--- MITgcm/doc/tag-index 2012/06/25 19:25:41 1.1675 +++ MITgcm/doc/tag-index 2017/01/10 15:51:00 1.2289 @@ -1,9 +1,3360 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1675 2012/06/25 19:25:41 heimbach Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.2289 2017/01/10 15:51:00 gforget Exp $ $Name: $ Notes on tags used in MITgcmUV ============================== +o pkg/mnc: + - mnc_utils.F: call ALL_PROC_DIE before 'stop', edit stop message +o pkg/autodiff: + - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER +o pkg/profiles: + - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F, + profiles_readparms.F: call ALL_PROC_DIE before 'stop' + - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER +o pkg/smooth: + - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop' + - smooth_init2d.F, smooth_init3d.F: move print statements to readparms + - smooth_readparms.F: add cleaner print statements from smooth_init?d.F +o pkg/exf: + - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE); + issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc + .EQ.UNSET_RL; generalize tests on interpMethod, nlat, and lon_inc to + all exf variables. + - summary: skip detailed field report if not used (empty file-name). +o tools/xmakedepend: + - In case line editor "ed" is missing, switch to "sed" command to clean-up + Makefile from previous dependencies (anything after "# DO NOT DELETE" line). +o pkg/exf: + - change definition of "hflux" input file to always include Short-Wave; + this is now consistent with hflux computation (if using bulk-formulae) + and hflux diagnostic & documentation (in EXF_FIELDS.h). + +checkpoint66b (2016/12/01) +o model & momentum pkgs: + - implement fully implicit bottom friction combined with implicit surf. + pressure, for now, only in hydrostic formulation: + + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h + and run with selectImplicitDrag=2 ; + + currently missing diagnostics of bottom drag and vert. viscosity tendency; + - partial implicit time-stepping (bot. friction + vert. visc first, then + surf. press) corresponding to selectImplicitDrag=1 should be applicable + to NH formulation but not available until we solve for surf. pressure + increment (instead of full etaN). + - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag + with implicit vertical viscosity. +o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model + - this is a first version that includes many regularisations that may + not all be necessary, to be sorted out, + - turned on by runtime parameter SEAICEuseLinRemapITD (true by default) + - change one verification experiment in seaice_itd to use and test new code + - seaice_growth: catch a case where the argument of log can be zero + or smaller (important for code stability) +o model/src: + - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F + & solve_pentadiagonal.F to enable to re-used inverse matrix for solving + similar A.X'=Y' system (with same matrix A) in subsequent calls; + switch based on errCode (In/Out) argument value; in calling routines, + initialise errCode before first call. + +checkpoint66a (2016/10/18) +o pkg/bling: + - BLING package now loads in atmospheric pCO2 file using exf package routines + Enable with #define USE_EXFCO2 in BLING_OPTIONS.h +o model/src & pkg/ptracers: + - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R & + GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and + implicitDiffusion (respectively) are used (even without momImplVertAdv + or temp,salt,PTRACERS_ImplVertAdv). +o model/src & generic_advdiff: + - add parenthesis in main diagonal calculation of implicit vertical + diffusion matrix (impldiff.F & gad_implicit_r.F). + This affects results at machine truncation level; update output of many + verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad). +o pkg/mom_commom & generic_advdiff: + - add deep atmosphere and anelastic scaling factor in implicit vertical + advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F). +o model/src: + - remove few unnecessary temp array copies in solve_tridiagonal.F + & solve_pentadiagonal.F + +checkpoint65z (2016/09/28) +o pkg/seaice: fix multithreading for seaice_fgmres.F + - remove unecessary variables from common blocks + - use extra dimension MAX_NO_THREADS for all variables of the Krylov space + basis, that are stored in commom blocks (including integer variable i1) + - clean up code a little by removing commented lines that refer to + original code + - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk. +o MITgcm manual: + - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex), + preliminary documentation for generic controls (8.3; ctrl.tex), + a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated + ecco_costfunction.tex +o pkg/ecco: + - update and cleanup list of CCP options + - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c' + is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM + - add checks that retired run-time options are not used, and in relation + to gencost_mask and gencost_errfile + - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and + gencost_nrecperiod + - fix m_eta computation for virtual salt flux case + - add m_horflux_vol case (selected via gencost_barfile) that computes + transports via cost_gencost_boxmean (gencost_flag=-3) + - use gencost_flag more systematically (i.e., avoid using gencost_name) + for code switches (aside from physical variable selection) +o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first + attempt appears to be a bit of a hack and my need some repair down the road +o pkg/exf: + - interpolation near South Pole: fix criteria on input field latitude. +o pkg/icefront & pkg/exf: + - move setting of icefront Sub-Glacial RunOff forcing (currently unused) + from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront) +o pkg/exf: + - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter + "exf_output_interp" (in namelist: EXF_NML_04); change output file name + (add suffix "_out" instead of a prefix); keep same record number as in + input file but always write record 1 first (to avoid a STOP in I/O S/R). + Change output file content by writing interpolated field before applying + land-sea mask (helpful for debug). + - 2 compon. vector interpolation with rotation: apply scaling factor on + each compon. (Eastward and Northward) just before rotation. +o pkg/bling: + - Cleaned package. Removed not needed code and comments. + - adjoint example now works + (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad) +o pkg/ptracers: + - add Bruno Deremble's code to complete the linear surface correction + for tracer conservation; + - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE. + +checkpoint65y (2016/07/29) +o pkg/debug (stats): + - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to + proc/thread mapping); + - fix Min & Max for case where 1 thread has only empty tiles; + - use RL variable to count number of wet grid points (with big domain, + can be too large to fit into integer*4). +o pkg/monitor: + - use RL variable to count number of wet grid points (but used only for del2) + - add new routine to compute Advective CFL within tracer time-stepping with + writing delayed until next monitor output. +o pkg/obcs: + - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW) +o pkg/cal: + - calandar-dump: treat case myTime < timePhase in the same way as in + eesupp/src/diff_phase_multiple.F (when not using calandar-dump). +o pkg/dic & seaice: + - fix compilation of ocean component for coupled atm+ocn model with + seaice dynamics & dic. + +checkpoint65x (2016/06/11) +o add a license text file in main MITgcm tree. +o added pkg/bling: + - intermediate complexity biogeochemical model + - see bling_description.txt for details + - verification experiment is global_oce_biogeo_bling (for now, in + Contrib/verification_other/); tested daily on baudelaire with gfortran. + - add entry point in pkg/gchem for new pkg "bling". +o pkg/seaice: fix tensile stength computation + - replace global field tensileStrength by tensileStrFac + - tensileStrFac can be computed once in S/R seaice_init_varia + - fortunately that does not affect any verification results + +checkpoint65w (2016/05/12) +o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles + with ECCO_CTRL_DEPRECATED defined +o verification/global_ocean.cs32x15: + - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3" + with "selectNHfreeSurf=1". +o model/src (non-hydrostatic free-surface): + - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1): + was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf. + - Calculate surface vertical velocity after 2-D solver adjustment (accounts + for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv + and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1. + This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux. + - Update output (changes at machine truncation level) of verification exp: + exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d), + short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d). +o pkg/seaice: ITD code + - fix picking up from a single category model by initialising + heff/area/hsnowITD = 0. in seaice_itd_pickup.F + - split a long warning message in seaice_check_pickup.F into two lines, + because NEC SX-ACE cannot deal with the long line. +o model/src: + - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3) +o pkg/seaice: + - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG +o pkg/seaice: + - add basal stress as parameterisation for grounding ice + following Lemieux et al. (2015) + - turn on by setting new parameter SEAICEbasalDragK2 to a value + larger than 0. Lemieux et al. (2015) recommend 15. + - The adjoint complains with extra recomputations so there is also a + new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in + order to postpone the problem + - compile the new code in lab_sea +o verification/halfpipe_streamice: + - update both TAF and OpenAD adm output (machine truncation differences) + +checkpoint65v (2016/04/08) +o verification/advect_xz: + - increase overlap size from 3 to 4 and add new secondary test for PQM + advection scheme (with mono & wino limiter). + - change main exp. to test PPM (with weno limiter) adv.scheme on Temp. +o model/src: + - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently + added phi0Ref) to set vertical axis origin and phiRef origin; + keep Ro_SeaLevel for backward compatibility (with a warning). + According to coordinate and fluid type: + OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top) + ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom) + OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top) + ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom) + - remove Ro_SeaLevel from ATM experiment parameter files; + - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the + complement; update output.txt (changes at machine truncation level). +o pkg/seaice/seaice_evp.F + - simplify computation of deltaZ and zetaZ to simple averaging following + Bouillon et al. (2013). This removes a lot of code, but also changes + verification experiment lab_sea.hb87 -> updated + +checkpoint65u (2016/03/14) +o pkg/generic_advdiff: + - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52) + with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP); + Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for + testing and not for actual use. +o model/src: + - add parameter "phi0Ref" to specify reference [pressure/geo] potential at + origin r = rF(1); + - add options (parameter selectP_inEOS_Zc) to select which pressure to use + in EOS for height coordinate: enable to include NH Pressure or to use + more accurate pressure vertical profile; options not linked to EOS type + (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type; + - start to implement variable gravity (along vertical): for now, only with + z-coords (not even z*). + - add Ideal Gas equation of state for height coordinate. + - update OpenAD output (affected at machine truncation level) of exp: + global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo. +o pkg/exf: + - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result + of exf interpolation (before any rescaling, rotation or interpolation + to velocity point) for each field that gets loaded from file. This option + identically mimics the input file organization (e.g. record numbers in year + by year input files) besides the change in horizontal grid. + - add rotateStressOnAgrid run-time switch so that wind stress fields + can be provided on the A-grid in zonal/meridional direction and + rotated on the fly. This only applies to the case when the exf + interpolation is off and rotateStressOnAgrid is false by default. +o model/src: + - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since + it's also used with pkg/atm_phys) and add few more parameters (but still + inactive, src code yet to come) + +checkpoint65t (2016/02/10) +o pkg/atm_phys: + - from Ruth Geen: add optical depth dependence on CO2 concentration. +o model/src: + - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic) + for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F. + Update output of exp. deep_anelastic (changes at truncation level). +o tools: + - add a hack in "remove_comments_sed" (used only with TAF) for recent + version of OpenMPI (shipped with FC.23): comment out the new header + file "mpif-sizeof.h" which causes problems to TAF. +o pkg/seaice: + - change the termination criterion so that maxits (SEAICElinearIterMax) + has an effect + - unify iteration parameters for implicit solvers (JFNK and Picard) + SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS + SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER + SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner + SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner + SEAICEnonLinTol replaces JFNKgamma_nonlin + - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN + - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and + use with SEAICEuseKrylov +o pkg/seaice/seaice_lsr.F + fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only + relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have + an effect. +o pkg/seaice: add two new parameters + - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this + parameter is not in any namelist) + - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as + a preconditioner for the non-linear Newton iteration of the JFNK + solver +o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT, + affects some experiments at truncation level: + - global_ocean.cs32x15.icedyn (11 digits), + - global_ocean.cs32x15.seaice (11 digits), + - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update + - also update global_ocean.cs32x15 adjoint and tangent-linear results +o pkg/salt_plume & pkg/thsice: + - for coupled set-up with pkg/thsice in ATM and pkg/salt_plume in OCN, + connect salt_plume flux to ATM-OCN coupling pkgs interface: + a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for + export to coupler interface) even without compiling pkg/salt_plume ; + b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field + (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH. +o pkg/dic: + - use the updated seaice fraction (from seaice pkgs) for DIC forcing + instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE + called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD); + - move also update with values from ATM-OCN Coupler in the same new S/R + (previously done in ocn_apply_import.F). +o tools/adjoint_options: + - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default) + has been changed on Jan 14, 2016. +o pkg/ggl90: + - add alternative discretisation of vertical shear (off by default), to + compute the mean (@ grid-cell center) of vertical shear compon instead of + vertical shear of mean flow (@ grid-cell center). + - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated + results on adjacent faces of cubed-sphere grids; this fix the restart. +o pkg/atm_compon_interf: + - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just + pass last value, stored directly before export to CPL ; + Note: this affects results of Coupled set-up where OCN uses useImportSLP=T + - remove atmSLPr from pickup files (no longer needed for restart) + +checkpoint65s (2016/01/13) +o eesupp & genmake2: + - first check for Function ETIME and, if it fails, then check for subroutine + ETIME and consistent output; use the appropriate version in timers.F +o model/src: + - to check restart test, add option to apply EXCH to U,V earlier, just before + integr_continuity; turned off by default. +o pkg/dic: + - remove CPP option USE_ATMOSCO2 (not needed) +o tools/tst_2+2: + - try to ignore difference between +0 and -0 in binary file, causing test + to fail for no good reason. +o eesupp & genmake2: + - put back modif from Jinxuan Zhu - change etime fct call to S/R call - + but also check (in genmake2) that test runs and returns meaningful results. +o coupler pkgs: + Finish implementation of optionally-exchanged variable switches (started on + Nov 12) with addition of few more exchanged fields, including 2-way exchange + of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice + advection in OCN component; this requires sequential coupling. + coupler (pkg/atm_ocn_coupler): + - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS + routines (useful for debug). + - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume + flux, DIC fields) if corresponding switch is ON. + - add option to export RunOff to OCN (to use for DIC river input) + - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting. + components (pkg/atm_ & ocn_compon_interf): + - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around + optionally exchanged fields; add a check & stop in cpl_readparms.F. + ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2; + OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice. + - rename: fracIce -> sIceFrac_cpl (<- match coupler var name) + + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime. + - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN. + - hold in common block coupler optionally-exchanged variable switch + and set default "useImportXXX" accordingly; + check & stop if inconsistent. + - add diagnostics for all imported fields from coupler (in both OCN & ATM); + this is intended to replace the OCN cplFldtave.* output files (not updated + to contain new additional exchanged fields). +o pkg/dic: + - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code. +o pkg/thsice: + - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading + and writing of thsice pickup files. +o pkg/atm_compon_interf: + - move all field individual export-call out of cpl_export_import_data.F + into new S/R ATM_EXPORT_FIELDS +o pkg/atm_compon_interf: + - store state variables (for now, only thSIce fields) just before beeing + exported (in cpl_export_import_data.F, like on ocean side) instead of from + atm_store_my_data.F like all exported fluxes. + - new version of pickup_cpl: write field names into meta file and read meta + file to find field postion in pickup. Also only write/read fields meeded for + restart (same logic as main pickup file ; also using pickupStrictlyMatch) +o pkg/dic: + - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3. +o pkg/seaice: add new parameter SEAICEpressReplFac to choose between + pressure replacement method (=1., default) or original Hibler (1979) (=0.) + value can be from domain [0,1] to average between the two methods +o pkg/atm_phys: + - allow to provide 2-d map of albedo and mixed-layer depth from files (but + hold fixed in time). + +checkpoint65r (2015/12/21) +o pkg/seaice: + fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK + solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated +o pkg/seaice: + - fix a bug in computing areaS in (J-J -> J-1) that affects runs + when SEAICEscaleSurfStress=.TRUE., + - apply areaW and areaS in S/R seaice_calc_lhs +o pkg/atm_phys: + - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes + (shortwave & longwave, net & downward) and diagnostics of temp. tendency + for individual contribution (convection, LSC cond, radiation) + - add Ruth Geen etal, GRL 2016, radiation options (see paper supp. + information); activated with: solar_exponent=0. and wv_exponent=-1. +o pkg/ggl90: + - within IDEMIX add upper limit for horizontal group velocity to + avoid instability problems in the explicit horizontal diffusion term for + long time steps or high resolution +o pkg/diagnostics: + - simplify setting of local-array size in diagstats_output.F: uses "numLevels" + (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels. +o testreport: + - remove "-v" (verbose option) in default mpirun command. +o pkg/seaice/seaice_growth: + - catch potential division by zero in ITD code, does not change + verification results +o pkg/ecco: + - retire old codes to the Attic. The calls to retired functions are + left in a commented form in case they ever need to be re-activated. + - ecco_check.F: issue warning if any old CPP option is + defined that corresponds to retired codes -- then stop. +o pkg/atm_compon_interf: + - change seaice fraction (use for OCN dic surf.flux) stored and sent to + coupler: use last time-step value instead of average over cplSendFrq_iter + time-step, similar to what is done for seaIceMass. + This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up. +o eesupp & genmake2: + - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME); + <= remove until a fix is found for some ifort version on ia32 machine. +o pkg/seaice/seaice_evp: + - refine residual computation + +checkpoint65q (2015/11/18) +o pkg/seaice/seaice_evp: + - fix residual computations so that they no longer affect the actual + simulation code + - fix seaice_readparams to be able to actually set new parameters + SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little +o model/src: + - fix wrong truncation (single prec) from "FLOAT" function in expressions + like: deltaT*FLOAT(myIter) when myIter is large: + a) replaced by DFLOAT (if not seen by TAF); + b) remove "FLOAT" and use implicit type conversion (if seen by TAF). +o pkg/aim_v23: + - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading + when pickupSuff is set ; do write rolling pickups + at the end of the run. +o pkg/atm_ocn_coupler + ocn_compon_interf: + - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential + coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ; + add corresponding call in DO_OCEANIC_PHYS. +o coupler pkgs: + Start a new way to set-up optionally-exchanged variables (previously, only + there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler + data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ; + send switch to ATM & OCN compon before reading their own "data.cpl" (so that + compononent param default can be set accordingly). + Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch + but rather applies to a group a fields (going both ways like for DIC) + and corresponds to an option of coupling config. + coupler (pkg/atm_ocn_coupler): + - change parameter file from "data" to "data.cpl" (in cpl_read_params.F), + and read namelist directly (without eessup S/R calls) instead of + in the very un-flexible old way, 1 param per line, in fixed order; + - add error-counter to track errors (e.g., missing "data.cpl") and to stop + cleanly in CPL_CHECK_CPLCONFIG + - add new coupling-exchange selectors (some not yet active) including + cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h + and ocnCpl_exchange_DIC=T in OCNIDS.h); + - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each + component ; called directly from coupler.F, after comp. registrations; + - rename few variable-ID names (in ATMIDS.h & OCNIDS.h): + atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name -> + -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName + components (pkg/atm_ & ocn_compon_interf): + - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding + CPP header file in all pkg source files. + - move checking of comp. configs out of cpl_exch_configs.F into new S/R + ATM/OCN_CHECK_CPLCONFIG; + - add error-counter to track errors (e.g., in "data.cpl") and to stop + cleanly in ATM/OCN_CHECK_CPLCONFIG; + - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors + from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and + before PACKAGES_READPARMS; + verification/cpl_aim+ocn/: + - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file + "data.cpl" for coupler (in input_cpl). +o eesupp/inc: + - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to: + #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F) + to always cumulate tile local-sum in the same order (still uses + MPI_Allreduce like standard code). + - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files + that are now identical to standard version (in eesupp/inc). +o pkg/shelfice: + - add SHELFICETransCoeffTFile for initializing spatially varying + heat and salt transfer coefficients +o pkg/atm_compon_interf & ocn_compon_interf: + - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous + S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA + - move bi,bj loops inside S/R OCN_STORE_MY_DATA +o pkg/atm_ocn_coupler: + - initialise to zero ATMVARS.h & OCNVARS.h arrays. +o pkg/rbcs: + - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows + to compile with maskLEN=1 when all tracers use the same RBCS-mask. + - add a short report (to STDOUT) about RBCS-mask settings. + +checkpoint65p (2015/10/23) +o pkg/seaice/seaice_evp.F: fix store directives and key computations, since + there is no adjoint test for EVP, we don't know what it does to the adjoint + solution, but at least there are no more recomputation warnings left +o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands + a chance of giving the same results as a fully converged VP (JFNK) solver +o tools/adjoint_options/adjoint_diva: + - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA +o pkg/streamice: + - spotted bug in streamice_driving_stress using dyG where should have been dxG +o pkg/exf: + - remove STOP statement that prevented to use wind or (wind-)stress + interpolation for constant-in-time forcing fields (wind/stress period = 0). +o pkg/seaice: + - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires + 5 additionals 2D fields and 6 new store directives + - change logic in seaice_readparms.F: EVP code can now be turned on in + various ways, setting SEAICE_deltaTev is no longer required, + alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev, + or SEAICEaEVPcoeff +o pkg/shelfice/shelfice_thermodynamics.F + - redefining uLoc/vLoc to u/v, instead of 2u/v +o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz + - this is an intermediate state of a truely converging EVP that has + the potential of outperforming implicit VP methods, I do not recommend + using it yet. + - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION + and all parameters are hardwired + - for convergence it still requires very smooth regularisations, that means, + if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is + different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also + specific averaging appears to be required, still subject to tuning + - still needs cleaning and I need to turn parameter into runtime parameters + - add code to compute and print residuals of iteration, compile with + defining ALLOW_SEAICE_EVP_RESIDUAL to enable it +o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq) + that entered with r1.54 on Sep04, 2015, -> update results + +checkpoint65o (2015/09/14) +o pkg/mom_vecinv & mom_common: + - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines + called from there. + - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this + allows to use Vector-Invariant form in deep atmos and anelastic formulation +o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015) + and Koenig-Beatty+Holland (2012) + - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth + - global 2D field tensileStrength, computed in seaice_calc_ice_strength + - requires an extra input argument for S/R seaice_calc_viscosities + - tensileStrength's depth dependence is different from Itkin et al. (2015) + (to be changed and played with, for now exponential) +o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.) + - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice + by AREA according to Connelly et al. (2004), JPO. + - For EVP and the LSR solver, the implicit part of the drag term is + the only non-zero term in the denominator when there is no ice (which + prevented running the model with zero ice-ocean drag). If + SEAICEscaleSurfStress = .TRUE., this results in a division by zero + (or zero main diagonals BU/BV) which need to be caught. A practical + consequence is that for open water, the momentum equation reduce + to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if + they happen to be zero, often leading to a non-zero solution over + open water. +o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more + efficient EVP method. + - introduce area-weighted averages for e12 (analogously to + seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits + remain, but also changing the order of terms in the previous average + changed the results as much) -> update experiment + - add SEAICE_DELTA_SMOOTHREG code + - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for + TEM-code + - adjust loop bounds so that only required fields are computed + - add new averaging code for zetaZ/deltaZ (again similar to + seaice_calc_viscosities.F), inactive by default for now (will change + results again), but will replace old code eventually +o eesupp/src: + - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F) + to always cumulate tile local-sum in the same order + (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h). + Still uses MPI_Allreduce (like standard code) but on array of tiles + and should be faster than GLOBAL_SUM_SEND_RECV code. + - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV + (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead. + - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.: + aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40, + fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example, + natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre, + tutorial_baroclinic_gyre and tutorial_held_suarez_cs. + +checkpoint65n (2015/07/29) +o pkg/thsice: + - add a warning when used with pkg/aim but without updating SST + (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ). +o pkg/offline: + - change where Offline-Fields are loaded, from load_fields_driver.F to + directly within FORWARD_STEP, just after updating iter number and time; + - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new + S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS; + These changes allow: + a) to recover exactly on-line results using deltaToffline=deltaTClock, + tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2) + both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous + time-step, both with GM & KPP files and with recomputing these fields; + b) no needs to switch on staggerTimeStep anymore; + c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf. + - update output of experiment tutorial_dic_adjoffline (only 3 digits left). +o pkg/offline: + - change (rarely used) offset-iteration parameter to an offset time (in s): + can easily recover previous offset-iter effect by setting offset-time + (offlineTimeOffset) to offset-iter x deltaToffline; + - do not turn-off Temp & Salinity surface relaxation when using KPP (used + in KPP as part of surface buoyancy forcing) in offline run. + - fix ptracers KPP non-local term in the case where KPP is re-computed. +o OpenAD + - Adding preliminary ggl90 test to OpenAD verification. + Config. with ggl90 currently diverges after 64 time steps + so will need more work to become more stable + - Adding preliminary kpp test to OpenAD verification. + required small tweakes in kpp_routines.F + - Merge and update from Krishna Narayanan's contrib area: + * Add one variable for preliminary OpenAD DIVA + * Add replacement time-stepping for OpenAD DIVA + * genmake2 flag -diva (but only for OpenAD; preliminary) + * required modifs for OAD_support + successful preliminary test for tutorial_global_oce_biogeo/ +o pkg/seaice: + - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr + - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising + delta with a smooth function in s/r seaice_calc_viscosity + (no effect on EVP) + - rename local suffix "sqr" into "sq" for more consistent variable names +o pkg/seaice: + add new parameter SEAICE_deltaMin that is used ***only*** + for regularizing Delta (and nothing else, like the parameter + which is also used for all sorts of things SEAICE_EPS). + Defaults to SEAICE_EPS for backward compatibility only. +o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with + the wrong key by inialising it before use -> fixes a recomputation + problem but does not fix the gradient +o pkg/layers: + - move resetting of flux arrays to outside the iLa loop + (this caused layers_diapycnal to not work with more than one layer coord.) + - fix bug in calculation of layers_recip_delta in layers_init_fixed.F +o pkg/layers: + - remove from common block 3D layers fields (used to diagnose transport + in tracer coords) and declare them as local arrays in layers_calc.F +o pkg/seaice: + - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it + in lab_sea forward experiment (changes results -> updated) + - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v +o pkg/seaice: modify seaice_lsr.F in order to improve the gradient + computations; for SEAICE_VECTORIZE_LSR + - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v) + sweep to the outside, + - remove store directives and add "CADJ loop sequential" directives + in analogy to model/src/solve_tridiagonal.F + - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop + boundaries to yield more readable code. This has also the charming side + effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without + SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in + seaice_lsr_tridiagu/v now requires either of these flags, vectorization + still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as + an additional option) + The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F + but the adjoint gradients (which are affected by this change) still explode. +o coupler (atm & ocn _compon_interf): + - avoid using Exch2 IO mapping if not suitable. + +checkpoint65m (2015/06/15) +o pkg/layers: + - clean-up old parameters setting (from Sep 2012): + + remove old parameters setting from common block (declared locally); + + stop if any old parameter is mixed with new parameters; + + check for valid or consistent parameter setting (e.g., layers_name) + - check that layers_bounds for Pot.Density are in the right range; + this is supposed to catch un-updated setting after recently shifting + potential density field "prho" by -1000 (now in "sigma" scale). +o pkg/layers: + - Added missing call to layers_fill for keeping track of tottend in + pkg/diagnostics/diagnostics_fill_state.F +o pkg/layers: + - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning + of diapycnal fluxes +o pkg/layers: + - reverted changes to interpolation to previous treatment; there + was never actually a problem +o pkg/layers: + - fix interpolation of layers tracers in the presence of partial cells + - add lots of new functionality to compute water mass transformation + (enabled by CPP flag LAYERS_THERMODYNAMICS) + - add new calls from main code (diags_oceanic_surf_flux.F, + thermodynamics.F, impldiff.F) and gad to save the necessary fields + for layers_thermodynamics calculations +o pkg/ptracers: + - add capability of stepping a passive tracer forward without advection + by setting PTRACERS_advScheme to 0. +o pkg/diagnostics: + - add few (threads) _BARRIER around any update of "diag_pkgStatus". +o pkg/layers: + - shift potential density field "prho" by -1000 for density layer averaging so + that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000); + Note that density bin boundaries (layers_bounds in data.layers) have + to be set accordingly (i.e., shifted, in sigma scale). +o pkg/layers: + - fix snap-shot output of layer thickness @ V.pt and output of pot.density + - fix calculation of layer non-weighted velocity and layer probability + - add diagnostics for pot.density used for layer averaging +o pkg/seaice: + - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure + positiveness, modify a few comments and improve variable names, + - the changed computation of deltaC affects most seaice-related + experiments at the truncation level. + seaice_itd.thermo is affected by far the most, with + only 7 digits of agreement remaining; update experiments. + +checkpoint65l (2015/05/04) +o pkg/shelfice: + - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set + factor drKp1 to zero where it is negative (ie. do not use + SHELFICEBoundaryLayer if hFacC>1) + - the same for factor drLoc in shelfice_forcing.F +o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem + with modules in ptracers, when using testreport option "-small_f" +o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD) + - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1)) +o verification/testreport + - add new option -small_f + with this option testreport first makes the target small_f (*.f files) + before running make (all). This is useful for explicit inlining when + all sources need to be full available. +o pkg/exf/exf_interp.F: + remove previous changes related to reverse (decreasing) input grids latitude + +checkpoint65k (2015/04/01) +o pkg/ecco: + fix missing cosphi initialization; use eccoiter in place of optimcycle; + if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL + instead of active read/write +o pkg/ctrl: + if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL + instead of active read/write. +o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F + return if .NOT.useAUTODIFF +o pkg/seaice: add CPP brackets (cost function related). +o model/src: + add useAUTODIFF run time switch. +o pkg/exf/exf_interp.F: + add code to allow input grids with latitude starting in the north (i.e. when + j=1 corresponds to northern edge of field); modify global_with_exf to test + this feature. +o verification/testreport: + - replace "grep -A3" with POSIX conformal sed command, because there are + implementations of grep that cannot do contextual searches + - replace "cat -n" by "nl" (two occurrences), because not all implementations + of "cat" have the option "-n" +o model/src: + add new file gsw_teos10.F that contains 3 functions, more or less a copy + of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to + convert from conservative to potential temperature. For now they are not + called anywhere. +o pkg/ggl90: make "useIDEMIX" useful + - re-organize code in s/r ggl90_calc a little to move computations that + are different for idemix into separate loops (changes verification + experiment idemix at truncation level, 12 digits remain -> updated) + - requires 2 new 2D fields KappaM, verticalShear + - make hFacI and recip_hFacI local 3D variables that are passed to + s/r ggl90_idemix + - fix and improve some comments + +checkpoint65j (2015/02/25) +o pkg/openad + - synchronize seawater.F with version in model/src: replace routine + body of sw_temp by calling sw_ptmp and fix/add a few comments. +o pkg/mnc: + - change default value of pickup_read/write_mnc params to FALSE + (since few features are missing in reading MNC pickup files). +o model/src: + - change default (background) vertical diffusivity for salt to be the + temperature (background) vertical diffusivity. + - change background vertical diffusivity in vertical mixing pkgs ggl90, + kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity. + This makes ptracers default diffusivity (that uses salt diffKr) more + consistent with vertical mixing schemes. +o verification/testreport: + - fix typo in "-pcls" option ; + - put temp files in /tmp (instead of in local dir) + - add option "-ncad" to use genmake2 new option "-nocat4ad" + - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM. +o pkg/ggl90 (idemix code): + - apply few fixes ; add some missing "_d 0" ; update output of exp. + global_ocean.90x40x15.idemix +o OpenAD + - enable active file I/O and begin removal of work-around code + for OpenAD for handling control variables (memory vs. active files) + - new CPP options file OPENAD_OPTIONS.h + - revert to genarr2d gradient check for hs94.1x64x5 + - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens) + - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5 +o tools/genmake2: + - add option for an alternative Makefile (from Martin) where multiple + source files are sent to TAF (instead of all in one file). +o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013) + - code provided by Carsten Eden as an extension of ggl90 + - so far the code is turned on within ggl90 by setting a CPP-flag at + compile time; a runtime flag implementation is not yet complete + - tested in new verification experiment global_ocean.90x40x15.idemix +o verification: + - reduce length of the AD test run by half for experiments + global_ocean.cs32x15 (std + thsice) and isomip + - enable active file I/O for OpenAD, adjust verifications accordingly + - halfpipe_streamice: change gradient check from genarr2d to gentim2d +o verification/testreport: + - fix two non-POSIX sed statements so that there are no error messages + on Mac OS X + - replace hostname -s with hostname | sed 's/\..*$//' +o model/src/seawater.F: + - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged + (following the matlab code), which would have avoided the bug caught + by Matt (see below) in the first place +o pkg/shelfice: + - implement alternative discretisation of quadratic drag (selectBotDragQuadr) + and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag. + - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin + ice-shelf case (i.e., within surface level). + - add config summary in shelfice_check.F + - remove global variable recip_SHELFICElatentHeat and replace by a local + variable recip_latentHeat + - introduce diagnostics for friction velocity uStar (in case of + SHELFICEuseGammaFrict) + - change verification experiment isomip.htd: + + start from pickup (as input_ad at nIter0=8640) + + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file + + test SHELFICEuseGammaFrict = .TRUE. + + test SHELFICEadvDiffHeatFlux = .TRUE. +o model/src: + - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to + in-situ Temp) and in routine SW_TEMP (in pkg/openad); + update output of experiments global_with_exf.yearly and isomip (all 6). +o pkg/shelfice: + - change setting of kTopC to also be zero where there is no ice-shelf. + - zero out surface forcing arrays (for now, for T & S + EmPmR) where + ice-shelf is. + - first attempt to get RealFreshWaterFlux effects: for now, only without + SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping. +o pkg/seaice: add the option to prescribe a fixed thickness PDF + for thermodynamic calculations + - because of divisions of the type 7/7 not exactly equal to 1, this change + affects results of some verification experiments by up to 4 digits: + global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume, + seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides + adjoint: lab_sea, lab_sea.noseaicedyn + -> updated + +checkpoint65i (2015/01/23) +o model/src: + - change units of frictionHeating field from W to W/m^2 + - fix bug in frictional heating from stratospheric drag in + S/R ATM_PHYS_TENDENCY_APPLY_V + - with synchronous time-stepping: move resetting to zero of frictionHeating + field from load_fields_driver.F to thermodynamics.F ; + - add diagnostics for frictional heating. +o model/src & gmredi K3D: + - add frictionHeating field to pickup-files (for synchronous time-stepping) + - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h + - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name + and name in pickup file). + - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F +o model/src: + - move (from ini_forcing.F) initialisation of all arrays in header file + FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart + (since Nov 2012) with option selectAddFluid=1. +o pkg/shelfice: + - change units (+ document) of newly added field "shelfIceMassDynTendency" + - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays. +o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers +o pkg/seaice: two new runtime parameters: + - SEAICE_cStar replaces the hard wired "20" in the strength formulation, + long overdue + - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012) + parameterization of tensil stress for fast ice (does not do anything yet) +o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method + for LSR: move checking overlaps out of JFNK-if-block +o pkg/atm_phys: + - move copy of grid and dynamical fields out of atm_phys_driver.F into + new S/R ATM_PHYS_DYN2PHYS. + - fix level height for Linear Free-Surf case (to be consistent with + fixed-in-time pressure levels). +o pkg/mom_common (bottomdrag): + - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center + to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG; + update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag. +o pkg/shelfice (u/v_drag): + - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG; + - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F + (now similar to shelfice_u_drag.F) + - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG + from mom_vecinv.F (similar to mom_fluxform calls). +o pkg/mom_common (bottomdrag): + - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG; + - add options for alternative discretisation of velocity norm in quadratic + bottom drag: averaging of grid-cell-center KE to U.point and V.point + (selectBotDragQuadr=0, original code) can produce noisy patterns; this + improves when averaging only the other component (e.g. vVel for U bottom + drag) using wet-point method (selectBotDragQuadr=2) or not (=1). + - add options (bottomVisc_pCell) to account for partial-cell in bottom + friction (no-slip BC) thus getting the true distance from the bottom; + off by default since this also reduces model stability (explicit bottom + friction). Changes produce different machine truncation with linear-drag + + no-slip BC: update output of experiments exp4.stevens (10 digits) and + front_relax (bvp & mxl, 10 & 11 digits). +o model/src & mom pkgs: + - add one more level to vertical viscosity local arrays (Nr+1, previously Nr) + since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k + - for now and until vertical mixing scheme are updated to fill up level Nr+1, + just copy level Nr value to level Nr+1. +o doc: + - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. +o pkg/shelfice: + - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, + SHELFICE.h: move array shelficemass to init_varia, initialise + from array shelficemassinit, which is set in init_fixed and + has option to be set from file; introduce array + shelficeMassDynTend array, set thru file in init_fixed + - NEW FILE: shelfice_step_icemass.F: update shelficemass from either + shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in + pkg/streamice + - shelfice_thermodynamics.F: call shelfice_step_icemass if + SHELFICEMassStepping = .true. + - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f + +checkpoint65h (2014/12/17) +o verification/global_ocean.90x40x15, global_ocean_ebm: + - update to generic controls. +o pkg/ctrl: + - ctrl_map_ini_genarr.F: test for igen>0 + - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. + - move gentim2d part of ctrl_map_ini_genarr.F to + new separate routine : ctrl_map_ini_gentim2d.F + - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: + add time variable weights and cyclic controls (time mean, + seasonal cycle, etc) capabilities to gentim2d +o pkg/ecco: + - move reading of error, conversion to weights from + ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei) +o global_oce_llc90, cs32: + - activte sbo. + - CTRL_SIZE.h : add maxCtrlProc. + - activate the new genctrl capabilities. + - update following reorganization of global_oce_input_fields.tar.gz +o pkg/ctrl/ctrl_ad_diff.list: + - add missing ctrl_init_rec.f +o tools/OAD_support/keepOriginal: + - add ctrl_init_rec.F +o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F: + - avoid recomputations of xx_gentim2d_dummy. +o momentum diagnostics: + - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and + mom_vecinv.F to timestep.F (to include Smag-3D contribution). +o pkg/seaice/seaice_lsr.F: + - fix computation of BU/BV, make sure they are non-zero, only necessary + for cubed sphere exchanges and SEAICE_OLx/y>0. + This makes calling s/r fill_cs_corner_rl obsolete (removed). +o verification/global_ocean.cs32x15/input.seaice + - add test for strong implicit coupling and restricted addtive Schwarz + methods for LSR + - update results/output.seaice.txt +o verification/tutorial_global_oce_biogeo: + - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up) + and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK); + update output_adm,_oadm,_tlm.txt +o pkg/dic: + - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h + - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn + for tracer 1 & 2 is set (to avoid double counting of dilution effect). +o verification/tutorial_global_oce_biogeo: + - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since + dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ; + update output_adm,_oadm,_tlm.txt +o eesupp/src: + - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F) + and call it in seaice_lsr when using nonzero SEAICE_OLx/y +o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing + LSR (following Hutchings et al. 2004) + - introduce zetaZ as a global variable (requires adjustments in + seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ + in seaice_calc_viscosities.F + - new flag SEAICEuseStrImpCpl (default off) + - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the + momentum equations + - JFNK-solver (preconditioner) adjusted to allow using this method + (where it does not have any positive effect) +o pkg/seaice + - add overlap for restrictive additive Schwartz method also to LSR, but + turn it off by default (because it only seems to work for non-cubed + sphere/llc topologies) +o pkg/autodiff + - add extra exchanges in addummy_in_steppging also for mnc output +o pkg/seaice: + - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F + to avoid stripes in the adjoint output (similar to addummy_in_stepping.F) +o pkg/obcs: + - add option to specify domain-connected piece Id along OB though files + (for now, only used to diagnose PhiVel; default =1 -> global correction) + - modify obcs_diag_balance.F to process each connected-part separately; + exclude OB where Id = 0 but keep the full divergence there (-> constant + Psi along this portion of OB and all inflow derived from grad(Phi)) + - add example of OB-conect files in verification/so_box_biogeo/input. +o pkg/diagnostics: + - improve treatment of Open-Boundaries in Velocity-Potential calculation: + a) use non zero matrix element across OB and solve for Phi 1 grid point + outside OB (i.e, where tracer OBCS are applied). + b) global imbalance of inFlow/outFlow across OB: instead of modifying + velocity across OB, spread it uniformly along the OB in the RHS. + +checkpoint65g (2014/11/19) +o pkg/diagnostcis: + - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param +o pkg/my82,pp81,kl10: + - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D + field diffKr as background diffusivity to set minimum diffusivity value. +o pkg/seaice: + - add new parameter SEAICEuseEVPrev (for revisited EVP by + Bouillon et al 2013) + - add SEAICE_evpAlpha/Beta to namelist + - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes + involve trivial re-ordering of divisions/multiplications that should not + have any effects, but ... they do change the results of lab_sea.hb87 so + that only 2 digits of agreement remain, in line with the general + instability/fragility of the evp-code. For now, I do not care and just + update the verification experiment +o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc) + - remove xx_genarr2d_numsmooth etc + - use xx_genarr2d_preproc etc instead + - carry out smooth_correl2D at initialization stage rather than during + time stepping. + - get smoothOpNb from xx_gentim2d_preproc +o global_oce_cs32 : + - add test of generic ecco capabilities. +o pkg/exf/exf_getsurfacefluxes.F : + - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior). +o pkg/ctrl,ecco : + - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED + is defined. +o pkg/seaice: add diagnostics for Delta (deformation parameter) +o model/src: + - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical + diffusivity (background) is specified but ignored. +o verification: + - in testreport, convert hostname to lower case for default output dir name +o model, pkg : add useCTRL, useECCO parameters (on/off run time switch). +o pkg/dic: add modifications from Hajoon: + - add iron sedimentation flux function of the flux of PO4 out of bottom layer + - light attenuation: add self-shading effect by climatological Chlorophyll + (read from file). +o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also + compiles when SEAICE_ALLOW_DYNAMICS is undefined +o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate + AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than + ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, + approach where CPP_OPTIONS.h includes an omnipotent + ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). +o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where + ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. +o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF + to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included + (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) +o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : + add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed + - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h + - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h + - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc +o pkg/ctrl,ecco,exf : + - remove variables associated with NON-generic costs, + unless ECCO_CTRL_DEPRECATED is defined. + - remove NON-generic NON-obcs controls, + unless ECCO_CTRL_DEPRECATED is defined. +o pkg/ctrl : added ctrl_local_params.h +o pkg/ecco : added ecco_local_params.h +o verification : added ECCO_CTRL_DEPRECATED to most as and oad + experiments, which will progressively be removed once the + experiments are revised to use only generic controls/costs. + +checkpoint65f (2014/10/13) +o pkg/ctrl, ecco, seaice : minor changes in headers +o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic + cost function and control capabilities added since checkpoint65c. +o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. +o pkg/ecco: increase modularity and improve logic + - ecco_toolbox.F (new) : basic operations that are often used, + including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk, + ecco_addcost, ecco_add, ecco_div, ecco_readbar. + - cost_gencal.F (new) : determine filnames and records. + - cost_genread.F, cost_generic.F : condense code using ecco_toolbox. + - cost_generic.F : use spzeroloc rather than hard-coded -9999, + and exploit the above functions leading to more compact code. + - cost_genread.F : rm un-necessary arguments, re-arrange args order. + - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj, + using_ers, using_gfo, using_mdt is now only defined within gencost) +o pkg/ecco: extend generic cost capabilities + - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost + capabilities via gencost_preproc (+ _c,_i,_r related params), + gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod, + gencost_outputlevel arguments to cost_generic + - pkg/ecco/cost_genread.F (new) : interface between cost_generic + and active_read, making room for gencost_preproc to take effect. + Added preproc code ('climmon') to replace GENERIC_BAR_MONTH. + - pkg/ecco/cost_generic.F : + compute and store misfit maks*(model-data) in localdif that is + then used in cost and for output, output misfit if outlev.GT.0 + - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip + rather gencost_barfile for deciding whether to write barfile + - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd + - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from + ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip + - pkg/ecco/ecco_summary.F : report gencost variables + - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs +o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA +o pkg/ecco: internal re-organization + - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl + (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter, + mv relevant variables definition from ecco_cost.h to ecco.h, + make sure gencost routines only include ecco.h) + - throughout : add missing CCP switches, rm unused variables, + and rm un-necessary CPP switches + - throughout gencost routines : replace modelstartdate with + gencost_startdate when needed + - cost_bp_read.F : use arguments, instead of common blocs + so that it can be used also by (new) cost_gencost_bpv4.F + - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0 + - ecco_phys.F : compute etanFull + - ecco_readparms.F : rename using_topex as using_tpj, add + bpv4-grace to gencost list, initialize added parameters + - ecco_summary.F : include SIZE.h needed for augmented ecco.h + +checkpoint65e (2014/09/28) +o pkg/obcs: + - replaced the just-added CPP options with run-time variables + (see pkg/obcs/OBCS_PARAMS.h for details) +o pkg/obcs: + - add additional CPP options for sponge boundary layers + (see pkg/obcs/OBCS_OPTIONS.h for details) +o pkg/atm_phys: + - implement simple (obliquity only, assuming circular planet orbit) + seasonal cycle for incoming insolation ; used when run-time parameter + "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula. +o pkg/exf, pkg/ecco, pkg/ctrl: + - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets + - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip + - implement gentim2d for xx_tauu, xx_tauv +o pkg/ctrl, pkg/ecco : + - fix and complement the generic controls implementation +o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F, + pkg/shelfice/shelfice_thermodynamics.F, + verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F, + verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F : + - add weight in CTRL_GET_GEN calls +o pkg/ctrl : + - ctrl_get_gen.F : add weight as input parameter, and apply + it directly rather than using smooth_correl2Dw (to be retired). + - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call +o pkg/ctrl : + - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, + ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) + - re-activate ctrl_summary (call in ctrl_init.F) +o pkg/ctrl/ctrl_cost_gen.F : + - fix CCP brackets, remove un-necessary myiter, mytime +o pkg/ecco, pkg/ctrl : + - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) + - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) + - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) + - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) + +checkpoint65d (2014/09/15) +o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : + - add xx_genarr2d_bounds,xx_genarr3d_bounds, + xx_genarr2d_numsmooth, xx_genarr3d_numsmooth +o pkg/ctrl/ctrl_map_ini_genarr.F : + - remove compilation failure + - replace hard coded example + - use ctrl_map_ini_gen2D, 3D +o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : + - on/off switch based upon xx_genarr2d_weight,3d +o src/packages_init_variables.F : + - regroup pkg/estimation calls + - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO + (moved to ctrl_init_variables) +o cost/cost_init_varia.F : + - remove ecco_cost_init_varia + (moved to ecco_init_varia) +o ctrl/ctrl_init_variables.F : + - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO + - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI +o ctrl/ctrl_map_ini.F : + - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini + (moved to ctrl_init_variables) +o ctrl/ctrl_map_ini_ecco.F : + - remove ECCO_PHYS (mv to ecco_init_varia) + - remove seaice_ctrl_map_ini (mv to ctrl_init_variables) +o ecco/ecco_ad_diff.list : + - add ecco_init_varia.f +o ecco/ecco_init_varia.F + - new routine +o pkg/streamice: + - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F + to streamice_init_fixed.F ; fix setting of STREAMICEisOn. + - from model/src, only call pkg/streamice routines if useStreamIce is TRUE. +o pkg/generic_advdiff: + - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. +o pkg/exf: + - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, + xxg_precip capability + - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch +o pkg/ctrl: + - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d +o model/src/load_fields_driver.F : + - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING + so xx_gentim2d can be applied to e.g. exf fields in a timely manner. +o OpenAD verification experiments: + - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h + in src files (to enable to skip the ECCO_CPPOPTIONS.h); + for now, only in pkgs used in OpenAD verification experiments. + - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg + specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) + instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). + This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. +o OpenAD verification tests: + - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); + - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for + tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. + - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) + and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). +o model/src & generic_advdiff: + - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S + forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model + dynamics requires valid tracer forcing only over tile interior but, for + some diagnostics, may need to extend it over 1 point in tile halo region. + - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid + tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max + setting in temp/salt/ptracer_integrate.F +o pkg/dic: + - multiply tracer tendencies by maskInC (if ussing OBCS) before updating + gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER + in gchem_forcing_sep.F +o pkg/autodiff & obcs: + - add storage of current OB values for U & V (was already done for T & S). + +checkpoint65c (2014/08/30) +o pkg/dic: + - take out of dic_atmos.F the initialisation part (corresponding to istate=0) + and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for + AD compilers (but still a Pb with multi-threading and Ajoint dependencies). +o verification: + - new experiment testing OBCS and DIC pkgs, using params & output from + tutorial_global_oce_biogeo but limited to a sub-domain around Drake + passage: take OBCS from the last year of a 2 yrs simulation and initial + conditions from t=1.yr while keeping the same forcing. +o model/src: + - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing + (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). +o pkg/diagnostics (Stats-Diags): + - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: + a) refine region where stats are computed, excluding where arrhFac=0 ; + b) fix missing interior mask (use with OBCS) in 3-D fields statistics; + c) extend regional stats over the region edges (for U or V pt location). +o pkg/gchem: + - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since + pkg/dic is currently changing/updating ptracers values beyond the OB). +o verification (hs94): + - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords + bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments + hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of + apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. +o pkg/ptracers: + - implement Adams-Bashforth on pTracers (instead of on tracer tendency), + switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) + - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer + with AB-2 code (so that it get tested). +o model/src: + - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) + with AB-2 code (previously only available with AB-3 code). + Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F + to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done + there, by calling CYCLE_AB_TRACER). +o pkg/generic_advdiff: + - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, + GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R + + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in + S/R temp/salt/ptracers_integrate.F +o model/src & pkg/ptracers: + - remove common block variables gT,gS (in DYNVARS.h), except when + USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. + - remove common block variable gPtr. +o model/src & pkgs: + - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R + ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, + IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, + GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T + + change accordingly all calling S/R. + - use local temperature/salinity/ptracer tendency array (without bi,bj) + in S/R temp/salt/ptracers_integrate.F +o pkg/seaice: + - move computation of stress contributions to rhsU/V in s/r seaice_lsr + to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code + - make u/vIceC local variables if SEAICE_CGRID is defined only to be used + in seaice_lsr + - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D + in s/r seaice_lsr_calc_coeffs +o pkg/mdsio: + - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long + (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is + too long (e.g., > MAX_LEN_FNAM/2 ) + +checkpoint65b (2014/08/12) +o pkg/matrix: + - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP +o model/src: + - fix initialisation of geothermalFile; compile geothermal-flux code in + natl_box verification experiment. +o model/src & pkg/down_slope: + - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). + - in dwnslp_apply.F, update tracer tendency instead of the future tracer + field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects + results at machine truncation level: update output of experiments + global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). +o pkg/diagnostics (Stats-Diags): + - do not cumulate the full volume when DIAGNOSTICS_FILL is + called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); + This fix the mean statistics when DIAGNOSTICS_FILL is called multiple + times (but Min,Max and StD are still wrong). +o model/src: + - add geothermal flux forcing: read in ini_forcing.F as time-constant + field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) +o model/src: + - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer + _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac + arrays are already updated while adjustments (filters, conv.adjustment) are + still applied later, in S/R TRACERS_CORRECTION_STEP. +o model/src: + - store in common bloc array "rhoInSitu" the virtual potential temperature + anomaly that is used to compute geopotential: this make the atmos code + more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F +o pkg/seaice/seaice_lsr.F + - rename integer variable ilcall to ipass (that's what it is called + in the residual diagnostics + - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the + default) for improved non-linear convergence of the first few steps + - adjust a few comments and add new ones to explain some of the store + directives +o pkg/generic_advdiff (& ptracers): + - re-work the code to check for valid advection scheme and for minimum + size of overlap (now stored in local common bloc in gad_advscheme.F) +o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics + - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 + - add an auxilliary variable "bet" and fix store directives and keys in + seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or + less exact gradients in my tests); but there are still + recomputation warning (although gradients are sort of OK), when + SEAICE_LSR_VECTORIZE is not defined, so this flag and + SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. + - update verification experiments lab_sea. + - change some comments in S/R seaice_calc_viscosities +o model/src: + - if staggerTimeStep=T, always apply exchange to velocity field in + do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F + (independent of using multi-dim advection or not); no effect on FWD run + but affects AD results (at machine truncation level): update output of + experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) + and isomip (oad: 12.d). +o pkg/generic_advdiff: + - stop if doAB_onGtGs is set to FALSE but ignored + - refine warning related to stability of tracer time-stepping + regarding internal wave dynamics. + - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition + on staggerTimeStep & implicitIntGravWave (will now get a warning + if potentially unstable). +o pkg/kl10: + - add new pkg "kl10" for mixing due to internal wave breaking, from + http://www.sciencedirect.com/science/article/pii/S1463500310000144 + (contribution from Jody Klymak), tested in verification experiment + verification/internal_wave/input.kl10/ +o isomip experiment: + - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up + (input.htd) and update the output. +o cd_code experiments: + - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & + #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) + global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and + update the corresponding output. +o pkg/seaice: + - reduce the number of include files and store directives in + S/R seaice_lsr_tridiagu/v + - change the order of loops in one case in S/R seaice_lsr_tridiagv + (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to + get rid off one store directive (a TAF bug?) + - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in + S/R seaice_lsr_tridiagv to change the loop range for consistency + - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v + - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in + S/R seaice_lsr_tridiagu/v (requires update of + offline_exf_seaice/input.dyn_jfnk) + +checkpoint65a (2014/07/27) +o model/src: + - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than + surrounding hFacC=1 @ edge of a step with different kSurfC on either side + (topo in p-coords, ice-shelf in z-coords); update output of experiments + tutorial_global_oce_in_p and isomip (both AD and OpenAD output). +o model/src: + - collect momentum forcing tendency into local 2-D array (passed as argument + to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE + parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); + affects results at machine truncation level (e.g., if using OBCS_SPONGE). + - collect T & S forcing tendency into local 2-D array (passed as argument to + apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. + affects results at machine truncation level (e.g., ocean: if using + SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist + correction due to vertical advection). + - update output of experiments: fizhi-cs-32x32x40 (13 digits), + global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: + seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), + obcs_ctrl (ad & fwd grd @ 12 & 7). +o pkg/ptracers & diagnostics: + - use ptracers (short) name (instead of long one) to make ptracers diagnostics + title (to avoid some unexpected truncation); sort out ptracers diags units. + - collect ptracer forcing tendency into local 2-D array (passed as argument + to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. + +checkpoint65 (2014/07/18) +o pkg/fizhi: + - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this + affects results at machine truncation level. Update output of experiments + fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). +o pkg/seaice: more clean up + - rename TAF common block tapes to be more consistent and remove + unnecessary duplicates + - add store directives to remove more recomputations, but use smaller + tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. + The idea behind this flag is to reduce the memory footprint when the + adjoint of the LSR is not required. As of now, defining the flag + SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by + a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). + For experiment offline_exf_seaice, this means on a linux box with gfortran + nearly a factor of 10 (but keep in mind there is mostly seaice code in + this experiment): + > size mitgcmuv_ad + text data bss dec hex + 5100659 1216 220458952 225560827 d71c8fb + 5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) + but only a moderate increase of 36% for global_ocean.cs32x15: + text data bss dec hex + 6695027 1648 1014578664 1021275339 3cdf6ccb + 6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER) + - note: there are still recomputations in global_ocean.cs32x15 and + offline_exf_seaice and the gradient agreement changes (gets a + little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) + - in general, the AD gradients still are wrong +o OpenAD + - clean up code_oad/ directories somewhat by moving files + dontCompile, dontTransform, keepOriginal to OAD_support/ +o model/src: + - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F + (not currently tested): add dissipation terms before NLFS rescaling of + tendencies (previously done after). +o pkg/diagnostics: + - write stats-diags in ascii file with more digits (same as in monitor). +o pkg/down_slope: + - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with + NLFS (not tested), use new recip_hFac value in order to conserve tracer. +o model/src: + - new file "apply_forcing.F" containing all the code previously in + external_forcing.F, but with new argument list: pass, as new argument, + the current level tendency array to update (instead of a direct update + of the common bloc array). Change the corresponding calls. + - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use + EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility). +o pkg/seaice/seaice_lsr, a little bit of clean up + - rearrange some code blocks, so that now all calculations for + setting up the right-hand-sides done within one single block + (I find that easier to read and understand) + - rearrange freedrift-code to reduce the number of ifdefs + - adjust some indentations and comments + +checkpoint64z (2014/07/10) +o model/src and several pkgs: + - change argument list of all S/R called from external_forcing.F and + called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F) + to pass, as argument, the current level tendency array to update + (instead of a direct update of the common bloc array). + - change also (in the same way) argument list of PTRACERS_APPLY_FORCING; + - rename taueddy_external_forcing.f to taueddy_tendency_apply.F +o pkg/seaice/seaice_lsr.F + - always initialize local arrays in seaice_lsr_tridiagu/v + - add more local tapes to seaice_lsr_tridiagu/v + - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but + keep it in bi/bj loop; this seems to be essential + - gradients are still wrong but only by 4-7 orders of magnitude + instead of 15 orders of magnitude, lab_sea improves a little +o pkg/seaice + - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that + generates unnecessary code in seaice_lsr_ad + - add more store directives in seaice_lsr to avoid unnecessary code + in seaice_lsr_ad + - exclude some residual computations in seaice_lsr when + ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code + in seaice_lsr_ad + - add more storing, a new tape (model/src/the_main_loop.F) and + another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey + and klockey should be checked by a specialist) + - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER ) + and update lab_sea after previous changes in pkg/seaice below +o pkg/autodiff: + - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and + viscFacInAd : run time parameters allowing for adjoint switches + note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F +o pkg/ecco: + - introduce cost_gencost_boxmean.F that computes a box mean + temperature (for use in adjoint sensitivity studies). +o model/src/set_defaults.F : initialize viscFacAdj to 1. +o pkg/mom_common/mom_calc_visc.F: + - ifdef ALLOW_AUTODIFF then include viscFacAdj factor. +o pkg/seaice/seaice_summary.F: + - statement for SEAICEadjMODE now in autodiff_readparms.F +o pkg/seaice: + - remove some store directives and add new ones in an effort to get + finally rid off the recomputation warnings. This is successful + when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are + defined (i.e. no extensive recomputation warnings left), but there + are still too many recomputations on the solver iteration level + - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h + - move definition of MPSEUDOTIMESTEPS into TAMC-block in + SEAICE_SIZE.h + - add a store directive in S/R seaice_calc_viscosities +o pkg/seaice (ITD code): + - fix definition of Hlimit for multi-threaded case + - use double precision arithmetic to compute Hlimit: this affects results; + update output of experiment seaice_itd. +o replace content of verification/seaice_itd + - instead of a 1D column use the configuration of offline_exf_seaice + to test the ice thickness distribution code with ridging + - this is a first shot at this experiment + - change of some defaults of ridging parameters SEAICEhStar (from + 100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F + and lot of new comments. + +checkpoint64y (2014/06/20) +o pkg/seaice/seaice_reg_ridge.F: + - modify the regularization of very small volumes of ice; only check + total volume HEFF, and do not apply correction to individual ice + classes because that leads to funny patterns in the heat and fw-fluxes + into the ocean. Adjust seaice_itd/results/output.txt + - replace nITD by SEAICE_multDim in loop-ranges +o pkg/exf: + - add code to process the case field period = -12. with UV interpolation. + - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec + into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F) +o verification/global_with_exf: + - switch all fields period to -12. (was previously untested) in input/data.exf + (but keep secondary test ".yearly" unchanged); update the reference output. +o pkg/cal: + - new calendar type "noLeapYear" for 365 days calendar without any leap year. +o pkg/exf: + - new integer parameter "exf_debugLev" (default set to main model debugLevel) + to replace logical switch "exf_verbose" + - report in STDOUT when loading a new record (if exf_debugLev >= 3) +o pkg/sbo: + - update from Katherine Quinn: evaluate mass directly from density and SSH + (budget using Finite Volume method) instead of from bottom pressure. + - allow testreport to collect few selected SBO output ; tested in exp. + global_ocean.90x40x15 (after updating the results, to include SBO output). + - fix some multi-threading issues (in output part). +o model/src & most packages: + - always call {PKG}_READPARMS even if corresponding use{PKG}=F; + - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R + PACKAGES_UNUSED_MSG to print a weak warning when parameter file + "data.{pkg}" exist ; and leave the S/R (return) just after. + - more standard LAND pkg interface (land_init_fixed.F, land_check.F). + + call LAND_READPARMS from packages_readparms.F +o pkg/seaice: + - remove code that resets useThSice in S/R seaice_readparms and + replace it by a warning in S/R seaice_check + - remove parameter MULTDIM, replace with nITD and runtime + parameter SEAICE_multDim (still hard-wired to nITD if + SEAICE_ITD is defined) + +checkpoint64x (2014/05/24) +o verification/lab_sea: + - update adjoint and TLM output following changes to pkg/salt_plume + - un-do the update after putting back local recip_Cp in few places. +o pkg/salt_plume: modifications by An Nguyen: + - add capability to do brine rejection (salt-plume) as function of + volume+tracers (instead of only salinity tracer). + - conserve volume by exchanging volume from each kLev to above to + accommodate in-coming brine volume + - store surface and klev exchanged fraction + volume in 4 new 3-d arrays + - switch KPP surf buoyancy due to brine forcing to 3-d + (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume) + - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t + - unrelatedly, also add ad-hoc capability to vary salt_plume scheme + in East/West Arctic. +o pkg/sbo: + - incorporate modifications from Katherine Quinn to enable the use of sbo + pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like + output for future testreport verification (unfinished). +o pkg/atm_phys: + - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R: + skip the reseting of t_ref & q_ref to initial t & q ; this preserve the + output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics. +o pkg/seaice + seaice_calc_ice_strength.F: modify expression to avoid divisions + (affects truncation) + seaice_do_ridging.F: clean up the insectarium + - fix a bug that was compensated by areaScaling (-> remove areaScaling code) + - added SEAICEsnowFracRidge to redistributed snow (2nd bug) + - set closing/openingRate to zero where no extra iteration is need (3rd bug) + - add some debugging information and error messages (warnings) +o model/src: modifications relatd to atmosphere p*: + - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F) + - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead + of vertical profile tRef in geopotential background and anomaly. + - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23 + and pkg/atm_phys. + - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40, + fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn. +o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt +o pkg/ptracers: compute ptracer source/sink due to linear free surface. + not used right now, but can be used in BGC packages to fix conservation. +o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by + other packages too. +o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by + SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix) +o model/src: + - since we have several heat capacity (even in model/src), define "recip_Cp" + as local variable (no longer in common block) to avoid any confusion. + - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords). +o pkg/exf: + - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local + air density as function of air Temp, Humidity and atm pressure. + +checkpoint64w (2014/05/02) +o verification: + - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice & + seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing + code from seaice_growth.F & seaice_advdiff.F to new ridging routines + seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient + (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea). +o model/src: for atmosphere in p* coords: + - store factor rStarFacC**atm_kappa (= pStarFacK) in common block + - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F), + but not yet activated. +o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation: + - move computation of opnWtrFrac = 1-AREA to before computing ice strength + - this changes the results (but not for any verification experiment, because + none tests this), but avoids having an extra field in the restart files +o pkg/seaice: remove global variable TICE (not needed) + - replace by TICES or local variable where necessary (cost_seaice_test, + seaice_diagnostics_state) + - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup + - use specific read/write routines for reading and writing individual leves + of a multilevel field +o pkg/ctrl & model/inc: + - move additional anomaly fields of control vars (related to options: + ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL) + from DYNVARS.h into new header file: CTRL_FIELDS.h +o pkg/seaice: some small modifications to the ridging code + - make fw2ObyRidge a global variable and add the freshwater flux to + seaice_growth + - pass actual thickness from seaice_prepare_ridging, so that it is + computed only in one place and compute it in the same way as in + seaice_growth + - initialise more fields in seaice_do_ridging that where cause floating + point exceptions over land +o pkg/seaice: preparations for ridging code and first real ridging code + - move most of "PART 1" of S/R seaice_growth into a new and separate + S/R seaice_reg_ridge that will both regularize the state variable after + advection call the actual ridging routine; + - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG, + d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust; + - remove ridging code from seaice_advdiff + - clean up remaining part 1 of seaice_growth in an attempt to make it + more readable (this is probably subjective) + - call seaice_itd_redist once in the initialisation phase to have the initial + conditions in the correct category + - finally: add new ridging routine for ITD code + +checkpoint64v (2014/04/11) +o pkg/ecco: + - add runtime parameters mdt[start,end]date[1,2] + - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile" +o pkg/seaice: + - make deltaC a global variable, so that it can be used in ridging code + - first step towards ridging: introduce new routines that compute + ice strength based on ridging parameters + - add diagnostic for HSNOWITD + - add opnWtrFrac as a global variable (required for ridging scheme) +o pkg/salt_plume + pkg/seaice/seaice_growth.F + - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice + AREA exceeds a threshold (code contributed by I.Fenty in 2011) +o verification/hs94.1x64x5: + - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h + - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests. +o autodiff: + - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, + and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h) + For now, only in pkgs used in verification/hs94.1x64x5. + - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage + which are specific to TAF/TAMC). + - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD: + since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad + is compiled), this simplifies/reduces which *_OPTIONS.h file to include. + - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when + building mitgcmuv_ad (make adAll). +o pkg/ecco: + - cost_gencost_seaicev4.F: + reformulate proxy cost as function of sst and local param SEAICE_freeze + change cost names from siv4-[sst,vol] to siv4-[deconc,exconc] + - add stop statement if old names siv4-[sst,vol] are used + - add snapshots + cost reports for atmospheric longwave + - remove factor 0.1 in front of wtau[u,v] + - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with + ALLOW_TMI_SST_COST_CONTRIBUTION +o pkg/atm_phys: + - add some diagnostics for Short-wave and for convection S/R. +o pkg/seaice/seaice_growth: + - fix a bug in the lateral melt parameterization for SEAICE_ITD + in seaice_growth; tempFrz needs to be computed inside the i/j-loop + - rearrange loop order for better vector code in the same code block + - rewrite the floeDiameter formula to have fewer divisions + - (miraculously) none of this changes the results of seaice_itd +o pkg/smooth: + - move param smooth2Ddiffnbt to pkg/ecco +o pkg/salt_plume: + - salt_plume_frac.F: + clean up local param names + reformulate (1-frac) to frac; original 1-frac was based on swfrac code +o pkg/rw: + - add RS version of S/R READ_MFLDS_LEV. +o pkg/streamice: + - fix the restart test by writing/reading pickup_streamice files. +o pkg/seaice: + - refine checks for jfnk-related parameters + - comment out if statement with SEAICEuseIMEX parameter as long as there + is no IMEX code to avoid confusion and surprises + +checkpoint64u (2014/03/07) +o verification/MLAdjust: + - rename secondary test suffix: + 1.leith -> A4FlxF + switch to flux-form & add side-drag + 0.leithD -> AhFlxF + switch to flux-form + 0.smag -> AhVrDv (use Vorticity-Div. visc form) + add side-drag + 0.leith -> AhStTn (use Strain-Tension visc form) + add side-drag +o pkg/mom_vecinv: + - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used + to be before mom_calc_visc.F) + - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed. + - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip): + this is simpler for the adjoint and for diagnostics. +o model/src + pkg/momentum: + - add input files for 2-D additional Western and Southern cell-edge wall + (e.g., to add "thin-wall" where it is =1). + - fix sideDrag option for thin-walls with Non-Lin Free-Surf + using 2nd hFacZ that is computed from initial (fix domain) hFac + - known limitations of thin wall implementation: not yet coded for sigma + coords; not working with CD-scheme neither. +o pkg/seaice: + - rename recently introduced parameters from (wrong name) AB to + BDF (backward difference time discretisation) + - retire runtime parameters SEAICEuseAB2, SEAICE_abEps +o tools/adjoint_options: + - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad") + +checkpoint64t (2014/02/01) +o pkg/ecco + - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and + runtime logical flag gencost_timevaryweight to read daily sea-ice sigma + - replace hard-coded record number and period which only work for monthly + with read-in runtime param that works for other periods (month,day,year) +o pkg/thsice + - corrected store directive fixes thsice adjoint gradient checks +o genmake2 & testreport: + - add genmake2 option "-oad" to generate a Makefile for OpenAD built and + in this case, use tools/adjoint_options/adjoint_oad as default AD optfile. + Update testreport accordingly. No need to set "export OPENAD=true" + in adjoint_options/adjoint_oad anymore (will be removed later). +o pkg/shelfice: + - put T & S shelfice forcing into model surfaceForcing_T,_S (for now, + only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F + so that surface forcing applies to k=kSurf if using pkg/shelfice. +o pkg/ctrl, pkg/grdchk, pkg/ecco: + - Changes to make GENARR more modular (i.e. invisible if not used) +o model/src/temp_integrate.F and salt_integrate.F + - re-include store directives that were removed on Dec 27th. +o model/src/external_forcing_surf.F + - add storage directives for EmPmR and PmEpR to avoid recomputation of + seaice_model in the adjoint that is problematic when seaice_model is + turned off in the adjoint. The resolved issue dated back to July when + EXTERNAL_FORCING_SURF call was moved. + Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly. +o pkg/exf/exf_check.F + - fix a small bug again (originally found by Wentao Liu, now found again) + - streamline error output +o pkg/streamice and aim_v23: + - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that + Apple's /usr/bin/cpp knows what to do: + Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) + Target: x86_64-apple-darwin13.0.0 + +checkpoint64s (2014/01/05) +o tools/adjoint_options: + - switch to fastopt.net TAF server (instead of default fastopt.de) for + AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default). +o model/src: + - remove some unnecessary TAF storage directives in forward_step.F and + in dynamics.F (note: not always removed by TAF, e.g., double storage + of kappaRU,kappaRV in former version of dynamics.F). +o model/src & pkg/ptracers: + - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F + salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F) + and remove ptracers_dwnslp_apply.F & ptracers_implicit.F + - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F) + - add fZon & fMer as output argument of S/R GAD_CALC_RHS. + - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad). +o useSingleCpuInput separates single-CPU input from single-CPU output; + for now only implemented for in exf_interp_read.F +o verification/advect_xy: + - fix missing EXCH call in local version of ini_salt.F and update output. +o momentum diagnostics: + - fix which deltaT is used in Total-Tendency diagnostics. + - fix typo in diagnostics for momentum tendency from AB. +o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the + SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8 + +checkpoint64r (2013/12/08) +o verification/*/results: + - Update reference output of experiments that were passing with just 13 digits + (make it easier to detect future changes in results) +o model/src & pkg/ptracers: + - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to + inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F + to inside ptracers_integrate.F ; remove ptracers_advection.F +o coupling interface pkgs: + [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler] + - change the config check to test the agreement of Ocean Depth + with ATM land/sea mask (instead of ATM orography); + - send to coupler the number of coupler time-steps to do for this run: + this allows to check for consistency and don't need anymore to be + specified in parameter file "data"; + in coupler: + - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask. + - improve report to log-file of config setting (pass log-file unit to few S/R) +o pkg/compon_communic: + - add coupling send/receive for non-tiled integer vector; + - add S/R to check and stop if any proc has an error (similar to + eesupp/src/stop_if_error.F but single thread and across Comm_World). +o pkg/exch2: + - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search + through list of all tiles my proc owns. +o model/src: + - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying + from rTrans) to simplify dependencies (no need to store rTrans anymore in + calling S/R); this affects AD results at machine truncation level: + update AD-output (TAF) of experiments: 1D_ocean_ice_column, + bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad). +o tools/build_options: + - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran +o coupling interface pkgs: + [compon_communic, atm_compon_interf & ocn_compon_interf] + - move declaration of local array "ibuf" out of header file "CPLR_SIG.h" + to each S/R that needs it; remove un-used variables. + - change component tile registration (cpl_register.F in both compon_interf + and mitcomponent_tile_register.F) to pass the full list of tiles + information (including bi,bj) in 1 vector (instead of in a bi,bj matrix). + - with pkg/exch2: adopt the same convention used for I/O to define mapping + towards coupler global array (unless W2_useE2ioLayOut=F): + a) can now use different tiling between atm & ocn comp. + b) no needs to modify the run-Off map when changing tiling (was needed + even if using the same tiling between atm & ocn). + c) will allow to run with blank-tiles in 1 component (e.g., for ocean + full land tiles); not yet tested. + - check for valid mapping from comp. tile to coupler global array + - improve report of tile registration results to log file. +o pkg/exch2: + - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler + tile-registration (CPL_REGISTER); + - activate (un-comment) definition and setting of "W2_tileIndex" list to + store the local bi,bj indices of each tile; + - also print bi,bj in local report to log file; + - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from + Jun 2009 modif of pkg/exch2). +o testing on baudelaire: + - run 2 tests at a time: no significant slow down (since enough cpu) and + get the full set of test done earlier + - switch the ifort test to "-devel" ; run the OpenAD test everyday. +o model/src/thermodynamics.F and routines called from it: + - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F & + gmredi_calc_wflow.F) to update eulerian velocity (input) into residual + velocity (outp) by adding bolus velocity. + - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute + mass transport from velocity + lateral grid cell area + - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER) + - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER) + in thermodynamics.F + - remove k from thermodynamics.F and move it to temp_integrate.F + salt_integrate.F and ptracers_integrate.F (now done inside the tracer + loop). + - compute locally (in thermodynamics.F) 3-D velocity field that is used to + advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT, + PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE, + GAD_IMPLICIT_R and PTRACERS_IMPLICIT + - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column, + global_ocean.90x40x15, tutorial_global_oce_biogeo and + tutorial_tracer_adjsens (+ TLM output). +o tools/OAD_support and (verification/*/) code_oad: + - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to + module conversion ; remove unneeded CPP_EEOPTIONS.h. + - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard + version (closer to model/inc/CPP_OPTIONS.h). +o model/src: + - remove parameter "useOldFreezing" from PARAMS.h and push it to the + retired list of parameters (routine FREEZE has been replace by surface + freezing (10.yrs ago) and by pkg/frazil (interior freezing). +o pkg/gmredi: + - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from + velocity (same scheme but affects machine truncation) for GM_AdvForm. + - update output of FWD experiments: front_relax.bvp, + global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce. + +checkpoint64q (2013/11/17) +o verification: + - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments + tutorial_global_oce_biogeo and global_ocean.90x40x15. + - generate new output (growth & melt) for seaice_itd experiment after + updating the input pickup_seaice files (previously wrong). +o pkg/cost: + - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL + (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads: + o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL + cannot be applied to var in common block). + o allows to get results independent of tile-per-proc setting (if using + slower GLOBAL_SUM_SEND_RECV option). + - update accordingly: seaice_cost_final.F, shelfice_cost_final.F, + thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea + forward gradients: update output). + - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL + S/R and, for most exp., also comment out GLOBAL_SUM_R8. +o pkg/mom_common: + - move to pkg/mom_common and model/src (previously in tutorial_deep_convection + code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and + viscosity are locally declared in dynmics.F and pass as argument to CALC_GW; + ensure that all field value that are used are set. +o tutorial_deep_convection (smag3d): + - add missing scaling in mom_calc_smag_3d.F; + - set smag3D_coeff in input.smag3d such that results do not change. +o pkg/dic: + - change dic_cost.F to compute cost on each tile first and then apply + GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments + tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output. + - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea. +o eesupp/src & pkg/mdsio: + - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F + (from pkg/mdsio) since they are no longer used for tape IO. + - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src + (+ keep a copy in pkg/atm_ocn_coupler). +o verification/isomip: + - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests. +o tools/build_options: + - optfile linux_amd64_ifort11, fast (no ieee) case: + to get a working restart for all experiments, add "-fp-model source" + to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default). + +checkpoint64p (2013/10/20) +o pkg/autodiff: + - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO + criteria, return to simple (default) tape IO format. +o pkg/mdsio (+ eesupp/src): + - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace + previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8); + - fix globalFile and singleCpuIO options using simpler global mapping. + - new pairs of scatter/gather vector S/R (one for each type, generated from + template) corresponding to simpler global mapping. + - adread_write.F: switch to new S/R (but leave old calls commented) and write + to globalFile when parameter globalFiles is set to True. + - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip. +o pkg/autodiff: + - adread_adwrite.F: add a hack for RS arrays (when RS=real*4); + with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is + missing, just add a STOP if array type do not match. +o pkg/exf: + - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice: + rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION + and rename array obsSIce to exf_iceFraction. +o tutorial_deep_convection: + - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe), + for now all in this exp. code dir. + - add secondary test using Smag-3D viscosity (keep very low backgroud visc for + testing) and flux-limter advection scheme for Temp. (no explicit diffusion). +o eesupp/src: + - added SINGLE_DISK_IO option because reading of parameter files on + very large number of processors did not work with existing set-up + +checkpoint64o (2013/09/25) +o pkg/atm_phys & atm_compon_interf: + - allows for coupling of gray-atmosphere (atm_phys) with ocean. +o tools/build_options: + - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran + & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also + remove CPP setting (was identical to genmake2 default). +o pkg/gmredi & model/src: Some updating and work done on the residual model. + - created new file model/src/calc_eddy_stress.F to calculate the eddy stress. + - fixed up the calculation of the eddy stress and how it is added to the + external forcing via taueddy_external_forcing.F + - at the moment, it is very experimental and only works with the variable eddy + diffusivity calculated in gmredi_k3d.F +o pkg/seaice/seaice_check.F: add a check to catch the case of specifying + lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice +o testreport (& tools/do_tst_2+2): + - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}' +o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11: + - remove CPP='cpp -traditional -P' (this is genmake2 default) + - add switch (for big setups) to use 'medium' memory-model (but leave it + commented out for now). Note: needed with FC 19 to compile big setups. +o pkg/atm_compon_interf: + - regroup per field origin (model & pkgs) the coupling storage routines + (which accumalate in time each coupling field) + - move bi,bj loops inside atm_store_my_data.F and store also wind-stress; + update accordingly + simplify aim_do_physics.F + +checkpoint64n (2013/08/26) +o pkg/bbl: + - update formulation to reduce dispersion of tracer properties in bbl + - replaced horizontal and vertical transport parameters with velocities + - changes results for verification/global_with_exf.yearly +o verification/halfpipe_streamice: + - change to matrix construction; update both Fwd & AD output. +o verification/tutorial_tracer_adjsens: + - OpenAD test: switch to vector-invariant momentum since fluxform with + rStar causes problems with OpenAD; update output. +o tools: + - genmake2: define a common prefix for all temp-file names ; move them + to local /tmp disk (but would be easy to move them back); + - xmakedepend: apply the same switch for temp-files. +o pkg/offline: + - changes for use with rStar (NLFS): assume that we continue to provide + UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid + output files) and apply r* scaling at each time-step (function of the time + varying Eta field); use normal pickup files (needed for restart with NLFS). +o adjoint with OpenAD: + - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new + package openad. This package has to be compiled for all runs with OpenAD + instead of specifying code_oad_all as a modification directory. + - link the fortran templates from tools/OAD_support to the build directory + for preprocessing to avoid conflicts between different setups compiled + simultaneously and simplify cleanup. +o pkg/exf: + - in exf_getforcing.F: comment out most of the EXCH calls (fields used by + main model or other pkgs are exchanged in EXF_MAPFIELDS). +o model/src: + - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline + (similar to do_fields_blocking_exchanges.F). +o tools/genmake2: + - remove TAF output src code just before calling staf (when not doing a fresh + built, will stop if things go wrong with staf). + - fix target "adobj" (left from TAF version-2 transition) +o pkg/diagnostics: + - add a parameter to track the status of pkg/diagnostics activation; + this replace/extend the use of logical param "settingDiags" (to check + when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call. + New S/R to print error message and stop when pkgStatus is not right. + - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F. + +checkpoint64m (2013/08/13) +o model/inc: + - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from + 8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) +o pkg/kpp & aim_v23: + - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. +o pkg/seaice: + - restore (last time on 2011/12/24) ability to compile pkg/seaice with + undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. + - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. +o eesupp/src: + - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) + in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). +o switch to TAF version-2: + - add flow directives to "freeze" naming convention for ad-routines that + are used in I/O routines of adjoint state and associated common blocks + that are used in adcommon.h (backward compatible with version-1) + - update all ad-optfiles (in tools/adjoint_options + few local to some + verification exp) to switch to latest TAF version (currently 2.5.5); + merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented + out except for diva). + - the major change with TAF version-2 is that both the differentiated + routines and the forward routines (new) are returned as part of the TAF + output source code. Update genmake2 accordingly. + - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient + with version-2 when compared to TLM or FWD gradient); other experiments + output show minor changes (machine truncation level); update the few AD & + TLM output with 12 matching digits only (some prior to version-2 switch). + +checkpoint64l (2013/08/05) +o model/src: + - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F + - main_do_loop.F: no longer includes additional (AUTODIFF) header files + when using TAF but only if using OpenAD. +o pkg/mom_common+fluxform+vecinv: + - always set horiz. viscosity arrays to background value before calling + MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC + only when using variable horiz. viscosity (useVariableVisc=T); + - simplify mom_vecinv.F (only 1 block for momViscosity). +o pkg/mom_common: variable horiz. viscosity in NH code + - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F) + from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h + - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, + useBiharmonicVisc & useVariableVisc. + - fix old bug (already in 1rst implementation of variable horizontal viscosity + in calc_gw.F, version 1.27, 2006/06/20): + horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 + even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. + - change background horiz viscosity in vertical momentum (gW) to always be + viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using + any type of variable viscosity, e.g., viscAh/4Grid) + - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of + viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing + horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since + default viscAh,viscA4 is zero). +o model/src: + - extend length of drC & recip_drC from Nr to Nr+1. +o Divided Adjoint (DIVA) with MPI: + - genmake2: do not create local ./mpi_headers dir when no file to copy into. + - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT + and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h. + +checkpoint64k (2013/07/23) +o tools/OAD_support: + - avoid the need for file "oadtempflile" in insertTemplateDir.bash + and remove it from genmake2. +o tools/build_options: + - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out + MPI_HEADER_FILES list (let genmake2 find the missing headers) +o verification/halfpipe_streamice: + - change to driving stress formulation; update both Fwd & AD output. +o tools/genmake2 and Divided Adjoint with MPI: + - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken); + - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set; + - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in + Makefile, which is set by genmake2, and check which mpi-headers are needed. + Note: need to update adjoint_options/adjoint_diva_mpi accordingly. + - update target "CLEAN" (to also remove ./mpi_headers/ dir). +o testreport: + - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, + perform additional runs (number of additional runs is "add_DIVA_runs" taken + from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h"). +o verification/lab_sea (AD test): + - change to test Divided Adjoint Run in this set-up (both standard AD test + and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test. +o pkg atm_ & ocn_compon_interf: + - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old + staggerTimeStep implementation) and disable (retired) corresponding + parameter. +o pkg/offline: + - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01]; + - add S/R OFFLINE_CHECK to print offline parameter summary + and stop if loading a file that is not used; + - enable to calculate GMRedi tensor, KPP mixing and convective index + when the corresponding file(s) is/are not specified (but pkg is used). + - comment out resetting of monitorFreq (to endTime) since it still useful + for monitoring CFL numbers and checking offline fields. +o OpenAD: + - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get + smaller standard output) and generate new (smaller) output (on baudelaire + using gfortran with -ieee) for exp. tutorial_tracer_adjsens +o model/src: + - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F), + (where external_forcing_adjust was called) and change list of arguments; + - merge external_forcing_adjust.F into external_forcing_surf.F + - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F) + which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX, + previously in file "balance_relax.F", now removed); remove corresponding + arrays in FFIELDS.h. + - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement + a hack for getting back surfaceForcingS (loaded from file) when using + ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up. + - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix + (was getting only 11 digits for AD-grad, due to different truncation + error in AD code). + +checkpoint64j (2013/07/04) +o pkg/offline: + - to enable the use of other features with pkg offline (e.g., obcs), + also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come. + - comment out "allowFreezing" (now active) in 2 offline testing exp. +o pkg/exf ALLOW_RUNOFTEMP + - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL + - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice + - changes verification/global_ocean.cs32x15/results/output.seaice.txt +o pkg/atm_phys: + - allows to add some damping on uVel,vVel (strength only function of k). +o verification, ad-tests: + - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, + global_ocean_ebm and offline_exf_seaice.thsice. +o verification/halfpipe_streamice: + - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused + flux input boundary conditions to be ignored; a fix for this bug changed + verification results for forward test. + - add adjoint test. +o pkg/ptracers: + - allow to restart without SOM pickup (resetting SOM to zero). +o pkg/gmredi: + - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added. + - It uses mixing length theory and suppression by steering level effects to + calculate a diffusivity used in the Redi tensor (see Bates et al., submitted + to JPO, for more details). + - It also uses the diffusivity to calculate an eddy induced streamfunction + based on a PV closure (rather than a buoyancy closure as in GM). + - New files added to pkg/gmredi: + gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy + induced overturning streamfunction (called from gmredi_calc_tensor) + gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required + for use in gmredi_k3d + gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate + the eddy diffusivity + +checkpoint64i (2013/06/18) +o pkg/cheapaml: + - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code + that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics) + with pkg/cheapaml. +o utils/python: add subpackage for cubed sphere function, first example is + simple cs.pcol to plot 2D fields on a map +o pkg/streamice: + - This is a new package in MITgcm, which solves dynamic equations for ice + sheets and ice streams + - At the moment it is independent of atmosphere/ocean dynamics, or any + other physical packages in MITgcm, even ShelfIce (although it is anticipat- + ed that this will change) + - There is a new verification exercise that tests it, halfpipe_streamice, + evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a + rectangular embayment + - halfpipe_streamice is forward-only for now, will have TAF test soon + - for questions, email dgoldber@mit.edu +o pkg/thsice: + - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing + of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40); + - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new + call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect ); + - allow precip from pkg/cheapaml to make snow over seaice. +o pkg/cfc: + - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC + - remove atmos CFC 2-D arrays from common bloc (now local variables) + - change some hard-coded constant to run time parameter for reading and + and interpolating atmospheric CFC ; keep same default as previously. + - more flexible reading of Atmos CFC (number of records no longer hard-coded) + - put arguments in standard order: myTime, myIter, myThid + - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of + atmospheric CFC ; fix for the case myIter < PTRACERS_iter0. + - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf + - new routine to print summary of CFC params and check for consistency. +o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff, + similar to thsice_advdiff. + Note that for the B-grid case the routine parameters uc/vc are overwritten. +o pkg/cfc: + - change time interpolation for atmospheric CFC-11 (now same as for CFC-12); + update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline. + - fix interpolation of atmphspheric CFC between Sorthern and Northern + hemisphere value. +o pkg/seaice: + - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml) +o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics; + so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE. + - requires an additional time level that is stored in the pickup + - you can start with AB2 from a pickup without this time level with + pickupStrictlyMatch = .false. + +checkpoint64h (2013/05/26) +o pkg/cheapaml: + - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux); + affect machine truncation (but exp cheapAML_box still pass with 13 digits). + - consistent treatment of uWind,vWind location: assume everywhere in + pkg/cheapaml that they are on C-grid (@ uVel,vVel location) + (Note: was already the case for Tair,Qair advection); + add option (INCONSISTENT_WIND_LOCATION) to recover old results. + - compute diabatic forcing only in the interior (excluding overlap regions) + - fill in array "Qsw" (for short-wave heating); + - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars + before any update (consistent with MITgcm state var diagnostics); + - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if + non periodic ; + adjusted for uWind,vWind (C-grid). +o pkg/seaice: + - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and + add explicitly pkg/exf in experiments that currently use pkg/seaice. + - allows to compile pkg/seaice without pkg/exf. +o tools/OAD_support: + - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds + of array "ourStepOf" in function rvNextAction (revolve.F90). +o pkg/aim_compon_interf renamed to pkg/atm_compon_interf + - change pkg name (to be used with other atmospheric physics pkg) + but by-pass CVS when making the new pkg so that we keep the CVS history. +o pkg/offline: + - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F + (previously called from pkg/dic_surfforcing_init.F) +o model/src: + - re-order sequence of calls within packages_init_variables.F, using + standard order, except for: + DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top), + CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom) +o new pkg: atm_phys + - add entry point and source code (previously in contrib + verification_other/atm_gray/code_gray/) for new pkg "atm_phys" + (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008). + - re-order sequence of calls within packages_readparms.F, + packages_init_fixed.F and packages_write_pickup.F + (but skip packages_init_variables.F because of TAF issues). + - update contrib/*/atm_gray/ experiment. +o pkg/seaice (ITD code): + - simplify and fix the writing of pickup-files for ITD case +o pkg/seaice (ITD code): + - introduce floe size dependent lateral melt for ITD case; + - cleaning (avoid division by zero, change to f77 syntax, remove tabs) + - update seaice_itd experiment main output. +o pkg/thsice: + - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and + declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F; + changed accordingly pkg/atm2d. + +checkpoint64g (2013/05/01) +o pkg/exf ALLOW_RUNOFTEMP + - if defined, river and glacier runoff temperature can be read-in from + runoftempfile; runoftempfile needs to have same format as runofffile +o pkg/thsice (& pkg/bulk_force): + - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account + for energy content of Precip + RunOff & Evap (like with pkg/exf). + - change computation domain to always be the interior (without overlap). + - fix bug (wrong overlap) when using EXF and stressReduction > 0. +o verification/tutorial_global_oce_biogeo: + - add preliminary OpenAD setup (still has problems) +o pkg/seaice: + - turn some parameters for choosing the convergence criterion of + the inexact Newton method (JFNK) into runtime parameters for convenience + - clean up seaice_calc_viscosities.F: remove/retire two options for + SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes + the results of lab_sea/input because a division has been replaced by + a multiplication with the reciprocal (sumNorm) + - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve + convergence of solver (changes results, of course), and to test some + new features +o model/src: + - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call. + - remove unused forcing field "dQdT" and associated parameter "dQdTFile". + - move forcing adjustment (balancing surface forcing) in specific S/R + where might also be applied exchanges (if needed) to forcing arrays. +o pkg/shelfice: + - allow to specify the Ice-Shelf mass per unit area (instead of + shelficeLoadAnomaly) and do the conversion from one to the other + - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA + to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and + (b) will be loaded in time (before calling INI_PRESSURE) in case it is + needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc + - update isomip experiment forward output (get machine truncation error + from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly) +o verification/offline_exf_seaice: + revise data.seaice in input.thermo and input_ad and update results accordingly + HO = 0.2, SEAICE_areaLossFormula = 2, + SEAICE_growMeltByConv = .TRUE., + SEAICE_doOpenWaterMelt = .TRUE., + Improve consistency with input.thsice and fix the spurious 500m ice corners +o verification/global_ocean.cs32x15: + - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0., + in icedyn (thsice+seaice-dyn) test and update output. +o verification/offline_exf_seaice: + - adjust list of tested variables (with testreport) and update + standard test output with better slection of monitored fields. +o pkg/cd_code: + - swtich off Adams-Bashforth on the 1rst iteration. Update output of + experiment lab_sea.hb87 +o tools/genmake2: + - change default makedepend from the system default to tools/xmakedepend: + When no makedepend is specified, select tools/xmakedepend it the test pass, + otherwise select the system default (if exist and pass the test) or + try to build cyrus-makedepend ; stop if none of the 3 works. +o pkg/exf & pkg/thsice: + - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account + for energy content of Precip + RunOff & Evap. Assumes: + 1) Rain has same temp as Air. + 2) Snow has no heat capacity (consistent with seaice & thsice pkgs) + 3) Run-Off comes at the temp of surface water (with same Cp) + 4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be + put directly into Latent Heat flux & should use water-vapor heat capacity. + 5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent + with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL). +o pkg/seaice: simplify the use of CPP flags in JFNK-related files + (compile when SEAICE_ALLOW_JFNK is defined) +o pkg/thsice: + - fix oceanic flux diagnostics & timeave (left from new sequence of calls + implementation): move THSICE_AVE call after the advection (called directly + from thsice_do_advect.F). +o verification/global_ocean.90x40x15 and OpenAD: + New experiment for OpenAD is identical to the one in input_ad except that + multiDimAdvection=.FALSE., + There is still an issue with this. +o pkg/thsice: + - account for ice velocity (ocean relative velocity) in turbulent heat flux + at the base of the ice; update output of global_ocean.cs32x15 (icedyn) + and offline_exf_seaice (main test). + +checkpoint64f (2013/03/31) +o verification/OpenAD: + - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran. +o verification/isomip, pkg/shelfice and OpenAD: + - add OpenAD setup to this exp and make shelfice package work with OpenAD +o verification/tutorial_global_oce_biogeo: + - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h) +o verification/offline_exf_seaice: + - replace adjoint experiment (now similar to fwd input.thermo/ setup). +o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD: + - add OpenAD setup to this exp and make ptracers package work with OpenAD +o pkg/seaice/seaice_evp.F: + mask the asymmetric contribution of the ice-ocean stress (when + the turningAngle is non-zero) over open water to avoid stripes + in the EVP-solutions after many EVP-substeps. This does not change + the verification experiment (because turningAngle=0 in that experiment), + but will affect other EVP solutions with turningAngle.ne.0 +o verification, AD & TLM output: + - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple + additions and multiplications which affect results at machine truncation + level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5, + lab_sea.noseaicedyn & offline_exf_seaice) and TLM output + (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12 + digits of matching. +o pkg/seaice: + modify lsr-algorithm so that it vectorizes AND converges by using a + "zebra" method: split vector loop into two with step size 2; this + solves a general convergence problem for the JFNK solver on a vector + computer. It has the potential to even improve convergence for + non-vector machines, but it does change the results so it is turned + off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and + SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h + +checkpoint64e (2013/03/05) +o pkg/ecco and several verification experiments: + Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F + from ecco package, and revert to unified routine in model/src/ + Adjust verification experiments accordingly, especially gloal_oce_llc90 + Should conclude long-standing work by Gael to reconsile the_main_loop with + ECCO and will enable OpenAD's revolve loop in ECCO setup. +o pkg/generic_advdiff: + - implement compressible flow method for multi-dim advection (similar to + gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since + TAF generates many recomputations) to use it; no yet coded with implicit + vertical advection. + - change experiment advect_cs (new output) and advect_xy (same output) + to test compressible flow multi-dim advection. +o pkg/generic_advdiff: + - fix SOM advection for unusual cases (linear Free-Surf in r*, other + cases where linear Free-Surf is not @ k=1, e.g., useShelfIce) +o pkg/seaice: + - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this + bug affects two verification experiments (lab_sea and lab_sea.hb87), + recover old (wrong) results by setting noSlipFac = 2. in + seaice_calc_strainrates.F; + - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0 + - add runtime parameter SEAICE_JFNKepsilon for that finite difference + gradient in the Jacobian times vector operation (s/r seaice_jacvec) + - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update) +o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code: + - new subroutines seaice_lsr_tridiagu/v + - introduce loop bounds i/jmin/max to be able to use a restricted + additive Schwarz method, but not used for now. + - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS + - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner +o OpenAD support + Reorganize S/R call for overall time-stepping loop to facilitate + OpenAD revolve loop replacement + (new S/R main_do_loop.F) +o model/src: + - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3; + - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R + ADAMS_BASHFORTH2. +o pkg/cheapaml: + - add new parameter (default=F, same as before) to disable full domain + (including land) periodicity in X & Y dir. + - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of + prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer + into single S/R CHEAPAML_TIMESTEP. + +checkpoint64d (2013/02/17) +o pkg/monitor (angular momentum): + - do not add Eta contribution to the total AM if using rigid-lid; + - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta). + - horizontal discretisation: compute Zonal wind contribution separately for + each component (instead of from cell centered averaged) and use the 4 + grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part. + - Check that AM is conserved with linear dynamics (momAdvection=F and linear + FreeSurf) if using vectorInvariant momentum. +o model/src (horizontal grid): + - move initialisation of all horizontal grid arrays to null value + from specific horizontal grid S/R to main S/R INI_GRID; + - add 2 new arrays to project model C-grid velocity on to zonal direction + (similar to AngleCosC & -AngleSinC but at U and V point location) and + compute them in S/R CALC_GRID_ANGLES. +o pkg/seaice: replace a hard coded parameter by a runtime parameter + SEAICE_JFNK_tolIter +o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in + preconditioner for JFNK (run LSR into the overlaps as far as possible, + i.e OLx/y-2, but overwrite the solution in the overlaps) + - extend loop range in seaice_calc_viscosity + - add new parameters SEAICE_OLx/y (default = OLx/y-2) + - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs + - slightly modify loops in tridiagonal solver lsr-preconditioner + - by default remove the extra exchange in seaice_preconditioner with a + replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE + - modify offline_exf_seaice so that old results without RAS are reproduced + for output.dyn_jfnk.txt + in seaice_fgmres.F (unrelated to RAS) + - add a cpp-flag option for a re-ordered mapping (potentially more + efficient), but because this changes the results, turn it off by + default + - replace the save statement by local common blocks +o utils/matlab: + - fix tile-offset in rdmnc.m when output was produced using EXCH2. + - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab) + instead of local script "load_cs.m". +o pkg/seaice: + - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected + to the scalarProductMetric and the unrolling. By chance this does not + change the verification experiment, because of the particular domain + decomposition +o pkg/diagnostics: + - change default missing_value from UNSET_RL to -999. +o pkg/layers: improve vectorization of layers_fluxcalc.F + - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu + time spent in this routine by more than a factor of 3 on an NEC-SX8 + - step 2: replace search algorithm by a bisection algorithm found in + Press et al. Numerical Recipes in Fortran. This algorithm can be + vectorized and finds the correct bin in approx. log2(Nlayers) steps. + For now, use this algorithm only for TARGET_NEC_SX defined. + - moved the search algorithm into a separate subroutine, that is kept + within the same file for automatic inlining. + - modified catching potential errors +o pkg/ecco: + - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY. +o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk : + - modifications for ALLOW_GENTIM2D_CONTROL + -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes. + -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid ) + -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc + -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F +o model/src: + - account for moist thermodynamics in (dry) potential temperature equation; + update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev) + and cpl_aim+ocn. + - also switch to standard compiler (gfortran, was using ifort previously) + for fizhi-cs experiments reference output. +o pkg/ctrl: + - 1st step toward generic time-varying control variable (2D) via CPP option + ALLOW_GENTIM2D_CONTROL + - note new namelist ctrl_nml_genarr in data.ctrl +o verification/global_ocean.cs32x15: + - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new + thsice calling sequence and update "output.icedyn.txt" output file. +o pkg/ptracers: + - from Ryan A.: code to allow to restart a tracer at regular time interval + specifying a reset frequency and a reset-phase (for each tracers). +o pkg/thsice: + - implement new sequence of calls for thsice+seaice: + previously: ice-Dyn,ice-Advect,ice-Thermo(thsice) + new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect + - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE" + in CPP_OPTIONS.h) to recover old sequence; + - update diagnostics for Intermediate State thsice diagnostics: now filled + just before advection (instead of just after advection in old sequence); + - update output of experiment offline_exf_seaice (standard test); + - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update + by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h +o pkg/aim_v23: + - use tiled array for aim_CO2 and surface wind speed for export to coupler; + - use standard pkg/mdsio routines to read & write CO2 pickup file; + - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F; + - Implement new sequence of calls for seaice advection (with thsice and + seaice diffusion): do ice advection after ice-Thermodynamic (previously + was done before); change aim_do_physics.F (split the bi,bj loops block); + - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence; +o pkg/thsice: + - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case + where just seaice diffusion is used without seaice-dynamics. + +checkpoint64c (2013/01/18) +o pkg/seaice: + - add a parameter JFNKres_tFac that can replace JFNKres_t + (= JFNKres_tFac*JFNKresidual before JFNK solver) + - add a line search option to the JFNK solver + - move update of u/vIce and computation of initial residual into a separate + routine (same file); makes the code a little easier to read (?) + - the line search requires computation of the residual and for some reason + I cannot do the update of u/vIce at the beginning of the Newton loop + without changing the results, so we move computation of the new residual + also to the end of the Newton loop, even without the line search +o pkg/mdsio: + - write missing value (corresponding to undefined array value) to meta files; + skip this if missing value is one (UNSET_RL would be a better value for the + case of undefined missing value but it's current the default missing-value); + Also update mdsio_read_meta.F (reading timeInterval & missing-value). +o pkg/exf & thsice: + - for diagnostics purpose, fill-up and update Qsw array (+ fill the + diagnostics) even when SHORTWAVE_HEATING is #undef; +o verification/cfc_example: + - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to + illustrate how to use it). +o verification/offline_exf_seaice: + in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing + files to only one time-record. + in input.thermo: narrow the 2 bands of low initial ice-concentration near + N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for + snapshot output; same mcPheePiston value as in thsice with + surf-current=0.2m/s. + in input.thsice: similar set-up as in input.thermo (channel with same seaice + initial conditions). +o verification/cfc_example: + - update file "data" with more standard choice (default rotationPeriod, + exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F, + set deltaTFreeSurf to deltaTtracer) and update the output. +o pkg/layers: + - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC; + - ensure that "layers_bolus" is switched to False when useGMRedi=False. +o verification/offline_exf_seaice: + - set all {field}period to zero for constant-in-time forcing (not tested + anywhere else). +o verification/offline_exf_seaice: + - dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice; + - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice. +o model/src: + - implement Finite-Volume method for (hydrostatic) presure gradient + from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate. +o pkg/seaice: implement EVP* by Lemieux et al. (2012). + - In order to be compatible with the default EVP code, this requires changing + the EVP code around a little; and because any small change immediately + breaks the lab_sea.hb87 verification experiment, the reference output is + updated two times (each time the remaining aggrement was only 2 digits): + - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt + - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt + The adjoint test lab_sea.evp also needed to be updated. + - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting + SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be + a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps + explicitly with SEAICEnEVPstarSteps (thereby overriding the default of + INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately + kept obscure, because I need to test it a little more. +o pkg/cheapaml: + - fix few incorrect type (_RL/_RS) in subroutine calls. +o pkg/seaice: + - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays + to _RL vector; this fixes JFNK code when compiling with "-use_r4" option. +o model/src: + - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4; + change (in input_ad*/data) select_rStar from 2 to 1 for AD verification + experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output) +o pkg/cheapaml: + - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and + update output of experiment cheapAML_box. + - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity, + and set them only in one place (cheapaml_readparms.F). + - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI" + - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms) + and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia). +o model/src/the_main_loop.F: + - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION. +o pkg/seaice: + - remove legacy branch code. + - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly. +o verification/*/code*/SEAICE_OPTIONS.h: + - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY, + SEAICE_CAP_HEFF). +o pkg/cheapaml: + - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time + to load new forcing fields. + - add missing "_d 0" where it's needed; + some editing (improve indentation). + - remove switch to "-r8" compiler option (no longer needed) in verification + cheapAML_box, keep same output (small trucation error differences). +o verification/offline_exf_seaice: + - add thermodynamics only test. +o verification/cheapAML_box: + - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test; + keep same output (same 14 digits for cg2d). + - switch on "-r8" compiler option (some numerical values are missing + the "_d 0") and update output (only 6 digits for cg2d were preserved). + +checkpoint64b (2012/12/24) +o pkg/cheapaml: + - remove un-used variables (Qnet,EmPmR) from pickup files. + - store tendency of advected variables into cheapaml pickup file + and fix the AB-2 restart. +o verification/offline_exf_seaice and lab_sea adjoint: + - switch to new code (#undef SEAICE_GROWTH_LEGACY). + - switch to 4 time steps in offline, consistent with lab_sea. + - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice. + - update results after change of experiment seaice. +o pkg/seaice: + - remove option SEAICE_MULTICATEGORY; has been replaced with run-time + parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is + still defined since SEAICE_multDim needs to be set to MULTDIM value (from + SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default. +o model/src: + - add run-time parameter to select CG2D solver minimum-residual solution + (in case of a poor convergence). +o pkg/seaice/seaice_lsr.F + - move calculation of matrix coefficients into new + S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same + file; the main purpose of this change is to be able to reuse the code + in S/R SEAICE_PRECONDITIONER + - modify the computation of the residual so that the mass of sea-ice + is not used twice; this simplifies the calculations, but since + the residual is never used except when LSR_mixIniGuess.ge.4---and this is + not tested in testreport---this does not affect the testreport results. +o verification/seaice_obcs: + - disable SEAICE_GROWTH_LEGACY; reset input files to match those of + verification/lab_sea/input.salt_plume; changes results/output.txt* +o model/src: + - adapt quasi-hydrostatic formulation to work with p or p* coordinate. +o pkg/seaice: + - improve description of parameters in seaice_fgmres.F and start + cleaning up the code + - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of + second argument + - add a metric based on grid cell area to SEAICE_SCALPROD; update + results of offline_exf_seaice.dyn_jfnk + - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD +o pkg/aim_v23: + - fix an other bug in dissipation heating (grid-cell area was missing). +o model/src + pkg/seaice: + - add global (multi-tile) linear solver for pair of tri-diagonal system + along X and Y lines, respectively for U and V component. + Note: 1) MPI and cube-exchange not yet coded. + 2) probably not accurate for poorly conditioned / large size problem. + - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver; + default: not compiled and not used. +o pkg/seaice: + - first attempt at a multi-threaded fgmres solver for the JFNK solver: + introduce bi/bj loops and use global_sum_tile_rl instead of + mpi_allreduce in seaice_fgmres.F + - improve diagnostics output for fgmres solver (seaice_fgmres.F) + - replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F) + - add a verification experiment for JFNK in offline_exf_seaice +o verification: + - change (for now, only fwd test) offline_exf_seaice experiment: + use a re-entrant channel with idealized coastline (trapezoidal shape) + at southern boundary to explore seaice dynamics and thermodynamics + with simple forcing. Main set-up has dynamics+thermo and SST relaxation; + secondary test (input.thsice) use thermodynamics only with SST relaxation. + - add seaice-dynamics only secondary test using LSR and pkg/thsice advection. +o pkg/exf: + - disable "sstExtrapol" when Nr=1 +o verification: + - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble) + to test pkg/cheapaml. +o pkg/aim_v23 & pkg/shap_filt: + - fix dissipation heating (erroneous gravity multiplication factor). +o pkg/seaice: + - remove unused field pressPre from jfnk solver + - rename two subroutines in seaice_preconditioner.F +o eesupp/src: + - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...) +o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again + - remove wrong parts of the rhs and the lhs (were in there + because I did not understand the concept of this preconditioner) + - add an exchange between u- and v-sweep. This increases communication + by a factor of two but improves the convergence of jfnk. Ideally, + one would like the u- and v-sweep to be independent. So far within + undocumented ifdefs + - reorganize the extra computations for printing the residuals +o tools/genmake2: + - comment out the "mpif.h" include in NetCDF test programm (for MPI built) + since it's not necessary (and was preventing to use MNC in some cases). + +checkpoint64a (2012/11/16) +o pkg/autodiff: + - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that + autodiff_readparms.F no longer depends on calling order (within + packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h): + rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd + and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd. +o pkg/obcs: + - adding tidal velocity forcing capability to obcs + for usage example, see verification/seaice_obcs/input.tides +o pkg/seaice: + - turn the LSR-relaxation parameters WFAU/V into runtime parameters + SEAICE_LSRrelaxU/V + - introduce runtime parameter SEAICEetaZmethod (=0 by default) +o pkg/aim_v23: + - implement heating from friction (bottom friction and stratospheric drag). +o pkg/shap_filt: + - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from + dissipation but only for Shap_funct=2, active when addFrictionHeating=T. +o model/src: + - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in + time-constant addMass field from file (addMassFile); + - support for heating due to friction (and Kinetic Energy dissipation): + add option, run-time switch and 3-D field array + support code ; each pkg + or S/R can add heating contribution (if there is a sink of KE); the sum is + accounted for as a Temperature tendency term (EXTERNAL_FORCING_T). +o pkg/seaice: + - complete merge of ITD code into seaice_growth.F + from MITgcm_contrib/torge/itd/code/ + no verification so far, but Torge Martin tested + "1-D test case and Beaufort set up; + deliver okay results after 1 model year." + - complete merge of SEAICE_SIZE.h into all relevant routines + - move computation of eta at Z-points into calc_viscosities + + introduce global field etaZ + + add different methods for computing etaZ, for now the old + method (simple averages of eta to Z-points) is hardwired + + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual, + seaice_preconditioner + - simplify computations for SEAICE_ZETA_SMOOTHREG + - seaice_preconditioner: + + replace one remaining press by pressLoc (mistake) + + adjust printing of residuals + - improve I/O of diagnostics of JFNK in seaice_jfnk.F: + + add (SEAICE.h) and rename some counters (initiliased in + seaice_init_fixed.F) + + add _BEGIN/END_MASTER (myThid) around print statements + + print total number of iterations and failures over SEAICE_monFreq + interval to STDOUT + - move control over output-messages by fgmres to seaice_jfnk to save + some operations + - move resetting initial guess for fgmres outside of seaice_fgmres_driver + in order to make restarts with sol .ne. zero (fgmres with restarts) + (seaice_jfnk.F, seaice_fgmres.F) + - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes + a serious convergence problem when open boundaries are involved +o pkg/ggl90: fix computation of control volumes for the case of + ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes + up half a grid cell from C-centered to W-centered (pointed out by C. Eden) +o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC +o pkg/autodiff + - Add inAdMode switch for SEAICEuseDYNAMICS: + SEAICEuseDYNAMICSinAdMode + (extend logic in ADAUTODIFF_INADMODE_SET) +o pkg/seaice + - Step 1 of merging ice-thickness distribution (ITD) code from + MITgcm_contrib/torge/itd/ (author: Torge Martin) + The code implements concept laid out in Thorndike et al. (1975); + code is enabled via CPP flag SEAICE_ITD + nITD (in SEAICE_SIZE.h) defines number of ice thickness categories; + code is not complete yet!! + - SEAICE_SIZE.h now included in almost all seaice routines +o verification (using seaice): + - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp. + global_ocean.cs32x15.seaice ; update results. + - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ; + - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp + offline_exf_seaice (previously compiling B-grid). +o pkg/exf: + - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow + to specify neither just 1 comp of wind or wind-stress, nor no surface momentum + forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind. +o pkg/layers (adjust changes from Sept 19): + - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F) + this allows to remove "layers_maxNum" dimension from all layers arrays. +o pkg/layers (adjust changes from Sept 19): + - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ; + - snap-shot extended to all type of layers (not just the 1rst type); + - remove layers variables when corresponding CPP option is undef. +o pkg/layers: + - rename pkg/layers variable and add new output (layer exist & un-weighted + velocity in layer) +o pkg/seaice: + - simplify (?) ocean-drag coefficent computations by using + the same routine in all three solvers (saves some code lines) + - remove global fields DRAGA and DRAGS from C-grid code and + declare them locally in lsr.F (the only place where they are + still used) + - update AD output of lab_sea.evp (very sensitive anyway). +o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics + (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK + and SEAICEuseJFNK=.true. A few things to note: + - involves a FGMRES, that is parallel but very inefficient, + because of many scalar products (global sums) in the Gram-Schmidt + orthogonalization method. Needs to be replaced. Original code + from J.-F. Lemieux + - preconditioner for FGMRES is a stripped down version of LSOR + - SOLV_MAX_ITERS is now used for LSOR as a solver and as a + preconditioner. For the preconditioner, the default is set to 10. + - Jacobian times vector is computed with finite differences + - marginally related to JFNK-solver: add a smooth regularization for + zeta with tanh that will improve convergence (Lemieux and Tremblay, + 2009) for any implicit solver (not implemented for EVP because EVP + does not need this regularization in the first place). Define + SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use. +o eesupp/src: + - check in genmake2 that intrinsic S/R flush is available. + - add S/R to flush IO unit (if intrinsic S/R flush is available) + - flush standard & error msg unit before MPI termination + - if debugMode, flush IO unit after printing msg +o pkg/ctrl: + - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call + to ctrl_set_unpack_xyz. + +checkpoint64 (2012/10/09) +o pkg/shelfice + - in mom_fluxform.F, mom_vecinv.F: + CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid) + Bug fix KappaRU -> KappaRV + does not change verification/isomip but may change other setups + (presumably constant KappaRU=KappaRV) + - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate) +o pkg/obcs: + - fixed some indexing bugs in obcs_seaice_sponge.F + - added obcs relaxation subroutines for HSALT and HSNOW + - changes verification/seaice_obcs/results/obcs_seaice_sponge.F +o pkg/seaice: + - add "multicategory" parameterization for snow in analogy to ice, + default is off for now. +o pkg/obcs: + - added obcs_seaice_sponge.F for obcs relaxation of seaice variables; + see verification/seaice_obcs/input.seaiceSponge for example application. + - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB + index setting by master-thread. This fix multi-threads Pb in previous modifs. +o pkg/layers : + - add diagnostics to pkg/layers + - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F + (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly. +o pkg/generic_advdiff/gad_implicit_r.F : + - fix ADVr diagnostics in case of both implicit vertical advection and diffusion. +o pkg/seaice/seaice_growth.F: + - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case. +o pkg/obcs: + - change default setting of OBCS_UVICE_OLD from defined to undef; + - use new parameter OB_indexNone for null index value (instead of hard-coded 0) + in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F; + - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z; + - change OB null index value (OB_indexNone) to -99 ; this fix the problem + with Southern & Western OB at a tile edge (at least in a simple set-up). +o pkg/obcs: + - change settings of OB index in case OB coincides with tile edge (shared by + 2 tiles), so that common OB location is registered by both tiles (instead of + only 1). However, for Southern and Western OB, index value = 0 is not + recognized as valid OB index (=default null value) and needs to be fixed. + - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting) + - new parameter "OB_indexNone" for null index value (for now, still zero) + to replace hard-coded null index value of zero. +o pkg/exch2: + - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON: + always check buffer-size (but outside the loop); move checking for valid + index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON, + print each tile and point connection only if |W2_printMsg|>= 2 and 3. +o pkg/ctrl (pack & unpack): + - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable + (locally defined) for different variables (+ remove the variable-specific + file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL + (to be extended to other local file names in ctrl.h). +o pkg/flt: + - add a FLT_Iter0 option (similar to PTRACERS_Iter0). +o pkg/mdsio: + - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing +o tools/genmake2: + - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE + (added by Alistair in version 1.51 for building without make depend); + - remove Header files list (H_SRC_FILES) from the dependence of targets + ad_input_code.f & ftl_input_code.f (not clear why it was added in the first + place in version 1.23): this save going through staf when unrelated header + file has been modified. + Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without + "make depend" step, still need to do "make links" before "make adtaf". +o eesupp/src (+ few pkg src files) & genmake2: + - finish to remove ALWAYS_USE_MPI in source code that TAF does not see; + - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2). + - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish + upper/lower case ; account for space between "#" and undef/define) +o pkg/flt (with exch2): + - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F; + - simplify threads synchronisation; fix (many issues) multi-threaded with MPI. + +checkpoint63s (2012/09/05) +o pkg/ecco: + - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets. + - add more relevant #ifdef ALLOW_SMOOTH ones. + - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D. +o pkg/ctrl: + - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D, + ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D. + - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag, + doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and + ctrlSmoothCorrel3D (new). + The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP. + - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist. + - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress + controls when useAtmWind, and vice versa. + - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers. + - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with + #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH. + - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with + #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH. + - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F: + replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D. +o pkg/smooth: + - remove un-necessary includes. + - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets. + Those CPP options were never defined, and not necessary. +o model/src: + - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi). + - standard treatment of useSMOOTH. +o pkg/autodiff: + - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode, + useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint. +o pkg/exch2: + - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template) + + start to remove ALWAYS_USE_MPI in source code that TAF does not see. + - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag + and tiles to process mapping. + - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h) + moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h; + rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX + from w2_eeboot.F to w2_readparms.F. +o eesupp/src: + - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of + ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F; + also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F + - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI + is defined (remove condition on usingMPI) to match cases where MPI_INIT + has been called. + - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used); + - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings + (so that on 1 proc, get same myPid independently of usingMPI) + - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and + useCubedSphereExchange with EXCH-1 (safer). + - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI). +o pkg/ggl90: + - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call) + used in ALLOW_GGL90_SMOOTH code. +o pkg/flt: + - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping + floats at the Southern end of the domain). +o eesupp/inc: + - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h); + but not used (and not to be used) anywhere, just for documentation. +o pkg/autodiff, exf, ptracers & seaice (AD & TL output): + - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since: + a) can damage previously written records in any other multi-record files. + b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S. +o tools/genmake2: + - define variable MAKE within Makefile and use it in place of 'make'; + - update AD_CONFIG.h (if needed) before building any of the executable + (forward, adjoint or tangent-lin); this involves a 2nd invocation of make; + and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h; + - always print usual warning comment 'this file is automatically generated' + from script convert_cpp_cmd2defines (+ remove this warning from genmake2). +o pkg/cheapaml: + - updated to correspond to the code used in accepted paper (Nico Wienders). +o pkg/exf: + added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch. + ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F) + and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h). +o pkg/exf, autodiff, ctrl, ecco and seaice: + remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones. +o pkg/ctrl, ecco: + allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL. + Depending on useAtmWind, one is inactive, and the other is active (see + exf_getffields.F/exf_getsurfacefluxes.F). +o tools/genmake2: + - improve error msg when failing in 2nd test of check_for_broken_Ff + - fix option '-makefile' short-name (-mf according to genmake2 -help) + - source local config file "genmake_local" just after processing the genmake2 + command arguments (previously done before processing arg). +o pkg/grdchk: + - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call + to this routine from cost_final has been dropped in g_cost_final) + - improve printed information (more explicit msg, no longer using "print *," + fix fcpertminus printed value). +o model/src: + - move call to COST_INIT_VARIA out of packages_init_variables.F directly + into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES): + this prevents getting cost-funct reset in adinitialise_varia recomputations. +o pkg/dic: + - move initialisation of "freefe" array from from dic_biotic_forcing.F to + fe_chem.F: this prevents TAF from dropping this initialisation in TLM code. +o pkg/grdchk: + - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid ) + - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0 +o pkg/autodiff/ctrl/grdchk : + - attempt to sort out what works and what does not, + with regard to I/O, and to warn/stop accordingly. +o pkg/grdchk: + - attempt to fix grdchk in the case of useSingleCpuIO. + - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )" + statements were moved from grdchk_main.F and into + grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F. + - a global sum is applied to record numbers icvrec/layer + out of grdchk_loc so that they be passed to I/O routines. +o pkg/smooth: + - fix recomputation that appeared with nlfs : use smooth_recip_hFacC, + smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case. +o verification/testreport: + - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive); + - can also use compressed (gzip) reference output file; + - change format (in pkg/grdchk) of TLM output (+ add forward gradient) + to be easier to collect by testreport. + - update existing TLM output (half out-of-date by more than 3 yrs). + - report NETCDF & LAPACK settings (from genmake2) in output dir. + - report run-time in each individual summary (previously only for AD test); + for TLM test, add also TAF version. + - add daily TLM test on (old) aces cluster + weekly test on baudelaire. + +checkpoint63r (2012/08/15) +o tools/genmake2: + - fix Makefile for target ftlall (+ update files to clean after make ftlall) +o pkg/ecco/ecco_cost_final.F : + - fix fc print statements (to stdout and costfunction0000) so + that the printed value is always after the global sum. +o pkg/seaice/seaice_dynsolver.F : + - fix ice strength assymptote at SEAICE_area_max<1 + (no change for the standard case of SEAICE_area_max=1) +o some cleaning: + - pkg source files: ensure that all *.F files from each pkg included the + corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which + only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment + code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding + includes; + - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used. + - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR + is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when + ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop. + - update option-file CPP_OPTIONS.h of all AD experiments: + * no longer include PACKAGES_CONFIG.h ; + * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ; + * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before + including ECCO_CPPOPTIONS.h). +o pkg/cost, pkg/ctrl, pkg/ecco option-file: + - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into + separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h, + not necessary accurate). + - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in + pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to + deliberately break compilation (a remainder that it needs to be customized) + - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h + - rename COST_CPPOPTIONS.h to COST_OPTIONS.h + - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h +o tools/genamke2: + - check for lapack. +o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies. + - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions + jointly. The exclusive ifdefs were removed, to add costs terms (when defined) + from both packages. + - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly. + - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs. + - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes + of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly. +o pkg/cost : add comments to explain special and/or untested setups. +o pkg/exf: + - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h + (previously, ALLOW_AUTODIFF_TAMC was controling this switch). +o verification/*/code_ad: + mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file: + - reccord when this file is included (define ECCO_CPPOPTIONS_H) + - remove the most obvious obsolete features (e.g., #define ALLOW_COST not + allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h) +o pkg/seaice : + - added possibility to change ice strength/PRESS0 relationship to + HEFF, according to the following run time parameters + SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0) + SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0) + SEAICEpresH0 :: HEFF threshold for ice strength (m) +o pkg/ggl90 : + - added run time flag mxlSurfFlag to include the code that ensure + mixing between first and second level (previously included as a comment) +o verification/1D_ocean_ice_column/input_ad/data.autodiff : + - add test of newly added dumpAdByRec=T option where + we write all records to one file per variable. +o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h : + - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES + to check that this code is ok with taf and compiles in adjoint. +o pkg/autodiff : + - added run time param dumpAdByRec : ad dump format switch. + If true then write all records to one file per variable. + Else write one file per record (remains the default). + - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly. +o pkg/seaice: + - Added SEAICEuseTILT run time switch : if set to + false then omit the tilt term in seaice dynamics. + - Fix free drift calculation. +o pkg/shelfice: + When initializing SHELFICEDragQuadratic, set default to be + consistent with shiCdrag in case SHELFICEuseGammaFrict is used, + but retain option to set it independently + (inconsistenty spotted by Veronique Dansereau) +o eesupp/inc: + - in EEPARAMS.h, add real-type constant for some frequently used simple number + (0,1,2,1/2), with name explicitly referring to RS/RL type. +o model/src: + - move balancing of relaxation terms to new S/R balance_relax.F. +o pkg/autodiff: + re-write active I/O high-level (control) S/R: + - rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL + - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R. + - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and + MDS_READ/WRITE_FIELD); change loops to multi-threads. + - update and merge active_file_control_slice.flow into active_file_control.flow + - update the calls in lower level S/R (active_file.F, active_file_g.F and + active_file_ad.F) keeping the argument list and function unchanged. + - also update lower-level "_LOC" version (call same S/R with "useCurrentDir + =.TRUE.") and remove high-level (control) _loc version (not called anymore). + - new low-level active I/O routines, one for each type (RL/RS), for active var + of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr); + fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the + right type. +o autodiff and RS=real*4: + - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf + ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ; + - change argument type of 3-D mask argument to _RS to match type in the call + (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued. +o pkg/thsice: + - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T. + - option to correct ocean fresh-water flux for imbalance of Atmos+Land + fresh-water flux: uniform correction or proportional to local precip. +o pkg/ctrl: + - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D + - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to + ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC + - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL + +checkpoint63q (2012/07/30) +o pkg/autodiff: + note about monitor and snap-shot of ad-variables: + a) need to apply ADEXCH before monitor or output of ad-vars to include + overlap contributions (was done for adjDump but missing for monitor). + b) since ADEXCH implies adding overlap values to interior array, machine + truncation error is expected when adding an ADEXCH call in the middle of + the time-stepping (although mathematically identical). + modifs: + - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars + declaration (adEddyPsiX,adEddyPsiY in adcommon.h). + - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to + apply ADEXCH before monitor or snap-shot of ad-variables: + =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy. + - implement new method (copy+adexch) for snap-shot and monitor of main model + ad-vars (initially not used by default -> output unchanged). + - change default (set to 2) to use new method and update few output_adm.txt + with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo + and both tutorial_tracer_adjsens tests). + - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice) + and turn off momDissip_In_AB in the 2 other (needed for stable AB-3). +o pkg/ctrl: + enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of + generic control variables via + #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL + Only required customization should be S/R ctrl_map_ini_genarr.F + (routine in repository contains example) +o pkg/exf: + - fix and refine checking of surface-relaxation setting when using EXF +o verification (adjoint exp): + - reduce length of simulation by half for experiment global_ocean.cs32x15 + (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output. +o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag) + - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers + of KE that can occur with aggressive optimization + + put quadratic bottom drag calculation in separated loops (only done if + using bottomDragQuadratic) +o model/src: CG2D_NSA + - clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF + and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE. + - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens), + change cg2d residual target to be expressed in Wunits (=> do not normalise + RHS ; this fix global_max Pb with TAF); update output. +o verification/tutorial_tracer_adjsens: + improve parameter consistency (and get rid of warnings): + - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf); + - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical) + - use staggerTimeStep (for stability) in som81; use default rotation period. +o pkg/exch2: + - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously + reset to 0 = 1 long line in X) +o pkg/mdsio: + - fix reading of dimensions from meta file for large-size domain +o model/src: + - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long); + - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using + Cubed-Sphere Exch with CS-corners inside the domain; + make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate + globalArea and to set hasWetCSCorners. + - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing + metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form. + - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if + useCDscheme and useCubedSphereExchange). +o pkg/seaice/seaice_growth.F : + - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly + for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0) + when the previous code was not correct. + - in all cases diagnoze the boundary condition mismatch to SIaaflux + - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add + that term to QNET (essentially to set the melt/freeze water to 0degC). + when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed. +o verification/global_ocean.cs32x15/input.seaice : + - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget. + - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces). + - update results (output.seaice.txt) accordingly. +o verification/lab_sea/input/data.seaice : + - remove SEAICEheatConsFix, which is now be tested + in global_ocean.cs32x15. The presently coded fix + is only consistent with real fresh water + nlfs. + - update results (output.txt) accordingly. +o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd). +o AD_CONFIG.h file: + - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h; + - remove #include "AD_CONFIG.h" from all included OPTIONS files and + add it explicitly in each fortran src file where it is needed. + motivation: header file AD_CONFIG.h is generated/modified after "make depend" + thus introducing potentially wrong dependency; therefore, better to include + it only where it's really needed, and after any other included OPTIONS file + (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN + or ALLOW_TANGENTLINEAR_RUN). + +checkpoint63p (2012/07/06) +o pkg/autodiff: + - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ; + - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters + which are now read from new parameter file "data.autodiff" (inAdExact + previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg) + - add file "data.autodiff" in all verification/*/input_ad/ directories. + - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward + mode (used in global_ocean.cs32x15.seaice_dynmix test exp.) +o verification/tutorial_tracer_adjsens/ + - add extra sub-verification which uses "SOM" advection scheme + (2nd Order-Moment Advection Scheme, Prather Limiter) with + #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h + and in data: + multiDimAdvection=.TRUE., + tempAdvScheme=81, + saltAdvScheme=81, +o model/src: + - introduce ALLOW_BALANCE_RELAX which allow the removal + of the global mean of relaxation terms by setting + balanceThetaClimRelax and balanceSaltClimRelax + - disable balanceEmPmR and balanceQnet in the case when useSeaice. + This case is now treated appropriately in seaice_growth.F +o pkg/seaice: + - do balanceEmPmR and balanceQnet based on the net fluxes + (SItflux) that enter the ocean+ice system rather than QNET + and EMPMR. Works best in real fresh water. + - SIatmFW, SIatmQnet, and SItflux computations had to be moved + out of the diagnotics bloc, and stored in global arrays. + +checkpoint63o (2012/06/29) +o vertical mixing schemes: + - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging) + - replace computation of density (in Function STATE1, opps_calc.F) by a call + to S/R FIND_RHO_SCALAR + - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC + and use it for N^2 calculation in ggl90_calc.F (save 2 density computations); + affects output (vermix.ggl90) at truncation level. +o testreport: + - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles + (nSx,nSy) for the number of threads (from eedata.mth) +o model/src: + - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part) + related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary). o verification/tutorial_tracer_adjsens/ - compile with ALLOW_CG2D_NSA - run with nonlinFreeSurf=3