--- MITgcm/doc/tag-index 2003/10/21 15:29:20 1.190 +++ MITgcm/doc/tag-index 2012/04/03 17:01:48 1.1644 @@ -1,26 +1,5684 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.190 2003/10/21 15:29:20 edhill Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1644 2012/04/03 17:01:48 jmc Exp $ +$Name: $ Notes on tags used in MITgcmUV ============================== +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 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/ + receive real*4 array (instead of real*8) to read/write 32.bit files. + (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S + and remove new mapping S/R) +o pkg/mdsio: in preparation for topology-generator within pkg/exch2: + - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.: + xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h + 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 (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. +o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros): + - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ; + - reduce number of macro definitions (keep only those which are used); + can always call directly the corrresponding S/R if needed. + - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix + _R4/_R8 to _RS/_RL when applied to _RS/_RL variable. + Fixed wrong type of arg in: + atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F + ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F + To fix: global_sum of var in common block is wrong (multi-threaded) in: + dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F + To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops) +o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd + "nlfs" mpi test is going to stop when checking for unconnected tile egdes. +o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error +o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile + edges are closed (zero depth); might happen with "blank tiles"; + for now, disabled if using OBCS. +o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi": + link *_mpi files from "MODS" dir) to return to a strait-forward behavior. +o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D) + to reduce length of 1.D array print in STDOUT. +o adjustment.cs-32x32x1: changed to oceanic test with 1 continent + + use 48 tiles (16x8): this will allow to test "blank tiles". +o start to test MPI + multi-threaded (change testreport to skip tests + where number of tiles do not match). +o genmake2: add option "-omp" to turn on Open-MP ; + passed to testreport (if using -mth) ; merge few (*+mth) optfiles. +o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them) + and keep the original tile numbering. Note: compatible with old + W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files. + +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: + switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE) + and generate new output. Note: new output is much closer to the old + one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from + the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007. +o pkg/fizhi: + - change to avoid indices going deliberately over array-bounds + - remove unnecessary MPI stuff + - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY" + - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE: + does not go over array-bounds and therefore returns reliable output. + - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls: + this S/R has 4 output arguments, which are used inside "get_alarm"; + when it is called with the same variable "ndum" in place of several + output arguments, this produces weird side effect inside "get_alarm" + (e.g., datein=dates(n) is overwritten by timein=times(n) since both + datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum" + address) and produces error. +o tools/gemake2: (March 27-29 2009) + with option "-mpi": link *_mpi files from "MODS" dir (this is what + testreport does). +o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output +o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F: + update lab_sea.lsr & lab_sea.salt_plume results +o pkg/seaice: + Major overhaul of the LSOR solver: change discretization from original + finite differences to finite volume. The old routine is still in the + file seaice_lsr.F and can be turned on with the CPP-flag + SEAICE_OLD_AND_BAD_DISCRETIZATION + Along with this change, the discretization of the strain rates is changed. + The same flag turns on the old discretization in seaice_calc_strainrates.F + All verification experiments with seaice are affected (except for + seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old + results by setting the above flag. + Further changes involve changes in defaults: + - ALLOW_FLOODING is defined and turned on by default + - SEAICEadvSnow = .true. is now the default + - SEAICEadvSalt = .true. is now the default + - SEAICEadvAge = .true. is now the default + - SEAICE_clipVelocities = .false. is now the default + (as per J. Zhang's recommendation) + - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE + 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 (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 + add more debugging diagnostics + seaice_evp: removed superfluous many metric terms of FV discretization + of stress divergence + affects lab_sea, lab_sea.hb87 + seaice_ocean_stress: removed superfluous many metric terms of FV discretization + of stress divergence for non-evp solver + (this part is not tested anywhere) + seaice_calc_strainrates: fixed a bug in no-slip boundary conditions, + they were effectively only half slip + affects lab_sea.hb87 + updated all relevant verification experiments (except lab_sea//output_adm.txt + which was left over, but fails at level 7 & 6) + +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 +o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids + that are not cubed-sphere grids +o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR +o pkg/ctrl: + fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low) +o non-hydrostatic (calc_gw.F): + fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec + update output of exp. global_ocean.cs32x15.viscA4 +o remove backward compatibility for thetaMin,phiMin + (replaced by xgOrigin,ygOrigin on Jan 27, 2009) +o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the + interpolated wind field not only for curvilineargrid=.true., but also + for a rotated grid (rotateGrid=.true.) +o pkg/exf: add capability to bypass interpolation for runoff + by setting yet another CPP-flag +o eesupp/src, B-grid exchange: + add simple (6 tiles, non MPI) CS exch + standard interface S/R. +o autodiff + new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV + allows to switch to single-prec common blocks; + corresponding switch occurs in tamc.h, integer isbyte + TAF store directivs "byte" and "kind" seem equivalent; + Most tamc.h have been updated correspondingly. + +checkpoint61i (2009/02/13) +o autodiff: + fix autodiff_sore/_restore indices for obcs + (spotted by I. Hoteit, M. Mazloff) +o pkg/autodiff, pkg/ctrl: + Add flag to reduce all tapelev I/O to single-prec. + In data.ctrl set + doSinglePrecTapelev = .TRUE. +o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2: + check in hack for SX8 compiler (for dxV, dyU); remove it afterwards. +o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for + real fresh water flux (not yet) +o pkg/mdsio & rw: + - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta) + - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX. +o pkg/flt: + - replace FLT_INIT by 3-steps standard initialization S/R: readparms, + init_fixed & ini_varia. + - clean-up & simplify linear interpolation S/R: + move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid. + - fix some indices (mainly vertical index) ; add IMPLICIT NONE. + - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R. + - add vert. coordinate & horiz. indices to output files. + - change vertical position in initial condition, from index to depth [m]. + - store horizontal (decimal) indices i,j in common block (instead of coord. x,y) + (easier to get to a curvilinear grid) ; delX,delY no longer used. +o pkg/ggl90: a few modifications: + - fix bottom boundary condition, and interpolation of KappaE + near top and bottom + - use same set of viscosity/diffusivity for TKE/momnetum/tracer + - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH) + - add a few options for mixing-length upper limit (--> mxlMaxFlag) +o rename thetaMin,phiMin -> xgOrigin,ygOrigin + (maintain temporary backward compatibility, until next checkpoint) + +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 +o pkg/obcs: fix loop ranges for balancing code +o pkg/flt: + - improve criteria for finding which tile owns a float. + - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case. +o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg + aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling + with ocean biogeo) +o pkg/flt: + - do some cleaning and fix the restart ; + - add output.txt in flt_example/results to get this pkg tested. +o genmake2: add an EXTENDED_SRC option and flag. + for now, cannot be turned on on command line (only through genmake_local) +o pkg/mdsio: read/write vector: + - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS + - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR + & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. + - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) + (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 (2008/12/29) +o pkg/flt: + - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) + + make OPTIONS file more standard. + - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) + - fix _BYTESWAPIO CPP-Flag + - standard reading of file-parameter "data.flt" + - fix argument list of S/R FLT_RESTART + still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F +o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell +o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to + a still unfixed compiler/optimization bug + +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. +o pkg/exf: add parameter for extrapolation of temp up to the surface + and option to prevent negative evap (in bulk_largeyeager04 only). +o Prather Advection scheme: fix tracer conservation for divergent flow + (e.g., when using NonLin Free-Surface). +o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead +o gmredi (Visbeck-variable-K): + - add more parameters to Visbeck-variable-K. + - use a 5 points average for dSigmaR in Visbeck-K calculation + (more "homogenous": same stencil and same weights as in dSigmaH) + - update output of ideal_2D_oce experiment. +o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 + (#undef REAL4_IS_SLOW) + - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 + coordinate variable + - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables + (surface forcing fields), removes some of the functionality + - model/src/write_grid.F: write _RS variables as RS-netcdf variables + - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but + probably not all: copy _RS surface flux fields to RL field before + calling DIAGNOSTICS_FILL + - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into + real*4 (CALL EXCH_*_RS) versions. + - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 + (generate new output). + +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 : + now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct) + previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output. +o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic + to be the same as with Z-coord. (i.e., m/s & no-units respectively). +o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc) +o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz + does not become too large (to avoid precision problems in implicit-diffusion + solver); update ideal_2D_oce output. +o pkg ggl90: + - in ggl90_cal.F: compute only one set of visc/diff, used to + step forward TKE/T/S/momentum + - default value of GGL90viscMax/GGL90diffMax larger and equal (to + have Prandlt =1) +o gmredi (fm07): + - add lower limit on Transition layer thickness + lower limit on 1/lambda + - allow to set few more params from data.gmredi +o pkg ggl90: + - add missing sqrt(2) factor in computation of mixing length + scale in ggl90_calc.F + (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) + +checkpoint61d (2008/09/25) +o adjoint modifs + - adapt to new field rhoInSitu + - allow to revert from StoreDynVars2D, StoreDynVars3D + to individual fields + (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) +o store 3-D (in-situ) density in commom block (DYNVARS.h) + - save 1 rho computation. + - no longer modify T & S inland when using down_slope pkg. +o gad_som : allow to switch to SOM advection for T & S without corresponding + pickup files (using new S/R: MDS_CHECK4FILE). +o keep removing _BEGIN/_END_MASTER between MDSIO S/R call + (for useSingleCpuIO to work in multi-threaded) +o pkg/shelfice: + - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute + with SHELFICEtopoFile in data.shelfice + - move code for reading ice shelf topography and modifying hFacC into separate + subroutines of the shelfice package + - separate initialisation of "fixed" and "variable" variables + - kTopC is not (yet) replaced by kSurfC, although this is possible +o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s +o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) + and rename: + ini_phiref.F --> set_ref_state.F (+ set anelastic factors) + ini_reference_state.F --> load_ref_files.F (- set anelastic factors) +o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) + +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). +o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) +o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) +o new pkg: down_slope + density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). + - presently, modify T & S inland (dwnslp_calc_rho.F). + can be avoided if rho was stored in common bloc and used in calc_phi_hyd. + - implementation for ocean in P-coords not tested. + - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. +o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) + (to facilitate conversion of oceanic pkg to p-coordinate). +o change FIND_RHO to FIND_RHO_2D : + pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. +o new pkg: cheapaml + +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). + - 3rd exchange no longer needed (tested with 24 tiles). + - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) + - exch_UV_A-grid readily available (but not yet tested). + comment out 3rd exch call and remove copy of V to U at SE & NE face-corners + (both are no longer needed) in exch_uv: no effect in forward run; but + get truncation error differences with adjoint exch. +o exch2: + - change index-bounds storage (moved from target to local tile, + more intuitive this way) ; rename/remove some variables. + - change utils/exch2/matlab-topology-generator & code_mods accordingly. + +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). +o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf + is exceeded +o testreport: modify syntax of awk, so that it works also with + awk, and not only with nawk and gawk + +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.) + Omission of this flag leads to incompatibility w.r.t. TAMC + To restore TAMC-compatibility, need following modifs: + * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility + * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY + Tested TAF version is 1.9.22 + N.B.: exch2 hand-written adjoint code currently not TAMC compatible + +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. +--->>> Future checkpoints will ommit this flag by default. +o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. +o pkg/grdchk: Add gradient check to etan0 perturbations. +o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). +o pkg/autodiff: more flexibility in zeroadj. + model/src: modifying do_oceanic_phys.F accordingly. +o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. +o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option + special setup of gmredi for which the adjoint is stable + enough for parameter optimization. +o bridging the gap between eddy stress and GM. + -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) + along with a change in CPP option (now ALLOW_EDDYPSI). + -> when using GM w/ GM_AdvForm: + The total eddy streamfunction (Psi = eddyPsi + K x Slope) + is applied either in the tracer Eq. or in momentum Eq. + depending on data.gmredi (intro. GM_InMomAsStress). + -> ALLOW_EDDYPSI_CONTROL for estimation purpose. + The key modifications are in model/src/taueddy_external_forcing.F + pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F + +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. +o pkg/mnc: add some attributes to standard 1D-coordinate variables +o pkg/diagnostics: enforce missing_value attribute for scalar variables at + mass points, when using mnc for output + - add runtime parameter (missing_value, missing_value_int) to override + default (which is the value of getcon('UNDEF')) +o pkg/mnc: prepare mnc for the actual use of missing values with the + diagnostics package: small fix in mnc_cw_readwrite.template and more + initialisation of never used fields + - replace mnc_common.h and mnc_id_header.h with corresponding upper case + versions +o pkg/thsice/thsice_ini_vars.F added default initial values so that + thermodynamics sea ice solver does not blow up when some initial fields + are missing. +o move from external_forcing_surf.F to ini_forcing.F + the p-coord. hack consisting in using pLoad to set phi0surf ; + update output of tutorial_global_oce_in_p (affected @ truncation level). +o Freshen up a bit hs94.1x64x5, notably: + remove rotationPeriod and tRef=5*0. (adjoint only), and add + exactConserv=.TRUE. +o pkg/generic_advdiff: + change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only + applies to files where Temperature & Salinity 2nd Order moments are used. +o pkg/ptracers: add second-order moment advection schemes (80 and 81); + this uses a dynamically allocated internal state data structure + (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) + and requires a fortran 90 compiler + +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: + - change bathymetry (put back seamounts in ACC, use hFacs) + - change EOS (POLY3 --> JMD95Z) + - use Bryan-Lewis vertical diffusivity + - use multidimensional advection + - remove old virtual virtual in dic pkg, now done through ptracer pkg + - change a couple of parameters in dic pkg +o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F +o pkg/obcs: change default to OBCSfixTopo = .true., + - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result + - replace "debugMode" with "debugLevel .GE. debLevB" +o implementation of TAF directives for gchem,cfc,dic +o remove "exp5" (replaced by tutorial_deep_convection). +o pkg/obcs: add code to fix topography gradients normal to open boundaries; + this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; + the code can be turned on by setting OBCSfixTopo = .true. in data.obcs + --> changes results in exp4, seaice_obcs +o tutorial_deep_convection : + update the set-up and increase resolution and domain size ; start + from pseudo initial conditions = output at t=120mn in order to see + something happening when running testreport. +o pkg/seaice: add os7mp as an advection scheme + add check for advection schemes + add a flag for restoring T and S underneath sea ice +o pkg/my82: add netcdf-support and diagnostics +o thsice pkg: + - Now hsMax limits snow height by turning it into ice following + flooding scheme (and now conserving energy) + - Slight rewriting of the formula in thsice_calc_thick.F + - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos + --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice + +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" ; + - various re-arrangement in initialisation & header file ; + - fix tutorial_global_oce_biogeo for multi-threaded test. +o pkg/dic: test for "pickup_dic" file when restarting ; + if no pickup-file, can restart with a re-initialised pH (same as it did + before) providing pickupStrictlyMatch is set to False. +o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP + + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP +o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2 + and staggerTimeStep is off (needed for stability of Internal-wave dynamics). +o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax, + & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers + (note: not clear to me what lambdaTr1ClimRelax is still used for ...) +o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which + scheme to use for vorticty-term ; + - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F + (with default selectVortScheme, return to original discretisation) + - remove weird combination (e.g.: upwindVorticity & highOrderVorticity) +o pkg/seaice: add a line to the summary to indicate grid type (B/C) +o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the + bottom ; only used with variable horizontal viscosity and non-hydrostatic. + also fix diagnostics VISCAHW & VISCA4W. + +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 +o pkg/shelfice: + - sort out freshwater flux; convert freshwater fluxes to mass fluxes + (kg/m^2/s), does not break tests, because in verification/isomip, + rhoConstFresh=rhoConst (by accident) + - rearrange computation of tLoc, sLoc, pLoc to make code more efficient + - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into + new file model/src/seawater.F, so that they are available for all pkgs. + - convert potential temperature into in-situ temperature. This changes the + isomip tests => update tests +o add a flag writePickupAtEnd (default=true) to be able to suppress + writing a pickup at the last timestep +o tools/mpack-1.6 : + - disable automake (not working) and autoconf (not needed). + - update to version 1.6.4 which fix MD5 code on some 64 bits platforms + also cleaner with much less compilation warnings. +o pkg/profiles: + rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg + (for "less than 32 characters name" compiler requirement) +o pkg/obcs and pkg/exf: added capability to specify seaice open boundary + conditions that have a different sampling frequency than S/T/U/V obcs +o pkg/diagnostics (stats-diags): + - fix global Min/Max in case 1 processor get only empty tiles +o genmake2: replace (4 times) + make genmake_tc_1.o >> genmake_warnings 2>&1 + with + COMM="$CC $CFLAGS -c genmake_tc_1.c" + echo $COMM >> genmake_warnings + $COMM >> genmake_warnings 2>&1 + to make genmake2 always see the value of CC as specified in the optfile. +o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid. + - add diagnostics for 1srt & 2nd Order moments and sub-grid variance. + - modify verification advect_cs test to test SOM-advection on CS-grid. +o pkg/ctrl: + - Rewrite of ctrl_map_ini_ecco.F, + introducing a generic routine (ctrl_map_ini_gen.F). + - Modification of ctrl_bound/adctrl_bound handling control vector bounds. + +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 + with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST. + - many small changes (integer format) for large number of diagnostics + - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with + a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23. +o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For + usingSphericalGrid, this allows to define the rotated grid coordinates + via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the + geographical coordinates according to the inverse of the rotation defined + by the Euler angles, so that Coriolis parameter and online-interpolation by + exf works with the geographical coordinates on XC/YC/XG/YG. + Naturally, this feature does not work with all packages, so some + combinations are prohibited in config_summary (flt, flt_zonal, ecco, + profiles), because there the coordinates are assumed to be regular + spherical grid coordinates. +o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc: + - introduce isopycnal diffusion coefficient control. +o tools/adjoint_options: + - additional control vector components. +o pkg/mnc: have mnc create marginally meaning full coordinate variables + (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 +o pkg/mypackage: + - add example of read/write pickup for state-var ; + - add entry points to the main code for state-vars diags & write-pickup. +o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year + transitions for useExfYearlyFields + - add new subroutine that determines the file to read from for + use*YearlyFields = .TRUE. and .FALSE. + - add a verification experiment to global_with_exf that tests + useExfYearlyFields with USE_EXF_INTERPOLATION defined +o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in + analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new + subroutines (which could be generated from a template, because they are + almost identical), for now they are included in obcs_prescribe_read.F for + simplicity +o pkg/exf: + - add a little more diagnostic to exf_interp_read (in analogy to + mds_read_field, can be turned off with debugLevel < debugLevA=1) + - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code + ugly but fast by unrolling short inner loops, inserting a unroll=8 + directive in routine lagran, and splitting a loop and making do while the + outermost loop (the latter requires the intoduction of index arrays) +o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice +o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver + http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html +o verification/seaice_obcs: updated for restart test and latest options +o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different + ice rheology (so-called truncated ellipse, that gets rid of tensile stress); + 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 (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 + advection scheme fluxes (was previously multiplied by deltaT). +o added verification/seaice_obcs both to test seaice open boundaries + and to provide an example matlab scrpt for generating them +o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume +o pkg/salt_plume: clean up salt_plume_frac.F to + remove redundancy in PlumeMethod 1 and 4 +o pkg/kpp: added saltplume diagnostics +o pkg/obcs and pkg/seaice: + - do not set uice and vice to zero when OB*icefile are unspecified + - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default + - moved seaice tracer obcs after call to seaice_growth +o pkg/salt_plume: added various options for salt plume depth + criterion and for vertical distribution of the salt + +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 ) +o pkg/seaice: + - add timescale for melting due to warm mixed layer as a means of + setting SEAICE_availHeatFrac more conveniently + - add a CPP-flag/runtime parameter check for flooding algorithm + - reformulated availHeat in seaice_growth.F to be independent of AREA +o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent + unit changes +o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint +o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC + SX vector computer. +o pkg/seaice: + - removed SEAICE_FFIELDS.h and seaice_get_forcing.F + seaice forcing fields can now be read only through pkg/exf + - removed some unused halos +o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP +o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL + or U/VICE from U/VWIND before computing U/VSTRESS + +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): + all experiments pass when compile with un-initialised var. checking option. +o added pkg/salt_plume +o script to test restart (for now, in MITgcm_contrib/jmc_script) +o pkg/seaice: new read/write pickup version. + read meta file and write only fields which are needed to restart. + ( same logic as main pickup file ; also using pickupStrictlyMatch ) +o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) +o lab_sea.hb87: modify the domain & update output.hb87.txt : + lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 + at j=1 & j=Ny+1 : this case is not treated correctly in the restart + process. Fixed here by closing the domain at the Northern boundary. +o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. +o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing + a set of consecutive levels in/from a 3-D array. +o pkg/ptracers: + 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 (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). + update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. +o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those + packages instead of reading ice cover and wind speed separately +o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h + (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad + to allow to compile customized code before the update) +o cleaning-up: + - fix CPP instruction syntax in pkg/obcs + - replace (some) call to MDSIO S/R with call to RW interface S/R ; and + add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio) + - fix some threads issue in IO parts. +o pkg/dic: + - add tons of "_d 0" (--> much better testreports !) + and then update outputs of tutorial_global_oce_biogeo +o pkg/mom_fluxform: + add a special version of momentum advection intended to conserve momentum + next to a bathymetry step or a coastline edge. (default = off = #undef) +o new read/write pickup version: + - for now, only implemented for main (mdsio) pickup file. + - write out only what is needed to restart; merge pickup_nh , pickup_ph + and main pickup together. + - read meta file; read only what is needed to restart; stop if a field + is missing (if pickupStrictlyMatch=T, = the default) or try to restart + if it make sense (even if the restart is not perfect). + - if no meta file, assume that pickup to read corresponds exactly to + a pickup that would currently be written. + - read pickup written in the old format (until checkpoint59i) if it + recognizes an old meta file (no field-list). + - add a meta file in exp. which starts from a pickup: 2 cases: + a) minimal meta file (with just file precision) + pickupStrictlyMatch=F + e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta + b) a meta file describing the content of the associated pickup file + e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta +o pkg/mdsio & pkg/rw: + - new routine to read a meta file ; new set of routine to read + Multiple-fields file (with meta file). +o added open boundary conditions capability for seaice + HSNOW, HSALT, UICE, and VICE + +checkpoint59i (2007/10/21) +o adjoint: + * fix multiDimAdvection adjoint + (partial recomputation problem by TAF for fVerT(:,:,kDown) + and comlev1 size definition (maxpass vs. max. number of tracers) + * verification/global_ocean.90x45x15 adjoint now tests + NLFS and multiDimAdvection using DST3 (=30) + * verification/lab_sea now tests multiDimAdvection using DST3 (=30) +o pkg/kpp: add "_d 0" to real constant (if missing); + update output of exp: natl_box (10.digits); vermix (std, 7.digits) + and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). +o prepare for "clever pickup" implementation: add new header file "RESTART.h" + for internal parameters related to restart process (formerly from PARAMS.h) + and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. +o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed + as argument. (only atm2d & obcs write_pickup have not yet been updated) +o pkg/monitor: + - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM + - fix mon_stats_rs (statistics over the full domain, even where field is zero) + - account for deep Atmosphere factor and density factor (anelastic) +o added open boundary conditions capability for seaice HEFF and AREA +o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) + thermodynamics + - requires a little reorganization, which affects the testreport results + of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, + so that now the conservative form is tested + - add a few comments +o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* +o add a little bit of code to gad_os7mp_adv_?.F to help vectorization +o add new diagnostics to seaice: advective, diffusive fluxes (only for + multidim-advection, for scheme 2 they are not filled) and transports, + thermodynamic growth rates +o change units of EmPmR (inside the code, + within coupling interface) + from m/s to kg/m2/s (mass flux) but leave input file unchanged. + Affects results @ truncation level (cg2d match) and update output of + experiments: lab_sea(6), global_ocean.90x40x15(10), + global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) + + adjoint results: global_ocean_ebm(11) and lab_sea (12). + Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). + Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). + +checkpoint59h (2007/09/29) +o pkg/exf: + - improve vectorization by moving if-statement out of loops in + exf_mapfields, exf_radiation + - exf_bulkformulae.F: introduce 2D fields and vectorize code +o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package +o testreport: + - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE + monitor & update offline_exf_seaice exp. output. + - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) +o pkg/seaice: + - bug fix in the evp solver: boundary conditions were affected be + masking of zMax/zMin (changes results) + - minor bug fix in boundary conditions in seaice_calc_strainrates + (changes results for no_slip) + - seaice_lsr.F: make interpolation of eta dependent on boundaries + - replace hardcoded lower limit for zeta (zMin) by runtime parameter + - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean + stress formulation and no-slip boundary conditions +o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP + in gad_calc_rhs.F ; add few safety stops in initialisation phase. +o pkg/seaice: a first HSALT time stepping equation has been checked in +o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV + in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem + without requiring DO-IF statements +o pkg/thsice: + use continuous power-law function for partition of energy between lateral + melting/freezing and thinning/thickening ; old code using step function + still available with #undef THSICE_FRACEN_POWERLAW + update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice +o testreport: change AD testing : check against results/output_adm.txt + using same scripts as for forward test. + +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") +o pkg/seaice: adding ice salinity HSALT as a prognostic variable +o pkg/seaice: changes for using pkg/seaice with pkg/obcs +o pkg/ecco: allow user defined cost function contributions +o testreport: + Allow to choose (per experiment) the list of tested output variables + and the main variable (used to issue a pass/FAIL ) ; + - for now, done by adding the specific list in file: [exp]/input/tr_checklist + - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; + Also modify printing of summary: + a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) + b) echo the list of tested variables in the individual summary.txt of + each experiment. +o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of + threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) + (but still depend on the tile decompostion of the domain). +o pkg/seaice: change a discretization detail to make the B-grid code + "more symmetric". This change is likely to remove all "ridges/leads" that + where quasi-aligned with the grid in B-grid solutions. It may also be + the solution to the stress coupling issues with the B-grid. +o each tested exp: add a "run" directory with a standard ".cvsignore" file ; + remove .cvsignore from input dir. (since testreport no longer run here). +o pkg/thsice: + - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" + - fix reshaping of sea-ice just after advection: + melt all the ice only if ice-volume is too small. + - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): + prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; + and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). +o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water + tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. +o define mass2rUnit & rUnit2mass as units conversion factor, used for surface + forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit + (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; + and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error + of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 + -> update output.txt +o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): + this affects truncation error: -> update output.txt of exp: + global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, + ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. + +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) +o pkg/ecco, ctrl, autodiff and mom_common: + internal parameter controls, completements of implementations +o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. +o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; + (not seem any difference in testing results). +o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains + at face corners. +o pkg/generic_advdiff: + - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) + loop range indices for computing vertical advection tendency + and do the calculation in the interior only (no overlap) ; + for now, only implemented for SOM advection (to save CPU time). + - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) +o exch2 adjoint + First set of changes: + - add exch2 hand-written adjoint templates + - exch2 hand-written no longer use TAF-flag 'nownew_arg' + This will require cleanup in pkg/autodiff/*.F + (changed routines currently kept separate in verif. code/) + - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC + that used to hide exch2 or cubed-sphere specific code + (commented via 'cph-exch2') +o pkg/seaice + - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. +o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update + output of global_ocean.cs32x15.thsice . + +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). +o starting implementation of Duffy et al. (GRL 1999) salt plume scheme + (#ifdef ALLOW_SALT_PLUME) +o gather_2d/scatter_2d: removed halo regions +o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 + scheme and the corresponding test case (under front_relax dir). For now, + only available with Skew-flux form and not yet tested in realistic set-up. + adjoint: store directives updated, but gradient checks deteriorated, + so maybe GM/Redi adjoint is now broken. +o seaice adjoint + * add AREA, HEFF, HSNOW as control variable + (should not change lab_sea results) + * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 +o pkg/seaice: + * added computation of saltFlux in seaice_growth; + For time being, sea ice salinity is assumed constant + contribution of snow flooding to freshening of sea ice is neglected. + SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it + defaults to 0.0 in order to maintain backward compatibility. + Typical values for SEAICE_salinity are 4 to 10 g/kg. + * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F + * added SEAICE_availHeatFrac, which specifies fraction of surface level + heat content used to melt or grow ice + * commented out cap of HICE: it helps keep ice thinner + * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option + * applied OBCS T/S mask to HEFFM sea ice mask + +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) +o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" + and change default value of parameter "GM_Small_Number"; + update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, + global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, + tutorial_global_oce_biogeo, tutorial_global_oce_latlon +o pkg/ecco: cost function when applying pkg/smooth to controls +o pkg/ctrl: add forcingPrecond run time parameter +o pkg/seaice: + - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code + - fix bug in metric terms of u-equation in LSR solver (implicit part), + changes verification/lab_sea + - rearrange implicit part of u-equation in LSR solver to make it easier to + read, understand, and debug. This causes changes at the truncation level. + - fix (serious) bug in the boundary conditions (sign error in the implicit + part) of the LSR solver. Changes all LSR results. + - fixed problem with HSNOW initialization to avoid thick snow when AREA + is initilized with small values - does not change lab_sea results. + - added HsnowFile initialization capability +o pkg/smooth: addition to model/src and pkg/ctrl so allow + initialization of pkg/smooth and application to control vector +o pkg/seaice: fix another bug in the LSR no-slip boundary conditons +o dependencies: pkg/profiles requires pkg/cal +o pkg/profiles: + - added option ALLOW_PROFILES_GENERICGRID + -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming + that interpolation information (grid points and coefficients) is provided + within the netcdf input files. + -> sample matlab scripts can be found in MITgcm_contrib/gael + that allow you to prepare netcdf input files. + - also modified: cleaner include statements, cleaner error print statements, + cleaner stops when error, and more tests of the netcdf input files consistency. +o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. +o pkg/seaice: + - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this + requires a new routine: seaice_diagnostics_fill.F + - make sure that seaice does not move if not forced (pressure replacement + method, Hibler and Ip, 1995), changes results + - and new damping criterion for EVP solver according to Hunke, JCP, 2001 + - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). + It is turned off by default (=-1.), because it changes the results. + - make it possible to read AREA from a file, too. + +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: + - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs + (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice +o pkg/obcs: + - bug fix for balance code +o pkg/seaice: + - allow values of SEAICE_elasticParm > 1 + - add new parameter SEAICE_evpTauRelax as an alternative + to SEAICE_elasticParm + - make lsr boundary conditions free slip (by default), changes result + - add code for no slip boundary conditions for lsr + - set minimum of zeta to zero (and not 4e8) (changes results) + - add a cap on AREA after advecting AREA if seaice_growth is not called +o change calculation of Visbeck K: + - no longer depend on tapering scheme; instead, compute slope (limited + by GM_maxSlope). this is equivalent to what was comuted before with + clipping or linear tappering. + - fix vertical averaging (wrong by 1/2 level) + - leave the old version (but will not be maintained) within + #ifdef OLD_VISBECK_CALC / #endif + - update output of exp. ideal_2D_oce +o change error catch in calc_r_star to improve vectorization +o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and + add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). +o adjoint: + Re-organized adjoint checkpointing according to Matt Mazloff + (but with modifs/completions/cleanups) + Storing is now bundled into large arrays to optimized I/O + (and second step in cleanup of the_main_loop) + +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: + - get rid of three more exchanges seaice_calc_viscosities (required + different loop boundaries in seaice_lsr and seaice_ocean_stress) + - bug fix in seaice_ocean_stress (update of lab_sea required) + - reduce loop boundaries to necessary minimum also in seaice_evp + - go back to the old way of computing deltaC/Z as the adjoint likes that + better +o Refresh of tutorial_global_oce_latlon (includes changing salinity-like + passive tracer to an Age Tracer) + update output.txt +o pkg/exf: + - implement A-grid / C-grid selection for wind-stress input files. + - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) + for now, in exf_bulk_largeyeager04.F only : + - change implementation for case where windspeed + 2. components wind-stress + are read-in. AND use rhoConstFresh to convert evap. +o pkg/seaice: + - use correct EXCH_UV for wind-forcing (on A-grid). + - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding + SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops. +o pkg/exf: + - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC) + EXF_INTERPOLATION: + - merge global_with_exf/code version of exf_interp_read.F + to the main code ; + - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when + reading the file ; Important: This options needs to be defined to recover + previous code. + otherwise, use fixed size array to read in (size=exf_interp_bufferSize). + - no longer loose real*8 precision along the way when using exf_iprec=64. +o pkg/seaice: rearrangement of common blocks (really needs more cleaning up) + - change discretisation of evp-solver in order to avoid another exchange + (changes lab_sea) and clean up a little + - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS) + help the adjoint (this also changes the results slightly) + - add a few "_d 0" where they had been missing in seaice_evp.F + - cleaning up: remove unused seaice_calc_rhs.F +o pkg/exf: some cleaning-up: + - change various "constants" into runtime parameters + - cleaned-up Large&Yeager04 routine which should eventually + replace exf_bulkformulae.F (changed names of S/R and CPP) + and merged various ALLOW_ATM_WIND options + only used with thsice pkg (in thsice_get_exf.F): + - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04) + which are used when useStabilityFct_overIce=TRUE (= the default) + - change default values of ice & snow emissivity and scale downward LW + by ice & snow emissivity. +o pkg/thsice: + fix few little problems, in thsice_calc_thickn.F: + - growth vertically (and not laterally) if iceFrac == iceMaskMax + - melt only laterally if hIce < hThinIce (as the comments say) + and in thsice_extend.F: + - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) + - start to form ice as soon as the minimum ice-volume is reachable. + update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice), + and cpl_aim+ocn +o pkg/kpp + - move computation of surface related input fields to KPP into a new + subroutine kpp_forcing_surf.F + - remove wrong (within bi,bj loops) EXCH calls. + - little cleaning (add argument myThid in last position, cvs header ...) + - for now, fix conservation problem by exchanging KPPviscAz (may not + be the best fix) +o pkg/seaice + - check for inconsistent evp parameter/cpp-flag combination + - remove leftover errIO flat for obsolete name list error handling +o OpenAD + - changed verification/OpenAD to full baroclinic setup (including GM/Redi) + +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 + himin0 -> hThinIce + hihig -> hThickIce + i0 -> i0swFrac + transCoef -> bMeltCoef + frac_energy -> fracMelting + add new parameters: hNewIceMax, fracFreezing, dhSnowLin + with default values (for now) that do not change the results. + remove old version of thsice vars advection in pkg/seaice. +o in FFIELDS.h: + - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD + - make pLoad & sIceLoad always available (but still only used if + ATMOSPHERIC_LOADING is #define). +o pkg/kpp: replaced _KPP_RL with _RL +o bug fixes for vertical diffusivity computations when both KPP and + 3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F + are no longer updating the vertical diffusivity array + (passed as argument) but are (re-) setting those arrays. +o pkg/seaice: fix bug in evp solver, while doing that + - change (improve?) discretization of stress computations for both + cgrid-lsr and evp solver + - add a new routine to compute strain rates + - the above changes lab_sea results + - add no slip conditions for evp solver (off by default), lsr-version + may follow + - fix exchange for shear at Z-points (does not change lab_sea) + - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp + (to force the user to pick a time step since there is not "safe" way + of choosing it) + - add principal stress diagnostics + - rearrange fields for evp a little to avoid having to call a: too many + exchanges and b: exchanges for stress trensor components which we do + not have. + - modify Hibler+Bryan (1987) stress coupling so that it reuses information + of evp, complete rewrite for lsr case (latter is does not yet work + in all cases) +o pkg/kpp: add code to have mixing in shelf ice caverns + - add myThid to all kpp routines (long overdue) + +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 + - move exf header files from lower_case.h to UPPER_CASE.h ; + add missing cvs Header & Name + - add adjoint routines and flow dirs for newly used exch_uv_agrid routines + - add namelist param. selectStressGridPosition, exf_monFreq + - retire many _CLIM routines, and remove data.exf_clim + + params moved to data.exf + + climsst, climsss now handled by exf_set_gen, i.e. + climss?period=0 refers to constant field, + climss?period=-12 to monthly forcing + - split up namelists in data.exf +o pkg/seaice: + - remove seaice_exch and seaice_exch_uv + - remove superfluous exchange of theta + - add myThid to seaice_budget_ocean/ice + - add new interface for atmospheric wind forcing (C-grid only) + + new routine + + two new field (taux, tauy for stress over ice) + + removed one global field (DAIRN) for C-grid case only +o pkg/thsise + - 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 (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 + diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file. +o Added capability for 3D specification of background vertical diffusion + coefficient. This is done by (i) #define ALLOW_3D_DIFFKR + in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime + "data" file that contains the 3D vertical diffusivity coefficients. +o ice dynamics (pkg/seaice) with thsice thermodynamics: + - add code within pkg thsice to advect & diffuse sea-ice fields + similar to (and will replace) what has been added in seaice_advdiff.F, + but: - conserving Mass, Heat & Salt. + - 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 (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). + - adapt utils/matlab/rdmds.m to read this format. + for now long-line format not yet supported by pkg/mdsio (& exch2). +o shelfice: add a few diagnostics + +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). + Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) + and tutorial_plume_on_slope (sensitive to truncation) +o seaice: if ALLOW_ATM_WIND is undefined use wind stress + directly to drive seaice model (C-grid only) +o exf: when input wind-stress (#undef ALLOW_ATM_WIND): + - reintroduce computation of wind from stress, + - compute tau (in exf_bulkformulae.F) from windstress averaged to + mass points to avoid tau = 0 + - fix serious bug: (1/3) in Fortran is not the same as (1./3.) +o rdmnc.m: make it work with "global" files created with gluemnc +o rdmnc.m : some improvements in dealing with singleton dimension + (tested on all testreport mnc output files). +o genmake2: disable pkg/profiles if netcdf test fails. +o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output. +o move call to cal_readparms up to make calendar parameters/variable available + to all packages + +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 +o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields + and portions thereof. See read_cs.txt for description and examples. +o utils/matlab/cs_grid/bk_line: to compute transport through passages, + add a script (grt_circ_bkl.m) to generate broken-line between 2 points, + following the great-circle arc between those 2 points. +o trap un-initialized variable with pathscale compiler on weddell.mit.edu + (thanks to Constantinos): fix few problems and get (almost) all exp to pass. +o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in + - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) + - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81) + - still needs work (not working with some options ; efficiency to improve) + and serious testing. + - use this scheme for temperature & salinity in 2 advection test exp.: + advect_xy & advect_xz, respectively. + +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. +o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent + momentum calculation. +o gad_advection: fix vertAdvecScheme (if different from advectionScheme) +o some cleaning: usePickupBeforeC35 no longer supported ; remove this option. + remove checkpoint.F and the_correction_step.F (no longer used); + do the k loop inside CYCLE_TRACER (supposed to be more efficient). +o add option (linFSConserveTr) to correct for tracer source/sink due to + Linear Free surface +o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine +o pkg/thsice: fix reading mnc-pickups + +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 + move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & + mdsio_write_field.F (S/R MDS_WRITE_FIELD); + - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD + - collect old S/R in one file: mdsio_rw_field.F (now just a call to + either MDS_READ_FIELD or MDS_WRITE_FIELD ) + - new S/R (to replace MDSWRITEMETA), which allows to write more + informations (variable names, time ...) to meta files. + - modify rdmds.m to give back the meta file content. +o pkg/diagnostics: change vertical interpolation to be safer, and more + flexible (define p-levels to interpolate to in data.diagnostics); + add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right + diagnostic pointer. +o pkg/seaice: more cleaning up of seaice_growth, added many comments +o pkg/exf: put runoff0 and runoff1 into the appropriate common block +o fix multi-category seaice: + - change cpp flag SEAICE_MULTILEVEL to more meaningful name: + SEAICE_MULTICATEGORY + - fix short wave heat flux +o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics + and allow to use EVP solver. Change forward lab_sea: test both EVP + solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) +o Initial check-in of lab_sea adjoint + (very similar to natl_box_adjoint/code_seaice) + * used C-grid and EVP solver + * used KPP, GM/Redi + * uses inAdExact=.TRUE. + * gradient checks fail for both ADM and TLM + due to sensitive snow melt code in seaice_grwoth (look for "JZ") + f.d. gradients actually seem more problematic than ADM, TLM gradients; + issue is related to forward mismatch between g77 an ifort +o pkg/seaice: overhaul of thermodynamics + - growth.F and groatb.F are replaced by new routine seaice_growth.F + - budget.F is replaced by two new routines seaice_budget_ocean/ice.F + - move a few global fields out of SEAICE.h into seaice_growth.F and + make them 2D (FICE/QNETO/ ...) + - remove FO (it is the same as QNETO) + - introduce a few local fields to avoid modifying external fields such + as atemp, etc. + +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 + genperiod=-12 means input file contains 12 monthly means +o CG2D: use pre-computed solver main-diagonal (stored in common block); + this affects truncation error ; generate new output file for exp. which + fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), + global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), + ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), + MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), + tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), + vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) +o start implementation of deep-atmosphere and anelastic formulation +o verification: remove 2nd copy of input files and use script "prepare_run" + to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) +o mom_common/vecinv/fluxform: fix a few initialisation isssues +o profiles: fix for multithreaded case + +o diagnostics: rename few diags: + s/'PRESSURE'/'RCENTER '/g + s/'TICE '/'oceFreez'/g + s/'TAUX '/'oceTAUX '/g + s/'TAUY '/'oceTAUY '/g + s/'SWFLUX '/'oceQsw '/g + s/DIFx/DFxE/g + s/DIFy/DFyE/g + and add few ocean-forcing diagnostics: + atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS +o modifications to pkg/seaice/growth.F and budget.F, which change results of + lab_sea experiment: HSNOW was sometimes treated as effective and sometimes + 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 (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 + computations of EVAP, PRECIP, HSNOW, and GHEFF +o add ability to read bathy, salt, and theta using MNC (off by def) +o add flooding algorithm and advection of HSNOW for pkg/seaice; + both are turned off by default and do no change any results +o seaice advection with pkg/thsice: a step toward the use of non-linear + advection scheme, but #ifdef or commented out for now (requires more EXCH). +o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens + (identical results) and the standard version of EXTERNAL_FIELDS_LOAD + in natl_box (affects results @ truncation level: update output.txt) +o multi-threading and IO: + - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. + - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls + (needed to work with SingleCpuIO): tested in all verif. exp. +o GAD: use simpler DST3 formulation as default (old version left within #ifdef) + affects the results (but none of the verification test uses this scheme). +o Adding some pkg/diagnostics capability to pkg/seaice + (will certainly be subject to changes) +o ctrl: adding new control variables: + lwflux, lwdown, evap, snowprecip, apressure, runoff + +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. +o clean-up multi-threaded problems (reported by debugger tcheck on ACES); + add (in global_with_exf/code) a version of EXF_INTERP_READ without + dynamical allocation (seems to work in multi-threaded). +o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using + 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 (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 + - remove stop for combination non-hydrostatic code and shelfice. That does + not mean, that the results are correct, but at least they are numerically + stable +o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) +o added adjoint exch routined for all exch*3d* routines + and updated flow directives + +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) + and clean-up reading/writing of pickup files. +o fix local version of read/write pickup (NH part) in rotating_tank/code +o simplify EXCH interface: + - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) + - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version +o added the regrid package +o shelfice: + - 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 (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. + - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); + - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls + to work with SingleCpuIO. +o add "_d 0" to real constant of pkg/cfc subroutines ; + update exp. cfc_exemple & tutorial_cfc_offline output files. +o multi-threading and IO: + - all threads call READ_FLD S/R (needed if using SingleCpuIO): + (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. + - barrier before and after reading. + - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) + - avoid using MDS_WRITELOCAL for LAND pkg output. + - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics + common-block variables ; Allows multi-threading with master-thread IO. +o change default MAX_NO_THREADS from 32 to 4 ; + and stop cleanly when MAX_NO_THREADS is too small. +o add S/R BAR_CHECK to check multi-threaded barrier synchronization + +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. + keep global_ocean.90x40x15 (for AD testing) with former secondary test + (".qshyd") as the main test (mv output.qshyd.txt to output.txt) +o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; + add MITgcm_tutorials (= code + all the tutorials) +o ecco, option to compute cost for total ssh (mean+anom) +o consistent with addition of ptracer and ssh in pkg/profiles +o profiles: adding ptracer and ssh +o testreport: change multi-test output-file name + (from output.txt.{name} to output.{name}.txt) +o profiles: now ok for mutli-tiles case +o seaice: add 4 parameters for different advection schemes for area, + (effective) seaice thickness, enthalphy, and snow height. Their default + is the standard parameter SEAICEadvScheme +o calc_gw: + - add cosFacU in zonal viscous flux (harmonic.visc.). + - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. + of tutorial_plume_on_slope. +o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). +o calc_gw: true flux-form, account for horizontal grid spacing. + update rotating_tank results, but not plume_on_slope (affected at + truncation level, 11 digits). + +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. + - fix for partial-cell & non-uniform dz; update plume_on_slope results. +o commit code to make SST/SSS weights spatially variable + (based on either variable in-situ or variable initial T/S weights) +o pkg/ecco: + * commit code to relax deviations of xx_theta, xx_salt to 5*sigma, + now based on horizontally varying weights wthetaLev, wsaltLev + * cost_averagesflags now returns year indices in addition to day, month + * sflux balance is performed on annual basis + (sflxumm, sfluxmm2, bal_sfluxmm) + * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, + including separate counting and multipliers +o pkg/rbcs + * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing + +checkpoint58k_post (2006/07/06) +o testreport: + - always build in dir. "build" (if not there, mkdir build instead of building + & running in input) + - run in dir run (if it exists), in build otherwise. + - call prepare_run (if input/prepare_run exists) + - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. +o pkg/exf modifications to interpolation and rotation routines for more + reasonable treatment of North Pole singularity: for tracers North Pole + value is set to northernmost zonal-mean value, for zonal velocity it is + set to zero, and for meridional velocity it is set to northernmost value. +o pkg/exf/exf_check_range.F + - add tile index to diagnostics and move stop statement to the very + end of the routine. +o pkg/diagnostics: (diagnostics_main_init.F) + define title of isomorphic variables according to the current config. +o pkg/thsice with pkg/seaice dynamics: +- fix domain of computation (interior only, required for exf) and do exchanges +- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient +o towards a standard way of dealing with multi-threading in MONITOR + and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. +o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) + to W momentum equation in nonhydrostatic and quasihydrostatic runs. +o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. +o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) +o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL + (problems ? with gradient check in bottom_ctrl_5x5 adjoint test) +o tracer advection: + - clean-up and simplify calc_common_factors.F + - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer + 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 (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 +o adjoint store dir. adjusted accordingly +o genmake2 + replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. + +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 + in the_main_loop.F to avoid Pb (e.g., when running fizhi test) +o vector_invariant: fix highOrderVorticity(=4.th.Order) advection + on CS-grid: no longer loosing mass. +o exf & curvilinear-grid: no longer modify longitude xC & xG. +o pkg/ggl90: fix sloppy output and fix a bug +o pkg/seaice: added SEAICEuseEVPpickup parameter + - Set to false in order to start EVP solver with + non-EVP pickup files when using SEAICEuseEVP + - fix sign error in diffusion in seaice_calc_rhs + +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 + o add non-self-adjoint cg2d_nsa + o update autodiff support routines + o re-initialise hfac after ctrl_depth_ini + o works for 5x5 box, doesnt work for global_ocean.90x40x15 +* Adding verification for 5x5 box (4-layer) bottom topography control + +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 +o pkg/ggl90: + - add parameter (minimum surface kinetic energy) + - fix bug (avoiding division by zero) +o couple pkg/thsice to pkg/seaice: + - modify advection in seaice to accomodate new scalar fields to be advected + - only muliDimAdection scheme work with seaice/thsice + - mapping of thsice-variables to seaice-variables, back and forth + - does not break the verification experiments, but does not give the + desired results either +o pkg/seaice + - make (default) second order advection a bit less confusing? + +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 + - add an additional formal parameter to thsice_solve4temp +o pkg/exf: + - add new fields wspeed, snowprecip (to be able to couple to thsice) + - correct Stefan-Boltzmann constant + - new parameter for longwave surface emittance + - separate some stuff from exf_bulkformulae into new routines + exf_radiation, exf_wind + - add new parameters and constants: longwave emissivity for ocean, ice + and snow, evaporation parameters over ice + - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute + either wind from stress or stress from wind +o pkg/thSIce: +- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F +- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND + and THSICE_CALC_THICKN +- for now, call to THSICE_GET_BULKF remains inside i,j loops. +- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h + to make debugging easier. +- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output +o pkg/bulk_force: + - clean-up comments and parameters ; + - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; +o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; + generate new output for test-experiment: aim.5l_cs.thSI +o results_ad : rename "output.txt_adm" to "output_adm.txt" and change + testreport accordingly + +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/ ) + * need to sort out init. of h0facc, etc. +o Make pkg/profile fully independent of ecco,cost, etc. stuff + to be able to use it in pure forward. + +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) + tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) + tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) + tutorial_global_oce_biogeo <- copy of dic_example + tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) + tutorial_plume_on_slope <- copy of plume_on_slope + tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) + tutorial_global_oce_optim <- empty for now (David ?) + tutorial_global_oce_in_p <- copy of global_ocean_pressure + some tutorials (R1) were already checked-in under tutorial_examples in release1_branch +o correct a sign problem in cost_scat.F +o obcs and ptracers: fix boundary conditions for advections schemes + with larger stencil +o thsice adjoint: start +o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for + completeness +o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING + and COSINEMETH_III, add comments in default CPP_OPTIONS.h +o ptracers adjoint: + * avoid extensive recomputatations + * fix missing re-init. of gptr (missed by TAF) +o obcs: add a flag (OBCSprintDiags, defaults is true) that allows + me to turn off the excessive output to STDOUT that this package produces +o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common + and add those terms in Vector-Invariant formulation. +o in ctrl pkg, if ALLOW_CAL, use monthly mean controls + if the control period (xx_hfluxperiod etc) is 0 +o in profiles pkg, clean routines and fix details +o in ecco pkg, reading ssh data: + fix problem in case the model does not start at iter0=0 +o fix mnc-pickup/restart for ptracers +o new package prifiles: + code to compute profile-based cost by Gael Forget + (modifs in ecco, ctrl, autodiff) +o Benign bug fix in initialization (spotted by M. Mazloff) of + ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F + +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 + documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in + SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only + with SEAICE_CGRID defined. +o move calendarDumps from "data" to "data.cal" and clean-up the code + with a simple call to pkg/cal S/R: CAL_TIME2WRITE +o add useEXF & useCAL flags (for now, set in hard-coded way) +o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum + (were missing in NH mode, and wrong in quasihydrostatic mode). + waiting for Chris updated version of calc_gw to add those CALLs. +o fix bug in quasihydrostatic S/R ; + add a test for this option: global_ocean.90x40x15.qshyd +o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs. + (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS) +o add on/off flag useOffLine for package OFFLINE +o seaice: + - modify advection so that it works also on the C-grid + - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes + problem in multi-tile runs with C-grid + - add flags for clipping ice velocities and/or masking solver forcing + - fix drag (ocean on ice) formulation and a bug that caused noise in the + C-grid solver + - added a few comments to seaice_diffusion.F + - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V + are now exclusive) + - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which + required re-ordering the code a little: + + make DAIRN global variable (defined in SEAICE) + + 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 (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: + + shrink lookup tables by factor of ~4 + + better error reporting when running out of lookup space + + able to handle longer path/file names (up to 500 chars) +o adjoint: + - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. + - TBD: "hidden" mom_vecinv recomp. in dynamics +o change forcing_In_AB to affects both T,S forcing and Momentum forcing + (allow to differentiate between forcing components using new integer flags: + momForcingOutAB=1/0 & tracForcingOutAB=1/0) + and add new flag to put Dissipation tendency out of Adams-Bashforth. +o ecco + - enable trend removal from SSH anomaly obs. +o adjoint + - a fix for PmEpR when #undef EXACT_CONSERV + - fix of "hidden" recomp. in thermodynamics (no TAF warnings) + - try to fix "hidden" recomp. in forward_step for NLFS + (NLFS seems broken sometimes after I checked it in) +o seaice: + - add c-grid version of the dynamic solver: + + three new routines that are the c-grid substitute lsr, dynsolver + and ostres + + put a few fields that were local to dynsolver into global common + blocks, so that I can move the computation of stresses etc into + seaice_lsr (saves coding but may break the adjoint). + - replace more hardwired parameters by runtime parameters + - add ice masks that mask the rhs of the implicit solvers where there + is no ice (commented out in seaice_dynsolver, because i am not sure + if this works properly), eventually this should replace the clipping + of ice velocities in seaice_dynsolver to +/-40cm/s. +o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly + include it only where its needed +o move balancing of fluxes before the call of external_forcing_surf +o seaice: + - correct units of turning angles (now they are really in degrees) + - move computation of GWATX/Y out of main routine into dynsolver + - initialize GWATX/Y in seaice_init +o Apply mask on Fresh-Water flux (needed for SSH forcing). + update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) +o seaice: add runtime flags for turning angles (default to zero) +o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean + and trend from exf forcing and ctrl control adjustments +o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF + (since checkpoint57x_post) +o change the default rotation period to 86164.s = the Earth rotation +o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) + and based on a reference stratification. Tested within hs94.cs-32x32x5. +o seaice advection: add code for choosing between the default (2nd order + central differences) and multiDim advection schemes provided by + pkg/generic_advdiff +o seaice: + - removed all references to SEAICE_GRID.h fields from + dynsolver, advect, diffus, lsr, without changing the results of lab_sea + (cubed-sphere configuration will change a little) + - grid computations in seaice_init are obsolete now. + - cleaned up code a little so that is easier to read (hopefully). + - added new (better?) discretizations of default advection and diffusion + (turn on with SEAICEuseFluxForm) + - replace 1 in 3d global fields by kSurface in growth.F + +checkpoint58a_post (2006/02/13) +o seaice: + - bug fix in advect.F +o shelfice: + - separate shelfice load anomaly from pload (breaks with time + dependent forcing), => introduce constant field shelficeLoadAnomaly. + Its default is 0., but it may be computed more cleverly from (unknown) + t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be + done offline. A good approximation of the pressure load anomaly is + necessary to avoid large initial adjustment processes underneath + deep-reaching shelfice. + - small fix in ISOMIP shelfice_thermodynamics + - add more sophisticated thermodynamics of Hellmer (1989), this is + now the default + - give a few constants more intuitive names +o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful + if bulk formulae are used in long integration (especially EmPmR). Turn + on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01 + if balancePrintMean, the imbalance that is substracted is printed to + STDOUT. +o fix bug (typo) in obcs_apply_eta.F +o add a new package shelfice which enables us to model the circulation + underneath shelf-ice with draughts of hundreds of meters. + - works + - to do: + include improved thermodynamics + + check whether kSurfC (from model/inc/SURFACE.h) can be used + instead of new field kTopC + + can we use topoFile, Ro_surf and existing code in ini_depth.F + instead of new field R_shelfIce and new code in ini_depth.F + and ini_mask_etc.F? + + adjust vertical mixing schemes? +o seaice pkg: + - add a cpp-flag to include a simple formula for a salinity dependent + freezing point of sea water at the surface + - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and + meridional stresses are now different (and hopefully correct) +o AIM pkg: change threshold on large-scale condensation to conserve Heat. + update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics + and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG) +o pkg/diagnostics: add options and parameters for regional-statistics + diagnostics ; define regions by reading a region-mask from a file + (might add other options later) +o pkg/bulk_force: + - add option and parameters to use AIM surface-flux formulae. + - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ; + others forcing fields (defined in PARM05, parameter file "data") are loaded + from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F). + - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F + - use the right EXCH call for uwind,vwind (to work on CS-grid). + - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h) + and parameters (note: calcWindStress replaces .NOT.readwindstress). + - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). + +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 + (*.[fFhc] + Makefile) used for the build within the executable + - requested by CNH but off by default + - adds a paltry <9MB to the mitgcmuv executable in most cases + - only writes the output when useEMBEDSRC in eedata is true +o clean up 3-dim. relaxation codes: + * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec + * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) + * Thanks to Tom Haine for testing! + +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 +o fix a bug in ptracers_external_fields_load +o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...) + affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) +o transfered surface NH pressure to eta field (if exactConserv). +o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign) + and update lab_sea output.txt file. +o completing 3-dim. relaxation code: additional term + 1/tau*( theta(i,j,k) - thetaStar(i,j,k) ) + in S/R EXTERNAL_FORCING_T (file external_forcing.F) + * At compile time, in "EXF_OPTIONS.h" set + #define ALLOW_CLIMTEMP_RELAXATION + #define ALLOW_CLIMSALT_RELAXATION + * At runtime in "data", under &PARM03 set (e.g., units in seconds) + tauThetaClimRelax3Dim = 15552000.0, + tauSaltClimRelax3Dim = 15552000.0, + * 3 cases: + 1) Use a constant-in-time 3-dim. field + 2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec. + 3) Real-time relax. to time-evolving prescribed field +o Adding Laplacian-type smoothness constraint on + initial and boundary (forcing) controls (ic, bc) + * enable at compile-time via + ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION + * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1 + * Absolute scale somewhat unclear so far + * no area weighting was included since no other cost term does so far + +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 (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) +o add new offset feature to offline pkg (plus minor cleanup) +o cfc fixes for final year of integration +o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should + be in GCHEM_OPTIONS). + +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) + - allows the vast majority of our tests to work with gfortran +o Non-Hydrostatic: + - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h + - fix exchange calls for CS-grid using the new EXCH_S3D_RL. +o Allow to apply AB on T,S rather than on AB(gT,gS): + - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 + - use the same arrays (gtNm,gsNm) to hold tracer field at previous + time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). + - need a "clever" read_pickup to restart from the other AB formulation +o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h +o remove some unused variables (reduces number of compiler warnings) +o adjoint + * Disable useVariableViscosity for adjoint for time being + (there are a number of extensive recomputations) + * Initialize certain variables needed for adjoint + +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. +o write grid-file(s) in only one format (MDS or MNC): default=MNC (if + using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc +o tracer advection scheme: + add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get + those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, + was not very convenient). + add implicit version for DST-3 & DST3_Flux_Limit vertical advection; + (further tests needed for the implicit DST & Flux-Limiter schemes). +o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef + and sRef for convenience, handy, when you want to initialize + ptracers in a large domain with a constant non-zero value. Also, + untangle ptracers_init.F a little. + +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 + identical results for a few days of testing +o add new parameter: sideDragFactor to enable half-slip-side BC + and change side-drag S/R to use viscosity from mom_calc_visc + (can switch back by setting sideDragFactor=0.); affects results at + truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), + global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). +o vorticity & strain are now computed without masking, to account for + no-slip-side BC in variable viscosity calculation ; mask is applied + anyway later on, before computing advection/coriolis terms. +o modify exp4 to test new obcs support for reading from external files + and for passive tracers +o fix behavior of ptracers_monitor when monitor output is written to a + netcdf-file; still not independent of monitor.F (writes in the same + file). +o change default value of tRef (put a uniform, meaningful value for ocean + & atmos) and initialize sRef (was missing, as Martin mentioned). +o Redefine viscC?Leith*. Change the coefficients of Leith viscosity + to be proportional to enstrophy dissipation length. Thus, + viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) + This is now consistent with Smagorinsky and with the manual. + +checkpoint57u_post +o OBCS and PTRACERS: add open boundary support for passive tracers + - either use homogenous (pseudo) v.Neumann conditions or prescribe + OB-values from file; this is not different from the way theta and salinity + are treated + - however, Orlanski-radiation conditions are not supported, and the model + will stop if you use pTracers and Orlanski at the same time. + - beefed up the rountine obcs_external_fields_load: now only those open + boundary values are overwritten with values from files for which there + are really files, otherwise the OB-fields remain untouched. This makes + it possible to use different OBs at different ends of the domain (as + with EXF) +o reduce number of exch calls in shap_filt (s2). +o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ + truncation level) 4/5 MLAdjust test results (11&12 digits match). + +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 + test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). +o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); + note that biharmonic viscosity + no-slip was not tested in any experiment. +o fix bug in non-linear free-surf side-drag ; generate new output for + global_ocean.cs32x15(+.thsice) & global_ocean_pressure. +o make mnc honor the writeBinaryPrec flag for most kinds of output +o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum +o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation + error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). +o add brackets in multi-terms sum to get same truncation, independent of + the face number (manage to get exactly same value of gU,gV at the cs-edge) + affects several test. exp. Update global_ocean.cs32x15 (+.thsice). +o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax + and viscA4Remax, which allow one to limit the minimum viscosity by specifying + a maximum grid-scale Reynolds number. Also, changes all length calculations + in the case of grid anisotropy to geometric mean of dx**2 and dy**2. + Suggested values of viscosity parameters found in mom_calc_visc. + Many new viscosity diagnostics available. + +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 + used simultaneously, and to be used in mom_vecinv and mom_fluxform. + Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) + and with Strain-Tension viscous term calculation (mom_hdissip.F). + The Strain-Tension form is now called with useStrainTensonVisc=.true. + ViscAhStrain and viscAhTension are now retired. +o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". +o In response to JMC's bug report, genmake2 now ignores any soft-links + that it finds in the *current* directory when searching for files. + Soft-links found in any other source directories will still work as + they did before. +o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls + a C routine to unlimit the stack size +o mnc-ify pkg/aim snapshot vars +o mnc-ify pkg/land as requested by Daniel +o various changes to mnc including: + - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format + - output can now be grouped so that all files within a group + change the ITER portion of their names in lock-step together + - can now read ("global") PER-FACE (in addition to PER-TILE) files + and works with both EXCH1 and EXCH2 (but needs more testing) + - writing works for all verification test cases w/ g77 on Linux + +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. +o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) +o remove MINIMAL_TAVE_OUTPUT option ; + add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). +o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src + allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) +o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) +o add time-dependent SST, SSS control +o cost terms in ecco/ modularized (new cost_generic.F) +o cost_averages routines are modularized (new cost_averagesgeneric.F) +o new infrastructure for seaice model vs. obs misfits in seaice/ + * driver from the_main_loop.F is seaice_cost_driver.F + * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) + * gradient check in Exp. 6a of natl_box_adjoint/ +o natl_box_adjoint input_seaice for Lab. Sea now available online via wget + (see README file) + +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 +o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) + update exp. cpl_aim+ocn output. +o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT + Needed for high-res. runs with large global files + to be able to limit tapelev size +o Changed some tests for adjoint: + * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT + * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT + * global_ocean.90x40x15/ back to default 3-level checkpointing +o Modifications to enable scripted COMMON to MODULE conversion + * verification/OpenAD/code/ has necessary scripts and description; + * converts, compiles and runs successfully; + +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) +o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) +o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F + (was already the case for dissipation with mom_vecinv, + and also the case for grad.PhiHyd when staggered-timeStep) + This will allow to put dissipation out-off the AB time-stepping. + Unfortunately, affects truncation error. Update output of exp. that "fails" + (cg2d matching number) and leave the others for later: front_relax(10), + 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 (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 + for ideal_2D_oce and lab_sea on linux_ia32_g77 +o set to #undef CTRL_SET_OLD_MAXCVARS_30 + in global1x1_tot/code_seaice_adj to access indices 32, 33 + (worth another tag) + +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. +o Implementing partitioning in time-mean and variable adjustment + for atmos. state. +o Time-mean constant error is now read in data.ecco (instead of hard-coded) +o in natl_box_adjoint: + * updated exp 1 to 10 + (but does not have time-mean vs. variable split results yet) +o updated global1x1/*_seaice_adj/ + to incorporate latest changes +o enable useSingleCpuIO for mdsio vector routines + (applies in particular to tapelev I/O) +o removed inefficient K-loop in all active_file*control*.F + +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 (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) +o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). + Affects results of exp. rotating_tank ; update output.txt. +o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor + and taking the square quantity and/or using a fraction-weight field. +o fix aim_diagnostics_init.F mate numbers. +o add mnc output capability to diagnostics/diagstat and update + our cvsignore files for the ACSII output generated + +checkpoint57k_post (2005/07/02) +o lab_sea now uses diagnostics package and provides a suite of + new EXF diagnostics output. + +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); + terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. + * extended diagnostics output + - now includes all EXF variables + - hs, hl moved to common block + - separate S/R for diagnostics, called after ctrl vector is added + - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet + - EXFqnet contains true Qnet (i.e. includes qsw) + * updated verif. lab_sea, global_with_exf + * Rearranging hflux (exf_mapfields -> exf_getforcing) + to ensure that diagnostics sees a true EXFqnet +o add matlab scripts for CS-grid vectors (in utils/cs_grid) +o diagnostics pkg: change pointers so that 1 diagnostic can be used + several times with different frequencies. +o mnc-ify the thsice package as requested by Daniel Enderton + - the monitor--MNC output needs work + - many attributes need to be added (most are currently blank) +o mnc-ify theaim_v23 package as requested by Daniel Enderton + - many attributes need to be added (most are currently blank) +o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) +o add Sadourny like discretization to the 4th.O vorticity advection scheme +o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. + update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, + fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). +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 (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 ; + add 1rst Order upwind vertical Shear. +o add a quick fix for A/B checkpointing in OFFLINE mode +o add IGNORE_TIME define and -ignore_time option to genmake2 as an + end-run around the C/Fortran linking horror in eesup/src/timers.F +o added pkg/runclock: allows user to terminate run based on wall clock +o added non-hydrostatic scaling parameter: nh_am2 +o pkg/my82: futile attempt to make results compiler-independent by adding + some "_d 0", etc. no effect. +o for mnc output, fill the 'T' coordinate var with myTime and create a + separate 'iter' variable for iteration count +o pkg/diagnostics: + add new capability: output of Global/Regional & per-level statistics ; + tested against monitor output (including land & thSIce) on various exp. +o make seaice-pkg I/O type flags (MNC/MDS) more standard. + +checkpoint57h_done (2005/05/19) + tag after changing user customized files (DIAGNOSTICS_SIZE.h, + data.diagnostics, data.gchem, data.ptracers) is done. + +o pkg/diagnostics: prepare for Global/Regional statistics. + add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h +o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE + and rename it: DIFFERENT_MULTIPLE + +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 (2005/05/12) + +o in mnc, let the user create the output dir if both mnc_outdir_date + and mnc_outdir_num are false +o add fflags() to pkg/diagnostics which allows one to specify, on a + per-file basis, the file precision [default behavior is unchanged] +o added diagnostics to pkg/kpp, including computation of mixed layer + depth based on a temperature/density criterion +o updated verification/natl_box to test the new pkg/kpp diagnostics +o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) +o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) +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 (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 (2005/04/15) + +o make lambda[Theta,Salt]ClimRelax spatially varying + (default remains spatially uniform constant based on tau) +o added new control variables + * init. uVel, vVel, etanN + * lambda[Theta,Salt]ClimRelax +o separate masks used for ctrl_pack/unpack 'from write_grid' output + (suggested by G. Forget) + +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 (2005/04/06) + +o mnc-ifying the seaice package +o introduced an alternative length scale calculation for use in the limiting + maximum viscosity (off by default, see mom_vi_hdissip.F for details) +o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S +o added modified Leith scheme with viscosity proportional to grad(Hdiv) + as well as grad(vort3). Made it compatible with both approximate form + for the cubed sphere and full form of these gradients. Added flag + useFullLeith to select between approximate and full form. +o add "d0" in getcon.F to reduce differences between compilers/platforms + update output.txt of exp. fizhi-gridalt-hs +o change port_rand funtion to allow to set the seed. +o fix obscure MNC bug involving conversion between reals and integers + - it caused no problems with certain (eg. gcc, ifc) compilers but the + new version is now more standards-compliant +o adjoint-related modifications + * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint + * 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 (2005/02/28) +o Adding eddy stress controls a la Ferreira et al. +checkpoint57e_pre (actually was tagged: eckpoint57e_pre) + +o fizhi pkg: fix AtoC and CtoA when called with same input & output array + update output.txt of exp. fizhi-gridalt-hs +o add more "Z" dimensions and associated coordinate vars to MNC +o pkg/exf: added twoDigitYear capability for option useExfYearlyFields +o parameter calendarDumps: when set, approximate months (30-31 days) and years + (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, + KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar + months and years. Requires pkg/cal. +o diagnostics: add pickup functionality + - off by default for backwards compatibility + - current version only uses MDSIO -- MNC will be added +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 (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 +o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up +o make genmake2 more portable by using ".$FS" instead of ".f" for more + of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) +o add coordinate variables to the MNC output from the diagnostics package +o change MNC-flags default value: true when useMNC=TRUE +o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F + the ability (off by default) to read the grid information using MNC +o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt +o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging +o do snap-shot diagnostics at the middle of the time-interval (instead of + at the end). +o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add + new test for AIM with thSIce + slab-ocean +o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) +o move state variable diagnostics to the beginning of the time step ; + (note: still needs some work specially for snap-shot diagnostics) + duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z + +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 (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 +o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer + results; update global_ocean_pressure & global_ocean.cs32x15 output.txt +o add saltFlux(+File) forcing capability with periodicExternalForcing +o allow to use pkg diagnostics for GM-Redi & ThSIce output +o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. +o improvements for the MNC output from DIAGNOSTICS: + - correct handling of the unlimitied dimension + - all dims now have associated coordinate variables + - variables located at U, V, and Corner ("Z") points are now written + with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that + *all* data points are output +o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice +o added pkg/seaice/seaice_monitor.F +o mdsio_readfield.F can now read files visible only to master MPI process. +o pkg/seaice: some test code for ice-modified ocean stress +o exf_getffields interpolation defaults to bilinear for all scalar forcing + fields (remains bicubic for wind velocity and stress). This avoids, e.g., + spurious negative numbers for precipitation and humidity. Will cause + some small numerical differences for integrations using pkg/exf/exf_interp.F. +o pkg/ctrl/ + * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O + May be enabled via doPackDiag + * introduce z-scaling of + + gradient (doZscalePack) and + + control (doZscaleUnpack) +o pkg/mdsio/ + * 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 (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 + general, EXCH2 grids are only aligned to a "local" coordinate system +o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) +o Implement instantaneous output within pkg diagnostics: + setting a negative frequency in data.diagnostics produces + "snap-shot" output (as opposed to time-average if freq > 0) +o move out off EQUIVALENCE all diagnostics that fizhi does not use ; + NOTE: change ptracer diagnostics name: use 2 characters to work with + more than 9 tracers. Add also diagnostics of advect & diffus flux. +o more CF compliance: convert all MNC 'iter' variables to 'T' so that it + becomes the coordinate variable for the 'T' dimension +o add CF-style coordinate variables to MNC + - just a first cut: numbers are meaningless on the cubesphere and + missing along the T axis but otherwise it works! +o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX +o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. +o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) + this is based directly on what the model compute, so that the content of + each diagnostics might be affected by switching options (e.g., implicitDiffusion) +o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) +o clean up build options files for SunOS, in particular + - remove -traditional from xmakedepend + - change -xarch=v9 to -xarch=native for f77 + - restore use of make (not gmake) + - add CC=gcc if using g77 +o changes per discussion of AM, JMC, & EH3 today: + - move redundant "grid" variables out of "state" -- in preparation of + creating proper CF-style coordinate variables and in recognition + that any/all grid variables can be easily copied (eg. w/NCO) from + the grid files into any of the other NetCDF files + - *always* output grid variables with MDSIO (this will eventually be + changed) + - output MNC grid file if useMNC is true +o every instance of _END_MASTER() has been found and replaced with + _END_MASTER( myThid ) in order to satisfy certain picky Sun + preprocessors +o re-arrange diagnostics pkg initialisation: + - allow each package to extend the available diagnostics list + - add some checking and fix small problems (multi-threaded, ...) + - new S/R diagnostics_fill (replace fill_diagnostics): + 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 (2004/12/10) +o this set of changes restores TAMC compatibility + tested for global_ocean.90x40x15 adjoint on trough + (what a pain) + +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 (2004/12/09) +o add horizontal bi-harmonic viscosity for vertical velocity + - new parameter viscA4W (defaults to viscA4) + - affects only non-hydrostatic code + - to be done: no-slip lateral boundary conditions +o switch back to "sflux = sflux - runoff" in exf_getforcing.F +o implement Implicit Vertical advection for pTracers +o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) + (implemented also for implicit vertical diffusion & advection) +o OBCS: extend application of tracer open boundary conditions + to a strip beyond the boundary of width Olx/Oly +o add call monitor to TAF set of required calls (flow directives) + and include in natl_box_adjoint +o untangle a few ifdefs related to cost, ctrl, autodiff + untangel a few ALLOW_ECCO_OPTIMIZATION +o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) + (theta2, salt2 in ecco_cost_weights) + +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 + - fix index bug nobcs in ctrl_init + - fix dummy fields filen in ctrl_pack + - add dummy weights for obcs +o lsopt: comment out fort.94 output +o optim: + - remove unnecessary header files + - adjusted namelists + - add xerbla.F to Makefile +o exf: + - multiple modifications of exf_check_range + - unit change in exf_init_runoff from [m/year] to [m/s] +o mdsio: + - i/o-vector change debugLevel from debLevA to debLevB + +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 + - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) + - clean up PTRACERS_WRITE_TIMEAVE a little +o add another verification experiment that tests both the cfc-pkg and + the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with + reactive tendencies treated inline with regular timestepping +o testreport previously did a lousy job of comparing small numbers, so + we (Ed and Martin) changed the way the cut-off of 1.e-12 is + implemented in the little c-progam tmp_cmpnum.c which is embedded in + testreport. +o ptracers_monitor: bug fix for MPI + +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 + GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING + gchemTendency is not needed because the timestep is done separately) + - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY + - GCHEM is now---more or less cleanly---separate from PTRACERS + - to bo done: handling of surfaceForcingPtr that is needed for KPP not + so clear to me how that should be done in a general way. +o CFC: improve formatting of output in CFC_ATMOS +o PTRACERS: + - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so + that ALL experiments with ptracers enable can be checked. This makes + GCHEM_MONITOR obsolete. + - include a runtime parameter PTRACERS_monitorFreq that defaults to + monitorFreq + - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true +o add PTRACERS (PTR0[1-5]) to testreport output +o exf_check_range: + * default changed to .TRUE. + * will check values for niter0 if debLevA, every timestep if debLevB + * STOP in exf_check_range if 'out of range' + * range chosen generous to allow for potential extema + TBD: a version with stricter range + permitted range would be runtime parameters +o GMredi: + - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; + - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. + - change the default GMREDI_OPTIONS.h: compile everything except Visbeck +o GCHEM: + - move call to GCHEM_FORCING_SEP, so that it is now called before + the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP + - introduced a useGCHEM runtime flag and applied it everywhere. + - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; + this flag is now only visible within GCHEM-pkg routines. + - moved gchem_forcing_int temporarily into ptracers_forcing, this will + be replaced by a 3D array that is computed before thermodynamics; for + this, the tracer ID iTracer had to be included into the parameter list + of ptracers_forcing + - set up forward_step to call gchem_forcing, that will replace + gchem_forcing_int in ptracers_forcing + - cleaning up +o small cleaning of exch2: remove files that are also in eesupp/src + +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 + * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup + * fully merged and updated from SIO code + windstress sign change affects + - exf_inscal_[u/v]stress + - sign of xx_tau[u/v] adjustments + - signs in cost_scat + * ctrl_get_gen: avoid update of tau[u/v] for first few days + * natl_box_adjoint updated and compressed + * 2-level checkpoint switch added + (tested in EXP. 1 of natl_box_adjoint) + * new switch doInitXX to avoid init. of xx_... in optimcycle=0 +o SVD + * first complete, non-hacked version for SVD calculations + * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... + performed via direct access files admtlm_vector.it???? + (via ctrl_[un]pack) + * optimcycle is used for ARPACK iteration counter + (note: adxx_... is iterated, rather than xx_...; latter is constant!) + * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms + and add linear transforms where necessary + * controls are initial/final SST, SSS (can be extended; need to check + ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F +o mdsio: filename info to both stderr, stdout +o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] + from sign change + +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 +o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity +o make all subroutines 30 or less characters in length for certain older + compilers to work (a thorough search only turns up two routines in + pkg/ptracers) +o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; + affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) + +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 + - added bits to verification/cpl_aim+ocn so that it can run on + ITRDA and other clusters without the mpirun "-wd" option +o fixed wayward endif in mom_fluxform.F that messed up cyclindrical + configuration +o give MNC the ability to create additional files rather than + exceeding a specified file size limit "MNC_MAX_FILESIZE" + - the default is just less than 2GB which is a practical limit + on many systems +o Compute the non-local term using either KPP vertical diffusivity (=default) + or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) + +checkpoint55h_post (2004/10/20) +o add verification test "vermix" +o remove all the *_ioinc flags and replace with the single global + outputTypesInclusive flag +o allow to set a vertical profile of vertical diffusivity for T & S +o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS +o useMNC moved from data.mnc to data.pkg + +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 + have been fixed to avoid recomp. of do_oceanic_phys + Works well for global_ocean.90x40x15, + but recomp. issue remains for carbon +o Updating adjoint output for natl_box_adjoint after + pkg/ecco has been modified (see taga c55d_post) + +checkpoint55f_post (2004/10/13) +o rename to timeave_init_fixed + +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 + checkpoint_lev1_directives.h +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 (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 (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 + the full 3D field is never actually stored) arrays to NetCDF files + with the correct (that is, the complete multi-dimensional) set of + array indicies + - used in mom_vecinv() to write the diagFreq output + - tested (demonstrated) in verification/aim.5l_cs +o further mnc-ification + - add verification/lab_sea to the list with mnc setups + - fix undefined mnc v-names in cd_code + - add kpp to mnc output (both snapshot and timeave) +o non-hydrostatic code + - added horizontal viscosity parameter viscAhW for w, that replaces viscAh + in calc_gw.F + - defaults to viscAh + - this is useful, when I want to use viscAh=0 (e.g., only biharmonic + friction or Leith) in non-hydrostatic mode, as long as there is + no biharmonic friction and/or Leigth or equivalent for vertical velocity. +o pkg/cost + extend simple cost functions to treat time mean quantities + (T,U,V) via cost_accumulate_state from cost_tile +o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to + be 2 times larger than the minimum size the advection scheme requires. + now get a perfect conservation of salt in advect_cs test-exp (updated) +o GGL90 (Gaspar's TKE mixed layer) + - add horizontal diffusion of TKE, requires exchanges in + do_fields_blocking_exchanges, horizontal diffusivity is zero by + default. In OPA there is no horizontal diffusion of TKE but the + mixing coefficients are computed from a horizontal average of TKE of + 6 points or so. I think that diffusion has a little more physical + justification. + - clean up ggl90_calc in the hope of reducing memory usage (this hope + was in vain) + - mask tke-variable in ggl90_init +o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) +o fix biharmonic diffusion on CS-grid. +o more obcs stuff + - added obcs_external_fields_load as an alternative to the EXF-pkg option + for reading boundary values. This routine is called from + obcs_prescribe_read + - updated obcs_check + - changed sponge layer relaxation parameter units for days to seconds + - turned off sponge layer by default + - changed argument list of OBCS_CALC to myTime+deltaTclock + - fixed about 35 bugs in obcs_external_fields_load + +checkpoint55c_post (2004/09/23) +o obcs stuff + - new runtime flags useOBCSprescribe, useOBCSbalance + - re-arranged obcs_calc + - moved exf_getobcs to obcs_prescibe_read + obcs_prescibe_read is called after ORLANSKI stuff + and independent of it (executable can contain all). + - updated obcs_check + - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. + These may be necessary only if tangential velocities are + prescribed at OB, not sure, needs testing. +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 (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)] + affects advect_cs results (for the wrong reason): update output.txt +o use a more standard discretization for biharmonic viscosity ; + (original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) + affects results of dome set-up: update output.txt +o fix gad_advection.F (CubedSphere part), back to version 1.23 +o fix bug in mom_vi_del2uv.F (CubedSphere part). + +checkpoint55a_post (2004/09/20) +o merged code to + * prescribe/read time-dependent open boundaries + (works in conjunction with exf, cal) + * sponge layer code for open boundaries + * each boundary N/S/E/W now has its own CPP option + (healthy for the adjoint) + +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) + - global_ocean.90x40x15: extended GMREDI_OPTIONS.h + - carbon: * remove tr1-related adjoint verification + * add ptracer as control variable +o remove all tr1-related code (ALLOW_PASSIVE_TRACER) + (adjoint stuff still has some tr1 'names', but all use ptracer arrays) + +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 + +o add two new packages + - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) + + subject to optimization (memory) + - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) + + subject to reordering (many GOTOs in the original code) + + so far opps is called for every (i,j) point, and then operates in + the vertical; one may want to reorder the scheme in order operate in + horizontal slabs at the cost of (a lot of) memory, at least ten new 3D + fields) +o overhaul of IO so that we now have flags for MDSIO and/or MNC + - all verification tests compile and run with linux_ia32_g77 + - defaults are compatible with current input files--nothing + should change if you were not previously using MNC + - MNC output has been added in numerous places (eg. timeave) + but there are still a few writes not yet do-able with MNC + (this is in progress) + - flags now allow for either/or/both use of MDSIO and MNC and + documentation will soon follow + - numerous small formatting cleanups for ProTeX +o add version info (via BUILD_INFO.h) to MNC and stdout + +checkpoint54e_post (2004/09/02) +o add two new packages + - pp81 (Packanowski and Philander, 1981), Richardson number and + stratification dependent mixing + - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme + - these scheme operate in a similar manner as KPP (without ghat, of + course), however there is only one diffusivity that is used for both + temperature and salinity (and passive tracers) +o add offline package +o add "verification/dic_example" which contains a dic-gchem-ptracer setup + provided by Stephanie Dutkiewicz +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 (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 + (i.e. leading to considerable offset over the years) +o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep +o start with no AB and no initial filtering (staggerTimeStep): + change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 +o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F + (external loading & cpl import/export stay in forward_step.F) +o update coupling interface to work with new staggerTimeStep +o change MDSIO ptracers_pickup. +o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); +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 (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 +o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) +o change Qnet to always be the net heat flux, (+upward). + affects (truncation error) output of natl_box exp.: updated +o define the max number of passive tracers in PTRACERS_SIZE.h +o start to test mnc routinely in exp0 +o add sea-ice loading (sIceLoad) as a new forcing field. + +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 +o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output +o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added +o staggerTimeStep & NLFS: rescale T & S surface tendencies. + affects (truncation error) output of lab_sea & natl_box exp.: updated +o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) + +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 (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 (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 +o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection +o new parameter "nShapS": allow to treat differently S from T (nShapT) +o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) +o restore adjointability + +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) +o AIM pkg: + - include stability function into surf.Flux derivative relative to Tsurf + - calculate clear-sky radiation & surface temp. change (for diagnostics) + +checkpoint53e_post +o merged cylindrical coord configuration +o added rotating_tank experiment +checkpoint53e_pre + +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 +o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. +o added Sadourny discretization of Coriolis + - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h + - re-enabled use of omega3 (useAbsVorticity) +o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for + vector-invariant equations + - note: does *NOT* yet use same variable visc. for no-slip BC's. +o recoded the lateral boundary conditions for non-hydrostatic w, this time + hopefully without new bugs + - still to do: biharmonic friction for non-hydrostatic w +o bug fix for mom_*_sidedrag: rA -> rAs,rAw +o regenerated output for global_ocean_ebm (using -ieee) +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 (2004/05/21) + +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 + - aim with thSIce: fix bug in snow-precip. +o changes to calc_gw.F + - bug fix for w^2 term near the bottom boundary + - (hopefully) improve the lateral slip boundary condtions for use with + partial/looped cells + - because the bug fix changes two verification experiments anyway (exp5 + and plume on slope), change the lateral boundary condition from half slip + to the value of no_slip_sides +o ebm package wasnt quite up to the parallel task. Fixed that. +o Adjoint of EBM package + verification + * TLM OK + * ADM not sufficient accuracy yet (needs further testing) + +checkpoint53b_post (2004/05/14) +o Commiting new energy balance model to repository + * package is pkg/ebm + * verif. is verification/global_ocean_ebm + * references are in ebm_driver.F +C * X. Wang, P. Stone and J. Marotzke, 1999: +C Global thermohaline circulation. Part I: +C Sensitivity to atmospheric moisture transport. +C J. Climate 12(1), 71-82 +C * X. Wang, P. Stone and J. Marotzke, 1999: +C Global thermohaline circulation. Part II: +C Sensitivity with interactive transport. +C J. Climate 12(1), 83-91 +C * M. Nakamura, P. Stone and J. Marotzke, 1994: +C Destabilization of the thermohaline circulation +C by atmospheric eddy transports. +C J. Climate 7(12), 1870-1882 +o Will need long integration testing. +checkpoint53b_pre (2004/05/14) + +o created pkg/mom_common in preparation for variable viscosity code +o renamed and split ini_mnc_io +o pkg/land: only liquid water can diffuse or run-off +o AIM using land: soil wetness availability account for snow +o added printMapIncludesZeros to EEPARMS namelist + +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 + TAMC problem with adjoint of KPP code. + (no success...) + Identical code works fine with TAF. +o Fixed verification/natl_box_adjoint experiments. + Initial conditions for Experiments 4 and 5 are now + set to "SEAICE_initialHEFF=0", which is more reasonable, + and hence gives results closer to that of Experiment 2. + Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. + +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_ + variables that is being autogenerated wrong. + Otherwise: + o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. + 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 (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 +o pkg/seaice modifications + - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost + of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer + and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm + - changed proxy for geostrophic velocity and updated + verification/lab_sea/results/* accordingly + - removed ADI dynamic solver from pkg/seaice + - replaced all occurrences of 1/CSTICE or 1/CSUICE + they caused a segmentation fault under certain circumstances + - removed unused field WATR +o bug fix in exf-package: + - u/vwind are defined at tracer/pressure points. The values of u/vwindmask + now reflect that. +o small fixes in the cal-package: + - set reference date to first of January for the 'model'-calendar + - failing of cal_CheckDate in cal_FullDate now actually results in a + warning +o small modifications in exf-package to increase flexibility: + - change climtempfreeze from a constant to a runtime parameter that + is specified in data.exf_clim (default = -1.9) + - introduce runtime parameter windstressmax (default = 2.0) that is + specified in data.exf +o fix in pkg/thsice: + - update Evap (Tsf changes) to be consistent with Latent heat flux + - maintain snow precipitation unchanged (even if Tsf >=0). + both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice + +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 + as a default +o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated +o re-work pkg/thsice interface with ocean & bulk_force pkg to allow + atmospheric model (AIM) to use it ; add a "slab ocean" component. +o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) +o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice +o extending useSingleCpuIO option to work with new exch2 I/O format + - old-style, missing-tile I/O is still accessible by defining CPP + option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h +o monitor package can write to NetCDF files and/or STDOUT +o fix re-definition bug in MNC_GRID_INIT_ALL() +o doc/api_reference added + - a framework for building an API Reference Manual using all + the "protex" comments embedded in the code + - see pkg/generic_advdiff, pkg/mnc for examples +o MNC: + - make myThid the last argument for all subroutines + - new default for the grid files: NO halos + - add useMNC and other run-time flags + - separate per-file-group handling of the unlimited dimension + - early initialization of MNC w/ flags read at the eeboot stage + and lookup tables set in initialize_fixed + - write all MNC output to a freshly-created directory +o thermodynamics sea-ice (thsice) is now tested with testreport. +o test exp. advect_cs: use the standard cs32 grid ; update output. +o Added functionality to grdchk: + pick global i,j,k position (or nearest wet) where to perform check. + +checkpoint52l_post (2004/03/11) +o new land formulation: + a) use ground enthalpy as prognostic variable to ensure exact + energy conservation. + b) account for water temperature and for latent heat of freezing + in all processes (rain, run-off, ground storage) + c) compute surface and ground temperature implicitly. +o aim_v23 modification for new land model: + 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 (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) +o no restoring terms under ice for pkg/seaice +o moved SEAICE_DO_DIAGS to S/R do_the_model_io +o bug fix for pkg/seaice pickups +o change MNC call locations and add coordinate attributes +o mask vorticity at the corner ; affects global_ocean.cs output +o fix ini_curvilinear_grid ; test CS experiments with mpi +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 (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 +o accuracy ctrlprec = 32 insuffient for gradient checks using + averaged fields (I/O via cost_averages) + -> use ctrl.h in active_file*.F to control I/O precision. +o paramter list of CALL ADTHE_MAIN_LOOP +o added initial do_the_model_io to ecco +o set all ...Freq to zero after cost_final + taveFreq, dumpFreq, pChkptFreq +o MAIN and ECCO differentiability restored + +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! + call do_the_model_io from the_main_loop with parameters + 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 (2004/02/03) + +o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and + error messages +o fix errorMessageUnit problem. remove old version of mdsio from eesup/src +o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating + debug output +o modfied mdsio_writefield.F to handle non-global files under exch2 +o update AIM Cubed-Sphere exp (aim.5l_cs): + use land, p*, and Franco.M forcing fields with fractional land-sea mask. +o update AIM Equatorial Channel exp: + use standard aim_v23 pkg and change the SST fields to be more realistic. +o globalFile now works with exch2 +o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and + mon_vort3.F to make exch2 friendly with >1 tile per cube face +o limit timeave output for hi-res integrations + +checkpoint52i_post (2004/01/21) +o removed CPP_EEOPTIONS.h from verification/*/code +o updated the tiling for global_ocean_pressure +checkpoint52i_pre (2004/01/20) + +o update aim.5l_LatLon using the standard aim_v23 pkg (instead of + the old pkg/aim). + +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 +o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed + old grid files, moved CPP_EEMACROS.h to pkg/exch2 +o added useSingleCPUIO flag to monitor.F and mon_out.F +o added temporary hack for sea-ice dynamics on the cube: + metric terms are ignored and it is assumed that + there is no sea-ice on cube faces 1, 2, 4, and 5. + +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 (2004/01/07) + +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) + to work with implicit vertical advection and AB ; +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 (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 +o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. +o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 + ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure +o added exf_offset_atemp for Celsius to Kelvin conversion of atemp +o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 +o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations + +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 + random number generator +o add infrastructure in model routines for fizhi and gridalt packages +o change global_ocean.cs32x15 because of Pb with GM on CS-grid. +o changes to permit hi-res, cubed-sphere, configuration + - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F + - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F + - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation + of surface winds for the cube + (A verification experiment, based on global_ocean.cs32x15, but with + pkg/seaice turned on and with on-the-fly interpolation from the NCEP + Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, + complete with example surface forcing files and matlab scripts to look + at the output and compare it with that of global_ocean.cs32x15.) +o packages pickup: $PKG_write_pickup called from packages_write_pickup ; + but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code + to conform to the common rule. +o check-in the first version of the coupler + interfaces for multi-components + set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. + - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). + - atmosphere: use pkg aim_v23 ; no sea-ice for now. + - ocean and atmos. share the same horizontal grid (no interpolation). + - exchanges between component and coupler is done in forward_step +o new verification experiment, cpl_aim+ocn: + coupled ocean - AIM atmosphere on cs32 grid. + +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 (2003/11/25) +o Fixing OPTIONS files for use of exf: + - ALLOW_ECCO not needed + - ECCO_CPPOPTIONS.h should not be included from + EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h + as has been the case in the past + - All cal/exf related options are currently set in + single header file. Should remain so until we + agree on a consistent new policy. +o Removed all CPP options for cal package. + cal has no more CPP options. +o modified STOREs in GAD_ADVECTION +o corrected key comp. for passkey + +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; + - light cleaning of bulk_force pkg (still needed with thsice). + - 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 (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) +o sort out interplay between tamc.h and PTRACERS_OPTIONS.h + (need info on NUMBER_OF_PTRACERS) +o missing PTRACERS headers in some routines +o default tamc.h in pkg/autodiff supposed to crash + to ensure proper customization + +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 + and is called in FORWARD_STEP (if allowFreezing=.TRUE.) + => new output.txt for global_ocean.cs32x15 & global_with_exf + - keep the old version of FREEZE for backward compatibility; + global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. + - corresponding modifs for TAF directives +o added surface flux output variables to TIMEAVE_STATVARS +o time-averaged output for pkg/ptracers +o fix problem with ECCO-related divided adjoint + snapshot file was missing some ad-variables, + but no warning issued by TAF + +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 (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 + but no input fields +o obcs adjoint not yet merged! +o adding ECCO global 1x1 and 2x2 degree configs +o updated/extended some store directives for seaice +o pkg/ecco now containes ecco-specific part of cost function +o top level routines the_main_loop, forward_step + supersede those in model/src/ + previous input data.cost now in data.ecco + (new namelist ecco_cost_nml) +o in ctrl/ cleaned some cross-dependencies and updated CPP options + +checkpoint51t_post (2003/11/04) +o this is the pre-merge tag of the ecco-branch + +checkpoint51s_post (2003/11/04) +o cleanup: removed various obsolete #define-s +o pkg/grdchk + - renamed 'ph-grd 3' to 'grad-res' + - merged from ecco-branch + (remaining bug fixes for obcs gradient checks) + - additional high-precision output for testreport + (grep for 'precision_grdchk_result') + +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 (2003/10/30) +o cd_code: + - moved cd_scheme.F -> cd_code_scheme.F + - separate read_checkpoint from cd_code_ini_vars.F + - separated cd_code part from write_checkpoint + - updated AD_SOURCE, generated .flow + - added CD_CODE_VARS.h to the_main_loop + - Moving cd_code specific store dir.s to pkg/cd_code +o ctrl package totally restructured + - pack/unpack now optional and decoupled from + xx_/adxx_ I/O + - ctrl_pack/unpack cleaned + (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) + - confined inclusion of AD_CONFIG.h to where necessary. +o genmake2: changed AD dependencies from SRCFILES to AD_FILES + +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 + called) is called *before* PACKAGES_INIT_VARIABLES. + This seems to be backwards since + 1) its important to initially zero the entire field including + the "halo" region + 2) zeroing needs to be done *before* reading pickup info + and the pickup call might or might not happen in any + particular run + - this needs an overhaul for R2 +o cleanup verification/*/code/GMREDI_OPTIONS.h +o cleanup testreport + +checkpoint51o_post (2003/10/27) +o bringing AD-related verif's up to date with genmake2 + - carbon/ + - global_ocean.90x40x15/ + - hs.94.1x64x5/ + - (front_relax/ ) +o (more) consistent directory structure for AD-related verif.'s +o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK +o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF +o bug fix in find_alpha.F for MDJWF: + - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for + change rho -> rho-rhoConst + - replace call find_rho to find_rhonum +o initialisation of rFlx extended to full array (required by TAF) + and shifted to thermodynamics +o removed PTRACERS.h in ptracers routine +o added surfacetendencyPtr to S/R parameter list pracers_forcing +o Correcting initialisations for fVerU, fVerV. +o helping TAF to recognize dependency on kUp for + fVerU, fVerV +o Replacing delZ by delR in pkg/ctrl/ +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 + it for adjoint/tl #defines + o re-worked the build logic in genmake2 to support AD_CONFIG.h + o removed tools/genmake since it no longer works + +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 + - subroutine FREEZE now limits only surface temperature + (this means new output.txt for global_ocean.90x40x15, + global_ocean.cs32x15, and global_with_exf) +o added surface flux output variables to TIMEAVE_STATVARS + +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: + - ALLOW_ADJOINT_RUN + - ALLOW_TANGENTLINEAR_RUN + - ALLOW_ECCO_OPTIMIZATION + +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 @@ -34,7 +5692,7 @@ 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 @@ -48,13 +5706,13 @@ - 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 @@ -66,7 +5724,7 @@ 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 @@ -74,12 +5732,12 @@ 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 @@ -91,7 +5749,7 @@ 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. @@ -101,7 +5759,7 @@ 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) @@ -114,7 +5772,7 @@ - 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 @@ -137,14 +5795,14 @@ - 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_... @@ -423,7 +6081,7 @@ 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) @@ -439,7 +6097,7 @@ 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: @@ -465,7 +6123,7 @@ 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 @@ -477,19 +6135,19 @@ - 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 @@ -501,7 +6159,7 @@ 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 @@ -518,7 +6176,7 @@ - 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. @@ -535,7 +6193,7 @@ - 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) @@ -564,7 +6222,7 @@ - #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 @@ -618,7 +6276,7 @@ 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() @@ -631,7 +6289,7 @@ 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) @@ -644,9 +6302,9 @@ 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) @@ -660,20 +6318,20 @@ - 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 @@ -683,13 +6341,13 @@ 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 @@ -707,9 +6365,9 @@ - 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 @@ -717,7 +6375,7 @@ 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 @@ -726,30 +6384,30 @@ - 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 @@ -758,17 +6416,17 @@ 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 @@ -795,7 +6453,7 @@ 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) @@ -809,7 +6467,7 @@ - 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). @@ -817,7 +6475,7 @@ - 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 @@ -829,7 +6487,7 @@ (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 @@ -849,13 +6507,13 @@ (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 @@ -920,7 +6578,7 @@ 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) @@ -928,13 +6586,13 @@ 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) @@ -946,11 +6604,11 @@ 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 @@ -959,7 +6617,7 @@ 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 @@ -969,7 +6627,7 @@ 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 @@ -988,14 +6646,14 @@ 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 @@ -1003,7 +6661,7 @@ 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 @@ -1017,7 +6675,7 @@ + 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, @@ -1025,18 +6683,18 @@ 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 @@ -1050,7 +6708,7 @@ (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 @@ -1058,7 +6716,7 @@ (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) @@ -1075,19 +6733,19 @@ 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). @@ -1098,7 +6756,7 @@ 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: @@ -1116,7 +6774,7 @@ 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 @@ -1127,7 +6785,7 @@ 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 @@ -1144,7 +6802,7 @@ - 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/ @@ -1153,10 +6811,10 @@ 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_... @@ -1169,7 +6827,7 @@ 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() @@ -1177,7 +6835,7 @@ 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 @@ -1187,7 +6845,7 @@ (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 @@ -1198,32 +6856,32 @@ 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. @@ -1231,18 +6889,18 @@ 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. @@ -1250,7 +6908,7 @@ 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? ) @@ -1259,11 +6917,11 @@ 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 @@ -1278,27 +6936,27 @@ 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 @@ -1308,7 +6966,7 @@ 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. @@ -1316,27 +6974,27 @@ 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