--- MITgcm/doc/tag-index 2008/05/09 21:51:26 1.989 +++ MITgcm/doc/tag-index 2010/10/16 17:23:12 1.1314 @@ -1,9 +1,1318 @@ -$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.989 2008/05/09 21:51:26 jmc Exp $ +$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1314 2010/10/16 17:23:12 jmc Exp $ $Name: $ Notes on tags used in MITgcmUV ============================== +o eesupp/src: + fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube +o pkg/seaice/seaice_growth.F + Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and + merging process. The merged routine has two branches, and one activates the 'evolution' + branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now). + In summary, here is what the '10/10 revision' did consist of + part 1: seaice_growth.F revisions 1.71 to 1.75 + - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged. + The emphasis here was on improving readability (e.g. by trying to use meaningful + variable names) and modularity (e.g. by adding arrays to store heff etc. updates). + part 1.5: + - revising the lab_sea experiment to make it a more useful (i.e. stable + and representative of an actual model run). This was done by generating a + (winter) pickup to start from, switching back the main experiment dynamic + solver from evp to lsr, having one of the experiments use the free drift solution. + part 2: seaice_growth.F revisions 1.76 to 1.85 + - Sorting out hard-coded constants that prevented heat and fresh water conservation. + - Sorting out the various fields units and sign (set early on and reset at the end) + to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and + fresh water stock is 'effective ice meters', and >0 implies more ice/snow. + - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks, + and simplifying logical expressions to further improve readibility. + part 3: seaice_growth.F revisions 1.86 to 1.89 + - Re-organize the blocks of code more logically. + - Merging the '_if.F' pieces that add something new. +o pkg/thsice: + - vectorize thsice_solve4temp and thsice_get_exf. + Problem: thsice_solve4temp has an unvectorizable statement that + might also be problematic for TAF + - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This + does not change the verifcation experiment, but will change all + experiments that have this flag undefined (not tested in verification); + a little reorganization to save a few 2D fields and recomputations +o pkg/obcs: add support for exch2 + - the position of the boundary and prescribed values are specified using + a global domain with exch2 facets stacked + - in x for N,S boundaries (like W2_mapIO=-1) + - in y for E,W boundaries (so E,W boundaries do not overlap) +o pkg/mdsio: add support for writing global sections with exch2 + file layout is as for obcs described above: + - for x-z sections, facets are stacked in x (like W2_mapIO=-1) + - for y-z sections, facets are stacked in y +o pkg/thsice: + - change a few routines for better vectorization: thsice_albedo.F, + thsice_step_temp.F, and in thsice_calc_thickn.F. Results are + not affected, but in particular the latter routine has changed + dramatically (not necessarily easier to read now). + - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops + iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF. +o verification/lab_sea: + - overhaul of the forward model experiments. The main motivation + for this revision is that lab_sea has proven quite fragile (when + changing the sea-ice code, and switching platforms) to a point + when failures were very hard to attribute to specific code problems. + - the suspected reason for this fragility is noise amplification by evp so, + to start with, we decided to replace evp with lsr in the main experiment. + - the input.lsr experiment thus became obsolete and was removed. + - it was replaced with the input.fd experiment that uses an + analytical "free drift" solution as the ice velocity field. + - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp) + will hopefully allow us to discriminate problems due to dynamic solvers + from problems due to the thermodynamic code. input.salt_plume (lsr) allows + us to test additional options, along with the salt plume package. + - Finally a pickup was generated (at the end of a one year run) to + make the tests more representative of an actual model run. Previously + the tests starting point was a 1m thickness of ice everywhere. +o pkg/seaice: + - introducing S\R seaice_freedrift.F that compute the + analytical solution to an approximate ice momentum + equation (i.e. the simple stress/coriolis balance). + - define SEAICE_ALLOW_FREEDRIFT to trigger the computation + of the free drift velocity field, and enable its use. + To actually use the free drift solution as the model ice + velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice. +o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata" + +checkpoint62l (2010/10/04) +o pkg/seaice: + -fix the USE_ORIGINAL_SBI version (for variable freezing point); + -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new + version (with USE_ORIGINAL_SBI undef); +o add hooks for new packages OASIS, the package will follow + (hooks exclude the seaice pkg for now) +o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO + Option to use mdsio_read_whalos.F/mdsio_write_whalos.F, + rather than mdsio_readvector.F/mdsio_writevector.F, within + adread_adwrite.F to read/write adjoint-related tapes to disk. +o eesupp and pkg/mdsio: ALLOW_WHIO + Option to write/read 2D fields to files including tiles halos. + The main purpose is for adjoint related "tape I/O". + The secondary purpose is for debugging phases. + A word on those rather specifically intended purposes. + The code was meant to be stripped down to the bare minimum. + Typically, there is a unique and basic mapping to the global + buffer (tile by tile, then proc by proc, then level by level), and + byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not + meant to generate user friendly outputs of various shapes and forms. + Rather it is intended, for the knowledgeabale developers, + to be largely independent of the many mdsio options, to allow + outputs of tiles+halos in debugging phases and in adjoint runs, + and to allow some flexibility in tuning (adoint) I/O depending on each + file system behavior. With regard to tuning, most of the potential knobs + (to leave files open, to allocate the I/O indep. of usesinglecpuio, + to specify directories, to specify the typical size of I/O calls, etc.) + are not yet included, and will be added if they prove useful. +o pkg/seaice: + fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F +o pkg/seaice: + new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty + code (seaice_budget_ice_if.F) which enable to recover old standard + code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined. + temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F. +o model/src (rStar): + use simple average (not area weighted) of rStarFac at U,V point when using + vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection) + update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20. + +checkpoint62k (2010/09/17) +o adjoint + * changed verification/global_ocean.cs32x15 ; adjoint now tests + Adams-Bashforth 3 + NLFS + RSTAR + * some more modifs required for ECCO-GODAE v4 +o pkg/seaice + add SEAICE_AGE_VOL option to use volume instead of area for + integrating SEAICE_AGE +o model/src: + first check-in of sigma & hybrid-sigma coordinate code ; also includes + non-linear free-surface parts ; but pressure-gradient not yet coded. +o pkg/ptracers: + option for ptracer to convert Salt Relax into additional EmP. + tested in exp. global_ocean.90x40x15.dwnslp (update output) + +checkpoint62j (2010/08/25) +o pkg/ggl90: + other minor changes: remove 3-D temp array gTKE (+ add argument myIter) +o pkg/dic: car_flux.F, phos_flux.F + - reduce number of exp-calls in order to improve performance + - clean up a little (replace fields by their macros, etc., fix + typo in CPP-flag) +o pkg/ggl90: minor changes + - GGL90diffKrS was removed --> always use GGL90diffKr + - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV + - hack of mxlMaxFlag=2 --> ensure mixing between first and second level + (commented out for now) + - change in max/min operations to ensure that smoothing is ok + - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr) + - always use diffKrNrT as background profile (i.e. never use diffKr field) +o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj) +o pkg/dic: + - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better + vectorization + - small bug fix in insol for the unlikely case of a cartesian grid + - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F + + now vectorize, which also removes adjoint recomputations; + + replace integer maksp1 by _RL maskp1 + + replace a**x by exp(x*log(a)) in phos_flux.F for speed + +checkpoint62i (2010/07/21) +o pkg/flt: + - with OBCS: stop floats which enter the OB region +o model/src: + - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones) + for implicit vertical advection. +o pkg/seaice: + - account for melting in seaice age evolution. + - remove double counting of seaice ridging effect on seaice age. + +checkpoint62h (2010/06/18) +o pkg/exch2: + - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1). +o tools/genmake2 + - remove "-pdefault" option: redundant with the use of "packages.conf"; + - remove file pkg/pkg_default : set the default as a pkg group + ("default_pkg_list") defined in pkg/pkg_groups; + - fix for case pkg/pkg_depend is missing (was hanging before); + - add option "-pgroups" to specify a different pkg_groups than the default. +o verification/adjustment.cs-32x32x1: + add a "minimal" set-up test (code_min & input_min) which only compiles + eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc. +o tools/genmake2 + - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg])) + - fix details of checking for mnc & profile pkg when NetCDF is unavailable. +o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these + files are nearly the same anyway. + Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04: + - redefinition of tau(i,i) (by a factor of ustar) + - 1./exf(Const/T) -> exf(-Const/T) (big change in the results) + - replace rhonil by rhoConstFresh in computation of evap (bug fix) + - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results) + - replace + rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh ) + shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j) + by + shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh ) + (changes results) + -> exf_bulkformulae v1.22, + update verification experiments lab_sea, offline_exf_seaice, seaice_obcs + (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13, + output.txt 1.63 + offline_exf_seaice: output.seaicetd.txt 1.7 + seaice_obcs: output.txt 1.10) + Step 2: do the actual merge and remove exf_bulk_largeyeager04.F + -> exf_bulkformulae v1.23, + unfortunately requires updating lab_sea.salt_plume (6 matching digits), + and global_ocean.cs32x15.icedyn (only 11 matching digits) + Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice. +o adjoint of exch-1: + - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list) + (note: was already like this when using EXCH-2) and remove flow dir + and hand-written AD version of high-level EXCH S/R (pkg/autodiff); + - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow); + - update pkg/exch2 diff list. + +checkpoint62g (2010/05/19) +o eesupp/src (exch-1): + - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F) + and remove argument "simulationMode"; same thing for all exch_*rx_cube.F + (renamed to exch1_*rx_cube.F). + - change accordingly exch_*_rx.template and AD version in pkg/autodiff + to call new exch1 S/R ; update Makefile and .cvsignore. + - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove + exch2_xy_rx later) + Note: after updating your code, need to run "make clean" in eesupp/src +o test experiment bottom_ctrl_5x5: + new output_adm.txt with fewer grdchk & less monitor output. +o model/src: + remove the call to ini_cori in initialise_varia.F (just keep the usual one + in initialise_fixed.F). More consistent with coriolis & horizontal grid + beeing treated in the same way (ini_grid is not called a 2nd time). +o pkg/exf: + - rewrite exf_bulk_largeyeager04.F for better vectorization, changes + global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated + - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now) + - cosmetic changes to exf_bulkformulae.F to make it look more like + exf_bulk_largeyeager04.F +o eesupp/src (exch-1): + - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1). + - Separate buffer filling and MPI sending: allow EXCH-1 to work for local + array (non-shared) when using MPI+MTH. Also reduces number of BARRIER + (even without using MPI). + - Message mode: move RecvAck setting (indicator of buffer being ready) + from send_put to recv_get S/R (was useless before, but not sure if + it's much more useful now); + - Switch the order of sync: MPI-proc 1rst and then threads; + - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead. + - fix AD code for communication mode ='get' (but not used). +o model/src: + initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does + not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp). +o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API +o pkg/ctrl: require a specific set of control variables and exf-flags for + adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied) +o model/src: + a) 1rst version of a new driver S/R to turn-off output freq and flags after the + 1rst forward sweep, to avoid over-writing output files during recomputations + recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?) + b) 2nd version: + - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO); + - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast, + writePickupAtEnd) + seaice & ptracers output; + - do not switch off MNC flags (otherwise, won't get admonitor netcdf file) +o model/src: + - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields. +o pkg/exch2: + - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ; + - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch). +o pkg/autodiff & exch2: + process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF + (for now, only if ALLOW_EXCH2 is defined). +o pkg/autodiff: + - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F + (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly. + + clean-up comments (_RS is not always real*4) + - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R) + - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2: + was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs. +o testreport (AD-tests): + no longer link files from dir "../input" (1rst link files from + "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad") + +checkpoint62f (2010/04/29) +o model/src/the_main_loop.F: + adjust store directives for seaice evp and multicategory according to + pkg/ecco/the_main_loop.F +o adjoint: + global_sum_ad was incomplete (noted many times by many people ;) + nice description by Jean U. as follows: + * allreduce(var) in global_sum.F can be interpreted as + reduce(sum) followed by broadcast of sum. + * The adjoint of that is + sum(adjoint) followed by broadcast(summed adjoint value) + or in other words, allreduce(sum, adjoint vars) + We were missing the sum(adjoint)! + Benign, except(!) for "global" scalars appearing in tile loops (bi,bj) + (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset). + The fix should produce 16-digit accuracy between + single-CPU multi-tile (e.g. nSx=2, nPx=1) and + multi-CPU single-tile (e.g. nSx=1, nPx-2) + We'll probably change this yet again shortly +o eesupp/src: + - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?) +o pkg/icefront + - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving + specification of addmass array based on a 2D field, which is added + at bottommost wet level at each horizontal location. +o model/src: + horizontal grid initialisation (other than curvilinear): add code for Exch2 IO + layout; (not always compatible with delX,delY setting; commented out for now). +o pkg/exch2: + change tile to processor setting (case nSy*nPy > 1): allows default model mapping + (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config. + +checkpoint62e (2010/04/15) +o pkg/obcs: + - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert). +o pkg/dic: + -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up; + (note: not presently tested in any forward verification exp.) + update tutorial_global_oce_biogeo AD output file. +o pkg/exf: + - account for the variation of albedo as a function of zenith angle + by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h +o build_options: + - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas" +o pkg/dic: + change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart: + - use binary pickup file for restart; + - initialise atmos-CO2 box from dic_pCO2 parameter; + - fix multi-threaded. +o pkg/rbcs: + - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ; + change (+ fix IO calls) type of array RBC_mask from _RL to _RS. + - add RBCS to exp4 passive tracer 01 (rbcs was previously untested) + and update output.txt +o pkg/kpp: + - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers; + - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS + (= ratio of KPP non-local (salt) flux relative to surface-flux) when + using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat '); + - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file + KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile). +o pkg/offline: + fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor + (bug was added in version 1.10 on 2007-08-23). +o pkg/offline: + - no need to specify periodicExternalForcing, etc ... to use offline pack + - offline input files no longer just single prec --> parameter offlineLoadPrec +o verification/lab_sea: + change AD test to multi-tile setup and update all 4 AD output. + NOTE: while cost function values remain very similar, + gradients are very different, although gradient checks are self-consistent + Should try to get to the bottom of this (cost function summation order?) +o pkg/dic: + in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid + a weakness of TAF that drops part of double precision in log10 derivative. + <= changes removed since problem has been fixed in current TAF version 1.9.71 + update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo. +o pkg/ecco: + add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F + update all 4 lab_sea AD output. + +checkpoint62d (2010/03/22) +o build_options: + remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles. +o remove unbalanced quote (single or double) in commented line of source code + (may cause some warning with some preprocessor/makedepend versions). +o pkg/seaice: + fix seaice_model.F for adjoint (gael) and update AD results of experiments + lab_sea (std + evp + noseaicedyn) and offline_exf_seaice. +o testreport: + add option '-runonly' (short: '-ro') to just do the run part (without make). +o eesupp: remove JAM communication code (obsolete). +o add option to genmake2 & testreport to switch "_RS" type to "real*4" + (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return + to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1 + (update also the output). + +checkpoint62c (2010/03/02) +o tools/build_options : + move (some) old optfiles from build_options/ to build_options/unsupported/ +o model/src and pkg/exf + surface relaxation -- separating data and data.exf options + The point is to ensure that we specify the surface relaxation + either in data or in data.exf (but not half and half) and to + avoid an accidental relaxation to 0 (which happened if a time + scale was specified but the file name was left empty) +o model/src model/inc and pkg/mom_common + ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity + => addition to the viscosity field as computed by others schemes +o tools/build_options: + - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile) + but keep the former optfile for few weeks for smooth transition +o pkg/ecco + - allow user defined cost function contributions + CPP: ALLOW_USERCOST_CONTRIBUTION + USAGE: compute contributions in cost_usercost_all.F + - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. + the two options are complementary. +o pkg/smooth + - migration from contrib to the main repository + +checkpoint62b (2010/01/26) +o pkg/monitor: + - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop + (in case someone forgot to update customized pieces of code) +o nonHydrostatic: + - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested); + - add a simple 2-D experiment (short_surf_wave) to test it. +o pkg/icefront: + adding the shell of, and the hooks to, a new package that + will model melting and freezing of vertical glacier ice fronts +o momentum: + add diagnostics of momentum tendency from Hydrostatic pressure gradient + (without surf.pressure term: would need a 2nd filling since implicit term). +o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace + two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR + cannot deal with the former +o cleaning: + - remove all (except OpenAD) old TLM output from results_ad dirs. + - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R) + - comment out maskH definition (replaced by maskInC) +o pkg/monitor: + - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl + & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs. + +checkpoint62a (2010/01/15) +o model/src: + - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4) +o pkg/diagnostics: + - add optional level number diagnostics (i.e., level number to be define + explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X". + - strictly check for valid parser-code(10) ; + - check if adding diag to the list from the right place. +o pkg/longstep: + - change parameters and fix tracer conservation with rstar/nonlinear free surface +o diagnostics: + - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer + S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics. +o pkg/diagnostics: + - Add option for writing vertical integral (sum of selected levels) of an output + field instead of writing output field levels. Activate this option on a per + output-file basis, by setting the 2nd character of fileflag to 'I'. + - Add field-specific information relative to level integral in 3rd postion + of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate + vertically (x level-thickness x hFac), "r"=same but without hFac. +o do_the_model_io: + - pass end-of-model-run flag as argument, from forward_step to diagnostics_write: + in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before + writing pickups and stopping. +o pkg/diagnostics (for now, only with mdsio): + - write time information to meta file (and modify accordingly rdmds.m) : + time-averaged diagnostics output: write starting and ending time of the + time-averaging interval ; snap-shot diagnostics output remains unchanged; +o pkg/timeave: + - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously + always Nr), now assumed to be equal to number of levels of averaged field; + only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F +o pkg/sbo: + - fix ocean bottom pressure global-average & 2-D time-ave output (was + neither initialised nor filled). + - add starting iteration in suffix of global-average output file + (to avoid over-writing the file after a restart) + - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb). +o time-average: + - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj) + (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf, + ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice) + this fix DIC_COST cumulative-time array (previously: bi,bj,k) + - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice) + - fix missing accumulation for pkg/opps. + - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0) + (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81); + - fix initialisation of time-ave vars and do only full time-step increment + (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81); +o pkg/layers: + - use standard RW pkg S/R to write the output + and remove local write_fld version (which had a problem). + - use simple cumulative-time array (no level index) to fix time-ave S/R calls. + - fix LAYERS_CALC argument list. +o pkg/timeave: + - store cumulative-time in a simple tiled array (drop the level index) + - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array. +o pkg/ocn,aim_compon_interf + - changes for multi-threaded coupled run. (tested with ifort-11 on danton) + +checkpoint62 (2009/12/23) +o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output. + (was not previously tested in any other exp.) +o pkg/monitor: + - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume: + mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one + (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics. + - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F). + - change del2 calculation. + - use interior masks (instead of maskH, <- to be remove). + - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing"). +o mask & obcs: + - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S). + - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F + (called after packages_init_fixed) +o pkg/obcs: + - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once. + Fixes bug in obcs+exf with nSx*nSy.GT.1 + - fix multi-tile handling in obcs balance code +o nonHydrostatic: + - Implement AB-3 for non-hydrostatic vertical momentum ; + (change ordering of var. stored in pickup file when using NH) + - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D. + - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x + (in prep. for new NH free surface form). +o pkg/obcs: + add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe +o model/src: + fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography + +checkpoint61z (2009/12/01) +o nonHydrostatic: + Fix missing vertical flux of vert. momentum near surface (k=1). This fixes + a spurious source of energy in simple baroclinic adjusment test case. + Update all non-hydrostatic exp output. +o model/src (3-d solver): + Change again 3-D solver free-surface RHS term when exactConserv=T: + simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1 + (which was not the case with previous formulation). + To recover previous version, just reset "oldFreeSurfTerm" to previous value. + Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW. +o nonHydrostatic: + - compatible with implicDiv2Dflow < 1 ; + implement implicit factor + for Non-Hydrostatic pressure gradient (similar to implicSurfPress). + - change 3-D solver to work with r* (for now, only with linear free-surf.) + - add few debug diagnostics (cg3d_x, residual) +o model/src: + fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b). + update output of exp. global_ocean.cs32x15.viscA4 +o update output of exp. global_ocean.cs32x15.icedyn after removing + #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h +o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) +o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output + for complex grids, for now only to "state", "adstate", "adexf", "adseaice" +o model: add Christopher Wolfe's implemetation of the single reduction cg2d + (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and + runtime flag useSRCGSolver. Modify verification experiment global_with_exf + to test this code +o pkg/cd_code: + Change defaut D-grid time-stepping to get the same for D-grid momentum as for + C-grid momentum. D-grid velocity used to be stepped forward in time with + Adams-Bashforth only on surface pressure term. Tests show that using AB on + D-grid coriolis term improves stability (as expected from CD-scheme paper). + To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h). + Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2), + lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD), + tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens. + Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2, + global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD. +o pkg/obcs: + - fix bug in initialisation (broken since Oct 1rst modification) + for useOBCSprescribe without useEXF. + +checkpoint61y (2009/11/15) +o pkg/seaice + - change (once again) the discretization for the evp solver: rather than + squaring the averages of strain rates, average the squares to give + a better approximation to VP behavior (in simple test); this breaks + verification experiments that use EVP (lab_sea and lab_sea.hb87) + --> update outputs +o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit) + to improve vectorization of adjoint code on TARGET_NEC_SX +o verification/vermix: + - change vermix to a more "classical" 1d column with high vertical + resolution, seasonal heat flux forcing and constant wind forcing + --> update outputs +o pkg/seaice + - fix diagnostics of principal stress components for EVP + - add optional diagnostics of non-linear convergence for LSOR solver + - make maximum zeta a runtime parameter +o model/src (3-d solver): + Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49), + which consisted in removing the Surf. Non-Hydrostatic pressure from the + whole column and adding it to Eta (inspired from Casualli, 1999): + Only affects 3-D solver initial guess and only if using ExactConserv, + but tests did show a degradation of solver convergence. For this reason, + decide to disable this piece of code. + to recover previous version, just set zeroPsNH = exactConserv (line 78). + Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW +o pkg/ggl90: + - fix previous modif (unfortunatly has not been documented here). +o pkg/seaice/autodiff: + - add CPP flag to include clipping of zeta in EVP code; + although clipping of zeta is not necessary for EVP and not recommended + it was done by default, now clipping is disabled by default + - modify computation and store zetaC/Z in seaice_evp for TAF + - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default) + - change seaice_calc_viscosities/strainrates for better + vectorization after AD by TAF + - rearrange common blocks in SEAICE.h once again for easier dumps of + adjoint output, adjust adcommon.h and g_common.h + - change flux form of default advection scheme for better vectorization + of adjoint code + - modify lab_sea/input.lsr to test the flux form of default advection + scheme +o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level + transition in checkpoint61r) + +checkpoint61x (2009/10/19) +o adjoint: adding two new verification experiments + * tutorial_global_biogeo: an online dic sensitivity experiment + (work with G. Forget) + * tutorial_dic_adjoffline: an offline dic sensitivity experiment + (an update of the Dutkiewicz et al., 2006 paper) + Both use the same CO2FLUX cost function, but different controls + Gradient checks look good, but some recomp. could still be traightened out + Should add xx_dic control variable to test at some point +o model/src: + add run-time parameters to check and/or mask initial Temp & Salt +o pkg/ptracers: + apply zonal filter (if used) to all passive tracers + +checkpoint61w (2009/10/12) +o adjoint: + * update and finish work on adjoint of dic package (G. Forget) + * start adjoint of offline package + * bug fix for cube-sphere TLM code (active_file_g.F) +o tutorial_global_oce_optim: + now tested with 4 tiles (change data.grdchk and update output_adm.txt) + and add SIZE.h_mpi for MPI testing +o pkg autodiff + - fix bug in autodiff_restore + - make genmake2 remove comments and empty lines from ad_input_code.f in + order to reduce file size (new script file remove_comments_sed) +o allows to specify vertical profile of vertical viscosity (viscArNr) +o pkg autodiff + autodiff_ini_model_io: comment out writing of grid information to netcdf + files, because at this time the grid fields are a bunch of zeros + (this is analogous to ini_mnc_vars.F) +o pkg seaice/autodiff: + left-over from removing the 3-time-level fields: + - small rearrangement of common blocks (SEAICE.h) + - fix field declaration in order to get meaningful output in + adseaice.*.nc (adcommon.h) +o pkg obcs: + - go through NH code only if nonHydrostatic=T + - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart) + - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields + => Update output of experiment seaice_obcs + - useOBCSbalance: code is wrong with multi-tile / proc: add a stop. + - fix NH+Orlanski restart (add wvel OBC value in pickup file) + - fix restart for useOBCSprescribe + useEXF +o pkg ctrl + - make obcs as control parameter work also with useSingleCPUio + - replace a few sny and snx by Ny and Nx to be consistent with + ctrl_set_globfld_x/yz.F +o pkg seaice + - re-introduce global field frWtrAtm for the case of + ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F) + - catch the case of an empty filename in seaice_cost_init_fixed.F +o pkg ecco: + - small bug fixes in the_main_loop + . fix order of monitor arguments + . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY + . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so + that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF + - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the + imbalance diagnostics for wmean_h/sflux = 0 + - add actual values to f_obcsn/s/w/e in ecco_cost_final.F + - catch the case of empty filenames in ecco_cost_init_fixed.F + and ecco_readparms.F + - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta) + to make this statement meaningfull in ecco_cost_weights.F +o pkg zonal_filt: + - change ZONAL_FILTER S/R interface (allows to filter 2-D fields) + - when using rStar, filter uVel*hFacW instead of uVel + (tested without topography: fix a Pb of growing instability with NLFS) +o pkg/aim/thsice: + -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F + (works as SST restoring) +o pkg/thsice: + -add specific parameter for salt restoring in slab mixed-layer + (by default equal to the temperature restoring) + +checkpoint61v (2009/09/21) +o pkg/kpp: + -add double diffusive contributions as a hack, turned off by default + for now, and the code can be excluded with a CPP-flag + EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX + -add a verification experiments to "vermix" to test this code +o pkg/mom_common: + Move computation of length scales to mom_init_fixed.F (avoid recomputation + at each time-steps*levels). +o pkg/layers: + Created a new package for computing volume fluxes in temperature or + [not yet implemented] density layers, e.g. for calculating residual + overturning circulations. +o pkg/diagnostics: + implement a RS type version for the set of DIAGNOSTICS-FILL subroutines +o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option) +o pkg/mdsio (& pkg/rw): rework high level S/R interface: + To avoid mixing type (RS/RL) of input/output array argument, + replace single mixed-type array with a pair from each type (RS/RL). +o setting pickupSuff force to start from a pickup (even if nIter0=0): this + is now implemented for all pkgs (previously only done for the main pickup) + +checkpoint61u (2009/08/25) +o pkg/obcs: + - change OB?eta from _RS to _RL and put them into a separate commen block + - add code to read OB?eta from a file via obcs_prescribe_read: the code + compiles and does not destroy any other experiments, the data is read + properly, but the code is not tested in actual applications +o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to + create a meaningful unit attribute for the time coordinate variable +o pkg/ebm: add plenty of missing "_d 0" ; + update results of experiment global_ocean_ebm (fwd + adjoint tests) + Notes: several pieces of code only works for (very) specific set up + (domain size, lat range, etc ...); should be documented & stop if one + of those assumptions is not meet. +o pkg/seaice: add missing "_d 0" in HSNOW initialisation + update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests) + and offline_exf_seaice (seaicetd + adjoint). +o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC): + update results of experiments: lab_sea (4 fwd tests + 3 adjoint), + seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2). +o few changes to pass when compiling with strick checking of arguments + across S/R (allow to find few bugs in S/R calls). +o pkg/seaice: + - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new + 2d-fields, for slightly better performance + +checkpoint61t (2009/07/22) +o pkg/seaice: + - remove unused variables in seaice_evp + - reduce number of SQRT in seaice_evp and seaice_calc_viscosities +o eeset_parms.F, open_copy_data_file.F & ini_parms.F: + named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT): + each processor opens a different file (a fix from Matt). +o cg2d: + use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F : + this reduces number of EXCH calls by 2 when using exch2. + For now, keep previous size array for gc2d_nsa.F to avoid Pb with store + directives and missing simple EXCH (exch_s3d_rx) adjoint code. +o pkg/thsice: + add code for Near Infra-Red albedo (from Jeff) + (turned on with run-time flag: thSIce_calc_albNIR, in data.ice). +o ini_model_io: + move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F + MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F + to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice. + +checkpoint61s (2009/06/30) +o pkg/exch2 (exch2_rxN_cube*): + remove last BARRIER (no need to synchronise after getting data from shared + buffer (get) as long as any change to buffer (put,recv) is between BARRIER) +o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH + and generate new output (for the 2 tests) using default rotationPeriod. +o pkg/exch2: + - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F + (was already the case with AUTODIFF_EXCH2 defined) + - add bj in exch2 arrays and S/R. + - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment + MLAdjust to exch2 (identical results except with MPI -> truncation diff); +o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep + - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY + GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT + - verification experiment natl_box.longstep +o build_options: ifort+mpi_aces optfile (following Constantinos advise): + allow different versions of ifort (8 or 9) and different versions + of mpi (mpich or mpich2) to be used with the same optfile. + requires to load a netcdf module and set MPI_INC_DIR (see comments inside + optfile). Change testing scripts (example_scripts/ACESgrid) accordingly. +o pkg/seaice: + fix previous modif (3-level field removed) for old-pickup reading + +checkpoint61r (2009/06/25) +o pkg/seaice: + - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps: + 1. introduce fields for time step (N-1) + 2. do not use levels 2 and 3 anymore (but keep them) + 3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This + includes changes to pkg/thsice/thsice_get_velocity.F, + model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and + pkg/obcs/obcs_apply_uvice.F. + - completely remove code for leap-frog time stepping for second order + advection + - adjusted adjoint accordingly; + gradient checks have improved by an order of magnitude! + +checkpoint61q (2009/06/22) +o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver + - the boundary conditions along open boundaries are unclear, because the + associated masks are set to zero and are thus treated as closed when + applying the slip-boundary conditions. + - move initialisation of grid variables from seaice_init_varia to _fixed +o adding doc/diags_changes.txt +o model/src: + do_the_model_io: rename few pkg S/R which are called from do_the_model_io, + to avoid "_diags" naming if no relation to pkg/diagnostics. + ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF + file and only call PLOT_FIELD_XYZ if debugMode=T. + remove few PLOT_FIELD_XY calls outside initialisation. + remove few unnecessary BARRIER. +o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling + of salt_plume package in Southern Ocean +o pkg/thsice: + - fix hOceMxL in overlap (needed for sea-ice advection); + update output of experiment global_ocean.cs32x15.icedyn. +o pkg/seaice: + - make the (placeholder-)tracer IceAge a little more meaningful + by avoiding ridging of age due to convergent ice flow + - add diagnostics for surface temperature, atmospheric and oceanic + heat flux, and atmospheric and oceanic ice growth + +checkpoint61p (2009/06/10) +o eesupp (global_max & global_sum): + - add one more element to buffer (start at index 0) for GL_MAX/SUM output; + - remove starting & endding barrier (no longer needed) +o pkg/mdsio, writelocal: + works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined + (remove the STOP): uses shared buffer IO to store data from all threads + and then let master-thread write nThreads tiles. +o pkg/mdsio (read/write field): + - tiled IO done in 1 piece (all levels at a time); + - new header file "MDSIO_BUFF_3D.h" with 3-D buffers. + - multi-threaded: allow to read/write local (non-shared) array + (was already working with singleCpuIO ; now works also without); + => no longer needs barrier call after reading a file (added inside + mds_read/write field). + - move barrier calls outside gather/scatter_2d to mds_read/write_field +o pkg/obcs/exf + - exf_getffieldrec.F: add a few ". _d 0" and + add code to catch the case fldperiod = 0. + - obcs_precribe_read.F: change if statements so that they match + the variable type (_RL) + - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to + exf_iprec) as part of namelist EXF_NML_01 +o pkg/mdsio: + - read/write tiled (local) files: read/write 1-level tile chunk at a time + (instead of segment of length sNx); expected to speed up tiled IO. +o pkg/exch2: + - take buffer copy from/to array out of S/R exch2_send/recv into new + S/R exch2_put/get ; Exch of local variable now works with MPI+MTH + (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h). + - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get) + - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds + (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by + including Topology header file (and common blocks). + - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1); + remove 2nd exch call in exch2_s3d_rx (no longer needed). + - document S/R arg. list (+ update some comments) +o pkg/seaice: + - added SEAICE_CLIM_AIR code, which permits modulation of surface air + temperature and humidity over sea ice based on climatological values. + - clean up computation of Hibler+Bryan (1987) stress coupling for the case + of LSR (this change is expected to change the results slightly because now + it uses slightly difference moduli from the second last LSR solution, but + that is more consistent with the stress computations; this part of the code + is not tested in the verification experiments) + - fix diagnostics for flux of ice in case of B-grid + - turn strain rates eij and press into global fields within global + common block in SEAICE.h for more straighforward diagnostics + - fix diagnostics for principal stress components, press, zeta, eta + to give something meaning full +o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate + new output (all 4 tests) using default rotationPeriod. +o pkg KPP: + - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions + - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1 + and normal grid from 1 to Nr) +o Fix computations of L4rdt in mom_calc_visc.F +o eesupp: + new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg): + should be called before a "stop" if we know that all process are going + to stop; if one Proc does call this S/R, will hang in MPI_FINALISE. + +checkpoint61o (2009/05/26) +o pkg/exch2: change check_depths to issue just a warning (instead of error+stop) +o model/src/ini_curvilinear_grid.F: + compute angleSin/CosC when they are not read from a file +o pkg/seaice: + add pseudo time stepping for LSOR +o pkg/exch2: + temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW +o pkg/seaice: + Adding separate sea ice albedo, drag coefficients, and HO in Southern + Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h +o SingleCpuIO: + fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used. +o pkg/seaice: + put exchanged variable in (local) common block for MPI+Multi-Threads + to work (necessary with exch1, and for now with exch2 too). +o verification: to get more experiments tested with mpi, mth and mpi+mth, + change tiling of: + aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15, + hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope + update output of exp: + exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5), + tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod) + + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU + (note: output.txt generated on faulks using only 1 tile) +o eesupp & mdsio (SingleCpuIO): + - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time + parameter "W2_useE2ioLayOut" (read from file "data.exch2"). + Note: was not effective for globalFile & useSingleCpuIO=F; now fixed. + - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc). + - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same + gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array). +o pkg/exch2: + - new code to set-up W2-Exch2 topology (replace matlab-topology-generator): + read parameter file "data.exch2" if it exists; otherwise try default regular + cube without blank-tile; new header file "W2_EXCH2_SIZE.h"; + - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible + with new code (not to be used, just as a backup solution). + - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2" + in utils/exch2/input. + +checkpoint61n (2009/05/12) +o eesupp & mdsio (SingleCpuIO): + - move mapping to global io-buffer inside gather_2d/scater_2d: this save + memory (1 less 2D global RL array); skip 1 buffer copy; and only send/ + receive real*4 array (instead of real*8) to read/write 32.bit files. + (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S + and remove new mapping S/R) +o pkg/mdsio: in preparation for topology-generator within pkg/exch2: + - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.: + xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h + when using exch2. Add S/R to map global io-buffer to global model array. + - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt. + +checkpoint61m (2009/04/29) +o write_utils : change WRITE_1D_R8 to WRITE_1D_RL + and add 3 other S/R for other types (R4,R8,RS). + Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument. +o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros): + - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ; + - reduce number of macro definitions (keep only those which are used); + can always call directly the corrresponding S/R if needed. + - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix + _R4/_R8 to _RS/_RL when applied to _RS/_RL variable. + Fixed wrong type of arg in: + atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F + ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F + To fix: global_sum of var in common block is wrong (multi-threaded) in: + dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F + To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops) +o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd + "nlfs" mpi test is going to stop when checking for unconnected tile egdes. +o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error +o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile + edges are closed (zero depth); might happen with "blank tiles"; + for now, disabled if using OBCS. +o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi": + link *_mpi files from "MODS" dir) to return to a strait-forward behavior. +o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D) + to reduce length of 1.D array print in STDOUT. +o adjustment.cs-32x32x1: changed to oceanic test with 1 continent + + use 48 tiles (16x8): this will allow to test "blank tiles". +o start to test MPI + multi-threaded (change testreport to skip tests + where number of tiles do not match). +o genmake2: add option "-omp" to turn on Open-MP ; + passed to testreport (if using -mth) ; merge few (*+mth) optfiles. +o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them) + and keep the original tile numbering. Note: compatible with old + W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files. + +checkpoint61l (2009/04/07) +o Overlaps had been forgotten in calculating ijk keys : fixed +o fix cyrus makedepend for gcc 4.4 +o experiment fizhi-cs-aqualev20: + switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE) + and generate new output. Note: new output is much closer to the old + one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from + the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007. +o pkg/fizhi: + - change to avoid indices going deliberately over array-bounds + - remove unnecessary MPI stuff + - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY" + - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE: + does not go over array-bounds and therefore returns reliable output. + - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls: + this S/R has 4 output arguments, which are used inside "get_alarm"; + when it is called with the same variable "ndum" in place of several + output arguments, this produces weird side effect inside "get_alarm" + (e.g., datein=dates(n) is overwritten by timein=times(n) since both + datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum" + address) and produces error. +o tools/gemake2: (March 27-29 2009) + with option "-mpi": link *_mpi files from "MODS" dir (this is what + testreport does). +o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output +o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F: + update lab_sea.lsr & lab_sea.salt_plume results +o pkg/seaice: + Major overhaul of the LSOR solver: change discretization from original + finite differences to finite volume. The old routine is still in the + file seaice_lsr.F and can be turned on with the CPP-flag + SEAICE_OLD_AND_BAD_DISCRETIZATION + Along with this change, the discretization of the strain rates is changed. + The same flag turns on the old discretization in seaice_calc_strainrates.F + All verification experiments with seaice are affected (except for + seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old + results by setting the above flag. + Further changes involve changes in defaults: + - ALLOW_FLOODING is defined and turned on by default + - SEAICEadvSnow = .true. is now the default + - SEAICEadvSalt = .true. is now the default + - SEAICEadvAge = .true. is now the default + - SEAICE_clipVelocities = .false. is now the default + (as per J. Zhang's recommendation) + - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE + is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS + - seaice_growth: replace computation of UG by a simple copy from wspeed + +checkpoint61k (2009/03/18) +o pkg/seaice: a few bug fixes mostly concerning the metric terms: + seaice_lsr: fixed a few metric terms, + affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs + add more debugging diagnostics + seaice_evp: removed superfluous many metric terms of FV discretization + of stress divergence + affects lab_sea, lab_sea.hb87 + seaice_ocean_stress: removed superfluous many metric terms of FV discretization + of stress divergence for non-evp solver + (this part is not tested anywhere) + seaice_calc_strainrates: fixed a bug in no-slip boundary conditions, + they were effectively only half slip + affects lab_sea.hb87 + updated all relevant verification experiments (except lab_sea//output_adm.txt + which was left over, but fails at level 7 & 6) + +checkpoint61j (2009/03/17) +o pkg/seaice: turn a few hard wired parameters into run time parameters +o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model + time in seconds as promised by the usints in seaice_monitor and exf_monitor +o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids + that are not cubed-sphere grids +o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR +o pkg/ctrl: + fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low) +o non-hydrostatic (calc_gw.F): + fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec + update output of exp. global_ocean.cs32x15.viscA4 +o remove backward compatibility for thetaMin,phiMin + (replaced by xgOrigin,ygOrigin on Jan 27, 2009) +o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the + interpolated wind field not only for curvilineargrid=.true., but also + for a rotated grid (rotateGrid=.true.) +o pkg/exf: add capability to bypass interpolation for runoff + by setting yet another CPP-flag +o eesupp/src, B-grid exchange: + add simple (6 tiles, non MPI) CS exch + standard interface S/R. +o autodiff + new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV + allows to switch to single-prec common blocks; + corresponding switch occurs in tamc.h, integer isbyte + TAF store directivs "byte" and "kind" seem equivalent; + Most tamc.h have been updated correspondingly. + +checkpoint61i (2009/02/13) +o autodiff: + fix autodiff_sore/_restore indices for obcs + (spotted by I. Hoteit, M. Mazloff) +o pkg/autodiff, pkg/ctrl: + Add flag to reduce all tapelev I/O to single-prec. + In data.ctrl set + doSinglePrecTapelev = .TRUE. +o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2: + check in hack for SX8 compiler (for dxV, dyU); remove it afterwards. +o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for + real fresh water flux (not yet) +o pkg/mdsio & rw: + - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta) + - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX. +o pkg/flt: + - replace FLT_INIT by 3-steps standard initialization S/R: readparms, + init_fixed & ini_varia. + - clean-up & simplify linear interpolation S/R: + move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid. + - fix some indices (mainly vertical index) ; add IMPLICIT NONE. + - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R. + - add vert. coordinate & horiz. indices to output files. + - change vertical position in initial condition, from index to depth [m]. + - store horizontal (decimal) indices i,j in common block (instead of coord. x,y) + (easier to get to a curvilinear grid) ; delX,delY no longer used. +o pkg/ggl90: a few modifications: + - fix bottom boundary condition, and interpolation of KappaE + near top and bottom + - use same set of viscosity/diffusivity for TKE/momnetum/tracer + - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH) + - add a few options for mixing-length upper limit (--> mxlMaxFlag) +o rename thetaMin,phiMin -> xgOrigin,ygOrigin + (maintain temporary backward compatibility, until next checkpoint) + +checkpoint61h (2009/01/27) +o pkg/diagnostics with "periodic averaging diagnostics": + fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. +o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82 +o pkg/obcs: fix loop ranges for balancing code +o pkg/flt: + - improve criteria for finding which tile owns a float. + - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case. +o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg + aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling + with ocean biogeo) +o pkg/flt: + - do some cleaning and fix the restart ; + - add output.txt in flt_example/results to get this pkg tested. +o genmake2: add an EXTENDED_SRC option and flag. + for now, cannot be turned on on command line (only through genmake_local) +o pkg/mdsio: read/write vector: + - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS + - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR + & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. + - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) + (drop to 4 digits matching for grad). But this test does not look very + reliable (was already failling on eddy, fc5, at 6.digits). Update output. + +checkpoint61g (2008/12/29) +o pkg/flt: + - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) + + make OPTIONS file more standard. + - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) + - fix _BYTESWAPIO CPP-Flag + - standard reading of file-parameter "data.flt" + - fix argument list of S/R FLT_RESTART + still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F +o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell +o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to + a still unfixed compiler/optimization bug + +checkpoint61f (2008/11/21) +o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; + update results of global_ocean.cs32x15.icedyn test. +o move getcon.F from model/src to pkg/fizhi. +o pkg/exf: add parameter for extrapolation of temp up to the surface + and option to prevent negative evap (in bulk_largeyeager04 only). +o Prather Advection scheme: fix tracer conservation for divergent flow + (e.g., when using NonLin Free-Surface). +o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead +o gmredi (Visbeck-variable-K): + - add more parameters to Visbeck-variable-K. + - use a 5 points average for dSigmaR in Visbeck-K calculation + (more "homogenous": same stencil and same weights as in dSigmaH) + - update output of ideal_2D_oce experiment. +o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 + (#undef REAL4_IS_SLOW) + - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 + coordinate variable + - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables + (surface forcing fields), removes some of the functionality + - model/src/write_grid.F: write _RS variables as RS-netcdf variables + - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but + probably not all: copy _RS surface flux fields to RL field before + calling DIAGNOSTICS_FILL + - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into + real*4 (CALL EXCH_*_RS) versions. + - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 + (generate new output). + +checkpoint61e (2008/10/23) +o gmredi (Visbeck-variable-K): + - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h + - change computation of Visbeck-K where Slope > Smax : + now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct) + previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output. +o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic + to be the same as with Z-coord. (i.e., m/s & no-units respectively). +o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc) +o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz + does not become too large (to avoid precision problems in implicit-diffusion + solver); update ideal_2D_oce output. +o pkg ggl90: + - in ggl90_cal.F: compute only one set of visc/diff, used to + step forward TKE/T/S/momentum + - default value of GGL90viscMax/GGL90diffMax larger and equal (to + have Prandlt =1) +o gmredi (fm07): + - add lower limit on Transition layer thickness + lower limit on 1/lambda + - allow to set few more params from data.gmredi +o pkg ggl90: + - add missing sqrt(2) factor in computation of mixing length + scale in ggl90_calc.F + (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) + +checkpoint61d (2008/09/25) +o adjoint modifs + - adapt to new field rhoInSitu + - allow to revert from StoreDynVars2D, StoreDynVars3D + to individual fields + (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) +o store 3-D (in-situ) density in commom block (DYNVARS.h) + - save 1 rho computation. + - no longer modify T & S inland when using down_slope pkg. +o gad_som : allow to switch to SOM advection for T & S without corresponding + pickup files (using new S/R: MDS_CHECK4FILE). +o keep removing _BEGIN/_END_MASTER between MDSIO S/R call + (for useSingleCpuIO to work in multi-threaded) +o pkg/shelfice: + - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute + with SHELFICEtopoFile in data.shelfice + - move code for reading ice shelf topography and modifying hFacC into separate + subroutines of the shelfice package + - separate initialisation of "fixed" and "variable" variables + - kTopC is not (yet) replaced by kSurfC, although this is possible +o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s +o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) + and rename: + ini_phiref.F --> set_ref_state.F (+ set anelastic factors) + ini_reference_state.F --> load_ref_files.F (- set anelastic factors) +o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) + +checkpoint61c (2008/08/30) +o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" + to add mass source/sink of fluid in the interior (3-D generalisation + of oceanic real-fresh water flux). +o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) +o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) +o new pkg: down_slope + density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). + - presently, modify T & S inland (dwnslp_calc_rho.F). + can be avoided if rho was stored in common bloc and used in calc_phi_hyd. + - implementation for ocean in P-coords not tested. + - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. +o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) + (to facilitate conversion of oceanic pkg to p-coordinate). +o change FIND_RHO to FIND_RHO_2D : + pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. +o new pkg: cheapaml + +checkpoint61b (2008/08/05) +o exch2: + change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) + - no longer depend on the order sequence (N,S,E,W). + - 3rd exchange no longer needed (tested with 24 tiles). + - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) + - exch_UV_A-grid readily available (but not yet tested). + comment out 3rd exch call and remove copy of V to U at SE & NE face-corners + (both are no longer needed) in exch_uv: no effect in forward run; but + get truncation error differences with adjoint exch. +o exch2: + - change index-bounds storage (moved from target to local tile, + more intuitive this way) ; rename/remove some variables. + - change utils/exch2/matlab-topology-generator & code_mods accordingly. + +checkpoint61a (2008/07/29) +o exch2/matlab-topology-generator: + fix bug in index bounds for N-S internal exchange (hard to tell if this + had any effect on the solution). +o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf + is exceeded +o testreport: modify syntax of awk, so that it works also with + awk, and not only with nawk and gawk + +checkpoint61 (2008/06/24) +o autodiff + Change default for TAF usage by removing argument '-nonew_arg' + This changes TAF subroutine argument list (ordering of active var.) + Omission of this flag leads to incompatibility w.r.t. TAMC + To restore TAMC-compatibility, need following modifs: + * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility + * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY + Tested TAF version is 1.9.22 + N.B.: exch2 hand-written adjoint code currently not TAMC compatible + +checkpoint60 (2008/06/19) +--->>> This is the last checkpoint for which generating the adjoint +--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" +--->>> by default. +--->>> Future checkpoints will ommit this flag by default. +o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. +o pkg/grdchk: Add gradient check to etan0 perturbations. +o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). +o pkg/autodiff: more flexibility in zeroadj. + model/src: modifying do_oceanic_phys.F accordingly. +o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. +o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option + special setup of gmredi for which the adjoint is stable + enough for parameter optimization. +o bridging the gap between eddy stress and GM. + -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) + along with a change in CPP option (now ALLOW_EDDYPSI). + -> when using GM w/ GM_AdvForm: + The total eddy streamfunction (Psi = eddyPsi + K x Slope) + is applied either in the tracer Eq. or in momentum Eq. + depending on data.gmredi (intro. GM_InMomAsStress). + -> ALLOW_EDDYPSI_CONTROL for estimation purpose. + The key modifications are in model/src/taueddy_external_forcing.F + pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F + +checkpoint59r (2008/05/29) +o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array + from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); + fix option to read coriolis(@ cell-corner) from files with CS-grid. +o pkg/mnc: add some attributes to standard 1D-coordinate variables +o pkg/diagnostics: enforce missing_value attribute for scalar variables at + mass points, when using mnc for output + - add runtime parameter (missing_value, missing_value_int) to override + default (which is the value of getcon('UNDEF')) +o pkg/mnc: prepare mnc for the actual use of missing values with the + diagnostics package: small fix in mnc_cw_readwrite.template and more + initialisation of never used fields + - replace mnc_common.h and mnc_id_header.h with corresponding upper case + versions +o pkg/thsice/thsice_ini_vars.F added default initial values so that + thermodynamics sea ice solver does not blow up when some initial fields + are missing. +o move from external_forcing_surf.F to ini_forcing.F + the p-coord. hack consisting in using pLoad to set phi0surf ; + update output of tutorial_global_oce_in_p (affected @ truncation level). +o Freshen up a bit hs94.1x64x5, notably: + remove rotationPeriod and tRef=5*0. (adjoint only), and add + exactConserv=.TRUE. o pkg/generic_advdiff: change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only applies to files where Temperature & Salinity 2nd Order moments are used. @@ -12,7 +1321,7 @@ (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) and requires a fortran 90 compiler -checkpoint59q +checkpoint59q (2008/05/06) o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) o Refresh tutorial_global_oce_biogeo, notably: @@ -47,7 +1356,7 @@ - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice -checkpoint59p +checkpoint59p (2008/04/10) o gchem / dic / cfc : - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); - add new parameter files: "data.dic" & "data.cfc" ; @@ -73,7 +1382,7 @@ bottom ; only used with variable horizontal viscosity and non-hydrostatic. also fix diagnostics VISCAHW & VISCA4W. -checkpoint59o +checkpoint59o (2008/03/07) o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). o change the loop ordering in most gad_*_adv_x.F to improve vectorization: move a few statemens out the main loop into separate loops @@ -114,7 +1423,7 @@ introducing a generic routine (ctrl_map_ini_gen.F). - Modification of ctrl_bound/adctrl_bound handling control vector bounds. -checkpoint59n +checkpoint59n (2008/02/09) o pkg/diagnostics: for large number of diagnostics, store diagnostic mate number in dedicate array "hdiag": - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST @@ -168,7 +1477,7 @@ for now this is only available for the C-grid code and also within #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code -checkpoint59m +checkpoint59m (2008/01/14) o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature o gad_som : fix flux output (& diagnostics) to have same units as other @@ -186,7 +1495,7 @@ o pkg/salt_plume: added various options for salt plume depth criterion and for vertical distribution of the salt -checkpoint59l +checkpoint59l (2007/12/18) o pkg/ptracers: new version of ptracers pickup: read meta file and write only fields which are needed to restart. ( same logic as main pickup file ; also using pickupStrictlyMatch ) @@ -208,7 +1517,7 @@ o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL or U/VICE from U/VWIND before computing U/VSTRESS -checkpoint59k +checkpoint59k (2007/11/30) o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. o fix un-initialised variable problem (in mom_vecinv & shap_filt): @@ -230,7 +1539,7 @@ use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). to-do: fix pkg/diagnostics when large number of diagnostics are defined. -checkpoint59j +checkpoint59j (2007/11/09) o in pkgs: dic, obcs, offline, rbcs: standard way to compute coeff. for time interpolation between 2 time reccords which retains full precision (& make results less dependent on compiler). @@ -273,7 +1582,7 @@ o added open boundary conditions capability for seaice HSNOW, HSALT, UICE, and VICE -checkpoint59i +checkpoint59i (2007/10/21) o adjoint: * fix multiDimAdvection adjoint (partial recomputation problem by TAF for fVerT(:,:,kDown) @@ -314,7 +1623,7 @@ Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). -checkpoint59h +checkpoint59h (2007/09/29) o pkg/exf: - improve vectorization by moving if-statement out of loops in exf_mapfields, exf_radiation @@ -347,7 +1656,7 @@ o testreport: change AD testing : check against results/output_adm.txt using same scripts as for forward test. -checkpoint59g +checkpoint59g (2007/09/17) o adjoint testing: in preparation for changing testreport: - output format: cost and grad written on separated lines - ad output results in directory "results" (instead of "results_ad") @@ -392,7 +1701,7 @@ global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. -checkpoint59f +checkpoint59f (2007/08/21) o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) o pkg/ctrl: ctrl_bound forces parameter corrections to stay in a bounded range (in forward mode) @@ -423,7 +1732,7 @@ o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update output of global_ocean.cs32x15.thsice . -checkpoint59e +checkpoint59e (2007/07/26) o exch2: new S/R that only use the cube-tracer (center-position) exchange: for B-grid vector (not yet tested) and C-grid vector (<- only used when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). @@ -453,7 +1762,7 @@ * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option * applied OBCS T/S mask to HEFFM sea ice mask -checkpoint59d +checkpoint59d (2007/06/21) o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array for {PKG} state variables, and called from DO_STATEVARS_DIAGS. (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) @@ -499,7 +1808,7 @@ It is turned off by default (=-1.), because it changes the results. - make it possible to read AREA from a file, too. -checkpoint59c +checkpoint59c (2007/06/04) o add S/R and diagnostics for oceanic mixed-layer depth o move GMRedi call after all vertical mixing schemes (including KPP) o pkg/thsice: @@ -532,7 +1841,7 @@ Storing is now bundled into large arrays to optimized I/O (and second step in cleanup of the_main_loop) -checkpoint59b +checkpoint59b (2007/05/16) o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): - export/import (between ocean & coupler) fields needed for ocean DIC. o pkg/seaice: @@ -603,7 +1912,7 @@ o OpenAD - changed verification/OpenAD to full baroclinic setup (including GM/Redi) -checkpoint59a +checkpoint59a (2007/05/01) o pkg/seaice: some parameter clarifications and a little bit of clean up o pkg/thsice: rename run-time parameters: himin -> hIceMin @@ -645,7 +1954,7 @@ o pkg/kpp: add code to have mixing in shelf ice caverns - add myThid to all kpp routines (long overdue) -checkpoint59 +checkpoint59 (2007/04/19) o pkg/exf: - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND & ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid @@ -671,7 +1980,7 @@ - 2nd set of modifs for thsice adjoint in conjunction with exf o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.) -checkpoint58y_post +checkpoint58y_post (2007/04/15) o Added capability for latitudinal dependence of Bryan and Lewis, 1979 vertical diffusivity, similar to that in MOM4; turned on using #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using @@ -687,7 +1996,7 @@ - better when using non-linear advection scheme (not yet fully tested) - can also be used in atmospheric set-up (for now, only the diffusion). -checkpoint58x_post +checkpoint58x_post (2007/04/04) o IO option for global-file compact format: - add options when generating topology (utils/exch2/matlab-topology-generator) - add I/O capability (pkg/mdsio). @@ -695,7 +2004,7 @@ for now long-line format not yet supported by pkg/mdsio (& exch2). o shelfice: add a few diagnostics -checkpoint58w_post +checkpoint58w_post (2007/03/13) o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref (and replace horiVertRatio in NH code). @@ -716,7 +2025,7 @@ o move call to cal_readparms up to make calendar parameters/variable available to all packages -checkpoint58v_post +checkpoint58v_post (2007/02/08) o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get useDynP_inEos_Zc tested. o pkg/exf: changes to properly interpolate/mask/scale initial fields @@ -735,7 +2044,7 @@ - use this scheme for temperature & salinity in 2 advection test exp.: advect_xy & advect_xz, respectively. -checkpoint58u_post +checkpoint58u_post (2007/01/12) o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. o testreport: add option "-skipdir" to skip some test. @@ -750,7 +2059,7 @@ o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine o pkg/thsice: fix reading mnc-pickups -checkpoint58t_post +checkpoint58t_post (2006/12/30) o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) o pkg/mdsio: - clean-up mdsio_readfield.F & mdsio_writefield_new.F and @@ -793,7 +2102,7 @@ - introduce a few local fields to avoid modifying external fields such as atemp, etc. -checkpoint58s_post +checkpoint58s_post (2006/12/11) o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F changed exf_set_gen.F so that genperiod=0 means input file is one time-constant field and @@ -827,7 +2136,7 @@ as actual snow thickness. It now refers everywhere to effective snow thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. -checkpoint58r_post +checkpoint58r_post (2006/11/17) o modifications to pkg/seaice/growth.F, which change results of lab_sea experiment: fixes pertain to melting snow over open water, to masking EVAP under sea ice, and to using the correct AREA variable for @@ -851,7 +2160,7 @@ o ctrl: adding new control variables: lwflux, lwdown, evap, snowprecip, apressure, runoff -checkpoint58q_post +checkpoint58q_post (2006/10/20) o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up 1/6-deg Southern Ocean configuration by 8% on IBM Datastar and high_res_cube configuration by 4% on Columbia. @@ -862,7 +2171,7 @@ single CPU io) so that TAF does not have to see EESUPPORT.h o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) -checkpoint58p_post +checkpoint58p_post (2006/09/08) o obcs: stop if obcs is used with useCDscheme = .true. o shelfice: - fix a sign error so that no slip at shelfice interface works @@ -873,7 +2182,7 @@ o added adjoint exch routined for all exch*3d* routines and updated flow directives -checkpoint58o_post +checkpoint58o_post (2006/08/28) o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; remove old subroutines (_XY_ & _XYZ_); update the adjoint version. o change controling S/R for writing pickup file (new S/R do_write_pickup) @@ -887,7 +2196,7 @@ - add a simple boundary layer scheme to reduce noise - fix the indexing in shelfice_u/v_drag so that there will be actually drag -checkpoint58n_post +checkpoint58n_post (2006/08/14) o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to local variable (not in common block). o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. @@ -908,7 +2217,7 @@ and stop cleanly when MAX_NO_THREADS is too small. o add S/R BAR_CHECK to check multi-threaded barrier synchronization -checkpoint58m_post +checkpoint58m_post (2006/07/17) o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. @@ -934,7 +2243,7 @@ update rotating_tank results, but not plume_on_slope (affected at truncation level, 11 digits). -checkpoint58l_post +checkpoint58l_post (2006/07/12) o calc_gw: - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V - remove side-drag for now (need to fix it); update plume_on_slope results. @@ -952,7 +2261,7 @@ o pkg/rbcs * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing -checkpoint58k_post +checkpoint58k_post (2006/07/06) o testreport: - always build in dir. "build" (if not there, mkdir build instead of building & running in input) @@ -985,7 +2294,7 @@ advection subroutine (but still not used within DST advection S/R) o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) -checkpoint58j_post +checkpoint58j_post (2006/06/15) o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields from file (collects calls previously in FORWARD_STEP) o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS @@ -993,7 +2302,7 @@ o genmake2 replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. -checkpoint58i_post +checkpoint58i_post (2006/06/14) o pkg/seaice: add parameter that allows to scale/turn off effect of seaice on wind stress (SEAICEstressFactor defaults to 1.) o Total number of Timers is finite (<=40): comment out 2 non-essential one @@ -1007,7 +2316,7 @@ non-EVP pickup files when using SEAICEuseEVP - fix sign error in diffusion in seaice_calc_rhs -checkpoint58h_post +checkpoint58h_post (2006/06/07) * Modifications for bottom topography control o replace hFacC by _hFacC at various places o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL @@ -1017,7 +2326,7 @@ o works for 5x5 box, doesnt work for global_ocean.90x40x15 * Adding verification for 5x5 box (4-layer) bottom topography control -checkpoint58g_post +checkpoint58g_post (2006/06/07) o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., used for mean seasonal cycle, mean diurnal cycle); add an example in verification/global_ocean.cs32x15/input.thsice/data.diagnostics @@ -1033,7 +2342,7 @@ o pkg/seaice - make (default) second order advection a bit less confusing? -checkpoint58f_post +checkpoint58f_post (2006/06/05) o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice to pkg/seaice): - new routines thsice_map_exf and thsice_get_exf provide the interface @@ -1064,7 +2373,7 @@ o results_ad : rename "output.txt_adm" to "output_adm.txt" and change testreport accordingly -checkpoint58e_post +checkpoint58e_post (2006/05/17) o SEAICE_CGRID adjoint done o R_STAR adjoint implemented. * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) @@ -1072,7 +2381,7 @@ o Make pkg/profile fully independent of ecco,cost, etc. stuff to be able to use it in pure forward. -checkpoint58d_post +checkpoint58d_post (2006/04/21) o upgrade simple test-experiment to tutorial example: step.1: duplicate the experiment and (step.2) will remove the old copy. tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) @@ -1112,7 +2421,7 @@ o Benign bug fix in initialization (spotted by M. Mazloff) of ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F -checkpoint58c_post +checkpoint58c_post (2006/03/23) o adjoint: finish NLFS adjoint and provide reference output in verification/global_ocean.90x40x15/results_ad_nlfs o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the @@ -1146,7 +2455,7 @@ + move computation of the viscosities eta and zeta into a new separate routine (because I need to recompute them in seaice_ocean_stress.F) -checkpoint58b_post +checkpoint58b_post (2006/03/13) o AIM+thSIce: fix sign of Short-Wave through the Ice ; update output.txt of exp. aim.5l_cs.thSI o various mnc cleanups and improvements: @@ -1209,7 +2518,7 @@ (turn on with SEAICEuseFluxForm) - replace 1 in 3d global fields by kSurface in growth.F -checkpoint58a_post +checkpoint58a_post (2006/02/13) o seaice: - bug fix in advect.F o shelfice: @@ -1262,7 +2571,7 @@ and parameters (note: calcWindStress replaces .NOT.readwindstress). - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). -checkpoint58 +checkpoint58 (2006/01/12) o add "--embed-source" option to genmake2 which, when the supporting tools can be compiled (as determined by genmake2) will turn on the embed_files package which then embeds the entire MITgcm source code @@ -1275,7 +2584,7 @@ * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) * Thanks to Tom Haine for testing! -checkpoint57z_post +checkpoint57z_post (2005/12/31) o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): affects output (@ truncation level) of exp. plume_on_slope ; updated. o fix the pickup behavior for obcs in combination with ptracers @@ -1306,13 +2615,13 @@ * Absolute scale somewhat unclear so far * no area weighting was included since no other cost term does so far -checkpoint57y_post +checkpoint57y_post (2005/12/08) First step for a NLFS adjoint o initially suppress rStar (new flag DISABLE_RSTAR_CODE) o new init. routines for calc_r_star, calc_surf_dr o still need to deal with ini_masks_etc o testreport seemed happy -checkpoint57y_pre +checkpoint57y_pre (2005/12/08) o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) @@ -1321,7 +2630,7 @@ o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should be in GCHEM_OPTIONS). -checkpoint57x_post +checkpoint57x_post (2005/12/04) o fix testreport Pb in multiple test experiment. o cleanup our namelist syntax in verification: - make it more F95 standards compliant (some work still needed) @@ -1341,7 +2650,7 @@ (there are a number of extensive recomputations) * Initialize certain variables needed for adjoint -checkpoint57w_post +checkpoint57w_post (2005/11/03) o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names fix the singleCpuIO RS version of MDSWRITEFIELD and add a WARNING if using globalFiles=T with multi-processors. @@ -1358,7 +2667,7 @@ ptracers in a large domain with a constant non-zero value. Also, untangle ptracers_init.F a little. -checkpoint57v_post +checkpoint57v_post (2005/10/13) o change dome exp. to use variable viscosity in side-drag terms. o remove all the files from the cfc_offline test since they are now incorporated into tutorial_cfc_offline which has been producing @@ -1399,7 +2708,7 @@ o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ truncation level) 4/5 MLAdjust test results (11&12 digits match). -checkpoint57t_post +checkpoint57t_post (2005/10/03) o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get same truncation, independent of the face number: affects affects several @@ -1422,7 +2731,7 @@ Suggested values of viscosity parameters found in mom_calc_visc. Many new viscosity diagnostics available. -checkpoint57s_post +checkpoint57s_post (2005/09/20) o Add clearing-house for viscosity calculations, mom_calc_visc and correct numerous bugs in LeithD and Smagorinsky discretizations. mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be @@ -1448,7 +2757,7 @@ and works with both EXCH1 and EXCH2 (but needs more testing) - writing works for all verification test cases w/ g77 on Linux -checkpoint57r_post +checkpoint57r_post (2005/09/07) o make MNC variable initialization happen earlier o add diagnostics for (almost) each term of the momentum Eq. o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. @@ -1468,7 +2777,7 @@ o natl_box_adjoint input_seaice for Lab. Sea now available online via wget (see README file) -checkpoint57q_post +checkpoint57q_post (2005/08/19) o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) o fix annoying months-old bug in mnc/mdsio output for seaice pkg - bug was reported by Jean-Michel and Ian Fenty @@ -1485,7 +2794,7 @@ * verification/OpenAD/code/ has necessary scripts and description; * converts, compiles and runs successfully; -checkpoint57p_post +checkpoint57p_post (2005/08/01) o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED (already the case for some pkgs, including recent MNC_init, e.g. thsice) @@ -1499,7 +2808,7 @@ global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). -checkpoint57o_post +checkpoint57o_post (2005/07/30) o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and (2) its ready to be documented during the 20050801 DocFest o MNC-ify the gmredi package -- tested and works w/ and w/o mnc @@ -1508,7 +2817,7 @@ in global1x1_tot/code_seaice_adj to access indices 32, 33 (worth another tag) -checkpoint57n_post +checkpoint57n_post (2005/07/29) o adding precip control xx_precip 32 o adding swflux control xx_swflux 33 o Replacing 10 forcing penalty cost routines by 1 generic. @@ -1524,13 +2833,13 @@ (applies in particular to tapelev I/O) o removed inefficient K-loop in all active_file*control*.F -checkpoint57m_post +checkpoint57m_post (2005/07/28) o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) and advect_cs (use EXCH-2 and standard cs-32 grid files). o pkg/exch2: filling of face-corner halo regions is optional (ifdef W2_FILL_NULL_REGIONS) and is turned off by default. -checkpoint57l_post +checkpoint57l_post (2005/07/14) tag before updating tutorials (pre-release-2) o add cos & sin of grid-direction orientation angle (curvilinear grid only, for output and interpolation of input fields onto model grid) @@ -1542,11 +2851,11 @@ o add mnc output capability to diagnostics/diagstat and update our cvsignore files for the ACSII output generated -checkpoint57k_post +checkpoint57k_post (2005/07/02) o lab_sea now uses diagnostics package and provides a suite of new EXF diagnostics output. -checkpoint57j_post +checkpoint57j_post (2005/06/30) o exf * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); @@ -1576,7 +2885,7 @@ o fix few little things to avoid floating error with -ftrapuv (ifort v9) (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) -checkpoint57i_post +checkpoint57i_post (2005/06/19) o Diagnostics package was changed: diagnostic allocation is now deactivated by setting an empty file name in the namelist (used to be by setting 0 frequency) o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; @@ -1595,7 +2904,7 @@ tested against monitor output (including land & thSIce) on various exp. o make seaice-pkg I/O type flags (MNC/MDS) more standard. -checkpoint57h_done +checkpoint57h_done (2005/05/19) tag after changing user customized files (DIAGNOSTICS_SIZE.h, data.diagnostics, data.gchem, data.ptracers) is done. @@ -1604,11 +2913,11 @@ o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE and rename it: DIFFERENT_MULTIPLE -checkpoint57h_post +checkpoint57h_post (2005/05/14) o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers o pkg/diagnostics: change output frequency, now in seconds (instead of Nb of iterations). This requires to change data.diagnostics. -checkpoint57h_pre +checkpoint57h_pre (2005/05/12) o in mnc, let the user create the output dir if both mnc_outdir_date and mnc_outdir_num are false @@ -1622,11 +2931,11 @@ o fix mnc flags in pkg/seaice so that they are "owned" by seaice, not mnc -- this mistake was found by JMC and is now corrected -checkpoint57g_post +checkpoint57g_post (2005/04/15) o add Adams-Bashforth 3rd Order time stepping: - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... -checkpoint57g_pre +checkpoint57g_pre (2005/04/15) o make lambda[Theta,Salt]ClimRelax spatially varying (default remains spatially uniform constant based on tau) @@ -1636,12 +2945,12 @@ o separate masks used for ctrl_pack/unpack 'from write_grid' output (suggested by G. Forget) -checkpoint57f_post +checkpoint57f_post (2005/04/06) o add parameter "baseTime" = model base time = time at iteration zero new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to account for baseTime shift o move Coriolis arrays from PARAMS.h to GRID.h -checkpoint57f_pre +checkpoint57f_pre (2005/04/06) o mnc-ifying the seaice package o introduced an alternative length scale calculation for use in the limiting @@ -1662,7 +2971,7 @@ * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 * mom_vi_hdissip: to be able to use Leith scheme in adjoint -checkpoint57e_post +checkpoint57e_post (2005/02/28) o Adding eddy stress controls a la Ferreira et al. checkpoint57e_pre (actually was tagged: eckpoint57e_pre) @@ -1680,7 +2989,7 @@ o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) -checkpoint57d_post +checkpoint57d_post (2005/02/11) o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing o modify verification/ideal_2D_oce so that it tests the creation of mnc output from the diagnostics package @@ -1702,10 +3011,10 @@ (note: still needs some work specially for snap-shot diagnostics) duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z -checkpoint57c_post +checkpoint57c_post (2005/01/27) o Change testing option (-ieee) to get closer agreement between g77 & ifort o generate new output.txt files on faulks with g77 & the new -ieee option -checkpoint57c_pre +checkpoint57c_pre (2005/01/27) o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); update output.txt of exp. global_ocean.90x40x15 @@ -1738,7 +3047,7 @@ * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F * N.B.: leave tiled I/O for tapelev (i.e. mds...vector) -checkpoint57b_post +checkpoint57b_post (2004/12/20) o simplify options in diagnostics_fill arguments (remove weird combinations) o fix MNC coordinate variables so that they now contain per-face index values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in @@ -1784,16 +3093,16 @@ look through the short list of active diag. (instead of the long list) create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active -checkpoint57a_post +checkpoint57a_post (2004/12/10) o this set of changes restores TAMC compatibility tested for global_ocean.90x40x15 adjoint on trough (what a pain) -checkpoint57a_pre +checkpoint57a_pre (2004/12/10) o some modifs in tools/build_options for sunos o call ctrl_pack for ctrl at end for optimcycle=0 -checkpoint57 +checkpoint57 (2004/12/09) o add horizontal bi-harmonic viscosity for vertical velocity - new parameter viscA4W (defaults to viscA4) - affects only non-hydrostatic code @@ -1811,7 +3120,7 @@ o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) (theta2, salt2 in ecco_cost_weights) -checkpoint56c_post +checkpoint56c_post (2004/12/03) o OBCS as control variables - update ctrl_ad_diff.list, obcs_ad_diff.list - remove balance of obcs controls from default @@ -1829,7 +3138,7 @@ o mdsio: - i/o-vector change debugLevel from debLevA to debLevB -checkpoint56b_post +checkpoint56b_post (2004/12/01) o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that is called from DO_THE_MODEL_IO - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE @@ -1844,7 +3153,7 @@ testreport. o ptracers_monitor: bug fix for MPI -checkpoint56a_post +checkpoint56a_post (2004/11/28) o GCHEM: finish reorganizating the package - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency (introduces another 3D-array for each passive tracer, but only if @@ -1889,7 +3198,7 @@ - cleaning up o small cleaning of exch2: remove files that are also in eesupp/src -checkpoint56 +checkpoint56 (2004/11/17) o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 o mnc: cleanup "full" files--fixes out-of-memory problem o ECCO-GODAE @@ -1919,7 +3228,7 @@ o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] from sign change -checkpoint55j_post +checkpoint55j_post (2004/11/10) o isolate dissipation tendency (allow to keep it out off AB) in V.I form. affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) o add consistent build directories and .cvsignore files to verification @@ -1930,7 +3239,7 @@ o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) -checkpoint55i_post +checkpoint55i_post (2004/10/28) o change arrays for total vertical diffusivity (2.D if explicit, 3.D if implicit) ; each ptracer uses its own background value. o added mnc/NetCDF output capability to ocn_compon_interf @@ -1945,7 +3254,7 @@ o Compute the non-local term using either KPP vertical diffusivity (=default) or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) -checkpoint55h_post +checkpoint55h_post (2004/10/20) o add verification test "vermix" o remove all the *_ioinc flags and replace with the single global outputTypesInclusive flag @@ -1953,7 +3262,7 @@ o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS o useMNC moved from data.mnc to data.pkg -checkpoint55g_post +checkpoint55g_post (2004/10/14) o Renaming carbon AD experiments to comply with testreport conventions o Updating adjoint of Held-Suarez hs94.1x64x5 o Fixing directives for non-ECCO forward_step, after ECCO directives @@ -1963,10 +3272,10 @@ o Updating adjoint output for natl_box_adjoint after pkg/ecco has been modified (see taga c55d_post) -checkpoint55f_post +checkpoint55f_post (2004/10/13) o rename to timeave_init_fixed -checkpoint55e_post +checkpoint55e_post (2004/10/13) o some delicate re-shuffle of store directives to avoid one extra call of do_oceanic_physics affects ecco_the_main_loop.F, do_oceanic_physics.F @@ -1974,14 +3283,14 @@ o NB: this may break global_ocean adjoint temporarily, but it is clear how to fix it. Will do later, need this now. -checkpoint55d_post +checkpoint55d_post (2004/10/11) o ECCO specific cost function terms (up-to-date with 1x1 runs) o ecco_cost_weights is modified to 1x1 runs o modifs to allow observations to be read in as single file or yearly files o enable to read exf forcing fields as either single file or yearly files (flag useExfYearlyFields) -checkpoint55d_pre +checkpoint55d_pre (2004/10/08) o switch between 2-level and 3-level checkpointing o add ability of MNC to write local and "partial" (eg. 2D slices where @@ -2029,7 +3338,7 @@ - changed argument list of OBCS_CALC to myTime+deltaTclock - fixed about 35 bugs in obcs_external_fields_load -checkpoint55c_post +checkpoint55c_post (2004/09/23) o obcs stuff - new runtime flags useOBCSprescribe, useOBCSbalance - re-arranged obcs_calc @@ -2043,7 +3352,7 @@ o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments which simplifies the calls and passes the ifc check-bounds test -checkpoint55b_post +checkpoint55b_post (2004/09/22) o add a 2D scalar, Z location, exchange_2 routine. o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] @@ -2054,7 +3363,7 @@ o fix gad_advection.F (CubedSphere part), back to version 1.23 o fix bug in mom_vi_del2uv.F (CubedSphere part). -checkpoint55a_post +checkpoint55a_post (2004/09/20) o merged code to * prescribe/read time-dependent open boundaries (works in conjunction with exf, cal) @@ -2062,7 +3371,7 @@ * each boundary N/S/E/W now has its own CPP option (healthy for the adjoint) -checkpoint55 +checkpoint55 (2004/09/17) o up-to-date adjoint of previous breaks - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix - global_ocean_ebm: adjoint still needs fix (TLM ok) @@ -2072,7 +3381,7 @@ o remove all tr1-related code (ALLOW_PASSIVE_TRACER) (adjoint stuff still has some tr1 'names', but all use ptracer arrays) -checkpoint54f_post +checkpoint54f_post (2004/09/16) o in verification/carbin/ remove experiment related to ALLOW_PASSIVE_TRACER (array tr1 etc) code_ad/ input_ad/ results_ad @@ -2098,21 +3407,21 @@ - numerous small formatting cleanups for ProTeX o add version info (via BUILD_INFO.h) to MNC and stdout -checkpoint54e_post +checkpoint54e_post (2004/09/02) o add two new packages - pp81 (Packanowski and Philander, 1981), Richardson number and stratification dependent mixing - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme - these scheme operate in a similar manner as KPP (without ghat, of course), however there is only one diffusivity that is used for both - temperature and salinity (and passive tracers)ç + temperature and salinity (and passive tracers) o add offline package o add "verification/dic_example" which contains a dic-gchem-ptracer setup provided by Stephanie Dutkiewicz o genmake2: add ability to search for C compilers and cleanup test output - fixes recent SX-6 problems and should help with others (eg. HP-UX) -checkpoint54d_post +checkpoint54d_post (2004/07/27) o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, leading to additional shift by 5 days each year of integration @@ -2128,7 +3437,7 @@ o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) -checkpoint54c_post +checkpoint54c_post (2004/07/18) o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr this affects (truncation error) output.txt of test-exp: global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box @@ -2139,7 +3448,7 @@ o start to test mnc routinely in exp0 o add sea-ice loading (sIceLoad) as a new forcing field. -checkpoint54b_post +checkpoint54b_post (2004/07/08) o add testreport "-j JOBS" option for parallel builds (tested and pretty impressive on Altix and Opteron systems) o diagnostics can now write NetCDF files through the mnc package @@ -2149,19 +3458,19 @@ affects (truncation error) output of lab_sea & natl_box exp.: updated o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) -checkpoint54a_post +checkpoint54a_post (2004/07/06) o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) + internal_wave (shift in writing cg2d_ini_res) -checkpoint54a_pre +checkpoint54a_pre (2004/07/05) o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice - modified verification/lab_sea and natl_box_adjoint accordingly -checkpoint54 -checkpoint53g_post +checkpoint54 (2004/07/02) +checkpoint53g_post (2004/07/02) o prepare splitting of thermodynamics: store convect.counter in common block o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave @@ -2170,7 +3479,7 @@ o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) o restore adjointability -checkpoint53f_post +checkpoint53f_post (2004/06/25) o modifications that affect AIM experiment results (update output.txt): - no advection of S at top interface Nr (pkg/generic_advdiff) - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) @@ -2183,7 +3492,7 @@ o added rotating_tank experiment checkpoint53e_pre -checkpoint53d_post +checkpoint53d_post (2004/06/14) o faulks upgraded: re-generate output.txt that have changed: global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box o Added Bryan and Lewis, 1979, vertical diffusivity profile @@ -2202,9 +3511,9 @@ o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation of mom_common/ - simple re-arrangement of instructions within computing loop -checkpoint53d_pre +checkpoint53d_pre (2004/05/21) -checkpoint53c_post +checkpoint53c_post (2004/05/21) o new version of coupler for AIM+thSIce and Ocean models - new fields (SSS,h_MixLayer ...) are exchanged through the coupler - land: change Evaporation of snow @@ -2221,7 +3530,7 @@ * TLM OK * ADM not sufficient accuracy yet (needs further testing) -checkpoint53b_post +checkpoint53b_post (2004/05/14) o Commiting new energy balance model to repository * package is pkg/ebm * verif. is verification/global_ocean_ebm @@ -2239,7 +3548,7 @@ C by atmospheric eddy transports. C J. Climate 7(12), 1870-1882 o Will need long integration testing. -checkpoint53b_pre +checkpoint53b_pre (2004/05/14) o created pkg/mom_common in preparation for variable viscosity code o renamed and split ini_mnc_io @@ -2247,7 +3556,7 @@ o AIM using land: soil wetness availability account for snow o added printMapIncludesZeros to EEPARMS namelist -checkpoint53a_post +checkpoint53a_post (2004/05/11) o restore TAMC compatiility for exf_constants.h (no usage of _d in .h) o Additional storing in KPP in an attempt to fix @@ -2260,7 +3569,7 @@ and hence gives results closer to that of Experiment 2. Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. -checkpoint53 +checkpoint53 (2004/05/06) o stable checkpoint with up to date adjoint TLM tests only run for 1st grdchk at the moment. Its unclear if this is a code problem or a problem with resetting code for g_ @@ -2270,7 +3579,7 @@ o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) are both still in chaos following their security messes. -checkpoint52n_post +checkpoint52n_post (2004/05/06) o various build (mostly genmake2) changes including: - ability to build/run more easily within Cygwin and MacOS X - more complicated Makefiles with a stronger dependence on Gnu Make @@ -2301,7 +3610,7 @@ - maintain snow precipitation unchanged (even if Tsf >=0). both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice -checkpoint52m_post +checkpoint52m_post (2004/04/18) o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; this does not change any of the results, because myIter=0 in swfrac always lead to jwtype=2 (the default anyway), but the call makes little sense @@ -2333,7 +3642,7 @@ o Added functionality to grdchk: pick global i,j,k position (or nearest wet) where to perform check. -checkpoint52l_post +checkpoint52l_post (2004/03/11) o new land formulation: a) use ground enthalpy as prognostic variable to ensure exact energy conservation. @@ -2344,7 +3653,7 @@ a) Treat separately land / ocean / sea-ice surface fluxes to allow implicit computation of land & sea-ice surface temp. b) add snow precipitation. -checkpoint52l_pre +checkpoint52l_pre (2004/03/11) o fix problem (when 1 tile is empty) in min/max monitor. o fix bug in timeAve (u,vZetatave in common block) @@ -2357,7 +3666,7 @@ o aim.5l_cs: modify sea-ice fraction input file ; update output o exf: Adding simple range check routine for exf fields after read -checkpoint52k_post +checkpoint52k_post (2004/02/23) o removed top-level directory "diags" - we migrated these functions to pkg/timeave a long time ago o fixed bug introduced in pkg/monitor @@ -2370,7 +3679,7 @@ taveFreq, dumpFreq, pChkptFreq o MAIN and ECCO differentiability restored -checkpoint52j_post +checkpoint52j_post (2004/02/18) o fix nchklev in tamc.h for global_ocean... o Bringing flow and store directives up-to-date o Really weird thing! @@ -2378,7 +3687,7 @@ starttime, niter0, instead of mytime, myiter, screws up the adjoint: TAF places a faulty re-call of initialise_varia after cost_final call which should not be there! -checkpoint52j_pre +checkpoint52j_pre (2004/02/03) o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and error messages @@ -2395,15 +3704,15 @@ mon_vort3.F to make exch2 friendly with >1 tile per cube face o limit timeave output for hi-res integrations -checkpoint52i_post +checkpoint52i_post (2004/01/21) o removed CPP_EEOPTIONS.h from verification/*/code o updated the tiling for global_ocean_pressure -checkpoint52i_pre +checkpoint52i_pre (2004/01/20) o update aim.5l_LatLon using the standard aim_v23 pkg (instead of the old pkg/aim). -checkpoint52h_pre +checkpoint52h_pre (2004/01/20) o shortened offending lines in exch2_send_rx?.template o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator o genmake2: add build & execute test for NetCDF code @@ -2414,13 +3723,13 @@ metric terms are ignored and it is assumed that there is no sea-ice on cube faces 1, 2, 4, and 5. -checkpoint52f_post +checkpoint52f_post (2004/01/09) o added exch2 cube routines to pkg/exch2 o modified hs94.cs-32x32x5 to use it o added new grid files to hs94.cs-32x32x5 -checkpoint52f_pre +checkpoint52f_pre (2004/01/07) -checkpoint52e_post +checkpoint52e_post (2004/01/07) o first attempt to solve vertical advection (momemtum & T,S) Implicitly for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) @@ -2428,7 +3737,7 @@ o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. o update output (gad_calc_rhs.F changes affect truncation error) of exp: front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box -checkpoint52e_pre +checkpoint52e_pre (2004/01/02) o fix bug in impldiff when Nr=1 or Nr=2. o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt @@ -2439,7 +3748,7 @@ o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations -checkpoint52d_post +checkpoint52d_post (2003/12/16) o re-tiled many expts to allow comparison in multi-processor mode - updated output accordingly - changed hs94.128x64x5 to use intial T from file rather than use the @@ -2468,11 +3777,11 @@ o new verification experiment, cpl_aim+ocn: coupled ocean - AIM atmosphere on cs32 grid. -checkpoint52d_pre +checkpoint52d_pre (2003/12/06) o surface flux time-av diagnostic modified for NLFS & RealFreshWater o add call to AIM pendant S/R in external_forcing & external_fields_load.F -checkpoint52c_post +checkpoint52c_post (2003/11/25) o Fixing OPTIONS files for use of exf: - ALLOW_ECCO not needed - ECCO_CPPOPTIONS.h should not be included from @@ -2486,7 +3795,7 @@ o modified STOREs in GAD_ADVECTION o corrected key comp. for passkey -checkpoint52b_post +checkpoint52b_post (2003/11/23) o new version: "thsice" of thermodynamic sea-ice pkg: - only 1 call from "forward_step"; conserve energy, fresh-water & salt. - modify fluxes but do not change theta directly; @@ -2494,7 +3803,7 @@ - add forcing fields + data files in global_ocean.cs32x15/inp_thsice + output_thsice.txt to test thsice & bulk_force pkgs. o put back grid & coriolis monitor output. -checkpoint52b_pre +checkpoint52b_pre (2003/11/23) o call "do_the_model_io" at the beginning (=> dump initial state) o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) @@ -2504,7 +3813,7 @@ o default tamc.h in pkg/autodiff supposed to crash to ensure proper customization -checkpoint52a_post +checkpoint52a_post (2003/11/17) o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp - moved surfaceTendencyTice from pkg/seaice to main code - subroutine FREEZE_SURFACE now limits only surface temperature @@ -2519,13 +3828,13 @@ snapshot file was missing some ad-variables, but no warning issued by TAF -checkpoint52a_pre +checkpoint52a_pre (2003/11/12) o some bug fixes for #undef REAL4_IS_SLOW checkpoint52 = ecco_c52_e35 o after testing adjoints of checkpoint51u_post -checkpoint51u_post +checkpoint51u_post (2003/11/06) o this is the post-merge tag of the ecco-branch (needs another clean checkout and re-testing) o various natl_box_adjoint configs and results @@ -2540,10 +3849,10 @@ (new namelist ecco_cost_nml) o in ctrl/ cleaned some cross-dependencies and updated CPP options -checkpoint51t_post +checkpoint51t_post (2003/11/04) o this is the pre-merge tag of the ecco-branch -checkpoint51s_post +checkpoint51s_post (2003/11/04) o cleanup: removed various obsolete #define-s o pkg/grdchk - renamed 'ph-grd 3' to 'grad-res' @@ -2552,12 +3861,12 @@ - additional high-precision output for testreport (grep for 'precision_grdchk_result') -checkpoint51r_post +checkpoint51r_post (2003/11/03) o cleaned up or removed CPP_OPTIONS.h files o updated results for some of the tests to reflect the new optfiles (-ieee: -O0 instead of -O3) -checkpoint51q_post +checkpoint51q_post (2003/10/30) o cd_code: - moved cd_scheme.F -> cd_code_scheme.F - separate read_checkpoint from cd_code_ini_vars.F @@ -2573,7 +3882,7 @@ - confined inclusion of AD_CONFIG.h to where necessary. o genmake2: changed AD dependencies from SRCFILES to AD_FILES -checkpoint51p_post +checkpoint51p_post (2003/10/30) o create initial cd_code package - WARNING: the initialization of fields within packages is broken because INI_FIELDS (where READ_CHECKPOINT is @@ -2588,7 +3897,7 @@ o cleanup verification/*/code/GMREDI_OPTIONS.h o cleanup testreport -checkpoint51o_post +checkpoint51o_post (2003/10/27) o bringing AD-related verif's up to date with genmake2 - carbon/ - global_ocean.90x40x15/ @@ -2609,7 +3918,7 @@ o helping TAF to recognize dependency on kUp for fVerU, fVerV o Replacing delZ by delR in pkg/ctrl/ -checkpoint51o_pre +checkpoint51o_pre (2003/10/24) o undid all of cp51 pending some cleanups and discussion o added the [#include "AD_CONFIG.h"] statement to all files that need @@ -2617,7 +3926,7 @@ o re-worked the build logic in genmake2 to support AD_CONFIG.h o removed tools/genmake since it no longer works -checkpoint51n_post +checkpoint51n_post (2003/10/23) o modifications to make FREEZE flux visible to pkg/kpp - moved surfaceTendencyTice from pkg/seaice to main code - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP @@ -2626,7 +3935,7 @@ global_ocean.cs32x15, and global_with_exf) o added surface flux output variables to TIMEAVE_STATVARS -checkpoint51n_pre +checkpoint51n_pre (2003/10/23) o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F o added [#include "AD_CONFIG.h"] to all files that use the following defines: @@ -2634,26 +3943,26 @@ - ALLOW_TANGENTLINEAR_RUN - ALLOW_ECCO_OPTIMIZATION -checkpoint51m_post +checkpoint51m_post (2003/10/21) o incorporating changes to get TAMC/TAF working in genmake2 - added new TAMC/TAF targets to the Makefile - various cleanups related to package handling - these changes should have no impact on the forward model -checkpoint51l_post +checkpoint51l_post (2003/10/20) o changes to pkg/cal and pkg/exf that allow and speed-up long integrations - faster algorithm for cal_addtime.F - higher precision arithmetic, where needed - pkg/exf *startdate variables changed from calendar date to model integration time -checkpoint51l_pre +checkpoint51l_pre (2003/10/17) o add salt flux to forcing fields (used when salty sea-ice forms or melts) o enable to apply restoring on S & T only in a latitude band. o update output (external_forcing_surf modif. change truncation errors) global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box -checkpoint51k_post +checkpoint51k_post (2003/10/16) o change default to: useNHMTerms=.FALSE. - new output.txt for atmos. exp (NHMTerms were wrong but now turned off): adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 @@ -2667,7 +3976,7 @@ removed the #include "PACKAGES_CONFIG.h" from it o fix a bug in mom_fluxform (from chk51j_post) -checkpoint51j_post +checkpoint51j_post (2003/10/10) o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ o adjusted some flow directives (dynamics, thermodynamics) o added cubed-sphere case to test cost function @@ -2681,13 +3990,13 @@ - pkg_ad_diff.list - pkg_ad_check_lev?_dir.h -checkpoint51i_post +checkpoint51i_post (2003/10/09) o merge of the branch-genmake2 - knowingly breaks the older genmake - automatic generation of all ALLOW_${PKG_NAME} defines - new testreport supersedes older testscript o large number of package inclusion and header cleanups -checkpoint51i_pre +checkpoint51i_pre (2003/10/08) o new output for adjoin of global ocean vector invariant o fix for checkpoint of thermodynamic seaice and bulk_force @@ -2699,7 +4008,7 @@ o modifications to clean up dic pkg o add pkg/cfc -checkpoint51g_post +checkpoint51g_post (2003/10/02) o provide links for ARPACK and ADM*TLM o start removing verification/vero/ o update AD-related stuff @@ -2707,12 +4016,12 @@ o adding to verification/global_ocean.90x40x15/ adjoint of vector invariant setup -checkpoint51f_post +checkpoint51f_post (2003/10/02) o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation of tracer Green's fucntions for ocean inversion project. -checkpoint51f_pre +checkpoint51f_pre (2003/08/07) o Added on-the-fly spatial interpolation capability "USE_EXF_INTERPOLATION" to pkg/exf. - This is a temporary Cartesian-grid hack until @@ -2724,7 +4033,7 @@ and pkg/kpp/kpp_transport_ptr.F for dealing with tracer non-local transport term. -checkpoint51e_post +checkpoint51e_post (2003/08/03) o pkg/mom_vecinv: - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) - add time-ave diagnostic of vorticity advection. @@ -2734,7 +4043,7 @@ o land pkg: read initial state from files. o AIM : add stratospheric drag in the upper level -checkpoint51d_post +checkpoint51d_post (2003/07/18) o change function ILNBLNK (=> last non-blank char.) to return zero (instead of the string length) when the string. char is empty o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) @@ -2747,7 +4056,7 @@ - new active_file_loc... and mdsio_..._loc routines - affected packages: autodiff, ctrl, grdchk, mdsio -checkpoint51c_post +checkpoint51c_post (2003/07/08) o introducing integer flag debugLevel - debLevZero: suppress all output - debLevA: standard @@ -2770,14 +4079,14 @@ - checked tapelev/comlev recomputations: OK << affects results of glob_oce_pressure (different truncation error) update output.txt of ideal_2D_oce & global_ocean_pressure -checkpoint48d_pre +checkpoint48d_pre (2003/02/08) o in preparation for r*: new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. pass the 2 comp. of the grad. as arguments to momentum S/R. but for the moment, only used if it does not change the results. o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP -checkpoint48c_post +checkpoint48c_post (2003/02/06) Modifications in treatment of initial flux forcing controls to avoid extra storing of flux fields. -checkpoint48c_pre +checkpoint48c_pre (2003/01/21) o Added tidal_basin_2d experiment (currently 1D!) o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) -checkpoint48b_post +checkpoint48b_post (2003/01/27) o r* coordinate added in #ifdef NONLIN_FRSURF block. (modification to pressure gradient not yet implemented) o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports (for U & V) that are used for vertical advection of momentum. -checkpoint48a_post +checkpoint48a_post (2003/01/24) o In preparation for r*, use temp. array to compute vertical transport in flux-form momentum pkg. => change results of few test-exp. Update output of: exp4, exp5, front_relax, global_ocean_pressure, lab_sea, natl_box & plume_on_slope -checkpoint48 +checkpoint48 (2003/01/23) o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') -checkpoint47j_post +checkpoint47j_post (2003/01/21) o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. o moved adexch from forward_step to addummy_in_stepping o added exch in ctrl_map_... @@ -3056,7 +4365,7 @@ re-activated full calculation of taperfct for case 'ac02' o updating verification/ adjoints of carbon, global_ocean.90x40x15 -checkpoint47i_post +checkpoint47i_post (2003/01/13) o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) @@ -3072,7 +4381,7 @@ S/R gmredi_slope_psi should be cleaned o verification/carbon now has exactConserv=.TRUE. -checkpoint47g_post +checkpoint47g_post (2003/01/10) o time-average AIM output: becomes independent from statvars time-average (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) o After TAF bug fix: @@ -3098,7 +4407,7 @@ in conjunction with data.gmredi parameters to be checked in in a few minutes under verification/carbon/code/ -checkpoint47f_post +checkpoint47f_post (2002/12/28) Merging from release1_p10: o modifications for using pkg/exf with pkg/seaice - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING @@ -3110,19 +4419,19 @@ - verification/lab_sea default experiment now uses pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf -checkpoint47e_post +checkpoint47e_post (2002/12/27) o created a tag prior to creating a branch -checkpoint47d_post +checkpoint47d_post (2002/12/16) o fixed bug in the oceanic pressure coordinates code: vertical viscosity at the bottom boundary had an erroneous half slip boundary condition o added bottom drag and no slip boundary condition capabilities to oceanic pressure coordinates code o added new verification experiment global_ocean_pressure, this experiment is also described in the tutorial section of the manual -checkpoint47d_pre +checkpoint47d_pre (2002/12/16) -checkpoint47c_post +checkpoint47c_post (2002/12/16) o Added a verification experiment for a global cubed-sphere ocean run - verification/global_ocean.cubed32x32x30 - uses pkg/therm_seaice and pkg/bulk_forcing @@ -3134,7 +4443,7 @@ NOTES: requires option NONLIN_FRSURF to be "#define". o update advect_xz/results/output.txt (left from checkpoint44g_post) -checkpoint47b_post +checkpoint47b_post (2002/12/05) Merging from release1_p9: o pkg/seaice - removed GOTO's and added taf directives @@ -3151,7 +4460,7 @@ - added missing matlab routines - added test of thermodynamics parallelization -checkpoint47a_post +checkpoint47a_post (2002/11/23) o new pkg: aim_v23 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. for now, keep the same surface forcing as before. @@ -3168,7 +4477,7 @@ - Two ifdef statements for compile time, ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE -checkpoint47 +checkpoint47 (2002/11/15) differentiable version of checkpoint46n_post o bug fix in quasihydrostaticterms o * "clean" adjoint code (in terms of extensive recomputations) @@ -3197,7 +4506,7 @@ - #define GM_VISBECK_VARIABLE_K - GM_taper_scheme = 'ldd97' -checkpoint46n_post +checkpoint46n_post (2002/11/12) Merging from release1_p8: o verification/natl_box: updating new external_fields_load routine @@ -3251,7 +4560,7 @@ the exf (and cal) package instead of the external_fields_load routine (cf README file). -checkpoint46m_post +checkpoint46m_post (2002/11/07) o modified testscript to return -- when there are no lines of "%MON" output o added new flag "quasiHydrostatic" for QH mode and new routine quasihydrostaticterms() @@ -3264,7 +4573,7 @@ o removed gravitySign from PARM04 o switched to g77/ifc from pgf77 in aim experiments -checkpoint46l_post +checkpoint46l_post (2002/11/01) o made convective adjustment work with pressure coordinates: - changed the direction of k-loop in convective_adjustment.F for the case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) @@ -3277,9 +4586,9 @@ at the beginning of find_rho, find_alpha, and find_beta, does a check of the entire slice, if CPP-option CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined -checkpoint46l_pre +checkpoint46l_pre (2002/10/23) -checkpoint46k_post +checkpoint46k_post (2002/10/23) o fixed the verification/global_ocean.90x40x15 experiment: - new bathymetry (the world according to A., JMC, and M.) - new initial fields and forcing fields (*.bin files) @@ -3293,20 +4602,20 @@ - read AIM physics parameters from a file (data.aimphys) - set defaults values = F.Molteni paper (Clim.Dyn., 2002) -checkpoint46j_post +checkpoint46j_post (2002/10/07) o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH o move wVel computation at the end of the time step, in S/R integr_continuity o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) o update timeave pkg for wVel diagnostic. -checkpoint46j_pre +checkpoint46j_pre (2002/09/27) -checkpoint46i_post +checkpoint46i_post (2002/09/25) o Clean up AIM package (and keep the results unchanged): include CPP_OPTION and use IMPLICT NONE in all routines ; declare all the variables _RL ; use _d 0 for all numerical constants. use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! -checkpoint46h_post +checkpoint46h_post (2002/09/25) o cleaned up the use of rhoNil and rhoConst. - rhoNil should only appear in the LINEAR equation of state, everywhere else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst @@ -3316,13 +4625,13 @@ value is 999.8 kg/m^3 o cleanup up external_forcing.F and external_forcing_surf.F - can now be used by both OCEANIC and OCEANICP -checkpoint46h_pre +checkpoint46h_pre (2002/09/18) Added code to convert surface volume flux (fresh water) into a mass flux when using P coordinates in the ocean (OCEANICP). Note: It assumes you have set rho0=rhoConst=density of fresh water. -checkpoint46g_post +checkpoint46g_post (2002/09/18) o Include a new diagnostic variable phiHydLow for the ocean model - in z-coordinates, it is the bottom pressure anomaly - in p-coordinates, it is the sea surface elevation @@ -3340,9 +4649,9 @@ - removed obsolete 'eqn' from the parameter list. o added two new verification experiments: gop and goz (4x4 degree global ocean, 15 layers in pressure and height coordinates) -checkpoint46g_pre +checkpoint46g_pre (2002/09/16) -checkpoint46f_post +checkpoint46f_post (2002/09/16) o Enable tangent linear (forward mode) gradient checks: - extended active file handling to g_... files - added TANGENT_SIMULATION to theSimulationMode @@ -3350,7 +4659,7 @@ o added tangent linear setup in verification/carbon/code_ftl o added adjoint setup in verification/front_relax/code_ad -checkpoint46e_post +checkpoint46e_post (2002/09/05) o Added new equation of state -> MDJWF - EOS of McDougall et al., 2002, JAOT, submitted - caveat: the equation of state is only valid for a smaller (more @@ -3359,30 +4668,30 @@ - added more check values for density in check_eos (ini_eos.F), some of the old check values are out of the range of the MDJWF-eos, so don't expect perfect matches for those -checkpoint46e_pre +checkpoint46e_pre (2002/08/19) -checkpoint46d_post +checkpoint46d_post (2002/08/19) o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and 'OCEANICP', also initialised field pressure correctly in ini_eos in the case of pressure coordinates. eosType='JMD95Z' in combination with buoyancyRelation='OCEANICP' now causes an error. o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) in find_alpha/beta. -checkpoint46d_pre +checkpoint46d_pre (2002/08/15) o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) so that JMD95Z and JMD95P give approptiate static stability in find_rho. -checkpoint46c_post +checkpoint46c_post (2002/08/15) o Changes necessary for ocean in p-coordinates - Added new buoyancy relation = 'OCEANICP' - Added new parameters = gravitySign (this used to be contained inside the factor dRdZ which I added when we first switched to R coordinates). X GM/Redi is not compatible (yet) X bottom drag and no-slip need to be debugged. -checkpoint46c_pre +checkpoint46c_pre (2002/08/07) -checkpoint46b_post +checkpoint46b_post (2002/08/07) o Added new equation of state -> JMD95Z and JMD95P - EOS of Jackett and McDougall, 1995, JAOT - moved all EOS parameters into EOS.h @@ -3391,17 +4700,17 @@ in-situ temperature (see JMD95) o Modified formatting for knudsen2.f in utils/knudsen2 and added unesco.f to be used with POLY3 -checkpoint46b_pre +checkpoint46b_pre (2002/07/31) -checkpoint46a_post +checkpoint46a_post (2002/07/31) o Added (atmospheric) pressure loading - new field in FFIELDS.h, etc... - new cpp flag ATMOSPHERIC_LOADING o Changed hFacC to _hFacC in calc_phi_hyd.F o Added SHORTWAVE_HEATING to some files for consistency -checkpoint46a_pre +checkpoint46a_pre (2002/07/13) -checkpoint46 +checkpoint46 (2002/07/13) further merges from release1_p5 o new ctrl package - adopted from ECCO environment to enable optimization @@ -3428,7 +4737,7 @@ o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) o incorporated hooks for sponge layer code (external_forcing.F) -checkpoint45d_post +checkpoint45d_post (2002/07/12) o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S (affects plume_on_slope "cg2d" output) @@ -3442,7 +4751,7 @@ - for each tracer, define internal flag for multiDimAdvection & A-B o monitor: change definition of KE to check conservation of Energy -checkpoint45c_post +checkpoint45c_post (2002/05/30) o Removed f90 comments ("!") o Modified initialisations to enable exf package for MITgcm (without invoking ECCO_PACKAGE). @@ -3450,7 +4759,7 @@ - enable centered differences - modified format of standard output -checkpoint45b_post +checkpoint45b_post (2002/05/30) o cleaned exchange calls in cg2d o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step o included CPP option SINGLE_LAYER_MODE in thermodynamics @@ -3462,7 +4771,7 @@ (corresponding adjustment of TAF tape initialisation). o in calc_diffusivity/calc_viscosity extended domain to full overlap. -checkpoint45a_post +checkpoint45a_post (2002/05/01) o compute Rho over the whole domain (extend iMin,jMin indices) o specific exchange for X-slice domain (case Ny=1) o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code @@ -3482,13 +4791,13 @@ (conflict on some platforms, e.g. IBM SP3) o modified carbon verif. -checkpoint44h_pre +checkpoint44h_pre (2002/03/14) o vertical grid option: allow to put the Interface at the middle between 2 cell-centers ; replace delZ in pkg/kpp by drF. o GM Advective form: Tracers are advected using the residual transport (= Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. -checkpoint44g_post +checkpoint44g_post (2002/03/05) o fix surface correction term in multiDimAdvection (affects plume_on_slope results) ; ifdef missing in thermodynamics.F @@ -3553,7 +4862,7 @@ o check parameters & config (chkpt44a_pre,post) o OBC and NonLin_FrSurf. -checkpoint44 +checkpoint44 (2002/01/18) o fix bug in mom_vi_del2uv o select when filters are applied ; add options to zonal_filter (data.zonfilt) o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) @@ -3561,13 +4870,13 @@ o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) o added some stuff for AD -checkpoint43 +checkpoint43 (2001/09/28) o added two new advection tests o added global 4x4 degree ocean test o added test of H&S94 with free surface on cube o some final mods for gradient check, adjoint,... -checkpoint42 +checkpoint42 (2001/09/27) Fixed AD-related problems: o Store directives up-to-date with re-arranged Adams-Bashforth (mainly thermodynamics.F) @@ -3579,11 +4888,11 @@ for the case ALLOW_KPP o Cleaned argument list for timestep_tracer.F -checkpoint41 +checkpoint41 (2001/09/27) o re-formatted/added comments in prologues of key subroutines to work with protex -checkpoint40 +checkpoint40 (2001/09/27) o moved calc_gs, calc_gt and calc_tr1 back to model/src o added FLT (floats) package from Arne along with demo. experiment o re-arranged Adams-Bashforth scheme for tracers to allow easier @@ -3592,7 +4901,7 @@ o modified multi-dim method to work on cube o bug fix in KPP (from DM) -checkpoint40pre9 +checkpoint40pre9 (2001/09/27) o added DST advection schemes o fix MPI bug on SGI's o modifications for non-linear free-surface @@ -3602,7 +4911,7 @@ o added/updated many matlab scripts o added multi-dimensional advection method for tracers -checkpoint40pre8 +checkpoint40pre8 (2001/09/05) o new package rw/ Added method for dumping intermediate local arrays: mdsio_writetile - same as mdsio_writefield except works from inside @@ -3621,14 +4930,14 @@ currently nothing implemented to switch this storing off in case fluxform is used since no CPP flag available). -checkpoint40pre7 +checkpoint40pre7 (2001/08/14) o bug fix in dynamics.F calc_viscosity called before k=1,Nr loop. o added some #ifdef's ALLOW_PASSIVE_TRACER o cleaned initialisations in ctrl_map_ini related to TAF -checkpoint40pre6 +checkpoint40pre6 (2001/08/13) o split dynamics into thermodynamics & dynamics o corresponding split of calc_diffusivity into calc_diffusivity, calc_viscosity @@ -3636,7 +4945,7 @@ o Added diffkr, kapgm to control variables o bug fix in gmredi_slope_limit for ldd97 -checkpoint40pre5 +checkpoint40pre5 (2001/07/31) o proper initialization of Adams-Bashforth time stepping + uses forward step for very first step of model (iter=0) o re-generated *all* output since almost all output is modified by this @@ -3650,7 +4959,7 @@ + this uses an alternative form of ini_curvilinear_grid.F which is not necessarily any better than the current one... -checkpoint40pre4 +checkpoint40pre4 (2001/07/30) o added re-initialisations of utrans,vtrans,rtrans in calc_common_factors which are crucial for TAF. o extended iMin,jMin range for calc_common_factors, @@ -3658,18 +4967,18 @@ o added option ALLOW_PASSIVE_TRACER o a few minor updates and fixes -checkpoint40pre3 +checkpoint40pre3 (2001/07/13) o created calc_gtr1.F for gad package o split the_main_loop and re-introduced forward_step o some recomputations of nIter0 for TAMC -checkpoint40pre2 +checkpoint40pre2 (2001/07/13) o Updated to latest branch of AJA, JMC o Added gradient check package o Added routines for passive tracer handling o Added carbon sequestration sensitivity experiment -checkpoint39 +checkpoint39 (2001/05/14) o Modifications and fixes to support TAMC (mainly missing or wrong directives) o Corrected common blocks when fooling TAMC to produce adjoint I/O @@ -3683,7 +4992,7 @@ (NB: this is not the full ECCO environment) o disabled some packages by default in genmake -checkpoint38 +checkpoint38 (2001/04/10) o see notes_c37_adj.txt o corrected wrong layer index in external_forcing_t o replaced the_main_loop/forward_step by the_main_loop @@ -3691,7 +5000,7 @@ (replaced criteria for initial/final state) o added runtime flag for pre-C35 pickups: usePickupBeforeC35 -checkpoint37 +checkpoint37 (2001/03/13) o mdsio.F routine split and packaged in pkg/mdsio (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not used unless genmake -disable=mdsio) @@ -3708,19 +5017,19 @@ o Non-Hydrostatic pickup file Pb fixed. o bug with Rigid-lid version (since c35) fixed. -checkpoint36 +checkpoint36 (2001/02/20) o implement Crank-Nickelson barotropic time-stepping o recover Time-Average diagnostics o fix Pb in checkpoint (PR#19) o AIM become a standard package ; clean unused CPP_kees -checkpoint35 +checkpoint35 (2001/02/08) o subtantial rewrite of dynamics.f o allows staggered time-stepping o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt o added bottom drag (linear + quadratic) -checkpoint34 +checkpoint34 (2001/01/30) o Modified exchange routines for correct reverse simulation. o Added verification output to comply with bug fix in impldiff.F as of c33 (exp2, natl_box). @@ -3731,7 +5040,7 @@ o Added routine GLOBAL_SUM_INT to global_sum.F o Added mdsio_gl.F for ECCO purposes. -checkpoint33 +checkpoint33 (2000/11/30) o Fixed bug in lower BC in impldiff.F o Fixed confusion about units of forcing arrays in FFIELDS.h namely Fu,Fv,Qnet,Qsw,EmPmR: @@ -3749,7 +5058,7 @@ possibly use them. o Corrected genmake to delete a temporary file during configuration -checkpoint32 +checkpoint32 (2000/11/13) o Scaling of forcing fields moved from external_forcing.F to external_fields_scale.F, called directly after loading fields. o Surface relaxation terms added to surface tendency fields in @@ -3760,7 +5069,7 @@ o Modifications and bug fixes in KPP package. o Verification experiment for KPP added (verification/nat_box/) -checkpoint31 +checkpoint31 (2000/09/11) o Packages interface brought in line with defined standard -> new routines packages_...F -> changes in initialise_fixed.F, initialise_varia.F @@ -3777,7 +5086,7 @@ - not yet tested for GMRedi. - not yet tested for KPP. -checkpoint30 +checkpoint30 (2000/07/13) o Updates for OBCs o New experiment for test OBCs (internal_wave) o New output.txt in verification/exp4/results/ @@ -3786,10 +5095,10 @@ o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) and entry for T90 in genmake -checkpoint29 +checkpoint29 (2000/06/21) o packaged KPP and GM/Redi -checkpoint28 +checkpoint28 (2000/06/09) o Corrected initialization of hFacMin for difference vertical coordinates o Modified calculation of partial cell thickness to more robust algorithm o config_summary.F: replaced write_1D_... by write_0D_... @@ -3802,7 +5111,7 @@ included store directives and tape key computations required for TAMC. o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC -checkpoint27 +checkpoint27 (2000/04/10) o fixed calc_isoslopes() to so that cancellation of terms in tensor formulation works properly with variable resolution. o restructured the calling tree between the_model_main() and dynamics() @@ -3810,7 +5119,7 @@ o introduced initialization file pSurfInitFile for free surface (cg2d_x) in new routine ini_psurf() -checkpoint26 +checkpoint26 (2000/04/05) o moved some #ifdef in optional routines to encompass everything except the argument declarations. This was using up some memory. o fixed macros like _ADT to work with both versions of Linux cpp @@ -3820,7 +5129,7 @@ (macros are now in eesupp/inc/CPP_EEMACROS.h) o patch for 2 processor JAM mode -checkpoint25 +checkpoint25 (2000/03/15) o updates for OBCs and NH o dramatically reduced memory usage o added "JAM" routines for use on Artic network @@ -3831,32 +5140,32 @@ an explicit free-surface option) o initial state input files for U and V -checkpoint24 +checkpoint24 (1999/08/02) o Removed some spurious "REAL"s o Updated KPP to latest version from JPL o Added a COS(latitude) in horizontal viscosity -checkpoint23 +checkpoint23 (1999/05/26) o Added del^4 diffusion for salt and temperature o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) -checkpoint22 +checkpoint22 (1999/05/18) o Made many small changes: implicit none, format(i5), etc... o Introduced KPP mixing scheme (compiles and runs but *not* tested) -checkpoint21 +checkpoint21 (1999/05/18) o Introduced new I/O package that supports direct-access records (mdsio.F) o Split-up mid-level I/O routines o Updated input data for experiments 0,1,2,4 and 5 o Finally removed the genmake.* scripts (everyone seems happy with genmake) -checkpoint20 +checkpoint20 (1999/03/22) o Tidied up open-boundaries some more o Added non-hydrostatic code o Fixed some input data o Modified MPI start-up to work in "coupled" context. -checkpoint19 +checkpoint19 (1998/12/15) o Tidied up directory structure for verification experiments. o Added new code for open boundaries. o Corrected advective terms near boundaries. @@ -3864,18 +5173,18 @@ o Implemented free-slip/no-slip BCs and del^4 dissipation. o Split default parameters out of ini_parms.F into set_defaults.F. -checkpoint18 +checkpoint18 (1998/11/30) o Further changes for optional code generation with CPP - ugh! -checkpoint17 +checkpoint17 (1998/11/03) o Beginning to incorporating modularity for supporting atmos. and ocean configs. o Small changes for TAMC complinace o New ultra simple test case. Barotropic box configuration "exp0". -checkpoint16 +checkpoint16 (1998/10/28) o Minor changes to exchange routines to support accumulation in reverse mode. Adjoint of an assignment is an addition. @@ -3883,7 +5192,7 @@ syntax) and by g77 under Linux ( 72 character limit ). -checkpoint15 +checkpoint15 (1998/09/29) Rewrote exchange routines to allow o General tile <-> tile connectivity. o TAMC reverse mode flag ( is this really needed? ) @@ -3892,11 +5201,11 @@ shmput/shmget, VIA, SYSV shmem and every other cool communication method. -checkpoint14 +checkpoint14 (1998/09/09) Consistent isomorphism chages made. These allow dynamical core to support both pressure and meters as a vertical coordinate. -checkpoint13 +checkpoint13 (1998/07/17) Release which corrects global_max problem and a couple of KGM time-averaging diagnostic errors. Also contains a double-gyre experiment setup as well as the baseline @@ -3911,27 +5220,27 @@ I don't want to commit the rDot to the main-trunk until we've actually tested it... -checkpoint12 +checkpoint12 (1998/07/08) Tidy up and added generic genmake script (formerly configure script). Released to testers. -checkpoint11 +checkpoint11 (1998/07/02) Re-arranged initialise() and introduced ini_vertical_grid() and ini_masks_etc(). -checkpoint10 +checkpoint10 (1998/07/01) Introduced the configure script. Separated out the diags package. Added template for writing time-averages of tile/intermediate quantities. Updated SIZE.h in exp2 and made the data big-endian. -checkpoint9 +checkpoint9 (1998/06/22) MPI fix. Filename changes (meta/data). salbin*y stuff. General tidy-up. SST.bin SSS.bin added to verification/exp2 -checkpoint8 +checkpoint8 (1998/06/22) Inludes time-dependant forcing and time-averaging. Works at 4x4 and 2.8125x2.8125 global @@ -3941,7 +5250,7 @@ model etc.. Configured for verification/exp2 - 4 degree global, two process. -checkpoint7 +checkpoint7 (1998/06/15) Created by cnh Simple 4 degree global simulation configuration. @@ -3949,27 +5258,27 @@ hydrography, bathymetry etc Does not include Heat Flux and E-P -checkpoint6 +checkpoint6 (1998/06/08) Created by cnh merged checkpoint5 with CD and spherical polar code. Still some problems with GM Redi abd full topography. -checkpoint5 +checkpoint5 (1998/06/08) Created by AJA contains updates to GM Redi and reordered timestepping loop for Implicit Diffusion. -checkpoint4 +checkpoint4 (1998/05/30) Created by cnh Contains memory saving macros ( _rdxc etc..) for when grid variations are limited. Contains polynomial coeffs for EOS and knudsen program for generation. -checkpoint3 +checkpoint3 (1998/05/26) Created by cnh Added extra flags for runtime options Added this file