--- MITgcm/doc/tag-index 2011/09/02 18:34:27 1.1500 +++ MITgcm/doc/tag-index 2013/07/01 16:55:57 1.1889 @@ -1,9 +1,2066 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1500 2011/09/02 18:34:27 jmc Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1889 2013/07/01 16:55:57 dimitri Exp $ $Name: $ Notes on tags used in MITgcmUV ============================== +o pkg/exf ALLOW_RUNOFTEMP + - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL + - added 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 + - update reference output_adm.txt +o tools/genmake2: + - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ; + refine usePROFILES switching off (only when NetCDF is not available). +o verification (atmospheric set-up): + - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration +o pkg/profiles : refine profiles and files handling. +o model/src and pkg/ecco : introduce run-time switch usePROFILES. +o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h : + - changes to use model/src/the_main_loop.F rather than the ecco version + in ecco type adjoint runs. +o model/src: + - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID + - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC + - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL) +o model/src: + - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before); + update output of test experiment bottom_ctrl_5x5. +o pkg/generic_advdiff: + - implement vertical bi-harmonic diffusion (for now, only for T & S and + only explicitly). +o verification/bottom_ctrl_5x5/ + update reference output (results changed quite some time ago, + not sure when; but new reference results look ok in terms of grdchk) +o verification/1D_ocean_ice_column/ + For verification purposes, the exact adjoint rather than an approx. + should be used (e.g., to comare against F.D. or TLM). + removed autodiff_inadmode*_ad.F routines in code_ad/ + Update results/ accordingly. +o pkg/cal: + - change cal_getdate.F so that output date is function of input time only + (less ambiguous, not mixed up with input iteration number). + - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP). +o pkg/diagnostics: + - implement calendarDumps also for stats-diags + - implement calendarDumps also for snap-shot output (negative freq) + - for now, ignores calendarDumps if non-zero phase-lag. + +checkpoint63n (2012/06/04) +o model/src: + - recompute rSurfW & S to ensure consistent column thickness (needed for rStar) + between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice; + - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more + similar to calc_r_star.F); update results of experiment internal_wave and + tutorial_global_oce_in_p (affected @ truncation level). +o pkg/shelfice: + - add parameterisation of advective-diffusive flux into the ice shelf + according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd + - simply eps3/3a computation +o eesupp: + - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange + between tiles, just fill-in edges assuming locally periodic subdomain) and + add corresponding exchange subroutines (EXCH0); + - new CG-solver version (_EX0) for disconnected-tiles special case. +o model/src (CG-solvers): + - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached + (similar final residual output and max-Iter number as with standard version); + - allows to store and use lowest-residual solution (standard & _SR versions); + - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...). + - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h) +o eesup/src: + - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef + ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012) +o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn + +checkpoint63m (2012/04/27) +o pkg/shelfice: + - account for partical cells in surface level below ice-shelf for hydrostatic + pressure calculion (set uniformFreeSurfLev to F); update isomip experiments. +o ad test experiments: + - update and rename to "ad_optfile.local" local AD-optfile specific to a + particular adjoint verification experiment (in verification/*/code_ad/) +o pkg/seaice & pkg/exf: + - Part two of ECCO-CLIVAR code merges. + Completes merge of seaice area relax. code. + Requires unified CPP option EXF_ALLOW_SEAICE_RELAX + to be set in EXF_OPTIONS.h since this pkg controls its I/O + (and avoids second CPP option in SEAICE_OPTIONS.h) + - change default value of costIceStart & costIceEnd to a valid date. + - add snowPrecip to HSNOW in seaice_growth +o pkg/ptracers: + - move ptracers summary and setup check into separated S/R ; add a check for + valid PTRACERS_Iter0 value (error+stop or just warning). +o pkg/cal (+ pkg/ecco): + - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used + as input; and for AD, unless both are not differentiable (e.g., k index)). +o model/src: + - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index + is everywhere k=1) to speed-up some calculations (by pass kSurf reference); + temporary set to usingZCoords value (to be changed to F when using shelfice). + - hydrostatic pressure: implement partial cell near the surface also for + Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on + usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code). +o pkg/ctrl/ctrl_init.F: + - add a formal parameter to s/r ctrl_init_rec to print + xx_$(ctrl_valiable)_file for easier debugging + - move call of cal_* routines into the if-block where they are really + needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having + to specify a startdate +o pkg/seaice: + - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and + global_ocean.cs32x15/code versions). + - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for + verification experiment global_ocean.cs32x15.seaice and update results. +o pkg/exf: + - new S/R EXF_GETFIELD_START to return starting-time of a forcing field + (according to useExfYearlyFields). +o pkg/cal: + - move calendar setting & summary (previously in cal_readparams.F) into new + S/R CAL_INIT_FIXED to be called later in the initialisation process, once + length of the simulation is set (after SET_PARMS call); This is an attempt + to fix Pb when, e.g.: pkg/longstep, modifies the length of the run. + - For safety: keep a record of pkg/cal parameter settings status + to allow to STOP if one pkg/cal S/R is called too early. + - add a stop in all basic pkg/cal subroutines if called before setting is done. + - modify cal_getdate.F: stop when nothing was returned; + if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2); + this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F. + +checkpoint63l (2012/04/04) +o pkg/bbl: + - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc); + update global_with_exf output.yearly.txt file. +o pkg/cal: + - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero. + - remove 2 unsused and very short (1 line only) functions ; + - remove unsused subroutines from AD-Diff list. +o model/src: + - start to implement clean wait to stop in initialization S/R (config_check.F, + packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage) +o folowing PRINT_MESSAGE changes: + - remove reminder multiple print to the same file (STDOUT) when multi-threads. +o pkg/bbl: + - modification so it can work with z* + - replace deltaT with dTtracerLev(k) for asynchronous time stepping + - global_with_exf/input.yearly verification; changes output.yearly.txt +o eesupp/src: + - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR); + writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1 + - CHECK_THREADS: specific code if using OpenMP threading: improve checking of + # of threads across processors (e.g., different env OMP_NUM_THREADS setting) + - improve special preliminary call to EESET_PARMS (if eedata is read 2 times). + - when using MPI, always set usingMPI=T ; set default accordingly and stop + if not consistent. + - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread + argument is zero (in case called within single-thread section). +o pkg/fizhi: + clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored + in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO. +o pkg/exch2: + - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to + activate EXCH_IGNORE_CORNERS in vector EXCH S/R). + - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS) + but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data + with bad ones coming from a not-yet-updated halo. + This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx. +o pkg/frazil: + move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F + http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html +o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy +o verification/lab_sea + * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING + * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL + * nTimeSteps 3 -> 4 + * changed reference output accordingly +o pkg/ctrl: + * fix ctrl_get_gen for xx_sst, xx_sss +o pkg/fizhi: + - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F + update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d) + - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE); + fix few out-of-bounds indices in referencing vars (initialise igrd to 1); + clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array). +o pkg/gmredi: + - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp +o pkg/fizhi: + - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the + (old)aces open64 tuv test. +o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F +o pkg/mom_vecinv: + - fix 1 loop range in mom_vecinv.F to be like all the other loops which + set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv + with non-lin free-surf). +o model/src: move k-loop outside of i/j-loops when (re-)computing R_low + in ini/update_masks_etc.F in order to avoid -O3 optimization problems with + some compilers (gfortran 4.6.0 on MacOS) +o momentum: + - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM + & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised + fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control. + +checkpoint63k (2012/03/17) +o model/src: + - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum + flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations. + - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version + (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp. +o model/src: solve_*diagonal.F + - replace division with multiplication by inverse (similar to original version) + update output of AD exp. global_ocean.90x40x15. + - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F + to enable the use of the vectorized & differentiable solve_tridiagonal.F + - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for + vertical advection (to get solve_tridiagonal tested in AD mode). +o pkg/seaice: ECCO-CLIVAR merge: + 1. seaice AREA relaxation + * CPP option: SEAICE_ALLOW_AREA_RELAXATION + * runtime flag: SEAICE_tauAreaObsRelax + 2. modified global mean cost imbalance code: CPP option + ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION +o another iteration on solve_*diagonal.F + Make choices independent of AUTODIFF + Default will be the adjoinable vectorized version. + Alternative choices are: + * non-adjoinable original version with low memory footprint: + #define SOLVE_DIAGONAL_LOWMEMORY + * still adjoinable but does not vectorize (k as inner-most loop): + #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef) +o testreport + - add option to use a home made wrapper around "make" + - remove MITGCM_IEEE env. variable (no longer active) +o pkg/shelfice + - improve computation of friction velocity for velocity dependent + exchange coefficients: include velocities into SHELFICEBoundaryLayer + block to average velocities vertically + - add TAF store directives for SHI_ALLOW_GAMMAFRICT +o Modify diagonal solvers, now three versions (upon request): + #ifndef SOLVE_DIAGONAL_AUTODIFF + 1. default version (dating back a while ago) + #else /* def SOLVE_DIAGONAL_AUTODIFF */ + # ifdef SOLVE_DIAGONAL_KINNER + 2. adjoinable version with k-innermost loop (G. Forget) + # else + 3. adjoinable vectorized version of 2. + # endif + #endif /* SOLVE_DIAGONAL_AUTODIFF */ + All flags are currently set within routines, but could/should be moved to CPP-options. + Array bounds for 1. are as before, for 2.,3. cover the entire domain + (could be changed for 1. too). +o verification/lab_sea (fwd): + - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY, + use 7 categories (except hb87), new solve4temp params (except salt_plume), + constant salinity (=4) or variable salinity (salt_plume) done through + SItracer. +o pkg/seaice: + - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0; + - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t, + SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz) + from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when + SEAICE_freeze got retired) but already better than previously with + SEAICE_freeze=123456.7 deg.C; + - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS + (safer multi-threaded setting); always set SEAICEuseEVP; + - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to + SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report); + stop if multiple specifications for the same coeff; make sure default + SEAICE_mcPheePiston is compatible with drF(1) & deltaT. +o pkg/obcs: + - allow to switch to upwind 1rst order advection scheme for the advective + flux computation at the open-boundary; disabled for adjoint built. +o pkg/ptracers: + - rename PTRACERS_RESTART.h -> PTRACERS_START.h + - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F + - add parameter to decide when to start a tracer; use internal flag to + know which tracer to step-forward; switch this internal flag at the top + of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled + for adjoint built. +o pkg/seaice: + - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ; + - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ; + - keep experiment offline_exf_seaice truly single category (set MULTDIM=1). +o pkg/ecco: + - fix writing of output file DiagnosCost_ClimSalt/Theta + and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc). +o pkg/seaice: + - add missing initialisation of COR_ICE array in dynsolver.F + - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is + compiled either way, and is tested in all exps (multidim was only tested + in lab_sea ad before). + - cosmetic change to prepare for future addition of ITD. no change to results. + no defaults change. + - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise). + - by lack of adequate verification experiments, I further used custom versions + of global_ocean.cs32x15 to test multicat or not, with pickup or not. All + should be correct. + - avoid recomputations in ad. +o array initialisation in adjoint mode: + 1) pkg/mom_common/mom_calc_ke.F: + add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC): + The S/R which calls MOM_CALC_KE initialises KE but in some recomputation + part this initialisation is gone, resulting in Floating Point Exception + (caught by open64 compiler with debug option). + 2) model/src/convective_weights.F + set output convectCount over the full array range (instead of doing + an update): this fix a similar issue when called within recomputation (adjoint) + which could by-pass the initialisation (normally done in the caller S/R). +o pkg/seaice: + - final version of turbulent flux params, as agreed at MIT ice meet: + SEAICE_mcPheePiston (default is ~ 0.000875) + SEAICE_mcPheeTaper (default is 0.) + SEAICE_frazilFrac (defualt is 1.) + SEAICE_mcPheeStepFunc (default is false) + - changes results at trunction error level + - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo +o added pkg/frazil: + - see frazil_description.tex for details + - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt +o pkg/shelfice/shelfice_thermodynamics.F + - fix exponents for velocity dependent exchange coefficients: change + from 2/3(=0) to 0.66666666666666667 + - move computation of velocity dependent exchange coefficients into + separate loop, so that it applies to both thermodynamics + - move some divisions by constants out of loops + +checkpoint63j (2012/02/16) +o pkg/seaice: + - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc. + - SItracer: added run time params, and allow coupling to ocn salinity. +o pkg/seaice: remove (almost) all divisions by constants within loops + in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d + results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only + those, caused by 1/QI -> recip_QI) -> update output.seaice.txt, + output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt +o pkg/seaice : + - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula + = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper. + - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148. + - add permanent SItflux diag that corresponds to TFLUX but includes + ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget. + - allow activation/testing of a fix for suspected missing term in + ocn-ice heat budget (to be confirmed). To test this, you want to + undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param + SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic. + - no change in results, fwd or ad. +o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below: + - switch to variable freezing point. + Results change : cg2d -> 1 digits; ad -> 3-6-6 digits. + - bug fix : the sublimation term that was missing is now activated. + Results change : cg2d -> 2 digits; ad -> 8-6-6 digits. + - bug fix : flooding sign term for SIsal0.NE.0. + Result change : cg2d -> 8 digits; ad -> 11-12-9 digits. +o pkg/seaice: + - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT + is now the default, and the old default constant freezing point is recovered + with SEAICE_tempFrz0 = -1.96, + SEAICE_dTempFrz_dS = 0., + - retire SEAICE_freeze (= the old way of specifycing the constant freezing point) + - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there. + - bug fix (thanks to M. Losch) : the sublimation term that was missing is now + activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM. + - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211) + was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail). + - bug fix (thanks to O. Jahn) : area loss for melting got messed up in + seaice_growth r149 for legacy branch (no results change). + - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code + from I. Fenty). + - results did not change except for global_ocean.cs32x15, mostly due to the + switch to variable freezing point (see above item for detail). +o pkg/thsice: + - fix and simplify interface to salt_plume pkg ; diagnose directly amount of + seawater freezing in thsice_calc_thickn (not used). +o pkg/seaice: turbulent flux term specification via run time params. + - replace CPP switches with run time switches to facilitate testing + - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, + GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR + - added runtime parameter : SEAICEturbFluxFormula + - move Mcphee constants to SEAICE_PARAMS.h + - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula; + SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); + remove seaice_summary call (moved to seaice_init_fixed) + - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on + SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms) + - seaice_summary.F : add missing report of read turbulent flux term set up + and SITRACER. + - seaice_check.F : check range; inform and stop if retired CPPs are used + (incl. SEAICE_AGE). + - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without + CPP switch, same computation as before for the different options. + - change results at the truncation level. +o pkg/seaice: + - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters: + useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and + SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY. + - update verification/*/input*/data.seaice: + to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY + code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ; + and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code, + set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0. +o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY): + - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same + algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0); + difference in results only due to machine truncation. + - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using + MaykutPolySatVap; keep MIN_LWDOWN. + - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation. + - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87, + + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits). +o pkg/salt_plume: + - isolate saltPlumeFlux array exch into a specific S/R called from + do_oceanic_phys.F + - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice. +o verification: + - move untested set-up to MITgcm_contrib/verification_other. +o pkg/seaice: + - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER. +o pkg/seaice: + - seaice_solve4temp.F (keeping results unchanged): + * add 2 future run-time params to select which saturation vapor pressure + formula is used and how post-iteration fluxes are set. + Temporary set these 2 params according to option SOLVE4TEMP_LEGACY; + * New piece of code (not used) to update surf. atmos. heat flux F_ia using + the linearized expression to stay consistent with tsurf finding. + - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x + can be < 0. +o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef): + - remove from F_ia (and from it's derivative dFiDTs1) the contribution of + conductive heat flux F_c , and add it explicitly when updating tsurf as + solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf + so that now F_ia has a consistent meaning through the entire routine. + This causes differences at truncation level: update output of fwd exp. + global_ocean.cs32x15.seaice. +o pkg/seaice: + - lots of editing/cleaning in seaice_solve4temp.F + better documentation + of arrays, sign/direction of fluxes; no effect on results. + - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K + in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part); + note: this should have been done before changing celsius2K default. + - to keep results unchanged, add back old value of celsius2K in verification + exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs + - replace hard coded seawater freezing temp in seaice_solve4temp.F (part + SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default + value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater + freezing temp is consistent with value in seaice_growth.F ; this causes + differences at machine truncation level: update lab_sea AD output (3/4). +o pkg/seaice: + - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask + and climsst/sss even when using seaice (to prevent calculation that might + use SST on land); does not affect any verification exp. + - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output + of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix. +o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness + over land (non-legacy code) +o vectorize salt_plume package: + - add extra code to salt_plume_frac and salt_plume_tendency_apply_s + - this code computes plumebk everywhere (also over land), thus requires + code to avoid divisions by zero and catch the case of kLev=Nr. + - efficiency of salt_plume_frac is still sub-optimal +o tools (genmake2): + - fix makefile NAME specification (option: -makefile NAME) by adding + "-f $MAKEFILE" in few places where it was missing including makedepend + command (contribution from Paul). + +checkpoint63i (2012/01/24) +o model/src: + - add factorized versions of some EOS code to find_rho.F, + define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX) +o model/src: + - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h; + - change default celsius2K from 273.16 to 273.15 + - to keep results unchanged, add back old value of celsius2K in verification + exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd), + global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm). +o model/src: add a little initialisation trick to find_rho.F and find_alpha.F + to make TAF generate vectorizable code +o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows. + Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers + have flags that do this more efficiently. +o pkg/diagnostics/diagstats_calc.F + - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact +o pkg/obcs (with exch2): + - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F) + and remove code (in obcs_readparms.F) which was based on EXCH of indices + (through buffer) and did not account for exch2 (e.g., CS-grid) topology. +o pkg/exf and seaice exp: + - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0) + so that switching off area & heff advection flags does not affect results. + - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h + - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef + EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update + results of verification experiments: 1D_ocean_ice_column(fwd), + global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8) + and offline_exf_seaice (all 4). +o pkg/seaice: + - remove array YNEG, RIVER, TMIX (replaced by local var) from common block; + remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef. + - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY) + but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and + not multi-dim advection; + - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and + SHORTWAVE_HEATING #undef. +o optim: make Makefile more robust (?) +o pkg/obcs: + * fix treatment of obcs_read_pickup for TAF +o pkg/shelfice: + * add missing initialisation of num_shifwflx + * new adjoint verification exp. for isomip + * change Prandtl and Schmidt numbers from generic formulations + (in terms of model diffus. and visc.) to separate runtime + parameters, with Holland and Jenkins (1999) default values. +o pkg/exf (interpolation): + - extended input field (2 rows) near the N & S poles: + * fill in with the symetric value (when even Nb of data in longitude) + * add average value at the poles only for scalar quantities ; for vector + component interpolation, skip the averaging and keep duplicated values, + unless the 2 components have same location (uvInterp=T) in which case + interpolate the 2 components together using S/R EXF_INTERP_UV. + - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field + together: this allows to account properly for local orientation when + averaging at N & S pole. + - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding + exf-interpolation near N & S poles. Undef by default. + - add debug check/print on 1rst iter if debugLevel >=2. +o pkg/exf: + - change masking flags definition (no longer "parameter"), put them in + common block and set them in S/R EXF_INIT_FIXED. + - change recognized masking flag from s,u,v to c,w,s since the mask + to use (maskC,W,S) depends on position on model grid and has little to + do with scalar/vector difference; fix masking if using P-coordinates. + - fix masking of wind-stress (was wrong if interpolated or read on A-grid) + and update results of exp. global_with_exf (x2). + - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef. +o pkg/obcs + - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate) +o pkg/exf (interpolation): + - assume periodicity in X only if input field cover full longitude range. + - improve search for lat. index (supposed to be faster, in ~log2(ny) steps, + and should vectorise). + - fix input lat of the 2 added row (in case we provide N.pole data). + +checkpoint63h (2011/12/30) +o pkg/seaice: + - change declaration of UVM from _RL to _RS in order to get B-grid + uIce,vIce monitor when _RS = real*4 +o pkg/offline: + - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags); + - compute vertical velocity if not read from file (switch on exactConserv + & staggerTimeStep); + - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq. +o verification: + - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input) + with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m": + fix Pb in yG definition @ 2 missing corners (previously yG was averaged); + - update output of exp. global_ocean.cs32x15.viscA4 after changing + grid-file angles (used here for coriolis-3d); + - remove (or gzip) few files not needed to run fizhi-cs experiments. +o pkg/exf (vector interpolation): + - rotate vector component toward local grid-axis orientation using grid-angles + (stored in GRID.h) instead of locally computed rotation angle; keep old code + available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default). +o pkg/seaice: + - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION + undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined. +o pkg/PKG_OPTIONS.h files: + - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h", + outside of the #ifdef ALLOW_THISPKG / #endif block. + - update verification/*/code/PKG_OPTIONS.h files. +o add a verification experiment (offline_exf_seaice/input.seaice) that test + the B-grid LSOR solver +o pkg/seaice: sort out emissivity and long wave radiation step 2: + - add emissivity for snow and ice as new run-time parameters + (unfortunately) that default to the corresponding exf values; this + changes results in most verification experiments so that for backward + compatibility these parameter have to be set explicitly to inconsistent + values (ugly); + - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired + emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp + until we agree how to handle this bug properly +o pkg/exf (interpolation): + - add a set of run-time param ({inputfield}_interpMethod), one for + each interpolated input field, to select the interpolation method + with a value of zero switching off the interpolation; + - print interpolation parameters to standard output; + - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined + (to use instead runoff_interpMethod=0 in data.exf). + - simplify default setting of interpolation parameters (for all fields, + set position to match model grid cell-center position, leading to trivial + interpolation in case of regular Lat-Lon grid) and fix for the case of + non-uniform delY. +o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for + within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1. + this factor is absolutely required, because the lw exitance (= out-going + long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown, + where the reflectivity rho = 1-emissivity for conservation reasons. Once + this is established, we can remove the CPP-Flag (if we want to). +o pkg/seaice: + - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and + ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined + - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity + what the name implies (and not emissivity*BoltzmannConstant), this means + the old default value of 5.5e-8 now means + 5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in + S/R exf_readparms + - FV-discretization of the B-grid LSOR solver, turn on with + SEAICE_LSRBNEW. This new solver also involves a slight re-organization + of the calling routine dynsolver, so that B and C-grid code look a + little more alike. + - fix index bugs in ostres.F (B-grid code) +o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better +o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the + default for SEAICE_emissivity, if useEXF; requires setting a wrong + parameter value in global_ocean.cs32x15/input.seaice/data.seaice for + backward compatiblity +o model/src: use sigmaR in calc_ivdc + +checkpoint63g (2011/12/16) +o pkg/seaice/seaice_growth.F: + fix heat conservation of the coupled ocean-seaice system. + when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of + solid vs liquid water treatment is resolved via QNET. +o pkg/seaice/seaice_growth.F: + add missing term for sublimation in saltFlux, which was breaking conservation. +o pkg/seaice/seaice_model.F: + Remove this patholigical case treatment in evolution branch, + where it is un-necessary and breaks conservation. + Update global_ocean.cs32x15/results accordingly for + output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt +o model/src: + useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in + external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE. +o pkg/obcs: + modify Stevens boundary conditions so that S/R obcs_calc_stevens computes + tendency for temperature and salinity that is then applied to update + theta and salt in S/R obcs_apply_ts; this requires proper masking of all + horizontal advection and diffusion contributions on the boundary (in + S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and + removing the mask in S/R timestep_tracer. The advantage of this approach is + that the updated tracer values include contributions from the surface + forcing and vertical diffusion. + This modification changes exp4.stevens because of vertical diffusion. +o model/src: + change non-curvilinear grid setting to also work with exch2 + blank tiles: + - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst + face dimensions. + - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units + as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID + and INI_SPHERICAL_POLAR_GRID. + change test-experiment global_ocean.90x40x15: + - split the domain in many more tiles (9x4 tiles of 10x10 each); + - switch to exch2 and remove 1 blank-tile (but only for MPI test). + - update results of both test (std & dwnslp). +o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in + tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation +o model/src: + - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS + and fix initialisation when using sigma-coords. +o model/src: + - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc. + to their current value at the beginning of forward_step.F": add a new run-time + switch "doResetHFactors" (default=false) and use it to do (or not) the resetting. + - set doResetHFactors=T in the following test exp: + global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS), + global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS) + and tutorial_global_oce_in_p (nonLinFS in p) +o pkg/ecco + - added IES cost term +o verification/advect_xz + - scale down the depth by 1/100 (from 200 km to just 2.km) + - add secondary test using divergent flow, r-star and implicit vertical advection. + - add note (check_conserve_TS.txt) and matlab script to check global + conservation of T & S with NonLin-FreeSurf and Adams-Bashforth. +o pkg/rbcs: + - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F). +o pkg/obcs (Stevens BCs): + - fix various problems in the phase speed computations of the Stevens + boundary conditions: + - sign error for western and southern boundaries, + - time tendencies were underestimated by factor of dTracerLev and some just + zero (for multidim advection schemes) -> now estimate time tendencies + from difference between previous (n) time level and the one before (n-1); + this requires storing a field per tracer per boundary, also in the pickup + files. + - replace deltaTmom in cflMer/Zon computation with dTracerLev + - set default phase velocity to cflMer/Zon + - update verification experiment exp4.stevens +o pkg/generic_advdiff (implicit_r): + - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf + (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F); + - fix implicit vertical diffusion or advection with NonLin FreeSurf + (was using current recip_hFacC instead of future recip_hFacC): set future + recip_hFac in thermodynamics.F and pass & use it in all vertical implicit + solver S/R ; + - fill diagnostics of vertical advective fluxes (computed from tendency) + when using implicit vert. advection; + - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion: + global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD), + tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD) + and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5. +o pkg/diagnostics: + - add diags for T & S tendency which goes through Adams-Bashforth. + +checkpoint63f (2011/11/30) +o pkg/obcs/obcs_calc_stevens.F: + - join some loops to reduce number of if-statements + - fix a bug in code for northern and southern boundaries. +o pkg/seaice/seaice_init_varia.F + - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and + caused zero ice-velocities for the B-grid code +o pkg/seaice/seaice_init_fixed.F + - fix a bug in the initialisation of the second metric terms + k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0. + - this affects all seaice configurations with useCurviLinearGrid = .true. + and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms + = .true. (default) + - the only verification experiment affected is global_ocean.cs32x15: + icedyn, seaice, and seaice_dynmix (AD) +o pkg/thsice/thsice_diagnostics_state.F + - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does + not contain garbage that can lead to surprises in diagstats_calc.F +o model/src: + - move bi,bj loops inside INTEGR_CONTINUITY ; + - call INTEGR_CONTINUITY directly from forward_step.F + (previously called from momentum_correction_step.F) + - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F, + forward_step.F and pkg/ecco/the_main_loop.F +o model/src/do_oceanic_phys.F: + - reset addMass to zero only if useICEFRONT ; + - separated k-loop for rhoInSitu calculation ; + - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P) + and at constant T,S (= WdRHOdP); + NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport + of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical + transport of locally-referenced potential density); + to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP) +o gluemnc: + - replace ncrcat with ncks when adding variables to *.glob.nc + - change the way variables without record dimensions are handled so that + files that have variables with and without record variables can be glued: + add a record dimension with a new unique name to be able to differentiate + between variable with and without a-prior record dimensions. Remove + this record dimension before adding the variable to the *.glob.nc file. + This procedure automatically works also for grid.*.nc files that do not + have any record dimension. +o verification/cpl_aim+ocn: + - generate new reference output on baudelaire (gfortran, mpich2) (previously + from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script. +o pkg/obcs/obcs_calc_stevens.F: + - add code for northern and southern boundaries. + - reorder some loops to save some operations and so that drFBar can be scalar +o model/src: + - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine + truncation) and add diagnostics for Adams-Bashforth tendency increment. + - update test-exp. AD output: + 1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl; + and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20, + front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5), + global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4), + matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre, + tutorial_global_oce_in_p, tutorial_global_oce_latlon and + tutorial_plume_on_slope. +o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX + that vectorises. This code uses 3 extra 2D fields, F90 array assignments + and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX + does not even come with an F77 compiler anymore, this should not be + a limitation + +checkpoint63e (2011/11/06) +o pkg/seaice adjoint of LSR: + - substantially rework STORE dirs. + - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED + this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields + and only perform SOLV_MAX_FIXED adjoint iters. + If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration + always goes to same record, meaning that the last forward field will be + the one used in the adjoint - an approximation. + - now produces non-zero LSR-related gradients, and acceptable gradients for + An's zonal (x-z) test case (to be checked in) + - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR + (but these are screwed up by the thermodynamics in the first place); + reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution; + output_adm.txt also reflects changes to seaice_lsr + - global_ocean.cs32x15: + * the "default" input_ad.seaice has been re-defined to always exclude dynamics + (output_adm.seaice.txt was updated) + * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift + (output_adm.seaice_dynmix.txt) +o test-exp. exp4+stevens: + - switch off pTracers and nonHydrostatic (restart problems with NH); update output +o pkg/seaice (lsr solver): + - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only); + update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15 + - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD) + - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution + into initial guess for linearised solver; use weight ~ (1/err)^2,4. + - compute (with new S/R) and print initial (+ free-driff sol. if available) + and final residual of linearised system. +o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity + (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F) +o pkg/obcs: Stevens BCs (still only for east and west) + - fix Stevens BCs by using intermediate velocities of previous + time step as "baroclinic" contribution rather velocity of one grid cell + inside the boundaries; more consistent but makes the entire treatment + more complicated, requires new pickup files and two new S/Rs: + obcs_copy_uv_n and obcs_save_uv_n + keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY + (undefined by default) + - silently move computation of some grid factors into separate loops to + save some recomputations + - add a hack for non-linear free surface + - add a verification experiment to exp4 that tests this code +o make gluemnc/xplodemnc work with (moron) non-GNU shell tools + +checkpoint63d (2011/10/25) +o pkg/obcs + seaice-dynamics: + - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before + solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB + values (consistent with an implicit method). + - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to + return to older implementation (same results as before); note that none of + the "experimental" OBCS_SEAICE options are implemented in the new version. + - switch test exp. seaice_obcs to use new version (update output). +o pkg/seaice: + - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS) + - add parenthesis in Water-Ice drag calculations (evp & lsr); + - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1; + and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice) + - update output of test exp lab_sea that uses evp or lsr (fwd+ad) + and global_ocean.cs32x15 (icedyn & seaice fwd+ad). +o pkg/layers: + - Include potential density as new coordinate (Thanks to David Munday) +o pkg/dic: + - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add + carbonate computation/output to CALC_PCO2_APPROX +o pkg/generic_advdiff + - make TAF generate code that vectorizes: + gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F +o model/src: + - improve vectorization also for adjoint code of + solve_tridiagonal and solve_pentadiagonal. As this requires up to + 5 new 3D-fields, this code is only turned on for the combination of + ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message + for singular matrix check (only for TARGET_NEC_SX). + - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to + ALLOW_AUTODIFF. This flag now needs to be set outside of + solve_tri/pentadiagonal.F +o pkg/exf: + - fix previous modif in exf_readparms.F (revision 1.66: treatment of + optional namelist EXF_NML_OBCS). + - add many debug-print (to trace down where pkg/cal error msg comes from) +o pkg/mom_vecinv/mom_vi_hdissip.F + - rearrange loops so that vectorization is improved and in particular + the adjoint routine vectorizes. The code is a little longer now, but I + think easier to read. + Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested. +o pkg/seaice: + - allow to specify initial seaice velocity from files (uIceFile,vIceFile) +o pkg/exch2: + - alternative code (without tile x tile matrix) for cumulated (global) sum; + used as default; keep using matrix version in adjustment.cs-32x32x1. +o tools/build_options: + - after merging some MPI and/or multi-threads specific optfiles so that + the modified default optfile support both built (using genmake2 -mpi + for the MPI built, using genmake2 -omp for OpenMP built), + move now obsolete optfiles to tools/build_options/unsupported/ + (add copy of email sent to support list in doc/optfiles_changes.txt) + +checkpoint63c (2011/09/28) +o pkg/ebm: + - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of + test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d) +o pkg/seaice (SItracer pickup) +* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER) + To be done: + - thorough testing of missing fields in S/R seaice_read_pickup + - thorough matching between generic tracers and specific fields used + (e.g. volume-weighted age, area-weighted age, salinity, ...) +o pkg/grdchk: + - all procs calculate and print finite-difference gradient (for testreport) + - change description output used by testreport; + - AD testing: also compare and report Finite-difference gradient; + => update all output_adm*.txt +o test exp. global_ocean_ebm: + - switch back useRealFreshWaterFlux (no problem anymore with run-off); + and turn on exactConserve; update (fwd) output. +o pkg/seaice (LSR): + - print to STDOUT number of solver iterations at SEAICE_monFreq interval. + - modify solver to deal cleanly with u/v switch at face edges (CS-grid): + * identical results with non-CS topology (but save up to half of EXCH calls) + * no much changes in cs-32 verification tests since no ice at face edges + (differences due to convergence criteria, since nb of iterations changed) + * expect some differences on lat-lon-cap grid. + update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice) +o pkg/exch2: + - add new CPP option to disable Cumul-Sum matrix (to save storage when using + many tiles); until alternative coding is added, just add a stop. +o pkg/kpp: + - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F + to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list). +o optfiles: + - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles + into corresponding standard one, which now support different build: + (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built) + - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael) o pkg/obcs (seaice): - add missing EXCH for uIce,vIce after applying OBCS; - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding