ -2424,7 +5241,7 @@ - changed argument list of OBCS_CALC to myTime+deltaTclock - fixed about 35 bugs in obcs_external_fields_load -checkpoint55c_post +checkpoint55c_post (2004/09/23) o obcs stuff - new runtime flags useOBCSprescribe, useOBCSbalance - re-arranged obcs_calc @@ -2438,7 +5255,7 @@ o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments which simplifies the calls and passes the ifc check-bounds test -checkpoint55b_post +checkpoint55b_post (2004/09/22) o add a 2D scalar, Z location, exchange_2 routine. o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] @@ -2449,7 +5266,7 @@ o fix gad_advection.F (CubedSphere part), back to version 1.23 o fix bug in mom_vi_del2uv.F (CubedSphere part). -checkpoint55a_post +checkpoint55a_post (2004/09/20) o merged code to * prescribe/read time-dependent open boundaries (works in conjunction with exf, cal) @@ -2457,7 +5274,7 @@ * each boundary N/S/E/W now has its own CPP option (healthy for the adjoint) -checkpoint55 +checkpoint55 (2004/09/17) o up-to-date adjoint of previous breaks - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix - global_ocean_ebm: adjoint still needs fix (TLM ok) @@ -2467,7 +5284,7 @@ o remove all tr1-related code (ALLOW_PASSIVE_TRACER) (adjoint stuff still has some tr1 'names', but all use ptracer arrays) -checkpoint54f_post +checkpoint54f_post (2004/09/16) o in verification/carbin/ remove experiment related to ALLOW_PASSIVE_TRACER (array tr1 etc) code_ad/ input_ad/ results_ad @@ -2493,7 +5310,7 @@ - numerous small formatting cleanups for ProTeX o add version info (via BUILD_INFO.h) to MNC and stdout -checkpoint54e_post +checkpoint54e_post (2004/09/02) o add two new packages - pp81 (Packanowski and Philander, 1981), Richardson number and stratification dependent mixing @@ -2507,7 +5324,7 @@ o genmake2: add ability to search for C compilers and cleanup test output - fixes recent SX-6 problems and should help with others (eg. HP-UX) -checkpoint54d_post +checkpoint54d_post (2004/07/27) o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, leading to additional shift by 5 days each year of integration @@ -2523,7 +5340,7 @@ o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) -checkpoint54c_post +checkpoint54c_post (2004/07/18) o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr this affects (truncation error) output.txt of test-exp: global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box @@ -2534,7 +5351,7 @@ o start to test mnc routinely in exp0 o add sea-ice loading (sIceLoad) as a new forcing field. -checkpoint54b_post +checkpoint54b_post (2004/07/08) o add testreport "-j JOBS" option for parallel builds (tested and pretty impressive on Altix and Opteron systems) o diagnostics can now write NetCDF files through the mnc package @@ -2544,19 +5361,19 @@ affects (truncation error) output of lab_sea & natl_box exp.: updated o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) -checkpoint54a_post +checkpoint54a_post (2004/07/06) o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) + internal_wave (shift in writing cg2d_ini_res) -checkpoint54a_pre +checkpoint54a_pre (2004/07/05) o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice - modified verification/lab_sea and natl_box_adjoint accordingly -checkpoint54 -checkpoint53g_post +checkpoint54 (2004/07/02) +checkpoint53g_post (2004/07/02) o prepare splitting of thermodynamics: store convect.counter in common block o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave @@ -2565,7 +5382,7 @@ o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) o restore adjointability -checkpoint53f_post +checkpoint53f_post (2004/06/25) o modifications that affect AIM experiment results (update output.txt): - no advection of S at top interface Nr (pkg/generic_advdiff) - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) @@ -2578,7 +5395,7 @@ o added rotating_tank experiment checkpoint53e_pre -checkpoint53d_post +checkpoint53d_post (2004/06/14) o faulks upgraded: re-generate output.txt that have changed: global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box o Added Bryan and Lewis, 1979, vertical diffusivity profile @@ -2597,9 +5414,9 @@ o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation of mom_common/ - simple re-arrangement of instructions within computing loop -checkpoint53d_pre +checkpoint53d_pre (2004/05/21) -checkpoint53c_post +checkpoint53c_post (2004/05/21) o new version of coupler for AIM+thSIce and Ocean models - new fields (SSS,h_MixLayer ...) are exchanged through the coupler - land: change Evaporation of snow @@ -2616,7 +5433,7 @@ * TLM OK * ADM not sufficient accuracy yet (needs further testing) -checkpoint53b_post +checkpoint53b_post (2004/05/14) o Commiting new energy balance model to repository * package is pkg/ebm * verif. is verification/global_ocean_ebm @@ -2634,7 +5451,7 @@ C by atmospheric eddy transports. C J. Climate 7(12), 1870-1882 o Will need long integration testing. -checkpoint53b_pre +checkpoint53b_pre (2004/05/14) o created pkg/mom_common in preparation for variable viscosity code o renamed and split ini_mnc_io @@ -2642,7 +5459,7 @@ o AIM using land: soil wetness availability account for snow o added printMapIncludesZeros to EEPARMS namelist -checkpoint53a_post +checkpoint53a_post (2004/05/11) o restore TAMC compatiility for exf_constants.h (no usage of _d in .h) o Additional storing in KPP in an attempt to fix @@ -2655,7 +5472,7 @@ and hence gives results closer to that of Experiment 2. Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. -checkpoint53 +checkpoint53 (2004/05/06) o stable checkpoint with up to date adjoint TLM tests only run for 1st grdchk at the moment. Its unclear if this is a code problem or a problem with resetting code for g_ @@ -2665,7 +5482,7 @@ o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) are both still in chaos following their security messes. -checkpoint52n_post +checkpoint52n_post (2004/05/06) o various build (mostly genmake2) changes including: - ability to build/run more easily within Cygwin and MacOS X - more complicated Makefiles with a stronger dependence on Gnu Make @@ -2696,7 +5513,7 @@ - maintain snow precipitation unchanged (even if Tsf >=0). both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice -checkpoint52m_post +checkpoint52m_post (2004/04/18) o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; this does not change any of the results, because myIter=0 in swfrac always lead to jwtype=2 (the default anyway), but the call makes little sense @@ -2728,7 +5545,7 @@ o Added functionality to grdchk: pick global i,j,k position (or nearest wet) where to perform check. -checkpoint52l_post +checkpoint52l_post (2004/03/11) o new land formulation: a) use ground enthalpy as prognostic variable to ensure exact energy conservation. @@ -2739,7 +5556,7 @@ a) Treat separately land / ocean / sea-ice surface fluxes to allow implicit computation of land & sea-ice surface temp. b) add snow precipitation. -checkpoint52l_pre +checkpoint52l_pre (2004/03/11) o fix problem (when 1 tile is empty) in min/max monitor. o fix bug in timeAve (u,vZetatave in common block) @@ -2752,7 +5569,7 @@ o aim.5l_cs: modify sea-ice fraction input file ; update output o exf: Adding simple range check routine for exf fields after read -checkpoint52k_post +checkpoint52k_post (2004/02/23) o removed top-level directory "diags" - we migrated these functions to pkg/timeave a long time ago o fixed bug introduced in pkg/monitor @@ -2765,7 +5582,7 @@ taveFreq, dumpFreq, pChkptFreq o MAIN and ECCO differentiability restored -checkpoint52j_post +checkpoint52j_post (2004/02/18) o fix nchklev in tamc.h for global_ocean... o Bringing flow and store directives up-to-date o Really weird thing! @@ -2773,7 +5590,7 @@ starttime, niter0, instead of mytime, myiter, screws up the adjoint: TAF places a faulty re-call of initialise_varia after cost_final call which should not be there! -checkpoint52j_pre +checkpoint52j_pre (2004/02/03) o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and error messages @@ -2790,15 +5607,15 @@ mon_vort3.F to make exch2 friendly with >1 tile per cube face o limit timeave output for hi-res integrations -checkpoint52i_post +checkpoint52i_post (2004/01/21) o removed CPP_EEOPTIONS.h from verification/*/code o updated the tiling for global_ocean_pressure -checkpoint52i_pre +checkpoint52i_pre (2004/01/20) o update aim.5l_LatLon using the standard aim_v23 pkg (instead of the old pkg/aim). -checkpoint52h_pre +checkpoint52h_pre (2004/01/20) o shortened offending lines in exch2_send_rx?.template o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator o genmake2: add build & execute test for NetCDF code @@ -2809,13 +5626,13 @@ metric terms are ignored and it is assumed that there is no sea-ice on cube faces 1, 2, 4, and 5. -checkpoint52f_post +checkpoint52f_post (2004/01/09) o added exch2 cube routines to pkg/exch2 o modified hs94.cs-32x32x5 to use it o added new grid files to hs94.cs-32x32x5 -checkpoint52f_pre +checkpoint52f_pre (2004/01/07) -checkpoint52e_post +checkpoint52e_post (2004/01/07) o first attempt to solve vertical advection (momemtum & T,S) Implicitly for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) @@ -2823,7 +5640,7 @@ o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. o update output (gad_calc_rhs.F changes affect truncation error) of exp: front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box -checkpoint52e_pre +checkpoint52e_pre (2004/01/02) o fix bug in impldiff when Nr=1 or Nr=2. o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt @@ -2834,7 +5651,7 @@ o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations -checkpoint52d_post +checkpoint52d_post (2003/12/16) o re-tiled many expts to allow comparison in multi-processor mode - updated output accordingly - changed hs94.128x64x5 to use intial T from file rather than use the @@ -2863,11 +5680,11 @@ o new verification experiment, cpl_aim+ocn: coupled ocean - AIM atmosphere on cs32 grid. -checkpoint52d_pre +checkpoint52d_pre (2003/12/06) o surface flux time-av diagnostic modified for NLFS & RealFreshWater o add call to AIM pendant S/R in external_forcing & external_fields_load.F -checkpoint52c_post +checkpoint52c_post (2003/11/25) o Fixing OPTIONS files for use of exf: - ALLOW_ECCO not needed - ECCO_CPPOPTIONS.h should not be included from @@ -2881,7 +5698,7 @@ o modified STOREs in GAD_ADVECTION o corrected key comp. for passkey -checkpoint52b_post +checkpoint52b_post (2003/11/23) o new version: "thsice" of thermodynamic sea-ice pkg: - only 1 call from "forward_step"; conserve energy, fresh-water & salt. - modify fluxes but do not change theta directly; @@ -2889,7 +5706,7 @@ - add forcing fields + data files in global_ocean.cs32x15/inp_thsice + output_thsice.txt to test thsice & bulk_force pkgs. o put back grid & coriolis monitor output. -checkpoint52b_pre +checkpoint52b_pre (2003/11/23) o call "do_the_model_io" at the beginning (=> dump initial state) o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) @@ -2899,7 +5716,7 @@ o default tamc.h in pkg/autodiff supposed to crash to ensure proper customization -checkpoint52a_post +checkpoint52a_post (2003/11/17) o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp - moved surfaceTendencyTice from pkg/seaice to main code - subroutine FREEZE_SURFACE now limits only surface temperature @@ -2914,13 +5731,13 @@ snapshot file was missing some ad-variables, but no warning issued by TAF -checkpoint52a_pre +checkpoint52a_pre (2003/11/12) o some bug fixes for #undef REAL4_IS_SLOW checkpoint52 = ecco_c52_e35 o after testing adjoints of checkpoint51u_post -checkpoint51u_post +checkpoint51u_post (2003/11/06) o this is the post-merge tag of the ecco-branch (needs another clean checkout and re-testing) o various natl_box_adjoint configs and results @@ -2935,10 +5752,10 @@ (new namelist ecco_cost_nml) o in ctrl/ cleaned some cross-dependencies and updated CPP options -checkpoint51t_post +checkpoint51t_post (2003/11/04) o this is the pre-merge tag of the ecco-branch -checkpoint51s_post +checkpoint51s_post (2003/11/04) o cleanup: removed various obsolete #define-s o pkg/grdchk - renamed 'ph-grd 3' to 'grad-res' @@ -2947,12 +5764,12 @@ - additional high-precision output for testreport (grep for 'precision_grdchk_result') -checkpoint51r_post +checkpoint51r_post (2003/11/03) o cleaned up or removed CPP_OPTIONS.h files o updated results for some of the tests to reflect the new optfiles (-ieee: -O0 instead of -O3) -checkpoint51q_post +checkpoint51q_post (2003/10/30) o cd_code: - moved cd_scheme.F -> cd_code_scheme.F - separate read_checkpoint from cd_code_ini_vars.F @@ -2968,7 +5785,7 @@ - confined inclusion of AD_CONFIG.h to where necessary. o genmake2: changed AD dependencies from SRCFILES to AD_FILES -checkpoint51p_post +checkpoint51p_post (2003/10/30) o create initial cd_code package - WARNING: the initialization of fields within packages is broken because INI_FIELDS (where READ_CHECKPOINT is @@ -2983,7 +5800,7 @@ o cleanup verification/*/code/GMREDI_OPTIONS.h o cleanup testreport -checkpoint51o_post +checkpoint51o_post (2003/10/27) o bringing AD-related verif's up to date with genmake2 - carbon/ - global_ocean.90x40x15/ @@ -3004,7 +5821,7 @@ o helping TAF to recognize dependency on kUp for fVerU, fVerV o Replacing delZ by delR in pkg/ctrl/ -checkpoint51o_pre +checkpoint51o_pre (2003/10/24) o undid all of cp51 pending some cleanups and discussion o added the [#include "AD_CONFIG.h"] statement to all files that need @@ -3012,7 +5829,7 @@ o re-worked the build logic in genmake2 to support AD_CONFIG.h o removed tools/genmake since it no longer works -checkpoint51n_post +checkpoint51n_post (2003/10/23) o modifications to make FREEZE flux visible to pkg/kpp - moved surfaceTendencyTice from pkg/seaice to main code - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP @@ -3021,7 +5838,7 @@ global_ocean.cs32x15, and global_with_exf) o added surface flux output variables to TIMEAVE_STATVARS -checkpoint51n_pre +checkpoint51n_pre (2003/10/23) o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F o added [#include "AD_CONFIG.h"] to all files that use the following defines: @@ -3029,26 +5846,26 @@ - ALLOW_TANGENTLINEAR_RUN - ALLOW_ECCO_OPTIMIZATION -checkpoint51m_post +checkpoint51m_post (2003/10/21) o incorporating changes to get TAMC/TAF working in genmake2 - added new TAMC/TAF targets to the Makefile - various cleanups related to package handling - these changes should have no impact on the forward model -checkpoint51l_post +checkpoint51l_post (2003/10/20) o changes to pkg/cal and pkg/exf that allow and speed-up long integrations - faster algorithm for cal_addtime.F - higher precision arithmetic, where needed - pkg/exf *startdate variables changed from calendar date to model integration time -checkpoint51l_pre +checkpoint51l_pre (2003/10/17) o add salt flux to forcing fields (used when salty sea-ice forms or melts) o enable to apply restoring on S & T only in a latitude band. o update output (external_forcing_surf modif. change truncation errors) global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box -checkpoint51k_post +checkpoint51k_post (2003/10/16) o change default to: useNHMTerms=.FALSE. - new output.txt for atmos. exp (NHMTerms were wrong but now turned off): adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 @@ -3062,7 +5879,7 @@ removed the #include "PACKAGES_CONFIG.h" from it o fix a bug in mom_fluxform (from chk51j_post) -checkpoint51j_post +checkpoint51j_post (2003/10/10) o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ o adjusted some flow directives (dynamics, thermodynamics) o added cubed-sphere case to test cost function @@ -3076,13 +5893,13 @@ - pkg_ad_diff.list - pkg_ad_check_lev?_dir.h -checkpoint51i_post +checkpoint51i_post (2003/10/09) o merge of the branch-genmake2 - knowingly breaks the older genmake - automatic generation of all ALLOW_${PKG_NAME} defines - new testreport supersedes older testscript o large number of package inclusion and header cleanups -checkpoint51i_pre +checkpoint51i_pre (2003/10/08) o new output for adjoin of global ocean vector invariant o fix for checkpoint of thermodynamic seaice and bulk_force @@ -3094,7 +5911,7 @@ o modifications to clean up dic pkg o add pkg/cfc -checkpoint51g_post +checkpoint51g_post (2003/10/02) o provide links for ARPACK and ADM*TLM o start removing verification/vero/ o update AD-related stuff @@ -3102,12 +5919,12 @@ o adding to verification/global_ocean.90x40x15/ adjoint of vector invariant setup -checkpoint51f_post +checkpoint51f_post (2003/10/02) o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation of tracer Green's fucntions for ocean inversion project. -checkpoint51f_pre +checkpoint51f_pre (2003/08/07) o Added on-the-fly spatial interpolation capability "USE_EXF_INTERPOLATION" to pkg/exf. - This is a temporary Cartesian-grid hack until @@ -3119,7 +5936,7 @@ and pkg/kpp/kpp_transport_ptr.F for dealing with tracer non-local transport term. -checkpoint51e_post +checkpoint51e_post (2003/08/03) o pkg/mom_vecinv: - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) - add time-ave diagnostic of vorticity advection. @@ -3129,7 +5946,7 @@ o land pkg: read initial state from files. o AIM : add stratospheric drag in the upper level -checkpoint51d_post +checkpoint51d_post (2003/07/18) o change function ILNBLNK (=> last non-blank char.) to return zero (instead of the string length) when the string. char is empty o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) @@ -3142,7 +5959,7 @@ - new active_file_loc... and mdsio_..._loc routines - affected packages: autodiff, ctrl, grdchk, mdsio -checkpoint51c_post +checkpoint51c_post (2003/07/08) o introducing integer flag debugLevel - debLevZero: suppress all output - debLevA: standard @@ -3165,14 +5982,14 @@ - checked tapelev/comlev recomputations: OK << affects results of glob_oce_pressure (different truncation error) update output.txt of ideal_2D_oce & global_ocean_pressure -checkpoint48d_pre +checkpoint48d_pre (2003/02/08) o in preparation for r*: new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. pass the 2 comp. of the grad. as arguments to momentum S/R. but for the moment, only used if it does not change the results. o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP -checkpoint48c_post +checkpoint48c_post (2003/02/06) Modifications in treatment of initial flux forcing controls to avoid extra storing of flux fields. -checkpoint48c_pre +checkpoint48c_pre (2003/01/21) o Added tidal_basin_2d experiment (currently 1D!) o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) -checkpoint48b_post +checkpoint48b_post (2003/01/27) o r* coordinate added in #ifdef NONLIN_FRSURF block. (modification to pressure gradient not yet implemented) o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports (for U & V) that are used for vertical advection of momentum. -checkpoint48a_post +checkpoint48a_post (2003/01/24) o In preparation for r*, use temp. array to compute vertical transport in flux-form momentum pkg. => change results of few test-exp. Update output of: exp4, exp5, front_relax, global_ocean_pressure, lab_sea, natl_box & plume_on_slope -checkpoint48 +checkpoint48 (2003/01/23) o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') -checkpoint47j_post +checkpoint47j_post (2003/01/21) o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. o moved adexch from forward_step to addummy_in_stepping o added exch in ctrl_map_... @@ -3451,7 +6268,7 @@ re-activated full calculation of taperfct for case 'ac02' o updating verification/ adjoints of carbon, global_ocean.90x40x15 -checkpoint47i_post +checkpoint47i_post (2003/01/13) o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) @@ -3467,7 +6284,7 @@ S/R gmredi_slope_psi should be cleaned o verification/carbon now has exactConserv=.TRUE. -checkpoint47g_post +checkpoint47g_post (2003/01/10) o time-average AIM output: becomes independent from statvars time-average (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) o After TAF bug fix: @@ -3493,7 +6310,7 @@ in conjunction with data.gmredi parameters to be checked in in a few minutes under verification/carbon/code/ -checkpoint47f_post +checkpoint47f_post (2002/12/28) Merging from release1_p10: o modifications for using pkg/exf with pkg/seaice - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING @@ -3505,19 +6322,19 @@ - verification/lab_sea default experiment now uses pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf -checkpoint47e_post +checkpoint47e_post (2002/12/27) o created a tag prior to creating a branch -checkpoint47d_post +checkpoint47d_post (2002/12/16) o fixed bug in the oceanic pressure coordinates code: vertical viscosity at the bottom boundary had an erroneous half slip boundary condition o added bottom drag and no slip boundary condition capabilities to oceanic pressure coordinates code o added new verification experiment global_ocean_pressure, this experiment is also described in the tutorial section of the manual -checkpoint47d_pre +checkpoint47d_pre (2002/12/16) -checkpoint47c_post +checkpoint47c_post (2002/12/16) o Added a verification experiment for a global cubed-sphere ocean run - verification/global_ocean.cubed32x32x30 - uses pkg/therm_seaice and pkg/bulk_forcing @@ -3529,7 +6346,7 @@ NOTES: requires option NONLIN_FRSURF to be "#define". o update advect_xz/results/output.txt (left from checkpoint44g_post) -checkpoint47b_post +checkpoint47b_post (2002/12/05) Merging from release1_p9: o pkg/seaice - removed GOTO's and added taf directives @@ -3546,7 +6363,7 @@ - added missing matlab routines - added test of thermodynamics parallelization -checkpoint47a_post +checkpoint47a_post (2002/11/23) o new pkg: aim_v23 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. for now, keep the same surface forcing as before. @@ -3563,7 +6380,7 @@ - Two ifdef statements for compile time, ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE -checkpoint47 +checkpoint47 (2002/11/15) differentiable version of checkpoint46n_post o bug fix in quasihydrostaticterms o * "clean" adjoint code (in terms of extensive recomputations) @@ -3592,7 +6409,7 @@ - #define GM_VISBECK_VARIABLE_K - GM_taper_scheme = 'ldd97' -checkpoint46n_post +checkpoint46n_post (2002/11/12) Merging from release1_p8: o verification/natl_box: updating new external_fields_load routine @@ -3646,7 +6463,7 @@ the exf (and cal) package instead of the external_fields_load routine (cf README file). -checkpoint46m_post +checkpoint46m_post (2002/11/07) o modified testscript to return -- when there are no lines of "%MON" output o added new flag "quasiHydrostatic" for QH mode and new routine quasihydrostaticterms() @@ -3659,7 +6476,7 @@ o removed gravitySign from PARM04 o switched to g77/ifc from pgf77 in aim experiments -checkpoint46l_post +checkpoint46l_post (2002/11/01) o made convective adjustment work with pressure coordinates: - changed the direction of k-loop in convective_adjustment.F for the case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) @@ -3672,9 +6489,9 @@ at the beginning of find_rho, find_alpha, and find_beta, does a check of the entire slice, if CPP-option CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined -checkpoint46l_pre +checkpoint46l_pre (2002/10/23) -checkpoint46k_post +checkpoint46k_post (2002/10/23) o fixed the verification/global_ocean.90x40x15 experiment: - new bathymetry (the world according to A., JMC, and M.) - new initial fields and forcing fields (*.bin files) @@ -3688,20 +6505,20 @@ - read AIM physics parameters from a file (data.aimphys) - set defaults values = F.Molteni paper (Clim.Dyn., 2002) -checkpoint46j_post +checkpoint46j_post (2002/10/07) o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH o move wVel computation at the end of the time step, in S/R integr_continuity o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) o update timeave pkg for wVel diagnostic. -checkpoint46j_pre +checkpoint46j_pre (2002/09/27) -checkpoint46i_post +checkpoint46i_post (2002/09/25) o Clean up AIM package (and keep the results unchanged): include CPP_OPTION and use IMPLICT NONE in all routines ; declare all the variables _RL ; use _d 0 for all numerical constants. use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! -checkpoint46h_post +checkpoint46h_post (2002/09/25) o cleaned up the use of rhoNil and rhoConst. - rhoNil should only appear in the LINEAR equation of state, everywhere else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst @@ -3711,13 +6528,13 @@ value is 999.8 kg/m^3 o cleanup up external_forcing.F and external_forcing_surf.F - can now be used by both OCEANIC and OCEANICP -checkpoint46h_pre +checkpoint46h_pre (2002/09/18) Added code to convert surface volume flux (fresh water) into a mass flux when using P coordinates in the ocean (OCEANICP). Note: It assumes you have set rho0=rhoConst=density of fresh water. -checkpoint46g_post +checkpoint46g_post (2002/09/18) o Include a new diagnostic variable phiHydLow for the ocean model - in z-coordinates, it is the bottom pressure anomaly - in p-coordinates, it is the sea surface elevation @@ -3735,9 +6552,9 @@ - removed obsolete 'eqn' from the parameter list. o added two new verification experiments: gop and goz (4x4 degree global ocean, 15 layers in pressure and height coordinates) -checkpoint46g_pre +checkpoint46g_pre (2002/09/16) -checkpoint46f_post +checkpoint46f_post (2002/09/16) o Enable tangent linear (forward mode) gradient checks: - extended active file handling to g_... files - added TANGENT_SIMULATION to theSimulationMode @@ -3745,7 +6562,7 @@ o added tangent linear setup in verification/carbon/code_ftl o added adjoint setup in verification/front_relax/code_ad -checkpoint46e_post +checkpoint46e_post (2002/09/05) o Added new equation of state -> MDJWF - EOS of McDougall et al., 2002, JAOT, submitted - caveat: the equation of state is only valid for a smaller (more @@ -3754,30 +6571,30 @@ - added more check values for density in check_eos (ini_eos.F), some of the old check values are out of the range of the MDJWF-eos, so don't expect perfect matches for those -checkpoint46e_pre +checkpoint46e_pre (2002/08/19) -checkpoint46d_post +checkpoint46d_post (2002/08/19) o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and 'OCEANICP', also initialised field pressure correctly in ini_eos in the case of pressure coordinates. eosType='JMD95Z' in combination with buoyancyRelation='OCEANICP' now causes an error. o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) in find_alpha/beta. -checkpoint46d_pre +checkpoint46d_pre (2002/08/15) o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) so that JMD95Z and JMD95P give approptiate static stability in find_rho. -checkpoint46c_post +checkpoint46c_post (2002/08/15) o Changes necessary for ocean in p-coordinates - Added new buoyancy relation = 'OCEANICP' - Added new parameters = gravitySign (this used to be contained inside the factor dRdZ which I added when we first switched to R coordinates). X GM/Redi is not compatible (yet) X bottom drag and no-slip need to be debugged. -checkpoint46c_pre +checkpoint46c_pre (2002/08/07) -checkpoint46b_post +checkpoint46b_post (2002/08/07) o Added new equation of state -> JMD95Z and JMD95P - EOS of Jackett and McDougall, 1995, JAOT - moved all EOS parameters into EOS.h @@ -3786,17 +6603,17 @@ in-situ temperature (see JMD95) o Modified formatting for knudsen2.f in utils/knudsen2 and added unesco.f to be used with POLY3 -checkpoint46b_pre +checkpoint46b_pre (2002/07/31) -checkpoint46a_post +checkpoint46a_post (2002/07/31) o Added (atmospheric) pressure loading - new field in FFIELDS.h, etc... - new cpp flag ATMOSPHERIC_LOADING o Changed hFacC to _hFacC in calc_phi_hyd.F o Added SHORTWAVE_HEATING to some files for consistency -checkpoint46a_pre +checkpoint46a_pre (2002/07/13) -checkpoint46 +checkpoint46 (2002/07/13) further merges from release1_p5 o new ctrl package - adopted from ECCO environment to enable optimization @@ -3823,7 +6640,7 @@ o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) o incorporated hooks for sponge layer code (external_forcing.F) -checkpoint45d_post +checkpoint45d_post (2002/07/12) o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S (affects plume_on_slope "cg2d" output) @@ -3837,7 +6654,7 @@ - for each tracer, define internal flag for multiDimAdvection & A-B o monitor: change definition of KE to check conservation of Energy -checkpoint45c_post +checkpoint45c_post (2002/05/30) o Removed f90 comments ("!") o Modified initialisations to enable exf package for MITgcm (without invoking ECCO_PACKAGE). @@ -3845,7 +6662,7 @@ - enable centered differences - modified format of standard output -checkpoint45b_post +checkpoint45b_post (2002/05/30) o cleaned exchange calls in cg2d o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step o included CPP option SINGLE_LAYER_MODE in thermodynamics @@ -3857,7 +6674,7 @@ (corresponding adjustment of TAF tape initialisation). o in calc_diffusivity/calc_viscosity extended domain to full overlap. -checkpoint45a_post +checkpoint45a_post (2002/05/01) o compute Rho over the whole domain (extend iMin,jMin indices) o specific exchange for X-slice domain (case Ny=1) o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code @@ -3877,13 +6694,13 @@ (conflict on some platforms, e.g. IBM SP3) o modified carbon verif. -checkpoint44h_pre +checkpoint44h_pre (2002/03/14) o vertical grid option: allow to put the Interface at the middle between 2 cell-centers ; replace delZ in pkg/kpp by drF. o GM Advective form: Tracers are advected using the residual transport (= Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. -checkpoint44g_post +checkpoint44g_post (2002/03/05) o fix surface correction term in multiDimAdvection (affects plume_on_slope results) ; ifdef missing in thermodynamics.F @@ -3948,7 +6765,7 @@ o check parameters & config (chkpt44a_pre,post) o OBC and NonLin_FrSurf. -checkpoint44 +checkpoint44 (2002/01/18) o fix bug in mom_vi_del2uv o select when filters are applied ; add options to zonal_filter (data.zonfilt) o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) @@ -3956,13 +6773,13 @@ o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) o added some stuff for AD -checkpoint43 +checkpoint43 (2001/09/28) o added two new advection tests o added global 4x4 degree ocean test o added test of H&S94 with free surface on cube o some final mods for gradient check, adjoint,... -checkpoint42 +checkpoint42 (2001/09/27) Fixed AD-related problems: o Store directives up-to-date with re-arranged Adams-Bashforth (mainly thermodynamics.F) @@ -3974,11 +6791,11 @@ for the case ALLOW_KPP o Cleaned argument list for timestep_tracer.F -checkpoint41 +checkpoint41 (2001/09/27) o re-formatted/added comments in prologues of key subroutines to work with protex -checkpoint40 +checkpoint40 (2001/09/27) o moved calc_gs, calc_gt and calc_tr1 back to model/src o added FLT (floats) package from Arne along with demo. experiment o re-arranged Adams-Bashforth scheme for tracers to allow easier @@ -3987,7 +6804,7 @@ o modified multi-dim method to work on cube o bug fix in KPP (from DM) -checkpoint40pre9 +checkpoint40pre9 (2001/09/27) o added DST advection schemes o fix MPI bug on SGI's o modifications for non-linear free-surface @@ -3997,7 +6814,7 @@ o added/updated many matlab scripts o added multi-dimensional advection method for tracers -checkpoint40pre8 +checkpoint40pre8 (2001/09/05) o new package rw/ Added method for dumping intermediate local arrays: mdsio_writetile - same as mdsio_writefield except works from inside @@ -4016,14 +6833,14 @@ currently nothing implemented to switch this storing off in case fluxform is used since no CPP flag available). -checkpoint40pre7 +checkpoint40pre7 (2001/08/14) o bug fix in dynamics.F calc_viscosity called before k=1,Nr loop. o added some #ifdef's ALLOW_PASSIVE_TRACER o cleaned initialisations in ctrl_map_ini related to TAF -checkpoint40pre6 +checkpoint40pre6 (2001/08/13) o split dynamics into thermodynamics & dynamics o corresponding split of calc_diffusivity into calc_diffusivity, calc_viscosity @@ -4031,7 +6848,7 @@ o Added diffkr, kapgm to control variables o bug fix in gmredi_slope_limit for ldd97 -checkpoint40pre5 +checkpoint40pre5 (2001/07/31) o proper initialization of Adams-Bashforth time stepping + uses forward step for very first step of model (iter=0) o re-generated *all* output since almost all output is modified by this @@ -4045,7 +6862,7 @@ + this uses an alternative form of ini_curvilinear_grid.F which is not necessarily any better than the current one... -checkpoint40pre4 +checkpoint40pre4 (2001/07/30) o added re-initialisations of utrans,vtrans,rtrans in calc_common_factors which are crucial for TAF. o extended iMin,jMin range for calc_common_factors, @@ -4053,18 +6870,18 @@ o added option ALLOW_PASSIVE_TRACER o a few minor updates and fixes -checkpoint40pre3 +checkpoint40pre3 (2001/07/13) o created calc_gtr1.F for gad package o split the_main_loop and re-introduced forward_step o some recomputations of nIter0 for TAMC -checkpoint40pre2 +checkpoint40pre2 (2001/07/13) o Updated to latest branch of AJA, JMC o Added gradient check package o Added routines for passive tracer handling o Added carbon sequestration sensitivity experiment -checkpoint39 +checkpoint39 (2001/05/14) o Modifications and fixes to support TAMC (mainly missing or wrong directives) o Corrected common blocks when fooling TAMC to produce adjoint I/O @@ -4078,7 +6895,7 @@ (NB: this is not the full ECCO environment) o disabled some packages by default in genmake -checkpoint38 +checkpoint38 (2001/04/10) o see notes_c37_adj.txt o corrected wrong layer index in external_forcing_t o replaced the_main_loop/forward_step by the_main_loop @@ -4086,7 +6903,7 @@ (replaced criteria for initial/final state) o added runtime flag for pre-C35 pickups: usePickupBeforeC35 -checkpoint37 +checkpoint37 (2001/03/13) o mdsio.F routine split and packaged in pkg/mdsio (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not used unless genmake -disable=mdsio) @@ -4103,19 +6920,19 @@ o Non-Hydrostatic pickup file Pb fixed. o bug with Rigid-lid version (since c35) fixed. -checkpoint36 +checkpoint36 (2001/02/20) o implement Crank-Nickelson barotropic time-stepping o recover Time-Average diagnostics o fix Pb in checkpoint (PR#19) o AIM become a standard package ; clean unused CPP_kees -checkpoint35 +checkpoint35 (2001/02/08) o subtantial rewrite of dynamics.f o allows staggered time-stepping o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt o added bottom drag (linear + quadratic) -checkpoint34 +checkpoint34 (2001/01/30) o Modified exchange routines for correct reverse simulation. o Added verification output to comply with bug fix in impldiff.F as of c33 (exp2, natl_box). @@ -4126,7 +6943,7 @@ o Added routine GLOBAL_SUM_INT to global_sum.F o Added mdsio_gl.F for ECCO purposes. -checkpoint33 +checkpoint33 (2000/11/30) o Fixed bug in lower BC in impldiff.F o Fixed confusion about units of forcing arrays in FFIELDS.h namely Fu,Fv,Qnet,Qsw,EmPmR: @@ -4144,7 +6961,7 @@ possibly use them. o Corrected genmake to delete a temporary file during configuration -checkpoint32 +checkpoint32 (2000/11/13) o Scaling of forcing fields moved from external_forcing.F to external_fields_scale.F, called directly after loading fields. o Surface relaxation terms added to surface tendency fields in @@ -4155,7 +6972,7 @@ o Modifications and bug fixes in KPP package. o Verification experiment for KPP added (verification/nat_box/) -checkpoint31 +checkpoint31 (2000/09/11) o Packages interface brought in line with defined standard -> new routines packages_...F -> changes in initialise_fixed.F, initialise_varia.F @@ -4172,7 +6989,7 @@ - not yet tested for GMRedi. - not yet tested for KPP. -checkpoint30 +checkpoint30 (2000/07/13) o Updates for OBCs o New experiment for test OBCs (internal_wave) o New output.txt in verification/exp4/results/ @@ -4181,10 +6998,10 @@ o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) and entry for T90 in genmake -checkpoint29 +checkpoint29 (2000/06/21) o packaged KPP and GM/Redi -checkpoint28 +checkpoint28 (2000/06/09) o Corrected initialization of hFacMin for difference vertical coordinates o Modified calculation of partial cell thickness to more robust algorithm o config_summary.F: replaced write_1D_... by write_0D_... @@ -4197,7 +7014,7 @@ included store directives and tape key computations required for TAMC. o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC -checkpoint27 +checkpoint27 (2000/04/10) o fixed calc_isoslopes() to so that cancellation of terms in tensor formulation works properly with variable resolution. o restructured the calling tree between the_model_main() and dynamics() @@ -4205,7 +7022,7 @@ o introduced initialization file pSurfInitFile for free surface (cg2d_x) in new routine ini_psurf() -checkpoint26 +checkpoint26 (2000/04/05) o moved some #ifdef in optional routines to encompass everything except the argument declarations. This was using up some memory. o fixed macros like _ADT to work with both versions of Linux cpp @@ -4215,7 +7032,7 @@ (macros are now in eesupp/inc/CPP_EEMACROS.h) o patch for 2 processor JAM mode -checkpoint25 +checkpoint25 (2000/03/15) o updates for OBCs and NH o dramatically reduced memory usage o added "JAM" routines for use on Artic network @@ -4226,32 +7043,32 @@ an explicit free-surface option) o initial state input files for U and V -checkpoint24 +checkpoint24 (1999/08/02) o Removed some spurious "REAL"s o Updated KPP to latest version from JPL o Added a COS(latitude) in horizontal viscosity -checkpoint23 +checkpoint23 (1999/05/26) o Added del^4 diffusion for salt and temperature o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) -checkpoint22 +checkpoint22 (1999/05/18) o Made many small changes: implicit none, format(i5), etc... o Introduced KPP mixing scheme (compiles and runs but *not* tested) -checkpoint21 +checkpoint21 (1999/05/18) o Introduced new I/O package that supports direct-access records (mdsio.F) o Split-up mid-level I/O routines o Updated input data for experiments 0,1,2,4 and 5 o Finally removed the genmake.* scripts (everyone seems happy with genmake) -checkpoint20 +checkpoint20 (1999/03/22) o Tidied up open-boundaries some more o Added non-hydrostatic code o Fixed some input data o Modified MPI start-up to work in "coupled" context. -checkpoint19 +checkpoint19 (1998/12/15) o Tidied up directory structure for verification experiments. o Added new code for open boundaries. o Corrected advective terms near boundaries. @@ -4259,18 +7076,18 @@ o Implemented free-slip/no-slip BCs and del^4 dissipation. o Split default parameters out of ini_parms.F into set_defaults.F. -checkpoint18 +checkpoint18 (1998/11/30) o Further changes for optional code generation with CPP - ugh! -checkpoint17 +checkpoint17 (1998/11/03) o Beginning to incorporating modularity for supporting atmos. and ocean configs. o Small changes for TAMC complinace o New ultra simple test case. Barotropic box configuration "exp0". -checkpoint16 +checkpoint16 (1998/10/28) o Minor changes to exchange routines to support accumulation in reverse mode. Adjoint of an assignment is an addition. @@ -4278,7 +7095,7 @@ syntax) and by g77 under Linux ( 72 character limit ). -checkpoint15 +checkpoint15 (1998/09/29) Rewrote exchange routines to allow o General tile <-> tile connectivity. o TAMC reverse mode flag ( is this really needed? ) @@ -4287,11 +7104,11 @@ shmput/shmget, VIA, SYSV shmem and every other cool communication method. -checkpoint14 +checkpoint14 (1998/09/09) Consistent isomorphism chages made. These allow dynamical core to support both pressure and meters as a vertical coordinate. -checkpoint13 +checkpoint13 (1998/07/17) Release which corrects global_max problem and a couple of KGM time-averaging diagnostic errors. Also contains a double-gyre experiment setup as well as the baseline @@ -4306,27 +7123,27 @@ I don't want to commit the rDot to the main-trunk until we've actually tested it... -checkpoint12 +checkpoint12 (1998/07/08) Tidy up and added generic genmake script (formerly configure script). Released to testers. -checkpoint11 +checkpoint11 (1998/07/02) Re-arranged initialise() and introduced ini_vertical_grid() and ini_masks_etc(). -checkpoint10 +checkpoint10 (1998/07/01) Introduced the configure script. Separated out the diags package. Added template for writing time-averages of tile/intermediate quantities. Updated SIZE.h in exp2 and made the data big-endian. -checkpoint9 +checkpoint9 (1998/06/22) MPI fix. Filename changes (meta/data). salbin*y stuff. General tidy-up. SST.bin SSS.bin added to verification/exp2 -checkpoint8 +checkpoint8 (1998/06/22) Inludes time-dependant forcing and time-averaging. Works at 4x4 and 2.8125x2.8125 global @@ -4336,7 +7153,7 @@ model etc.. Configured for verification/exp2 - 4 degree global, two process. -checkpoint7 +checkpoint7 (1998/06/15) Created by cnh Simple 4 degree global simulation configuration. @@ -4344,27 +7161,27 @@ hydrography, bathymetry etc Does not include Heat Flux and E-P -checkpoint6 +checkpoint6 (1998/06/08) Created by cnh merged checkpoint5 with CD and spherical polar code. Still some problems with GM Redi abd full topography. -checkpoint5 +checkpoint5 (1998/06/08) Created by AJA contains updates to GM Redi and reordered timestepping loop for Implicit Diffusion. -checkpoint4 +checkpoint4 (1998/05/30) Created by cnh Contains memory saving macros ( _rdxc etc..) for when grid variations are limited. Contains polynomial coeffs for EOS and knudsen program for generation. -checkpoint3 +checkpoint3 (1998/05/26) Created by cnh Added extra flags for runtime options Added this file