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$Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.1284 2010/06/30 17:51:36 jmc Exp $ |
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$Name: $ |
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|
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Notes on tags used in MITgcmUV |
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============================== |
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|
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checkpoint62i (2010/07/21) |
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o pkg/flt: |
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- with OBCS: stop floats which enter the OB region |
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o model/src: |
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- use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones) |
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for implicit vertical advection. |
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o pkg/seaice: |
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- account for melting in seaice age evolution. |
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- remove double counting of seaice ridging effect on seaice age. |
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|
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checkpoint62h (2010/06/18) |
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o pkg/exch2: |
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- remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1). |
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o tools/genmake2 |
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- remove "-pdefault" option: redundant with the use of "packages.conf"; |
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- remove file pkg/pkg_default : set the default as a pkg group |
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("default_pkg_list") defined in pkg/pkg_groups; |
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- fix for case pkg/pkg_depend is missing (was hanging before); |
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- add option "-pgroups" to specify a different pkg_groups than the default. |
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o verification/adjustment.cs-32x32x1: |
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add a "minimal" set-up test (code_min & input_min) which only compiles |
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eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc. |
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o tools/genmake2 |
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- extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg])) |
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- fix details of checking for mnc & profile pkg when NetCDF is unavailable. |
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o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these |
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files are nearly the same anyway. |
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Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04: |
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- redefinition of tau(i,i) (by a factor of ustar) |
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- 1./exf(Const/T) -> exf(-Const/T) (big change in the results) |
37 |
- replace rhonil by rhoConstFresh in computation of evap (bug fix) |
38 |
- replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results) |
39 |
- replace |
40 |
rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh ) |
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shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j) |
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by |
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shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh ) |
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(changes results) |
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-> exf_bulkformulae v1.22, |
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update verification experiments lab_sea, offline_exf_seaice, seaice_obcs |
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(lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13, |
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output.txt 1.63 |
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offline_exf_seaice: output.seaicetd.txt 1.7 |
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seaice_obcs: output.txt 1.10) |
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Step 2: do the actual merge and remove exf_bulk_largeyeager04.F |
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-> exf_bulkformulae v1.23, |
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unfortunately requires updating lab_sea.salt_plume (6 matching digits), |
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and global_ocean.cs32x15.icedyn (only 11 matching digits) |
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Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice. |
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o adjoint of exch-1: |
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- pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list) |
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(note: was already like this when using EXCH-2) and remove flow dir |
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and hand-written AD version of high-level EXCH S/R (pkg/autodiff); |
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- provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow); |
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- update pkg/exch2 diff list. |
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|
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checkpoint62g (2010/05/19) |
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o eesupp/src (exch-1): |
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- split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F) |
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and remove argument "simulationMode"; same thing for all exch_*rx_cube.F |
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(renamed to exch1_*rx_cube.F). |
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- change accordingly exch_*_rx.template and AD version in pkg/autodiff |
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to call new exch1 S/R ; update Makefile and .cvsignore. |
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- replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove |
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exch2_xy_rx later) |
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Note: after updating your code, need to run "make clean" in eesupp/src |
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o test experiment bottom_ctrl_5x5: |
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new output_adm.txt with fewer grdchk & less monitor output. |
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o model/src: |
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remove the call to ini_cori in initialise_varia.F (just keep the usual one |
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in initialise_fixed.F). More consistent with coriolis & horizontal grid |
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beeing treated in the same way (ini_grid is not called a 2nd time). |
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o pkg/exf: |
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- rewrite exf_bulk_largeyeager04.F for better vectorization, changes |
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global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated |
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- fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now) |
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- cosmetic changes to exf_bulkformulae.F to make it look more like |
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exf_bulk_largeyeager04.F |
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o eesupp/src (exch-1): |
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- Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1). |
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- Separate buffer filling and MPI sending: allow EXCH-1 to work for local |
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array (non-shared) when using MPI+MTH. Also reduces number of BARRIER |
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(even without using MPI). |
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- Message mode: move RecvAck setting (indicator of buffer being ready) |
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from send_put to recv_get S/R (was useless before, but not sure if |
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it's much more useful now); |
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- Switch the order of sync: MPI-proc 1rst and then threads; |
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- take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead. |
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- fix AD code for communication mode ='get' (but not used). |
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o model/src: |
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initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does |
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not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp). |
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o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API |
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o pkg/ctrl: require a specific set of control variables and exf-flags for |
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adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied) |
102 |
o model/src: |
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a) 1rst version of a new driver S/R to turn-off output freq and flags after the |
104 |
1rst forward sweep, to avoid over-writing output files during recomputations |
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recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?) |
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b) 2nd version: |
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- add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO); |
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- switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast, |
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writePickupAtEnd) + seaice & ptracers output; |
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- do not switch off MNC flags (otherwise, won't get admonitor netcdf file) |
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o model/src: |
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- new S/R rotate_uv2en_rl (..._rs) that rotates vector fields. |
113 |
o pkg/exch2: |
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- remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ; |
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- add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch). |
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o pkg/autodiff & exch2: |
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process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF |
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(for now, only if ALLOW_EXCH2 is defined). |
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o pkg/autodiff: |
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- include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F |
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(not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly. |
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+ clean-up comments (_RS is not always real*4) |
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- fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R) |
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- add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2: |
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was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs. |
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o testreport (AD-tests): |
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no longer link files from dir "../input" (1rst link files from |
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"../input_ad.[xx]" if secondary test "xx" and then from "../input_ad") |
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|
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checkpoint62f (2010/04/29) |
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o model/src/the_main_loop.F: |
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adjust store directives for seaice evp and multicategory according to |
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pkg/ecco/the_main_loop.F |
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o adjoint: |
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global_sum_ad was incomplete (noted many times by many people ;) |
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nice description by Jean U. as follows: |
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* allreduce(var) in global_sum.F can be interpreted as |
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reduce(sum) followed by broadcast of sum. |
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* The adjoint of that is |
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sum(adjoint) followed by broadcast(summed adjoint value) |
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or in other words, allreduce(sum, adjoint vars) |
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We were missing the sum(adjoint)! |
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Benign, except(!) for "global" scalars appearing in tile loops (bi,bj) |
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(noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset). |
145 |
The fix should produce 16-digit accuracy between |
146 |
single-CPU multi-tile (e.g. nSx=2, nPx=1) and |
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multi-CPU single-tile (e.g. nSx=1, nPx-2) |
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We'll probably change this yet again shortly |
149 |
o eesupp/src: |
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- fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?) |
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o pkg/icefront |
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- ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving |
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specification of addmass array based on a 2D field, which is added |
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at bottommost wet level at each horizontal location. |
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o model/src: |
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horizontal grid initialisation (other than curvilinear): add code for Exch2 IO |
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layout; (not always compatible with delX,delY setting; commented out for now). |
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o pkg/exch2: |
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change tile to processor setting (case nSy*nPy > 1): allows default model mapping |
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(myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config. |
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|
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checkpoint62e (2010/04/15) |
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o pkg/obcs: |
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- fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert). |
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o pkg/dic: |
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-fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up; |
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(note: not presently tested in any forward verification exp.) |
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update tutorial_global_oce_biogeo AD output file. |
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o pkg/exf: |
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- account for the variation of albedo as a function of zenith angle |
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by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h |
172 |
o build_options: |
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- rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas" |
174 |
o pkg/dic: |
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change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart: |
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- use binary pickup file for restart; |
177 |
- initialise atmos-CO2 box from dic_pCO2 parameter; |
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- fix multi-threaded. |
179 |
o pkg/rbcs: |
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- clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ; |
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change (+ fix IO calls) type of array RBC_mask from _RL to _RS. |
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- add RBCS to exp4 passive tracer 01 (rbcs was previously untested) |
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and update output.txt |
184 |
o pkg/kpp: |
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- add diagnostics for KPP non-local flux of Temp, Salinity and pTracers; |
186 |
- change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS |
187 |
(= ratio of KPP non-local (salt) flux relative to surface-flux) when |
188 |
using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat '); |
189 |
- change pkg/offline to read-in average KPPghat*KPPdiffKzS from file |
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KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile). |
191 |
o pkg/offline: |
192 |
fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor |
193 |
(bug was added in version 1.10 on 2007-08-23). |
194 |
o pkg/offline: |
195 |
- no need to specify periodicExternalForcing, etc ... to use offline pack |
196 |
- offline input files no longer just single prec --> parameter offlineLoadPrec |
197 |
o verification/lab_sea: |
198 |
change AD test to multi-tile setup and update all 4 AD output. |
199 |
NOTE: while cost function values remain very similar, |
200 |
gradients are very different, although gradient checks are self-consistent |
201 |
Should try to get to the bottom of this (cost function summation order?) |
202 |
o pkg/dic: |
203 |
in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid |
204 |
a weakness of TAF that drops part of double precision in log10 derivative. |
205 |
<= changes removed since problem has been fixed in current TAF version 1.9.71 |
206 |
update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo. |
207 |
o pkg/ecco: |
208 |
add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F |
209 |
update all 4 lab_sea AD output. |
210 |
|
211 |
checkpoint62d (2010/03/22) |
212 |
o build_options: |
213 |
remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles. |
214 |
o remove unbalanced quote (single or double) in commented line of source code |
215 |
(may cause some warning with some preprocessor/makedepend versions). |
216 |
o pkg/seaice: |
217 |
fix seaice_model.F for adjoint (gael) and update AD results of experiments |
218 |
lab_sea (std + evp + noseaicedyn) and offline_exf_seaice. |
219 |
o testreport: |
220 |
add option '-runonly' (short: '-ro') to just do the run part (without make). |
221 |
o eesupp: remove JAM communication code (obsolete). |
222 |
o add option to genmake2 & testreport to switch "_RS" type to "real*4" |
223 |
(if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return |
224 |
to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1 |
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(update also the output). |
226 |
|
227 |
checkpoint62c (2010/03/02) |
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o tools/build_options : |
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move (some) old optfiles from build_options/ to build_options/unsupported/ |
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o model/src and pkg/exf |
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surface relaxation -- separating data and data.exf options |
232 |
The point is to ensure that we specify the surface relaxation |
233 |
either in data or in data.exf (but not half and half) and to |
234 |
avoid an accidental relaxation to 0 (which happened if a time |
235 |
scale was specified but the file name was left empty) |
236 |
o model/src model/inc and pkg/mom_common |
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ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity |
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=> addition to the viscosity field as computed by others schemes |
239 |
o tools/build_options: |
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- rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile) |
241 |
but keep the former optfile for few weeks for smooth transition |
242 |
o pkg/ecco |
243 |
- allow user defined cost function contributions |
244 |
CPP: ALLOW_USERCOST_CONTRIBUTION |
245 |
USAGE: compute contributions in cost_usercost_all.F |
246 |
- note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. |
247 |
the two options are complementary. |
248 |
o pkg/smooth |
249 |
- migration from contrib to the main repository |
250 |
|
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checkpoint62b (2010/01/26) |
252 |
o pkg/monitor: |
253 |
- change back mon_printstats_rl.F & mon_stats_rl.F and add a stop |
254 |
(in case someone forgot to update customized pieces of code) |
255 |
o nonHydrostatic: |
256 |
- add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested); |
257 |
- add a simple 2-D experiment (short_surf_wave) to test it. |
258 |
o pkg/icefront: |
259 |
adding the shell of, and the hooks to, a new package that |
260 |
will model melting and freezing of vertical glacier ice fronts |
261 |
o momentum: |
262 |
add diagnostics of momentum tendency from Hydrostatic pressure gradient |
263 |
(without surf.pressure term: would need a 2nd filling since implicit term). |
264 |
o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace |
265 |
two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR |
266 |
cannot deal with the former |
267 |
o cleaning: |
268 |
- remove all (except OpenAD) old TLM output from results_ad dirs. |
269 |
- remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R) |
270 |
- comment out maskH definition (replaced by maskInC) |
271 |
o pkg/monitor: |
272 |
- change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl |
273 |
& mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs. |
274 |
|
275 |
checkpoint62a (2010/01/15) |
276 |
o model/src: |
277 |
- bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4) |
278 |
o pkg/diagnostics: |
279 |
- add optional level number diagnostics (i.e., level number to be define |
280 |
explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X". |
281 |
- strictly check for valid parser-code(10) ; |
282 |
- check if adding diag to the list from the right place. |
283 |
o pkg/longstep: |
284 |
- change parameters and fix tracer conservation with rstar/nonlinear free surface |
285 |
o diagnostics: |
286 |
- in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer |
287 |
S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics. |
288 |
o pkg/diagnostics: |
289 |
- Add option for writing vertical integral (sum of selected levels) of an output |
290 |
field instead of writing output field levels. Activate this option on a per |
291 |
output-file basis, by setting the 2nd character of fileflag to 'I'. |
292 |
- Add field-specific information relative to level integral in 3rd postion |
293 |
of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate |
294 |
vertically (x level-thickness x hFac), "r"=same but without hFac. |
295 |
o do_the_model_io: |
296 |
- pass end-of-model-run flag as argument, from forward_step to diagnostics_write: |
297 |
in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before |
298 |
writing pickups and stopping. |
299 |
o pkg/diagnostics (for now, only with mdsio): |
300 |
- write time information to meta file (and modify accordingly rdmds.m) : |
301 |
time-averaged diagnostics output: write starting and ending time of the |
302 |
time-averaging interval ; snap-shot diagnostics output remains unchanged; |
303 |
o pkg/timeave: |
304 |
- S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously |
305 |
always Nr), now assumed to be equal to number of levels of averaged field; |
306 |
only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F |
307 |
o pkg/sbo: |
308 |
- fix ocean bottom pressure global-average & 2-D time-ave output (was |
309 |
neither initialised nor filled). |
310 |
- add starting iteration in suffix of global-average output file |
311 |
(to avoid over-writing the file after a restart) |
312 |
- use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb). |
313 |
o time-average: |
314 |
- use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj) |
315 |
(pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf, |
316 |
ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice) |
317 |
this fix DIC_COST cumulative-time array (previously: bi,bj,k) |
318 |
- fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice) |
319 |
- fix missing accumulation for pkg/opps. |
320 |
- cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0) |
321 |
(pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81); |
322 |
- fix initialisation of time-ave vars and do only full time-step increment |
323 |
(i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81); |
324 |
o pkg/layers: |
325 |
- use standard RW pkg S/R to write the output |
326 |
and remove local write_fld version (which had a problem). |
327 |
- use simple cumulative-time array (no level index) to fix time-ave S/R calls. |
328 |
- fix LAYERS_CALC argument list. |
329 |
o pkg/timeave: |
330 |
- store cumulative-time in a simple tiled array (drop the level index) |
331 |
- add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array. |
332 |
o pkg/ocn,aim_compon_interf |
333 |
- changes for multi-threaded coupled run. (tested with ifort-11 on danton) |
334 |
|
335 |
checkpoint62 (2009/12/23) |
336 |
o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output. |
337 |
(was not previously tested in any other exp.) |
338 |
o pkg/monitor: |
339 |
- clean-up _RL/_RS version: add specific S/R for statistics with mask & volume: |
340 |
mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one |
341 |
(mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics. |
342 |
- use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F). |
343 |
- change del2 calculation. |
344 |
- use interior masks (instead of maskH, <- to be remove). |
345 |
- shorter monitor suffix for forcing stats ("forcing" instead of "extforcing"). |
346 |
o mask & obcs: |
347 |
- define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S). |
348 |
- move global area computation from ini_masks_etc.F to ini_linear_phisurf.F |
349 |
(called after packages_init_fixed) |
350 |
o pkg/obcs: |
351 |
- move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once. |
352 |
Fixes bug in obcs+exf with nSx*nSy.GT.1 |
353 |
- fix multi-tile handling in obcs balance code |
354 |
o nonHydrostatic: |
355 |
- Implement AB-3 for non-hydrostatic vertical momentum ; |
356 |
(change ordering of var. stored in pickup file when using NH) |
357 |
- move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D. |
358 |
- add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x |
359 |
(in prep. for new NH free surface form). |
360 |
o pkg/obcs: |
361 |
add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe |
362 |
o model/src: |
363 |
fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography |
364 |
|
365 |
checkpoint61z (2009/12/01) |
366 |
o nonHydrostatic: |
367 |
Fix missing vertical flux of vert. momentum near surface (k=1). This fixes |
368 |
a spurious source of energy in simple baroclinic adjusment test case. |
369 |
Update all non-hydrostatic exp output. |
370 |
o model/src (3-d solver): |
371 |
Change again 3-D solver free-surface RHS term when exactConserv=T: |
372 |
simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1 |
373 |
(which was not the case with previous formulation). |
374 |
To recover previous version, just reset "oldFreeSurfTerm" to previous value. |
375 |
Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW. |
376 |
o nonHydrostatic: |
377 |
- compatible with implicDiv2Dflow < 1 ; + implement implicit factor |
378 |
for Non-Hydrostatic pressure gradient (similar to implicSurfPress). |
379 |
- change 3-D solver to work with r* (for now, only with linear free-surf.) |
380 |
- add few debug diagnostics (cg3d_x, residual) |
381 |
o model/src: |
382 |
fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b). |
383 |
update output of exp. global_ocean.cs32x15.viscA4 |
384 |
o update output of exp. global_ocean.cs32x15.icedyn after removing |
385 |
#define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h |
386 |
o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) |
387 |
o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output |
388 |
for complex grids, for now only to "state", "adstate", "adexf", "adseaice" |
389 |
o model: add Christopher Wolfe's implemetation of the single reduction cg2d |
390 |
(d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and |
391 |
runtime flag useSRCGSolver. Modify verification experiment global_with_exf |
392 |
to test this code |
393 |
o pkg/cd_code: |
394 |
Change defaut D-grid time-stepping to get the same for D-grid momentum as for |
395 |
C-grid momentum. D-grid velocity used to be stepped forward in time with |
396 |
Adams-Bashforth only on surface pressure term. Tests show that using AB on |
397 |
D-grid coriolis term improves stability (as expected from CD-scheme paper). |
398 |
To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h). |
399 |
Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2), |
400 |
lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD), |
401 |
tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens. |
402 |
Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2, |
403 |
global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD. |
404 |
o pkg/obcs: |
405 |
- fix bug in initialisation (broken since Oct 1rst modification) |
406 |
for useOBCSprescribe without useEXF. |
407 |
|
408 |
checkpoint61y (2009/11/15) |
409 |
o pkg/seaice |
410 |
- change (once again) the discretization for the evp solver: rather than |
411 |
squaring the averages of strain rates, average the squares to give |
412 |
a better approximation to VP behavior (in simple test); this breaks |
413 |
verification experiments that use EVP (lab_sea and lab_sea.hb87) |
414 |
--> update outputs |
415 |
o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit) |
416 |
to improve vectorization of adjoint code on TARGET_NEC_SX |
417 |
o verification/vermix: |
418 |
- change vermix to a more "classical" 1d column with high vertical |
419 |
resolution, seasonal heat flux forcing and constant wind forcing |
420 |
--> update outputs |
421 |
o pkg/seaice |
422 |
- fix diagnostics of principal stress components for EVP |
423 |
- add optional diagnostics of non-linear convergence for LSOR solver |
424 |
- make maximum zeta a runtime parameter |
425 |
o model/src (3-d solver): |
426 |
Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49), |
427 |
which consisted in removing the Surf. Non-Hydrostatic pressure from the |
428 |
whole column and adding it to Eta (inspired from Casualli, 1999): |
429 |
Only affects 3-D solver initial guess and only if using ExactConserv, |
430 |
but tests did show a degradation of solver convergence. For this reason, |
431 |
decide to disable this piece of code. |
432 |
to recover previous version, just set zeroPsNH = exactConserv (line 78). |
433 |
Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW |
434 |
o pkg/ggl90: |
435 |
- fix previous modif (unfortunatly has not been documented here). |
436 |
o pkg/seaice/autodiff: |
437 |
- add CPP flag to include clipping of zeta in EVP code; |
438 |
although clipping of zeta is not necessary for EVP and not recommended |
439 |
it was done by default, now clipping is disabled by default |
440 |
- modify computation and store zetaC/Z in seaice_evp for TAF |
441 |
- add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default) |
442 |
- change seaice_calc_viscosities/strainrates for better |
443 |
vectorization after AD by TAF |
444 |
- rearrange common blocks in SEAICE.h once again for easier dumps of |
445 |
adjoint output, adjust adcommon.h and g_common.h |
446 |
- change flux form of default advection scheme for better vectorization |
447 |
of adjoint code |
448 |
- modify lab_sea/input.lsr to test the flux form of default advection |
449 |
scheme |
450 |
o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level |
451 |
transition in checkpoint61r) |
452 |
|
453 |
checkpoint61x (2009/10/19) |
454 |
o adjoint: adding two new verification experiments |
455 |
* tutorial_global_biogeo: an online dic sensitivity experiment |
456 |
(work with G. Forget) |
457 |
* tutorial_dic_adjoffline: an offline dic sensitivity experiment |
458 |
(an update of the Dutkiewicz et al., 2006 paper) |
459 |
Both use the same CO2FLUX cost function, but different controls |
460 |
Gradient checks look good, but some recomp. could still be traightened out |
461 |
Should add xx_dic control variable to test at some point |
462 |
o model/src: |
463 |
add run-time parameters to check and/or mask initial Temp & Salt |
464 |
o pkg/ptracers: |
465 |
apply zonal filter (if used) to all passive tracers |
466 |
|
467 |
checkpoint61w (2009/10/12) |
468 |
o adjoint: |
469 |
* update and finish work on adjoint of dic package (G. Forget) |
470 |
* start adjoint of offline package |
471 |
* bug fix for cube-sphere TLM code (active_file_g.F) |
472 |
o tutorial_global_oce_optim: |
473 |
now tested with 4 tiles (change data.grdchk and update output_adm.txt) |
474 |
and add SIZE.h_mpi for MPI testing |
475 |
o pkg autodiff |
476 |
- fix bug in autodiff_restore |
477 |
- make genmake2 remove comments and empty lines from ad_input_code.f in |
478 |
order to reduce file size (new script file remove_comments_sed) |
479 |
o allows to specify vertical profile of vertical viscosity (viscArNr) |
480 |
o pkg autodiff |
481 |
autodiff_ini_model_io: comment out writing of grid information to netcdf |
482 |
files, because at this time the grid fields are a bunch of zeros |
483 |
(this is analogous to ini_mnc_vars.F) |
484 |
o pkg seaice/autodiff: |
485 |
left-over from removing the 3-time-level fields: |
486 |
- small rearrangement of common blocks (SEAICE.h) |
487 |
- fix field declaration in order to get meaningful output in |
488 |
adseaice.*.nc (adcommon.h) |
489 |
o pkg obcs: |
490 |
- go through NH code only if nonHydrostatic=T |
491 |
- fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart) |
492 |
- move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields |
493 |
=> Update output of experiment seaice_obcs |
494 |
- useOBCSbalance: code is wrong with multi-tile / proc: add a stop. |
495 |
- fix NH+Orlanski restart (add wvel OBC value in pickup file) |
496 |
- fix restart for useOBCSprescribe + useEXF |
497 |
o pkg ctrl |
498 |
- make obcs as control parameter work also with useSingleCPUio |
499 |
- replace a few sny and snx by Ny and Nx to be consistent with |
500 |
ctrl_set_globfld_x/yz.F |
501 |
o pkg seaice |
502 |
- re-introduce global field frWtrAtm for the case of |
503 |
ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F) |
504 |
- catch the case of an empty filename in seaice_cost_init_fixed.F |
505 |
o pkg ecco: |
506 |
- small bug fixes in the_main_loop |
507 |
. fix order of monitor arguments |
508 |
. change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY |
509 |
. move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so |
510 |
that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF |
511 |
- replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the |
512 |
imbalance diagnostics for wmean_h/sflux = 0 |
513 |
- add actual values to f_obcsn/s/w/e in ecco_cost_final.F |
514 |
- catch the case of empty filenames in ecco_cost_init_fixed.F |
515 |
and ecco_readparms.F |
516 |
- fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta) |
517 |
to make this statement meaningfull in ecco_cost_weights.F |
518 |
o pkg zonal_filt: |
519 |
- change ZONAL_FILTER S/R interface (allows to filter 2-D fields) |
520 |
- when using rStar, filter uVel*hFacW instead of uVel |
521 |
(tested without topography: fix a Pb of growing instability with NLFS) |
522 |
o pkg/aim/thsice: |
523 |
-Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F |
524 |
(works as SST restoring) |
525 |
o pkg/thsice: |
526 |
-add specific parameter for salt restoring in slab mixed-layer |
527 |
(by default equal to the temperature restoring) |
528 |
|
529 |
checkpoint61v (2009/09/21) |
530 |
o pkg/kpp: |
531 |
-add double diffusive contributions as a hack, turned off by default |
532 |
for now, and the code can be excluded with a CPP-flag |
533 |
EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX |
534 |
-add a verification experiments to "vermix" to test this code |
535 |
o pkg/mom_common: |
536 |
Move computation of length scales to mom_init_fixed.F (avoid recomputation |
537 |
at each time-steps*levels). |
538 |
o pkg/layers: |
539 |
Created a new package for computing volume fluxes in temperature or |
540 |
[not yet implemented] density layers, e.g. for calculating residual |
541 |
overturning circulations. |
542 |
o pkg/diagnostics: |
543 |
implement a RS type version for the set of DIAGNOSTICS-FILL subroutines |
544 |
o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option) |
545 |
o pkg/mdsio (& pkg/rw): rework high level S/R interface: |
546 |
To avoid mixing type (RS/RL) of input/output array argument, |
547 |
replace single mixed-type array with a pair from each type (RS/RL). |
548 |
o setting pickupSuff force to start from a pickup (even if nIter0=0): this |
549 |
is now implemented for all pkgs (previously only done for the main pickup) |
550 |
|
551 |
checkpoint61u (2009/08/25) |
552 |
o pkg/obcs: |
553 |
- change OB?eta from _RS to _RL and put them into a separate commen block |
554 |
- add code to read OB?eta from a file via obcs_prescribe_read: the code |
555 |
compiles and does not destroy any other experiments, the data is read |
556 |
properly, but the code is not tested in actual applications |
557 |
o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to |
558 |
create a meaningful unit attribute for the time coordinate variable |
559 |
o pkg/ebm: add plenty of missing "_d 0" ; |
560 |
update results of experiment global_ocean_ebm (fwd + adjoint tests) |
561 |
Notes: several pieces of code only works for (very) specific set up |
562 |
(domain size, lat range, etc ...); should be documented & stop if one |
563 |
of those assumptions is not meet. |
564 |
o pkg/seaice: add missing "_d 0" in HSNOW initialisation |
565 |
update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests) |
566 |
and offline_exf_seaice (seaicetd + adjoint). |
567 |
o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC): |
568 |
update results of experiments: lab_sea (4 fwd tests + 3 adjoint), |
569 |
seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2). |
570 |
o few changes to pass when compiling with strick checking of arguments |
571 |
across S/R (allow to find few bugs in S/R calls). |
572 |
o pkg/seaice: |
573 |
- seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new |
574 |
2d-fields, for slightly better performance |
575 |
|
576 |
checkpoint61t (2009/07/22) |
577 |
o pkg/seaice: |
578 |
- remove unused variables in seaice_evp |
579 |
- reduce number of SQRT in seaice_evp and seaice_calc_viscosities |
580 |
o eeset_parms.F, open_copy_data_file.F & ini_parms.F: |
581 |
named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT): |
582 |
each processor opens a different file (a fix from Matt). |
583 |
o cg2d: |
584 |
use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F : |
585 |
this reduces number of EXCH calls by 2 when using exch2. |
586 |
For now, keep previous size array for gc2d_nsa.F to avoid Pb with store |
587 |
directives and missing simple EXCH (exch_s3d_rx) adjoint code. |
588 |
o pkg/thsice: |
589 |
add code for Near Infra-Red albedo (from Jeff) |
590 |
(turned on with run-time flag: thSIce_calc_albNIR, in data.ice). |
591 |
o ini_model_io: |
592 |
move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F |
593 |
MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F |
594 |
to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice. |
595 |
|
596 |
checkpoint61s (2009/06/30) |
597 |
o pkg/exch2 (exch2_rxN_cube*): |
598 |
remove last BARRIER (no need to synchronise after getting data from shared |
599 |
buffer (get) as long as any change to buffer (put,recv) is between BARRIER) |
600 |
o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH |
601 |
and generate new output (for the 2 tests) using default rotationPeriod. |
602 |
o pkg/exch2: |
603 |
- always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F |
604 |
(was already the case with AUTODIFF_EXCH2 defined) |
605 |
- add bj in exch2 arrays and S/R. |
606 |
- can now use pkg/exch2 for regular (non CS) set-up; switch test experiment |
607 |
MLAdjust to exch2 (identical results except with MPI -> truncation diff); |
608 |
o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep |
609 |
- adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY |
610 |
GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT |
611 |
- verification experiment natl_box.longstep |
612 |
o build_options: ifort+mpi_aces optfile (following Constantinos advise): |
613 |
allow different versions of ifort (8 or 9) and different versions |
614 |
of mpi (mpich or mpich2) to be used with the same optfile. |
615 |
requires to load a netcdf module and set MPI_INC_DIR (see comments inside |
616 |
optfile). Change testing scripts (example_scripts/ACESgrid) accordingly. |
617 |
o pkg/seaice: |
618 |
fix previous modif (3-level field removed) for old-pickup reading |
619 |
|
620 |
checkpoint61r (2009/06/25) |
621 |
o pkg/seaice: |
622 |
- clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps: |
623 |
1. introduce fields for time step (N-1) |
624 |
2. do not use levels 2 and 3 anymore (but keep them) |
625 |
3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This |
626 |
includes changes to pkg/thsice/thsice_get_velocity.F, |
627 |
model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and |
628 |
pkg/obcs/obcs_apply_uvice.F. |
629 |
- completely remove code for leap-frog time stepping for second order |
630 |
advection |
631 |
- adjusted adjoint accordingly; |
632 |
gradient checks have improved by an order of magnitude! |
633 |
|
634 |
checkpoint61q (2009/06/22) |
635 |
o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver |
636 |
- the boundary conditions along open boundaries are unclear, because the |
637 |
associated masks are set to zero and are thus treated as closed when |
638 |
applying the slip-boundary conditions. |
639 |
- move initialisation of grid variables from seaice_init_varia to _fixed |
640 |
o adding doc/diags_changes.txt |
641 |
o model/src: |
642 |
do_the_model_io: rename few pkg S/R which are called from do_the_model_io, |
643 |
to avoid "_diags" naming if no relation to pkg/diagnostics. |
644 |
ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF |
645 |
file and only call PLOT_FIELD_XYZ if debugMode=T. |
646 |
remove few PLOT_FIELD_XY calls outside initialisation. |
647 |
remove few unnecessary BARRIER. |
648 |
o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling |
649 |
of salt_plume package in Southern Ocean |
650 |
o pkg/thsice: |
651 |
- fix hOceMxL in overlap (needed for sea-ice advection); |
652 |
update output of experiment global_ocean.cs32x15.icedyn. |
653 |
o pkg/seaice: |
654 |
- make the (placeholder-)tracer IceAge a little more meaningful |
655 |
by avoiding ridging of age due to convergent ice flow |
656 |
- add diagnostics for surface temperature, atmospheric and oceanic |
657 |
heat flux, and atmospheric and oceanic ice growth |
658 |
|
659 |
checkpoint61p (2009/06/10) |
660 |
o eesupp (global_max & global_sum): |
661 |
- add one more element to buffer (start at index 0) for GL_MAX/SUM output; |
662 |
- remove starting & endding barrier (no longer needed) |
663 |
o pkg/mdsio, writelocal: |
664 |
works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined |
665 |
(remove the STOP): uses shared buffer IO to store data from all threads |
666 |
and then let master-thread write nThreads tiles. |
667 |
o pkg/mdsio (read/write field): |
668 |
- tiled IO done in 1 piece (all levels at a time); |
669 |
- new header file "MDSIO_BUFF_3D.h" with 3-D buffers. |
670 |
- multi-threaded: allow to read/write local (non-shared) array |
671 |
(was already working with singleCpuIO ; now works also without); |
672 |
=> no longer needs barrier call after reading a file (added inside |
673 |
mds_read/write field). |
674 |
- move barrier calls outside gather/scatter_2d to mds_read/write_field |
675 |
o pkg/obcs/exf |
676 |
- exf_getffieldrec.F: add a few ". _d 0" and |
677 |
add code to catch the case fldperiod = 0. |
678 |
- obcs_precribe_read.F: change if statements so that they match |
679 |
the variable type (_RL) |
680 |
- add a separate exf_iprec_obcs to exf_set_obcs (by default equal to |
681 |
exf_iprec) as part of namelist EXF_NML_01 |
682 |
o pkg/mdsio: |
683 |
- read/write tiled (local) files: read/write 1-level tile chunk at a time |
684 |
(instead of segment of length sNx); expected to speed up tiled IO. |
685 |
o pkg/exch2: |
686 |
- take buffer copy from/to array out of S/R exch2_send/recv into new |
687 |
S/R exch2_put/get ; Exch of local variable now works with MPI+MTH |
688 |
(tested by removing commom block statement in SOLVE_FOR_PRESSURE.h). |
689 |
- ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get) |
690 |
- simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds |
691 |
(which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by |
692 |
including Topology header file (and common blocks). |
693 |
- implement EXCH_IGNORE_CORNERS in scalar exchange (rx1); |
694 |
remove 2nd exch call in exch2_s3d_rx (no longer needed). |
695 |
- document S/R arg. list (+ update some comments) |
696 |
o pkg/seaice: |
697 |
- added SEAICE_CLIM_AIR code, which permits modulation of surface air |
698 |
temperature and humidity over sea ice based on climatological values. |
699 |
- clean up computation of Hibler+Bryan (1987) stress coupling for the case |
700 |
of LSR (this change is expected to change the results slightly because now |
701 |
it uses slightly difference moduli from the second last LSR solution, but |
702 |
that is more consistent with the stress computations; this part of the code |
703 |
is not tested in the verification experiments) |
704 |
- fix diagnostics for flux of ice in case of B-grid |
705 |
- turn strain rates eij and press into global fields within global |
706 |
common block in SEAICE.h for more straighforward diagnostics |
707 |
- fix diagnostics for principal stress components, press, zeta, eta |
708 |
to give something meaning full |
709 |
o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate |
710 |
new output (all 4 tests) using default rotationPeriod. |
711 |
o pkg KPP: |
712 |
- add flag (LimitHblStable) to avoid limiting BL depth under stable conditions |
713 |
- fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1 |
714 |
and normal grid from 1 to Nr) |
715 |
o Fix computations of L4rdt in mom_calc_visc.F |
716 |
o eesupp: |
717 |
new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg): |
718 |
should be called before a "stop" if we know that all process are going |
719 |
to stop; if one Proc does call this S/R, will hang in MPI_FINALISE. |
720 |
|
721 |
checkpoint61o (2009/05/26) |
722 |
o pkg/exch2: change check_depths to issue just a warning (instead of error+stop) |
723 |
o model/src/ini_curvilinear_grid.F: |
724 |
compute angleSin/CosC when they are not read from a file |
725 |
o pkg/seaice: |
726 |
add pseudo time stepping for LSOR |
727 |
o pkg/exch2: |
728 |
temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW |
729 |
o pkg/seaice: |
730 |
Adding separate sea ice albedo, drag coefficients, and HO in Southern |
731 |
Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h |
732 |
o SingleCpuIO: |
733 |
fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used. |
734 |
o pkg/seaice: |
735 |
put exchanged variable in (local) common block for MPI+Multi-Threads |
736 |
to work (necessary with exch1, and for now with exch2 too). |
737 |
o verification: to get more experiments tested with mpi, mth and mpi+mth, |
738 |
change tiling of: |
739 |
aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15, |
740 |
hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope |
741 |
update output of exp: |
742 |
exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5), |
743 |
tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod) |
744 |
+ ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU |
745 |
(note: output.txt generated on faulks using only 1 tile) |
746 |
o eesupp & mdsio (SingleCpuIO): |
747 |
- remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time |
748 |
parameter "W2_useE2ioLayOut" (read from file "data.exch2"). |
749 |
Note: was not effective for globalFile & useSingleCpuIO=F; now fixed. |
750 |
- move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc). |
751 |
- fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same |
752 |
gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array). |
753 |
o pkg/exch2: |
754 |
- new code to set-up W2-Exch2 topology (replace matlab-topology-generator): |
755 |
read parameter file "data.exch2" if it exists; otherwise try default regular |
756 |
cube without blank-tile; new header file "W2_EXCH2_SIZE.h"; |
757 |
- update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible |
758 |
with new code (not to be used, just as a backup solution). |
759 |
- add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2" |
760 |
in utils/exch2/input. |
761 |
|
762 |
checkpoint61n (2009/05/12) |
763 |
o eesupp & mdsio (SingleCpuIO): |
764 |
- move mapping to global io-buffer inside gather_2d/scater_2d: this save |
765 |
memory (1 less 2D global RL array); skip 1 buffer copy; and only send/ |
766 |
receive real*4 array (instead of real*8) to read/write 32.bit files. |
767 |
(new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S |
768 |
and remove new mapping S/R) |
769 |
o pkg/mdsio: in preparation for topology-generator within pkg/exch2: |
770 |
- Change declaration of SingleCpuIO buffer, reduced to only 1 dim.: |
771 |
xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h |
772 |
when using exch2. Add S/R to map global io-buffer to global model array. |
773 |
- uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt. |
774 |
|
775 |
checkpoint61m (2009/04/29) |
776 |
o write_utils : change WRITE_1D_R8 to WRITE_1D_RL |
777 |
and add 3 other S/R for other types (R4,R8,RS). |
778 |
Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument. |
779 |
o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros): |
780 |
- ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ; |
781 |
- reduce number of macro definitions (keep only those which are used); |
782 |
can always call directly the corrresponding S/R if needed. |
783 |
- everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix |
784 |
_R4/_R8 to _RS/_RL when applied to _RS/_RL variable. |
785 |
Fixed wrong type of arg in: |
786 |
atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F |
787 |
ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F |
788 |
To fix: global_sum of var in common block is wrong (multi-threaded) in: |
789 |
dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F |
790 |
To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops) |
791 |
o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd |
792 |
"nlfs" mpi test is going to stop when checking for unconnected tile egdes. |
793 |
o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error |
794 |
o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile |
795 |
edges are closed (zero depth); might happen with "blank tiles"; |
796 |
for now, disabled if using OBCS. |
797 |
o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi": |
798 |
link *_mpi files from "MODS" dir) to return to a strait-forward behavior. |
799 |
o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D) |
800 |
to reduce length of 1.D array print in STDOUT. |
801 |
o adjustment.cs-32x32x1: changed to oceanic test with 1 continent |
802 |
+ use 48 tiles (16x8): this will allow to test "blank tiles". |
803 |
o start to test MPI + multi-threaded (change testreport to skip tests |
804 |
where number of tiles do not match). |
805 |
o genmake2: add option "-omp" to turn on Open-MP ; |
806 |
passed to testreport (if using -mth) ; merge few (*+mth) optfiles. |
807 |
o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them) |
808 |
and keep the original tile numbering. Note: compatible with old |
809 |
W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files. |
810 |
|
811 |
checkpoint61l (2009/04/07) |
812 |
o Overlaps had been forgotten in calculating ijk keys : fixed |
813 |
o fix cyrus makedepend for gcc 4.4 |
814 |
o experiment fizhi-cs-aqualev20: |
815 |
switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE) |
816 |
and generate new output. Note: new output is much closer to the old |
817 |
one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from |
818 |
the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007. |
819 |
o pkg/fizhi: |
820 |
- change to avoid indices going deliberately over array-bounds |
821 |
- remove unnecessary MPI stuff |
822 |
- perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY" |
823 |
- new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE: |
824 |
does not go over array-bounds and therefore returns reliable output. |
825 |
- in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls: |
826 |
this S/R has 4 output arguments, which are used inside "get_alarm"; |
827 |
when it is called with the same variable "ndum" in place of several |
828 |
output arguments, this produces weird side effect inside "get_alarm" |
829 |
(e.g., datein=dates(n) is overwritten by timein=times(n) since both |
830 |
datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum" |
831 |
address) and produces error. |
832 |
o tools/gemake2: (March 27-29 2009) |
833 |
with option "-mpi": link *_mpi files from "MODS" dir (this is what |
834 |
testreport does). |
835 |
o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output |
836 |
o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F: |
837 |
update lab_sea.lsr & lab_sea.salt_plume results |
838 |
o pkg/seaice: |
839 |
Major overhaul of the LSOR solver: change discretization from original |
840 |
finite differences to finite volume. The old routine is still in the |
841 |
file seaice_lsr.F and can be turned on with the CPP-flag |
842 |
SEAICE_OLD_AND_BAD_DISCRETIZATION |
843 |
Along with this change, the discretization of the strain rates is changed. |
844 |
The same flag turns on the old discretization in seaice_calc_strainrates.F |
845 |
All verification experiments with seaice are affected (except for |
846 |
seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old |
847 |
results by setting the above flag. |
848 |
Further changes involve changes in defaults: |
849 |
- ALLOW_FLOODING is defined and turned on by default |
850 |
- SEAICEadvSnow = .true. is now the default |
851 |
- SEAICEadvSalt = .true. is now the default |
852 |
- SEAICEadvAge = .true. is now the default |
853 |
- SEAICE_clipVelocities = .false. is now the default |
854 |
(as per J. Zhang's recommendation) |
855 |
- B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE |
856 |
is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS |
857 |
- seaice_growth: replace computation of UG by a simple copy from wspeed |
858 |
|
859 |
checkpoint61k (2009/03/18) |
860 |
o pkg/seaice: a few bug fixes mostly concerning the metric terms: |
861 |
seaice_lsr: fixed a few metric terms, |
862 |
affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs |
863 |
add more debugging diagnostics |
864 |
seaice_evp: removed superfluous many metric terms of FV discretization |
865 |
of stress divergence |
866 |
affects lab_sea, lab_sea.hb87 |
867 |
seaice_ocean_stress: removed superfluous many metric terms of FV discretization |
868 |
of stress divergence for non-evp solver |
869 |
(this part is not tested anywhere) |
870 |
seaice_calc_strainrates: fixed a bug in no-slip boundary conditions, |
871 |
they were effectively only half slip |
872 |
affects lab_sea.hb87 |
873 |
updated all relevant verification experiments (except lab_sea//output_adm.txt |
874 |
which was left over, but fails at level 7 & 6) |
875 |
|
876 |
checkpoint61j (2009/03/17) |
877 |
o pkg/seaice: turn a few hard wired parameters into run time parameters |
878 |
o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model |
879 |
time in seconds as promised by the usints in seaice_monitor and exf_monitor |
880 |
o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids |
881 |
that are not cubed-sphere grids |
882 |
o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR |
883 |
o pkg/ctrl: |
884 |
fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low) |
885 |
o non-hydrostatic (calc_gw.F): |
886 |
fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec |
887 |
update output of exp. global_ocean.cs32x15.viscA4 |
888 |
o remove backward compatibility for thetaMin,phiMin |
889 |
(replaced by xgOrigin,ygOrigin on Jan 27, 2009) |
890 |
o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the |
891 |
interpolated wind field not only for curvilineargrid=.true., but also |
892 |
for a rotated grid (rotateGrid=.true.) |
893 |
o pkg/exf: add capability to bypass interpolation for runoff |
894 |
by setting yet another CPP-flag |
895 |
o eesupp/src, B-grid exchange: |
896 |
add simple (6 tiles, non MPI) CS exch + standard interface S/R. |
897 |
o autodiff |
898 |
new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV |
899 |
allows to switch to single-prec common blocks; |
900 |
corresponding switch occurs in tamc.h, integer isbyte |
901 |
TAF store directivs "byte" and "kind" seem equivalent; |
902 |
Most tamc.h have been updated correspondingly. |
903 |
|
904 |
checkpoint61i (2009/02/13) |
905 |
o autodiff: |
906 |
fix autodiff_sore/_restore indices for obcs |
907 |
(spotted by I. Hoteit, M. Mazloff) |
908 |
o pkg/autodiff, pkg/ctrl: |
909 |
Add flag to reduce all tapelev I/O to single-prec. |
910 |
In data.ctrl set |
911 |
doSinglePrecTapelev = .TRUE. |
912 |
o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2: |
913 |
check in hack for SX8 compiler (for dxV, dyU); remove it afterwards. |
914 |
o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for |
915 |
real fresh water flux (not yet) |
916 |
o pkg/mdsio & rw: |
917 |
- add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta) |
918 |
- add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX. |
919 |
o pkg/flt: |
920 |
- replace FLT_INIT by 3-steps standard initialization S/R: readparms, |
921 |
init_fixed & ini_varia. |
922 |
- clean-up & simplify linear interpolation S/R: |
923 |
move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid. |
924 |
- fix some indices (mainly vertical index) ; add IMPLICIT NONE. |
925 |
- more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R. |
926 |
- add vert. coordinate & horiz. indices to output files. |
927 |
- change vertical position in initial condition, from index to depth [m]. |
928 |
- store horizontal (decimal) indices i,j in common block (instead of coord. x,y) |
929 |
(easier to get to a curvilinear grid) ; delX,delY no longer used. |
930 |
o pkg/ggl90: a few modifications: |
931 |
- fix bottom boundary condition, and interpolation of KappaE |
932 |
near top and bottom |
933 |
- use same set of viscosity/diffusivity for TKE/momnetum/tracer |
934 |
- add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH) |
935 |
- add a few options for mixing-length upper limit (--> mxlMaxFlag) |
936 |
o rename thetaMin,phiMin -> xgOrigin,ygOrigin |
937 |
(maintain temporary backward compatibility, until next checkpoint) |
938 |
|
939 |
checkpoint61h (2009/01/27) |
940 |
o pkg/diagnostics with "periodic averaging diagnostics": |
941 |
fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. |
942 |
o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82 |
943 |
o pkg/obcs: fix loop ranges for balancing code |
944 |
o pkg/flt: |
945 |
- improve criteria for finding which tile owns a float. |
946 |
- fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case. |
947 |
o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg |
948 |
aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling |
949 |
with ocean biogeo) |
950 |
o pkg/flt: |
951 |
- do some cleaning and fix the restart ; |
952 |
- add output.txt in flt_example/results to get this pkg tested. |
953 |
o genmake2: add an EXTENDED_SRC option and flag. |
954 |
for now, cannot be turned on on command line (only through genmake_local) |
955 |
o pkg/mdsio: read/write vector: |
956 |
- singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS |
957 |
- singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR |
958 |
& MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. |
959 |
- affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) |
960 |
(drop to 4 digits matching for grad). But this test does not look very |
961 |
reliable (was already failling on eddy, fc5, at 6.digits). Update output. |
962 |
|
963 |
checkpoint61g (2008/12/29) |
964 |
o pkg/flt: |
965 |
- move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) |
966 |
+ make OPTIONS file more standard. |
967 |
- rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) |
968 |
- fix _BYTESWAPIO CPP-Flag |
969 |
- standard reading of file-parameter "data.flt" |
970 |
- fix argument list of S/R FLT_RESTART |
971 |
still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F |
972 |
o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell |
973 |
o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to |
974 |
a still unfixed compiler/optimization bug |
975 |
|
976 |
checkpoint61f (2008/11/21) |
977 |
o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; |
978 |
update results of global_ocean.cs32x15.icedyn test. |
979 |
o move getcon.F from model/src to pkg/fizhi. |
980 |
o pkg/exf: add parameter for extrapolation of temp up to the surface |
981 |
and option to prevent negative evap (in bulk_largeyeager04 only). |
982 |
o Prather Advection scheme: fix tracer conservation for divergent flow |
983 |
(e.g., when using NonLin Free-Surface). |
984 |
o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead |
985 |
o gmredi (Visbeck-variable-K): |
986 |
- add more parameters to Visbeck-variable-K. |
987 |
- use a 5 points average for dSigmaR in Visbeck-K calculation |
988 |
(more "homogenous": same stencil and same weights as in dSigmaH) |
989 |
- update output of ideal_2D_oce experiment. |
990 |
o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 |
991 |
(#undef REAL4_IS_SLOW) |
992 |
- pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 |
993 |
coordinate variable |
994 |
- pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables |
995 |
(surface forcing fields), removes some of the functionality |
996 |
- model/src/write_grid.F: write _RS variables as RS-netcdf variables |
997 |
- model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but |
998 |
probably not all: copy _RS surface flux fields to RL field before |
999 |
calling DIAGNOSTICS_FILL |
1000 |
- model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into |
1001 |
real*4 (CALL EXCH_*_RS) versions. |
1002 |
- tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 |
1003 |
(generate new output). |
1004 |
|
1005 |
checkpoint61e (2008/10/23) |
1006 |
o gmredi (Visbeck-variable-K): |
1007 |
- fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h |
1008 |
- change computation of Visbeck-K where Slope > Smax : |
1009 |
now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct) |
1010 |
previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output. |
1011 |
o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic |
1012 |
to be the same as with Z-coord. (i.e., m/s & no-units respectively). |
1013 |
o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc) |
1014 |
o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz |
1015 |
does not become too large (to avoid precision problems in implicit-diffusion |
1016 |
solver); update ideal_2D_oce output. |
1017 |
o pkg ggl90: |
1018 |
- in ggl90_cal.F: compute only one set of visc/diff, used to |
1019 |
step forward TKE/T/S/momentum |
1020 |
- default value of GGL90viscMax/GGL90diffMax larger and equal (to |
1021 |
have Prandlt =1) |
1022 |
o gmredi (fm07): |
1023 |
- add lower limit on Transition layer thickness + lower limit on 1/lambda |
1024 |
- allow to set few more params from data.gmredi |
1025 |
o pkg ggl90: |
1026 |
- add missing sqrt(2) factor in computation of mixing length |
1027 |
scale in ggl90_calc.F |
1028 |
(see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) |
1029 |
|
1030 |
checkpoint61d (2008/09/25) |
1031 |
o adjoint modifs |
1032 |
- adapt to new field rhoInSitu |
1033 |
- allow to revert from StoreDynVars2D, StoreDynVars3D |
1034 |
to individual fields |
1035 |
(switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) |
1036 |
o store 3-D (in-situ) density in commom block (DYNVARS.h) |
1037 |
- save 1 rho computation. |
1038 |
- no longer modify T & S inland when using down_slope pkg. |
1039 |
o gad_som : allow to switch to SOM advection for T & S without corresponding |
1040 |
pickup files (using new S/R: MDS_CHECK4FILE). |
1041 |
o keep removing _BEGIN/_END_MASTER between MDSIO S/R call |
1042 |
(for useSingleCpuIO to work in multi-threaded) |
1043 |
o pkg/shelfice: |
1044 |
- disentangle parameters: retire shelfIceFile in data/PARM05 and substitute |
1045 |
with SHELFICEtopoFile in data.shelfice |
1046 |
- move code for reading ice shelf topography and modifying hFacC into separate |
1047 |
subroutines of the shelfice package |
1048 |
- separate initialisation of "fixed" and "variable" variables |
1049 |
- kTopC is not (yet) replaced by kSurfC, although this is possible |
1050 |
o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
1051 |
o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
1052 |
and rename: |
1053 |
ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
1054 |
ini_reference_state.F --> load_ref_files.F (- set anelastic factors) |
1055 |
o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) |
1056 |
|
1057 |
checkpoint61c (2008/08/30) |
1058 |
o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" |
1059 |
to add mass source/sink of fluid in the interior (3-D generalisation |
1060 |
of oceanic real-fresh water flux). |
1061 |
o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) |
1062 |
o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) |
1063 |
o new pkg: down_slope |
1064 |
density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). |
1065 |
- presently, modify T & S inland (dwnslp_calc_rho.F). |
1066 |
can be avoided if rho was stored in common bloc and used in calc_phi_hyd. |
1067 |
- implementation for ocean in P-coords not tested. |
1068 |
- add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. |
1069 |
o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) |
1070 |
(to facilitate conversion of oceanic pkg to p-coordinate). |
1071 |
o change FIND_RHO to FIND_RHO_2D : |
1072 |
pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. |
1073 |
o new pkg: cheapaml |
1074 |
|
1075 |
checkpoint61b (2008/08/05) |
1076 |
o exch2: |
1077 |
change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) |
1078 |
- no longer depend on the order sequence (N,S,E,W). |
1079 |
- 3rd exchange no longer needed (tested with 24 tiles). |
1080 |
- same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) |
1081 |
- exch_UV_A-grid readily available (but not yet tested). |
1082 |
comment out 3rd exch call and remove copy of V to U at SE & NE face-corners |
1083 |
(both are no longer needed) in exch_uv: no effect in forward run; but |
1084 |
get truncation error differences with adjoint exch. |
1085 |
o exch2: |
1086 |
- change index-bounds storage (moved from target to local tile, |
1087 |
more intuitive this way) ; rename/remove some variables. |
1088 |
- change utils/exch2/matlab-topology-generator & code_mods accordingly. |
1089 |
|
1090 |
checkpoint61a (2008/07/29) |
1091 |
o exch2/matlab-topology-generator: |
1092 |
fix bug in index bounds for N-S internal exchange (hard to tell if this |
1093 |
had any effect on the solution). |
1094 |
o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf |
1095 |
is exceeded |
1096 |
o testreport: modify syntax of awk, so that it works also with |
1097 |
awk, and not only with nawk and gawk |
1098 |
|
1099 |
checkpoint61 (2008/06/24) |
1100 |
o autodiff |
1101 |
Change default for TAF usage by removing argument '-nonew_arg' |
1102 |
This changes TAF subroutine argument list (ordering of active var.) |
1103 |
Omission of this flag leads to incompatibility w.r.t. TAMC |
1104 |
To restore TAMC-compatibility, need following modifs: |
1105 |
* use adoptfile tools/adjoint_options/adjoint_tamc_compatibility |
1106 |
* use CPP option #define AUTODIFF_TAMC_COMPATIBILITY |
1107 |
Tested TAF version is 1.9.22 |
1108 |
N.B.: exch2 hand-written adjoint code currently not TAMC compatible |
1109 |
|
1110 |
checkpoint60 (2008/06/19) |
1111 |
--->>> This is the last checkpoint for which generating the adjoint |
1112 |
--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" |
1113 |
--->>> by default. |
1114 |
--->>> Future checkpoints will ommit this flag by default. |
1115 |
o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. |
1116 |
o pkg/grdchk: Add gradient check to etan0 perturbations. |
1117 |
o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). |
1118 |
o pkg/autodiff: more flexibility in zeroadj. |
1119 |
model/src: modifying do_oceanic_phys.F accordingly. |
1120 |
o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. |
1121 |
o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option |
1122 |
special setup of gmredi for which the adjoint is stable |
1123 |
enough for parameter optimization. |
1124 |
o bridging the gap between eddy stress and GM. |
1125 |
-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) |
1126 |
along with a change in CPP option (now ALLOW_EDDYPSI). |
1127 |
-> when using GM w/ GM_AdvForm: |
1128 |
The total eddy streamfunction (Psi = eddyPsi + K x Slope) |
1129 |
is applied either in the tracer Eq. or in momentum Eq. |
1130 |
depending on data.gmredi (intro. GM_InMomAsStress). |
1131 |
-> ALLOW_EDDYPSI_CONTROL for estimation purpose. |
1132 |
The key modifications are in model/src/taueddy_external_forcing.F |
1133 |
pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F |
1134 |
|
1135 |
checkpoint59r (2008/05/29) |
1136 |
o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array |
1137 |
from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); |
1138 |
fix option to read coriolis(@ cell-corner) from files with CS-grid. |
1139 |
o pkg/mnc: add some attributes to standard 1D-coordinate variables |
1140 |
o pkg/diagnostics: enforce missing_value attribute for scalar variables at |
1141 |
mass points, when using mnc for output |
1142 |
- add runtime parameter (missing_value, missing_value_int) to override |
1143 |
default (which is the value of getcon('UNDEF')) |
1144 |
o pkg/mnc: prepare mnc for the actual use of missing values with the |
1145 |
diagnostics package: small fix in mnc_cw_readwrite.template and more |
1146 |
initialisation of never used fields |
1147 |
- replace mnc_common.h and mnc_id_header.h with corresponding upper case |
1148 |
versions |
1149 |
o pkg/thsice/thsice_ini_vars.F added default initial values so that |
1150 |
thermodynamics sea ice solver does not blow up when some initial fields |
1151 |
are missing. |
1152 |
o move from external_forcing_surf.F to ini_forcing.F |
1153 |
the p-coord. hack consisting in using pLoad to set phi0surf ; |
1154 |
update output of tutorial_global_oce_in_p (affected @ truncation level). |
1155 |
o Freshen up a bit hs94.1x64x5, notably: |
1156 |
remove rotationPeriod and tRef=5*0. (adjoint only), and add |
1157 |
exactConserv=.TRUE. |
1158 |
o pkg/generic_advdiff: |
1159 |
change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
1160 |
applies to files where Temperature & Salinity 2nd Order moments are used. |
1161 |
o pkg/ptracers: add second-order moment advection schemes (80 and 81); |
1162 |
this uses a dynamically allocated internal state data structure |
1163 |
(#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) |
1164 |
and requires a fortran 90 compiler |
1165 |
|
1166 |
checkpoint59q (2008/05/06) |
1167 |
o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) |
1168 |
(from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) |
1169 |
o Refresh tutorial_global_oce_biogeo, notably: |
1170 |
- change bathymetry (put back seamounts in ACC, use hFacs) |
1171 |
- change EOS (POLY3 --> JMD95Z) |
1172 |
- use Bryan-Lewis vertical diffusivity |
1173 |
- use multidimensional advection |
1174 |
- remove old virtual virtual in dic pkg, now done through ptracer pkg |
1175 |
- change a couple of parameters in dic pkg |
1176 |
o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F |
1177 |
o pkg/obcs: change default to OBCSfixTopo = .true., |
1178 |
- set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result |
1179 |
- replace "debugMode" with "debugLevel .GE. debLevB" |
1180 |
o implementation of TAF directives for gchem,cfc,dic |
1181 |
o remove "exp5" (replaced by tutorial_deep_convection). |
1182 |
o pkg/obcs: add code to fix topography gradients normal to open boundaries; |
1183 |
this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; |
1184 |
the code can be turned on by setting OBCSfixTopo = .true. in data.obcs |
1185 |
--> changes results in exp4, seaice_obcs |
1186 |
o tutorial_deep_convection : |
1187 |
update the set-up and increase resolution and domain size ; start |
1188 |
from pseudo initial conditions = output at t=120mn in order to see |
1189 |
something happening when running testreport. |
1190 |
o pkg/seaice: add os7mp as an advection scheme |
1191 |
add check for advection schemes |
1192 |
add a flag for restoring T and S underneath sea ice |
1193 |
o pkg/my82: add netcdf-support and diagnostics |
1194 |
o thsice pkg: |
1195 |
- Now hsMax limits snow height by turning it into ice following |
1196 |
flooding scheme (and now conserving energy) |
1197 |
- Slight rewriting of the formula in thsice_calc_thick.F |
1198 |
- Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos |
1199 |
--> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice |
1200 |
|
1201 |
checkpoint59p (2008/04/10) |
1202 |
o gchem / dic / cfc : |
1203 |
- add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); |
1204 |
- add new parameter files: "data.dic" & "data.cfc" ; |
1205 |
- various re-arrangement in initialisation & header file ; |
1206 |
- fix tutorial_global_oce_biogeo for multi-threaded test. |
1207 |
o pkg/dic: test for "pickup_dic" file when restarting ; |
1208 |
if no pickup-file, can restart with a re-initialised pH (same as it did |
1209 |
before) providing pickupStrictlyMatch is set to False. |
1210 |
o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP |
1211 |
+ fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP |
1212 |
o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2 |
1213 |
and staggerTimeStep is off (needed for stability of Internal-wave dynamics). |
1214 |
o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax, |
1215 |
& lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers |
1216 |
(note: not clear to me what lambdaTr1ClimRelax is still used for ...) |
1217 |
o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which |
1218 |
scheme to use for vorticty-term ; |
1219 |
- compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F |
1220 |
(with default selectVortScheme, return to original discretisation) |
1221 |
- remove weird combination (e.g.: upwindVorticity & highOrderVorticity) |
1222 |
o pkg/seaice: add a line to the summary to indicate grid type (B/C) |
1223 |
o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the |
1224 |
bottom ; only used with variable horizontal viscosity and non-hydrostatic. |
1225 |
also fix diagnostics VISCAHW & VISCA4W. |
1226 |
|
1227 |
checkpoint59o (2008/03/07) |
1228 |
o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). |
1229 |
o change the loop ordering in most gad_*_adv_x.F to improve vectorization: |
1230 |
move a few statemens out the main loop into separate loops |
1231 |
o pkg/shelfice: |
1232 |
- sort out freshwater flux; convert freshwater fluxes to mass fluxes |
1233 |
(kg/m^2/s), does not break tests, because in verification/isomip, |
1234 |
rhoConstFresh=rhoConst (by accident) |
1235 |
- rearrange computation of tLoc, sLoc, pLoc to make code more efficient |
1236 |
- move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into |
1237 |
new file model/src/seawater.F, so that they are available for all pkgs. |
1238 |
- convert potential temperature into in-situ temperature. This changes the |
1239 |
isomip tests => update tests |
1240 |
o add a flag writePickupAtEnd (default=true) to be able to suppress |
1241 |
writing a pickup at the last timestep |
1242 |
o tools/mpack-1.6 : |
1243 |
- disable automake (not working) and autoconf (not needed). |
1244 |
- update to version 1.6.4 which fix MD5 code on some 64 bits platforms |
1245 |
also cleaner with much less compilation warnings. |
1246 |
o pkg/profiles: |
1247 |
rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg |
1248 |
(for "less than 32 characters name" compiler requirement) |
1249 |
o pkg/obcs and pkg/exf: added capability to specify seaice open boundary |
1250 |
conditions that have a different sampling frequency than S/T/U/V obcs |
1251 |
o pkg/diagnostics (stats-diags): |
1252 |
- fix global Min/Max in case 1 processor get only empty tiles |
1253 |
o genmake2: replace (4 times) |
1254 |
make genmake_tc_1.o >> genmake_warnings 2>&1 |
1255 |
with |
1256 |
COMM="$CC $CFLAGS -c genmake_tc_1.c" |
1257 |
echo $COMM >> genmake_warnings |
1258 |
$COMM >> genmake_warnings 2>&1 |
1259 |
to make genmake2 always see the value of CC as specified in the optfile. |
1260 |
o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid. |
1261 |
- add diagnostics for 1srt & 2nd Order moments and sub-grid variance. |
1262 |
- modify verification advect_cs test to test SOM-advection on CS-grid. |
1263 |
o pkg/ctrl: |
1264 |
- Rewrite of ctrl_map_ini_ecco.F, |
1265 |
introducing a generic routine (ctrl_map_ini_gen.F). |
1266 |
- Modification of ctrl_bound/adctrl_bound handling control vector bounds. |
1267 |
|
1268 |
checkpoint59n (2008/02/09) |
1269 |
o pkg/diagnostics: for large number of diagnostics, store diagnostic mate |
1270 |
number in dedicate array "hdiag": |
1271 |
- new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST |
1272 |
with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST. |
1273 |
- many small changes (integer format) for large number of diagnostics |
1274 |
- start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with |
1275 |
a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23. |
1276 |
o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For |
1277 |
usingSphericalGrid, this allows to define the rotated grid coordinates |
1278 |
via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the |
1279 |
geographical coordinates according to the inverse of the rotation defined |
1280 |
by the Euler angles, so that Coriolis parameter and online-interpolation by |
1281 |
exf works with the geographical coordinates on XC/YC/XG/YG. |
1282 |
Naturally, this feature does not work with all packages, so some |
1283 |
combinations are prohibited in config_summary (flt, flt_zonal, ecco, |
1284 |
profiles), because there the coordinates are assumed to be regular |
1285 |
spherical grid coordinates. |
1286 |
o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc: |
1287 |
- introduce isopycnal diffusion coefficient control. |
1288 |
o tools/adjoint_options: |
1289 |
- additional control vector components. |
1290 |
o pkg/mnc: have mnc create marginally meaning full coordinate variables |
1291 |
(that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 |
1292 |
o pkg/mypackage: |
1293 |
- add example of read/write pickup for state-var ; |
1294 |
- add entry points to the main code for state-vars diags & write-pickup. |
1295 |
o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year |
1296 |
transitions for useExfYearlyFields |
1297 |
- add new subroutine that determines the file to read from for |
1298 |
use*YearlyFields = .TRUE. and .FALSE. |
1299 |
- add a verification experiment to global_with_exf that tests |
1300 |
useExfYearlyFields with USE_EXF_INTERPOLATION defined |
1301 |
o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in |
1302 |
analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new |
1303 |
subroutines (which could be generated from a template, because they are |
1304 |
almost identical), for now they are included in obcs_prescribe_read.F for |
1305 |
simplicity |
1306 |
o pkg/exf: |
1307 |
- add a little more diagnostic to exf_interp_read (in analogy to |
1308 |
mds_read_field, can be turned off with debugLevel < debugLevA=1) |
1309 |
- improve vectorizability of exf_interp for TARGET_NEC_SX, makes code |
1310 |
ugly but fast by unrolling short inner loops, inserting a unroll=8 |
1311 |
directive in routine lagran, and splitting a loop and making do while the |
1312 |
outermost loop (the latter requires the intoduction of index arrays) |
1313 |
o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice |
1314 |
o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver |
1315 |
http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html |
1316 |
o verification/seaice_obcs: updated for restart test and latest options |
1317 |
o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different |
1318 |
ice rheology (so-called truncated ellipse, that gets rid of tensile stress); |
1319 |
for now this is only available for the C-grid code and also within |
1320 |
#ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code |
1321 |
|
1322 |
checkpoint59m (2008/01/14) |
1323 |
o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) |
1324 |
and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature |
1325 |
o gad_som : fix flux output (& diagnostics) to have same units as other |
1326 |
advection scheme fluxes (was previously multiplied by deltaT). |
1327 |
o added verification/seaice_obcs both to test seaice open boundaries |
1328 |
and to provide an example matlab scrpt for generating them |
1329 |
o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume |
1330 |
o pkg/salt_plume: clean up salt_plume_frac.F to |
1331 |
remove redundancy in PlumeMethod 1 and 4 |
1332 |
o pkg/kpp: added saltplume diagnostics |
1333 |
o pkg/obcs and pkg/seaice: |
1334 |
- do not set uice and vice to zero when OB*icefile are unspecified |
1335 |
- OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default |
1336 |
- moved seaice tracer obcs after call to seaice_growth |
1337 |
o pkg/salt_plume: added various options for salt plume depth |
1338 |
criterion and for vertical distribution of the salt |
1339 |
|
1340 |
checkpoint59l (2007/12/18) |
1341 |
o pkg/ptracers: new version of ptracers pickup: |
1342 |
read meta file and write only fields which are needed to restart. |
1343 |
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
1344 |
o pkg/seaice: |
1345 |
- add timescale for melting due to warm mixed layer as a means of |
1346 |
setting SEAICE_availHeatFrac more conveniently |
1347 |
- add a CPP-flag/runtime parameter check for flooding algorithm |
1348 |
- reformulated availHeat in seaice_growth.F to be independent of AREA |
1349 |
o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent |
1350 |
unit changes |
1351 |
o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint |
1352 |
o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC |
1353 |
SX vector computer. |
1354 |
o pkg/seaice: |
1355 |
- removed SEAICE_FFIELDS.h and seaice_get_forcing.F |
1356 |
seaice forcing fields can now be read only through pkg/exf |
1357 |
- removed some unused halos |
1358 |
o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP |
1359 |
o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL |
1360 |
or U/VICE from U/VWIND before computing U/VSTRESS |
1361 |
|
1362 |
checkpoint59k (2007/11/30) |
1363 |
o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between |
1364 |
dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. |
1365 |
o fix un-initialised variable problem (in mom_vecinv & shap_filt): |
1366 |
all experiments pass when compile with un-initialised var. checking option. |
1367 |
o added pkg/salt_plume |
1368 |
o script to test restart (for now, in MITgcm_contrib/jmc_script) |
1369 |
o pkg/seaice: new read/write pickup version. |
1370 |
read meta file and write only fields which are needed to restart. |
1371 |
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
1372 |
o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) |
1373 |
o lab_sea.hb87: modify the domain & update output.hb87.txt : |
1374 |
lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 |
1375 |
at j=1 & j=Ny+1 : this case is not treated correctly in the restart |
1376 |
process. Fixed here by closing the domain at the Northern boundary. |
1377 |
o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. |
1378 |
o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing |
1379 |
a set of consecutive levels in/from a 3-D array. |
1380 |
o pkg/ptracers: |
1381 |
use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). |
1382 |
to-do: fix pkg/diagnostics when large number of diagnostics are defined. |
1383 |
|
1384 |
checkpoint59j (2007/11/09) |
1385 |
o in pkgs: dic, obcs, offline, rbcs: |
1386 |
standard way to compute coeff. for time interpolation between 2 time reccords |
1387 |
which retains full precision (& make results less dependent on compiler). |
1388 |
update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. |
1389 |
o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those |
1390 |
packages instead of reading ice cover and wind speed separately |
1391 |
o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h |
1392 |
(keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad |
1393 |
to allow to compile customized code before the update) |
1394 |
o cleaning-up: |
1395 |
- fix CPP instruction syntax in pkg/obcs |
1396 |
- replace (some) call to MDSIO S/R with call to RW interface S/R ; and |
1397 |
add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio) |
1398 |
- fix some threads issue in IO parts. |
1399 |
o pkg/dic: |
1400 |
- add tons of "_d 0" (--> much better testreports !) |
1401 |
and then update outputs of tutorial_global_oce_biogeo |
1402 |
o pkg/mom_fluxform: |
1403 |
add a special version of momentum advection intended to conserve momentum |
1404 |
next to a bathymetry step or a coastline edge. (default = off = #undef) |
1405 |
o new read/write pickup version: |
1406 |
- for now, only implemented for main (mdsio) pickup file. |
1407 |
- write out only what is needed to restart; merge pickup_nh , pickup_ph |
1408 |
and main pickup together. |
1409 |
- read meta file; read only what is needed to restart; stop if a field |
1410 |
is missing (if pickupStrictlyMatch=T, = the default) or try to restart |
1411 |
if it make sense (even if the restart is not perfect). |
1412 |
- if no meta file, assume that pickup to read corresponds exactly to |
1413 |
a pickup that would currently be written. |
1414 |
- read pickup written in the old format (until checkpoint59i) if it |
1415 |
recognizes an old meta file (no field-list). |
1416 |
- add a meta file in exp. which starts from a pickup: 2 cases: |
1417 |
a) minimal meta file (with just file precision) + pickupStrictlyMatch=F |
1418 |
e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta |
1419 |
b) a meta file describing the content of the associated pickup file |
1420 |
e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta |
1421 |
o pkg/mdsio & pkg/rw: |
1422 |
- new routine to read a meta file ; new set of routine to read |
1423 |
Multiple-fields file (with meta file). |
1424 |
o added open boundary conditions capability for seaice |
1425 |
HSNOW, HSALT, UICE, and VICE |
1426 |
|
1427 |
checkpoint59i (2007/10/21) |
1428 |
o adjoint: |
1429 |
* fix multiDimAdvection adjoint |
1430 |
(partial recomputation problem by TAF for fVerT(:,:,kDown) |
1431 |
and comlev1 size definition (maxpass vs. max. number of tracers) |
1432 |
* verification/global_ocean.90x45x15 adjoint now tests |
1433 |
NLFS and multiDimAdvection using DST3 (=30) |
1434 |
* verification/lab_sea now tests multiDimAdvection using DST3 (=30) |
1435 |
o pkg/kpp: add "_d 0" to real constant (if missing); |
1436 |
update output of exp: natl_box (10.digits); vermix (std, 7.digits) |
1437 |
and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). |
1438 |
o prepare for "clever pickup" implementation: add new header file "RESTART.h" |
1439 |
for internal parameters related to restart process (formerly from PARAMS.h) |
1440 |
and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. |
1441 |
o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed |
1442 |
as argument. (only atm2d & obcs write_pickup have not yet been updated) |
1443 |
o pkg/monitor: |
1444 |
- use GLOBAL_SUM_TILE instead of _GLOBAL_SUM |
1445 |
- fix mon_stats_rs (statistics over the full domain, even where field is zero) |
1446 |
- account for deep Atmosphere factor and density factor (anelastic) |
1447 |
o added open boundary conditions capability for seaice HEFF and AREA |
1448 |
o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) |
1449 |
thermodynamics |
1450 |
- requires a little reorganization, which affects the testreport results |
1451 |
of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, |
1452 |
so that now the conservative form is tested |
1453 |
- add a few comments |
1454 |
o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* |
1455 |
o add a little bit of code to gad_os7mp_adv_?.F to help vectorization |
1456 |
o add new diagnostics to seaice: advective, diffusive fluxes (only for |
1457 |
multidim-advection, for scheme 2 they are not filled) and transports, |
1458 |
thermodynamic growth rates |
1459 |
o change units of EmPmR (inside the code, + within coupling interface) |
1460 |
from m/s to kg/m2/s (mass flux) but leave input file unchanged. |
1461 |
Affects results @ truncation level (cg2d match) and update output of |
1462 |
experiments: lab_sea(6), global_ocean.90x40x15(10), |
1463 |
global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) |
1464 |
+ adjoint results: global_ocean_ebm(11) and lab_sea (12). |
1465 |
Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). |
1466 |
Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). |
1467 |
|
1468 |
checkpoint59h (2007/09/29) |
1469 |
o pkg/exf: |
1470 |
- improve vectorization by moving if-statement out of loops in |
1471 |
exf_mapfields, exf_radiation |
1472 |
- exf_bulkformulae.F: introduce 2D fields and vectorize code |
1473 |
o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package |
1474 |
o testreport: |
1475 |
- allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE |
1476 |
monitor & update offline_exf_seaice exp. output. |
1477 |
- AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) |
1478 |
o pkg/seaice: |
1479 |
- bug fix in the evp solver: boundary conditions were affected be |
1480 |
masking of zMax/zMin (changes results) |
1481 |
- minor bug fix in boundary conditions in seaice_calc_strainrates |
1482 |
(changes results for no_slip) |
1483 |
- seaice_lsr.F: make interpolation of eta dependent on boundaries |
1484 |
- replace hardcoded lower limit for zeta (zMin) by runtime parameter |
1485 |
- add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean |
1486 |
stress formulation and no-slip boundary conditions |
1487 |
o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP |
1488 |
in gad_calc_rhs.F ; add few safety stops in initialisation phase. |
1489 |
o pkg/seaice: a first HSALT time stepping equation has been checked in |
1490 |
o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV |
1491 |
in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem |
1492 |
without requiring DO-IF statements |
1493 |
o pkg/thsice: |
1494 |
use continuous power-law function for partition of energy between lateral |
1495 |
melting/freezing and thinning/thickening ; old code using step function |
1496 |
still available with #undef THSICE_FRACEN_POWERLAW |
1497 |
update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice |
1498 |
o testreport: change AD testing : check against results/output_adm.txt |
1499 |
using same scripts as for forward test. |
1500 |
|
1501 |
checkpoint59g (2007/09/17) |
1502 |
o adjoint testing: in preparation for changing testreport: |
1503 |
- output format: cost and grad written on separated lines |
1504 |
- ad output results in directory "results" (instead of "results_ad") |
1505 |
o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
1506 |
o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
1507 |
o pkg/ecco: allow user defined cost function contributions |
1508 |
o testreport: |
1509 |
Allow to choose (per experiment) the list of tested output variables |
1510 |
and the main variable (used to issue a pass/FAIL ) ; |
1511 |
- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
1512 |
- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
1513 |
Also modify printing of summary: |
1514 |
a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
1515 |
b) echo the list of tested variables in the individual summary.txt of |
1516 |
each experiment. |
1517 |
o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
1518 |
threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
1519 |
(but still depend on the tile decompostion of the domain). |
1520 |
o pkg/seaice: change a discretization detail to make the B-grid code |
1521 |
"more symmetric". This change is likely to remove all "ridges/leads" that |
1522 |
where quasi-aligned with the grid in B-grid solutions. It may also be |
1523 |
the solution to the stress coupling issues with the B-grid. |
1524 |
o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
1525 |
remove .cvsignore from input dir. (since testreport no longer run here). |
1526 |
o pkg/thsice: |
1527 |
- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
1528 |
- fix reshaping of sea-ice just after advection: |
1529 |
melt all the ice only if ice-volume is too small. |
1530 |
- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
1531 |
prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
1532 |
and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
1533 |
o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
1534 |
tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
1535 |
o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
1536 |
forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
1537 |
(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
1538 |
and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
1539 |
of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
1540 |
-> update output.txt |
1541 |
o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
1542 |
this affects truncation error: -> update output.txt of exp: |
1543 |
global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
1544 |
ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
1545 |
|
1546 |
checkpoint59f (2007/08/21) |
1547 |
o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
1548 |
o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
1549 |
a bounded range (in forward mode) |
1550 |
o pkg/ecco, ctrl, autodiff and mom_common: |
1551 |
internal parameter controls, completements of implementations |
1552 |
o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
1553 |
o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
1554 |
(not seem any difference in testing results). |
1555 |
o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
1556 |
at face corners. |
1557 |
o pkg/generic_advdiff: |
1558 |
- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
1559 |
loop range indices for computing vertical advection tendency |
1560 |
and do the calculation in the interior only (no overlap) ; |
1561 |
for now, only implemented for SOM advection (to save CPU time). |
1562 |
- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
1563 |
o exch2 adjoint |
1564 |
First set of changes: |
1565 |
- add exch2 hand-written adjoint templates |
1566 |
- exch2 hand-written no longer use TAF-flag 'nownew_arg' |
1567 |
This will require cleanup in pkg/autodiff/*.F |
1568 |
(changed routines currently kept separate in verif. code/) |
1569 |
- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
1570 |
that used to hide exch2 or cubed-sphere specific code |
1571 |
(commented via 'cph-exch2') |
1572 |
o pkg/seaice |
1573 |
- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
1574 |
o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
1575 |
output of global_ocean.cs32x15.thsice . |
1576 |
|
1577 |
checkpoint59e (2007/07/26) |
1578 |
o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
1579 |
for B-grid vector (not yet tested) and C-grid vector (<- only used |
1580 |
when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). |
1581 |
o starting implementation of Duffy et al. (GRL 1999) salt plume scheme |
1582 |
(#ifdef ALLOW_SALT_PLUME) |
1583 |
o gather_2d/scatter_2d: removed halo regions |
1584 |
o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
1585 |
scheme and the corresponding test case (under front_relax dir). For now, |
1586 |
only available with Skew-flux form and not yet tested in realistic set-up. |
1587 |
adjoint: store directives updated, but gradient checks deteriorated, |
1588 |
so maybe GM/Redi adjoint is now broken. |
1589 |
o seaice adjoint |
1590 |
* add AREA, HEFF, HSNOW as control variable |
1591 |
(should not change lab_sea results) |
1592 |
* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
1593 |
o pkg/seaice: |
1594 |
* added computation of saltFlux in seaice_growth; |
1595 |
For time being, sea ice salinity is assumed constant |
1596 |
contribution of snow flooding to freshening of sea ice is neglected. |
1597 |
SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
1598 |
defaults to 0.0 in order to maintain backward compatibility. |
1599 |
Typical values for SEAICE_salinity are 4 to 10 g/kg. |
1600 |
* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
1601 |
* added SEAICE_availHeatFrac, which specifies fraction of surface level |
1602 |
heat content used to melt or grow ice |
1603 |
* commented out cap of HICE: it helps keep ice thinner |
1604 |
* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
1605 |
* applied OBCS T/S mask to HEFFM sea ice mask |
1606 |
|
1607 |
checkpoint59d (2007/06/21) |
1608 |
o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
1609 |
for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
1610 |
(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
1611 |
o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
1612 |
and change default value of parameter "GM_Small_Number"; |
1613 |
update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
1614 |
global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
1615 |
tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
1616 |
o pkg/ecco: cost function when applying pkg/smooth to controls |
1617 |
o pkg/ctrl: add forcingPrecond run time parameter |
1618 |
o pkg/seaice: |
1619 |
- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
1620 |
- fix bug in metric terms of u-equation in LSR solver (implicit part), |
1621 |
changes verification/lab_sea |
1622 |
- rearrange implicit part of u-equation in LSR solver to make it easier to |
1623 |
read, understand, and debug. This causes changes at the truncation level. |
1624 |
- fix (serious) bug in the boundary conditions (sign error in the implicit |
1625 |
part) of the LSR solver. Changes all LSR results. |
1626 |
- fixed problem with HSNOW initialization to avoid thick snow when AREA |
1627 |
is initilized with small values - does not change lab_sea results. |
1628 |
- added HsnowFile initialization capability |
1629 |
o pkg/smooth: addition to model/src and pkg/ctrl so allow |
1630 |
initialization of pkg/smooth and application to control vector |
1631 |
o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
1632 |
o dependencies: pkg/profiles requires pkg/cal |
1633 |
o pkg/profiles: |
1634 |
- added option ALLOW_PROFILES_GENERICGRID |
1635 |
-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
1636 |
that interpolation information (grid points and coefficients) is provided |
1637 |
within the netcdf input files. |
1638 |
-> sample matlab scripts can be found in MITgcm_contrib/gael |
1639 |
that allow you to prepare netcdf input files. |
1640 |
- also modified: cleaner include statements, cleaner error print statements, |
1641 |
cleaner stops when error, and more tests of the netcdf input files consistency. |
1642 |
o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
1643 |
o pkg/seaice: |
1644 |
- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
1645 |
requires a new routine: seaice_diagnostics_fill.F |
1646 |
- make sure that seaice does not move if not forced (pressure replacement |
1647 |
method, Hibler and Ip, 1995), changes results |
1648 |
- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
1649 |
- SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). |
1650 |
It is turned off by default (=-1.), because it changes the results. |
1651 |
- make it possible to read AREA from a file, too. |
1652 |
|
1653 |
checkpoint59c (2007/06/04) |
1654 |
o add S/R and diagnostics for oceanic mixed-layer depth |
1655 |
o move GMRedi call after all vertical mixing schemes (including KPP) |
1656 |
o pkg/thsice: |
1657 |
- ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs |
1658 |
(melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice |
1659 |
o pkg/obcs: |
1660 |
- bug fix for balance code |
1661 |
o pkg/seaice: |
1662 |
- allow values of SEAICE_elasticParm > 1 |
1663 |
- add new parameter SEAICE_evpTauRelax as an alternative |
1664 |
to SEAICE_elasticParm |
1665 |
- make lsr boundary conditions free slip (by default), changes result |
1666 |
- add code for no slip boundary conditions for lsr |
1667 |
- set minimum of zeta to zero (and not 4e8) (changes results) |
1668 |
- add a cap on AREA after advecting AREA if seaice_growth is not called |
1669 |
o change calculation of Visbeck K: |
1670 |
- no longer depend on tapering scheme; instead, compute slope (limited |
1671 |
by GM_maxSlope). this is equivalent to what was comuted before with |
1672 |
clipping or linear tappering. |
1673 |
- fix vertical averaging (wrong by 1/2 level) |
1674 |
- leave the old version (but will not be maintained) within |
1675 |
#ifdef OLD_VISBECK_CALC / #endif |
1676 |
- update output of exp. ideal_2D_oce |
1677 |
o change error catch in calc_r_star to improve vectorization |
1678 |
o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
1679 |
add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
1680 |
o adjoint: |
1681 |
Re-organized adjoint checkpointing according to Matt Mazloff |
1682 |
(but with modifs/completions/cleanups) |
1683 |
Storing is now bundled into large arrays to optimized I/O |
1684 |
(and second step in cleanup of the_main_loop) |
1685 |
|
1686 |
checkpoint59b (2007/05/16) |
1687 |
o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
1688 |
- export/import (between ocean & coupler) fields needed for ocean DIC. |
1689 |
o pkg/seaice: |
1690 |
- get rid of three more exchanges seaice_calc_viscosities (required |
1691 |
different loop boundaries in seaice_lsr and seaice_ocean_stress) |
1692 |
- bug fix in seaice_ocean_stress (update of lab_sea required) |
1693 |
- reduce loop boundaries to necessary minimum also in seaice_evp |
1694 |
- go back to the old way of computing deltaC/Z as the adjoint likes that |
1695 |
better |
1696 |
o Refresh of tutorial_global_oce_latlon (includes changing salinity-like |
1697 |
passive tracer to an Age Tracer) + update output.txt |
1698 |
o pkg/exf: |
1699 |
- implement A-grid / C-grid selection for wind-stress input files. |
1700 |
- clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) |
1701 |
for now, in exf_bulk_largeyeager04.F only : |
1702 |
- change implementation for case where windspeed + 2. components wind-stress |
1703 |
are read-in. AND use rhoConstFresh to convert evap. |
1704 |
o pkg/seaice: |
1705 |
- use correct EXCH_UV for wind-forcing (on A-grid). |
1706 |
- change SEAICE_OPTIONS.h to limit the number of option combinations (regarding |
1707 |
SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops. |
1708 |
o pkg/exf: |
1709 |
- default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC) |
1710 |
EXF_INTERPOLATION: |
1711 |
- merge global_with_exf/code version of exf_interp_read.F |
1712 |
to the main code ; |
1713 |
- Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when |
1714 |
reading the file ; Important: This options needs to be defined to recover |
1715 |
previous code. |
1716 |
otherwise, use fixed size array to read in (size=exf_interp_bufferSize). |
1717 |
- no longer loose real*8 precision along the way when using exf_iprec=64. |
1718 |
o pkg/seaice: rearrangement of common blocks (really needs more cleaning up) |
1719 |
- change discretisation of evp-solver in order to avoid another exchange |
1720 |
(changes lab_sea) and clean up a little |
1721 |
- replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS) |
1722 |
help the adjoint (this also changes the results slightly) |
1723 |
- add a few "_d 0" where they had been missing in seaice_evp.F |
1724 |
- cleaning up: remove unused seaice_calc_rhs.F |
1725 |
o pkg/exf: some cleaning-up: |
1726 |
- change various "constants" into runtime parameters |
1727 |
- cleaned-up Large&Yeager04 routine which should eventually |
1728 |
replace exf_bulkformulae.F (changed names of S/R and CPP) |
1729 |
and merged various ALLOW_ATM_WIND options |
1730 |
only used with thsice pkg (in thsice_get_exf.F): |
1731 |
- implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04) |
1732 |
which are used when useStabilityFct_overIce=TRUE (= the default) |
1733 |
- change default values of ice & snow emissivity and scale downward LW |
1734 |
by ice & snow emissivity. |
1735 |
o pkg/thsice: |
1736 |
fix few little problems, in thsice_calc_thickn.F: |
1737 |
- growth vertically (and not laterally) if iceFrac == iceMaskMax |
1738 |
- melt only laterally if hIce < hThinIce (as the comments say) |
1739 |
and in thsice_extend.F: |
1740 |
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
1741 |
- start to form ice as soon as the minimum ice-volume is reachable. |
1742 |
update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice), |
1743 |
and cpl_aim+ocn |
1744 |
o pkg/kpp |
1745 |
- move computation of surface related input fields to KPP into a new |
1746 |
subroutine kpp_forcing_surf.F |
1747 |
- remove wrong (within bi,bj loops) EXCH calls. |
1748 |
- little cleaning (add argument myThid in last position, cvs header ...) |
1749 |
- for now, fix conservation problem by exchanging KPPviscAz (may not |
1750 |
be the best fix) |
1751 |
o pkg/seaice |
1752 |
- check for inconsistent evp parameter/cpp-flag combination |
1753 |
- remove leftover errIO flat for obsolete name list error handling |
1754 |
o OpenAD |
1755 |
- changed verification/OpenAD to full baroclinic setup (including GM/Redi) |
1756 |
|
1757 |
checkpoint59a (2007/05/01) |
1758 |
o pkg/seaice: some parameter clarifications and a little bit of clean up |
1759 |
o pkg/thsice: rename run-time parameters: |
1760 |
himin -> hIceMin |
1761 |
himin0 -> hThinIce |
1762 |
hihig -> hThickIce |
1763 |
i0 -> i0swFrac |
1764 |
transCoef -> bMeltCoef |
1765 |
frac_energy -> fracMelting |
1766 |
add new parameters: hNewIceMax, fracFreezing, dhSnowLin |
1767 |
with default values (for now) that do not change the results. |
1768 |
remove old version of thsice vars advection in pkg/seaice. |
1769 |
o in FFIELDS.h: |
1770 |
- replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD |
1771 |
- make pLoad & sIceLoad always available (but still only used if |
1772 |
ATMOSPHERIC_LOADING is #define). |
1773 |
o pkg/kpp: replaced _KPP_RL with _RL |
1774 |
o bug fixes for vertical diffusivity computations when both KPP and |
1775 |
3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F |
1776 |
are no longer updating the vertical diffusivity array |
1777 |
(passed as argument) but are (re-) setting those arrays. |
1778 |
o pkg/seaice: fix bug in evp solver, while doing that |
1779 |
- change (improve?) discretization of stress computations for both |
1780 |
cgrid-lsr and evp solver |
1781 |
- add a new routine to compute strain rates |
1782 |
- the above changes lab_sea results |
1783 |
- add no slip conditions for evp solver (off by default), lsr-version |
1784 |
may follow |
1785 |
- fix exchange for shear at Z-points (does not change lab_sea) |
1786 |
- retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp |
1787 |
(to force the user to pick a time step since there is not "safe" way |
1788 |
of choosing it) |
1789 |
- add principal stress diagnostics |
1790 |
- rearrange fields for evp a little to avoid having to call a: too many |
1791 |
exchanges and b: exchanges for stress trensor components which we do |
1792 |
not have. |
1793 |
- modify Hibler+Bryan (1987) stress coupling so that it reuses information |
1794 |
of evp, complete rewrite for lsr case (latter is does not yet work |
1795 |
in all cases) |
1796 |
o pkg/kpp: add code to have mixing in shelf ice caverns |
1797 |
- add myThid to all kpp routines (long overdue) |
1798 |
|
1799 |
checkpoint59 (2007/04/19) |
1800 |
o pkg/exf: |
1801 |
- fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND & |
1802 |
ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid |
1803 |
- move exf header files from lower_case.h to UPPER_CASE.h ; |
1804 |
add missing cvs Header & Name |
1805 |
- add adjoint routines and flow dirs for newly used exch_uv_agrid routines |
1806 |
- add namelist param. selectStressGridPosition, exf_monFreq |
1807 |
- retire many _CLIM routines, and remove data.exf_clim |
1808 |
+ params moved to data.exf |
1809 |
+ climsst, climsss now handled by exf_set_gen, i.e. |
1810 |
climss?period=0 refers to constant field, |
1811 |
climss?period=-12 to monthly forcing |
1812 |
- split up namelists in data.exf |
1813 |
o pkg/seaice: |
1814 |
- remove seaice_exch and seaice_exch_uv |
1815 |
- remove superfluous exchange of theta |
1816 |
- add myThid to seaice_budget_ocean/ice |
1817 |
- add new interface for atmospheric wind forcing (C-grid only) |
1818 |
+ new routine |
1819 |
+ two new field (taux, tauy for stress over ice) |
1820 |
+ removed one global field (DAIRN) for C-grid case only |
1821 |
o pkg/thsise |
1822 |
- 2nd set of modifs for thsice adjoint in conjunction with exf |
1823 |
o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.) |
1824 |
|
1825 |
checkpoint58y_post (2007/04/15) |
1826 |
o Added capability for latitudinal dependence of Bryan and Lewis, 1979 |
1827 |
vertical diffusivity, similar to that in MOM4; turned on using |
1828 |
#define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using |
1829 |
diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file. |
1830 |
o Added capability for 3D specification of background vertical diffusion |
1831 |
coefficient. This is done by (i) #define ALLOW_3D_DIFFKR |
1832 |
in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime |
1833 |
"data" file that contains the 3D vertical diffusivity coefficients. |
1834 |
o ice dynamics (pkg/seaice) with thsice thermodynamics: |
1835 |
- add code within pkg thsice to advect & diffuse sea-ice fields |
1836 |
similar to (and will replace) what has been added in seaice_advdiff.F, |
1837 |
but: - conserving Mass, Heat & Salt. |
1838 |
- better when using non-linear advection scheme (not yet fully tested) |
1839 |
- can also be used in atmospheric set-up (for now, only the diffusion). |
1840 |
|
1841 |
checkpoint58x_post (2007/04/04) |
1842 |
o IO option for global-file compact format: |
1843 |
- add options when generating topology (utils/exch2/matlab-topology-generator) |
1844 |
- add I/O capability (pkg/mdsio). |
1845 |
- adapt utils/matlab/rdmds.m to read this format. |
1846 |
for now long-line format not yet supported by pkg/mdsio (& exch2). |
1847 |
o shelfice: add a few diagnostics |
1848 |
|
1849 |
checkpoint58w_post (2007/03/13) |
1850 |
o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: |
1851 |
rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref |
1852 |
(and replace horiVertRatio in NH code). |
1853 |
Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) |
1854 |
and tutorial_plume_on_slope (sensitive to truncation) |
1855 |
o seaice: if ALLOW_ATM_WIND is undefined use wind stress |
1856 |
directly to drive seaice model (C-grid only) |
1857 |
o exf: when input wind-stress (#undef ALLOW_ATM_WIND): |
1858 |
- reintroduce computation of wind from stress, |
1859 |
- compute tau (in exf_bulkformulae.F) from windstress averaged to |
1860 |
mass points to avoid tau = 0 |
1861 |
- fix serious bug: (1/3) in Fortran is not the same as (1./3.) |
1862 |
o rdmnc.m: make it work with "global" files created with gluemnc |
1863 |
o rdmnc.m : some improvements in dealing with singleton dimension |
1864 |
(tested on all testreport mnc output files). |
1865 |
o genmake2: disable pkg/profiles if netcdf test fails. |
1866 |
o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output. |
1867 |
o move call to cal_readparms up to make calendar parameters/variable available |
1868 |
to all packages |
1869 |
|
1870 |
checkpoint58v_post (2007/02/08) |
1871 |
o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get |
1872 |
useDynP_inEos_Zc tested. |
1873 |
o pkg/exf: changes to properly interpolate/mask/scale initial fields |
1874 |
o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields |
1875 |
and portions thereof. See read_cs.txt for description and examples. |
1876 |
o utils/matlab/cs_grid/bk_line: to compute transport through passages, |
1877 |
add a script (grt_circ_bkl.m) to generate broken-line between 2 points, |
1878 |
following the great-circle arc between those 2 points. |
1879 |
o trap un-initialized variable with pathscale compiler on weddell.mit.edu |
1880 |
(thanks to Constantinos): fix few problems and get (almost) all exp to pass. |
1881 |
o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in |
1882 |
- enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) |
1883 |
- used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81) |
1884 |
- still needs work (not working with some options ; efficiency to improve) |
1885 |
and serious testing. |
1886 |
- use this scheme for temperature & salinity in 2 advection test exp.: |
1887 |
advect_xy & advect_xz, respectively. |
1888 |
|
1889 |
checkpoint58u_post (2007/01/12) |
1890 |
o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. |
1891 |
o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. |
1892 |
o testreport: add option "-skipdir" to skip some test. |
1893 |
o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent |
1894 |
momentum calculation. |
1895 |
o gad_advection: fix vertAdvecScheme (if different from advectionScheme) |
1896 |
o some cleaning: usePickupBeforeC35 no longer supported ; remove this option. |
1897 |
remove checkpoint.F and the_correction_step.F (no longer used); |
1898 |
do the k loop inside CYCLE_TRACER (supposed to be more efficient). |
1899 |
o add option (linFSConserveTr) to correct for tracer source/sink due to |
1900 |
Linear Free surface |
1901 |
o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine |
1902 |
o pkg/thsice: fix reading mnc-pickups |
1903 |
|
1904 |
checkpoint58t_post (2006/12/30) |
1905 |
o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) |
1906 |
o pkg/mdsio: |
1907 |
- clean-up mdsio_readfield.F & mdsio_writefield_new.F and |
1908 |
move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & |
1909 |
mdsio_write_field.F (S/R MDS_WRITE_FIELD); |
1910 |
- fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD |
1911 |
- collect old S/R in one file: mdsio_rw_field.F (now just a call to |
1912 |
either MDS_READ_FIELD or MDS_WRITE_FIELD ) |
1913 |
- new S/R (to replace MDSWRITEMETA), which allows to write more |
1914 |
informations (variable names, time ...) to meta files. |
1915 |
- modify rdmds.m to give back the meta file content. |
1916 |
o pkg/diagnostics: change vertical interpolation to be safer, and more |
1917 |
flexible (define p-levels to interpolate to in data.diagnostics); |
1918 |
add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right |
1919 |
diagnostic pointer. |
1920 |
o pkg/seaice: more cleaning up of seaice_growth, added many comments |
1921 |
o pkg/exf: put runoff0 and runoff1 into the appropriate common block |
1922 |
o fix multi-category seaice: |
1923 |
- change cpp flag SEAICE_MULTILEVEL to more meaningful name: |
1924 |
SEAICE_MULTICATEGORY |
1925 |
- fix short wave heat flux |
1926 |
o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics |
1927 |
and allow to use EVP solver. Change forward lab_sea: test both EVP |
1928 |
solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) |
1929 |
o Initial check-in of lab_sea adjoint |
1930 |
(very similar to natl_box_adjoint/code_seaice) |
1931 |
* used C-grid and EVP solver |
1932 |
* used KPP, GM/Redi |
1933 |
* uses inAdExact=.TRUE. |
1934 |
* gradient checks fail for both ADM and TLM |
1935 |
due to sensitive snow melt code in seaice_grwoth (look for "JZ") |
1936 |
f.d. gradients actually seem more problematic than ADM, TLM gradients; |
1937 |
issue is related to forward mismatch between g77 an ifort |
1938 |
o pkg/seaice: overhaul of thermodynamics |
1939 |
- growth.F and groatb.F are replaced by new routine seaice_growth.F |
1940 |
- budget.F is replaced by two new routines seaice_budget_ocean/ice.F |
1941 |
- move a few global fields out of SEAICE.h into seaice_growth.F and |
1942 |
make them 2D (FICE/QNETO/ ...) |
1943 |
- remove FO (it is the same as QNETO) |
1944 |
- introduce a few local fields to avoid modifying external fields such |
1945 |
as atemp, etc. |
1946 |
|
1947 |
checkpoint58s_post (2006/12/11) |
1948 |
o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F |
1949 |
changed exf_set_gen.F so that |
1950 |
genperiod=0 means input file is one time-constant field and |
1951 |
genperiod=-12 means input file contains 12 monthly means |
1952 |
o CG2D: use pre-computed solver main-diagonal (stored in common block); |
1953 |
this affects truncation error ; generate new output file for exp. which |
1954 |
fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), |
1955 |
global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), |
1956 |
ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), |
1957 |
MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), |
1958 |
tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), |
1959 |
vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) |
1960 |
o start implementation of deep-atmosphere and anelastic formulation |
1961 |
o verification: remove 2nd copy of input files and use script "prepare_run" |
1962 |
to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) |
1963 |
o mom_common/vecinv/fluxform: fix a few initialisation isssues |
1964 |
o profiles: fix for multithreaded case |
1965 |
|
1966 |
o diagnostics: rename few diags: |
1967 |
s/'PRESSURE'/'RCENTER '/g |
1968 |
s/'TICE '/'oceFreez'/g |
1969 |
s/'TAUX '/'oceTAUX '/g |
1970 |
s/'TAUY '/'oceTAUY '/g |
1971 |
s/'SWFLUX '/'oceQsw '/g |
1972 |
s/DIFx/DFxE/g |
1973 |
s/DIFy/DFyE/g |
1974 |
and add few ocean-forcing diagnostics: |
1975 |
atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS |
1976 |
o modifications to pkg/seaice/growth.F and budget.F, which change results of |
1977 |
lab_sea experiment: HSNOW was sometimes treated as effective and sometimes |
1978 |
as actual snow thickness. It now refers everywhere to effective snow |
1979 |
thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. |
1980 |
|
1981 |
checkpoint58r_post (2006/11/17) |
1982 |
o modifications to pkg/seaice/growth.F, which change results of |
1983 |
lab_sea experiment: fixes pertain to melting snow over open water, to |
1984 |
masking EVAP under sea ice, and to using the correct AREA variable for |
1985 |
computations of EVAP, PRECIP, HSNOW, and GHEFF |
1986 |
o add ability to read bathy, salt, and theta using MNC (off by def) |
1987 |
o add flooding algorithm and advection of HSNOW for pkg/seaice; |
1988 |
both are turned off by default and do no change any results |
1989 |
o seaice advection with pkg/thsice: a step toward the use of non-linear |
1990 |
advection scheme, but #ifdef or commented out for now (requires more EXCH). |
1991 |
o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens |
1992 |
(identical results) and the standard version of EXTERNAL_FIELDS_LOAD |
1993 |
in natl_box (affects results @ truncation level: update output.txt) |
1994 |
o multi-threading and IO: |
1995 |
- replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. |
1996 |
- remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls |
1997 |
(needed to work with SingleCpuIO): tested in all verif. exp. |
1998 |
o GAD: use simpler DST3 formulation as default (old version left within #ifdef) |
1999 |
affects the results (but none of the verification test uses this scheme). |
2000 |
o Adding some pkg/diagnostics capability to pkg/seaice |
2001 |
(will certainly be subject to changes) |
2002 |
o ctrl: adding new control variables: |
2003 |
lwflux, lwdown, evap, snowprecip, apressure, runoff |
2004 |
|
2005 |
checkpoint58q_post (2006/10/20) |
2006 |
o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up |
2007 |
1/6-deg Southern Ocean configuration by 8% on IBM Datastar and |
2008 |
high_res_cube configuration by 4% on Columbia. |
2009 |
o clean-up multi-threaded problems (reported by debugger tcheck on ACES); |
2010 |
add (in global_with_exf/code) a version of EXF_INTERP_READ without |
2011 |
dynamical allocation (seems to work in multi-threaded). |
2012 |
o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using |
2013 |
single CPU io) so that TAF does not have to see EESUPPORT.h |
2014 |
o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
2015 |
|
2016 |
checkpoint58p_post (2006/09/08) |
2017 |
o obcs: stop if obcs is used with useCDscheme = .true. |
2018 |
o shelfice: |
2019 |
- fix a sign error so that no slip at shelfice interface works |
2020 |
- remove stop for combination non-hydrostatic code and shelfice. That does |
2021 |
not mean, that the results are correct, but at least they are numerically |
2022 |
stable |
2023 |
o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) |
2024 |
o added adjoint exch routined for all exch*3d* routines |
2025 |
and updated flow directives |
2026 |
|
2027 |
checkpoint58o_post (2006/08/28) |
2028 |
o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; |
2029 |
remove old subroutines (_XY_ & _XYZ_); update the adjoint version. |
2030 |
o change controling S/R for writing pickup file (new S/R do_write_pickup) |
2031 |
and clean-up reading/writing of pickup files. |
2032 |
o fix local version of read/write pickup (NH part) in rotating_tank/code |
2033 |
o simplify EXCH interface: |
2034 |
- change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) |
2035 |
- not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version |
2036 |
o added the regrid package |
2037 |
o shelfice: |
2038 |
- add a simple boundary layer scheme to reduce noise |
2039 |
- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
2040 |
|
2041 |
checkpoint58n_post (2006/08/14) |
2042 |
o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
2043 |
local variable (not in common block). |
2044 |
o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
2045 |
- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
2046 |
- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
2047 |
to work with SingleCpuIO. |
2048 |
o add "_d 0" to real constant of pkg/cfc subroutines ; |
2049 |
update exp. cfc_exemple & tutorial_cfc_offline output files. |
2050 |
o multi-threading and IO: |
2051 |
- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
2052 |
(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
2053 |
- barrier before and after reading. |
2054 |
- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
2055 |
- avoid using MDS_WRITELOCAL for LAND pkg output. |
2056 |
- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
2057 |
common-block variables ; Allows multi-threading with master-thread IO. |
2058 |
o change default MAX_NO_THREADS from 32 to 4 ; |
2059 |
and stop cleanly when MAX_NO_THREADS is too small. |
2060 |
o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
2061 |
|
2062 |
checkpoint58m_post (2006/07/17) |
2063 |
o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
2064 |
and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
2065 |
o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
2066 |
keep global_ocean.90x40x15 (for AD testing) with former secondary test |
2067 |
(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
2068 |
o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
2069 |
add MITgcm_tutorials (= code + all the tutorials) |
2070 |
o ecco, option to compute cost for total ssh (mean+anom) |
2071 |
o consistent with addition of ptracer and ssh in pkg/profiles |
2072 |
o profiles: adding ptracer and ssh |
2073 |
o testreport: change multi-test output-file name |
2074 |
(from output.txt.{name} to output.{name}.txt) |
2075 |
o profiles: now ok for mutli-tiles case |
2076 |
o seaice: add 4 parameters for different advection schemes for area, |
2077 |
(effective) seaice thickness, enthalphy, and snow height. Their default |
2078 |
is the standard parameter SEAICEadvScheme |
2079 |
o calc_gw: |
2080 |
- add cosFacU in zonal viscous flux (harmonic.visc.). |
2081 |
- put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. |
2082 |
of tutorial_plume_on_slope. |
2083 |
o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). |
2084 |
o calc_gw: true flux-form, account for horizontal grid spacing. |
2085 |
update rotating_tank results, but not plume_on_slope (affected at |
2086 |
truncation level, 11 digits). |
2087 |
|
2088 |
checkpoint58l_post (2006/07/12) |
2089 |
o calc_gw: |
2090 |
- take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V |
2091 |
- remove side-drag for now (need to fix it); update plume_on_slope results. |
2092 |
- fix for partial-cell & non-uniform dz; update plume_on_slope results. |
2093 |
o commit code to make SST/SSS weights spatially variable |
2094 |
(based on either variable in-situ or variable initial T/S weights) |
2095 |
o pkg/ecco: |
2096 |
* commit code to relax deviations of xx_theta, xx_salt to 5*sigma, |
2097 |
now based on horizontally varying weights wthetaLev, wsaltLev |
2098 |
* cost_averagesflags now returns year indices in addition to day, month |
2099 |
* sflux balance is performed on annual basis |
2100 |
(sflxumm, sfluxmm2, bal_sfluxmm) |
2101 |
* for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, |
2102 |
including separate counting and multipliers |
2103 |
o pkg/rbcs |
2104 |
* add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing |
2105 |
|
2106 |
checkpoint58k_post (2006/07/06) |
2107 |
o testreport: |
2108 |
- always build in dir. "build" (if not there, mkdir build instead of building |
2109 |
& running in input) |
2110 |
- run in dir run (if it exists), in build otherwise. |
2111 |
- call prepare_run (if input/prepare_run exists) |
2112 |
- run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. |
2113 |
o pkg/exf modifications to interpolation and rotation routines for more |
2114 |
reasonable treatment of North Pole singularity: for tracers North Pole |
2115 |
value is set to northernmost zonal-mean value, for zonal velocity it is |
2116 |
set to zero, and for meridional velocity it is set to northernmost value. |
2117 |
o pkg/exf/exf_check_range.F |
2118 |
- add tile index to diagnostics and move stop statement to the very |
2119 |
end of the routine. |
2120 |
o pkg/diagnostics: (diagnostics_main_init.F) |
2121 |
define title of isomorphic variables according to the current config. |
2122 |
o pkg/thsice with pkg/seaice dynamics: |
2123 |
- fix domain of computation (interior only, required for exf) and do exchanges |
2124 |
- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient |
2125 |
o towards a standard way of dealing with multi-threading in MONITOR |
2126 |
and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. |
2127 |
o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) |
2128 |
to W momentum equation in nonhydrostatic and quasihydrostatic runs. |
2129 |
o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. |
2130 |
o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) |
2131 |
o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL |
2132 |
(problems ? with gradient check in bottom_ctrl_5x5 adjoint test) |
2133 |
o tracer advection: |
2134 |
- clean-up and simplify calc_common_factors.F |
2135 |
- make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer |
2136 |
advection subroutine (but still not used within DST advection S/R) |
2137 |
o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
2138 |
|
2139 |
checkpoint58j_post (2006/06/15) |
2140 |
o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
2141 |
from file (collects calls previously in FORWARD_STEP) |
2142 |
o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS |
2143 |
o adjoint store dir. adjusted accordingly |
2144 |
o genmake2 |
2145 |
replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. |
2146 |
|
2147 |
checkpoint58i_post (2006/06/14) |
2148 |
o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
2149 |
on wind stress (SEAICEstressFactor defaults to 1.) |
2150 |
o Total number of Timers is finite (<=40): comment out 2 non-essential one |
2151 |
in the_main_loop.F to avoid Pb (e.g., when running fizhi test) |
2152 |
o vector_invariant: fix highOrderVorticity(=4.th.Order) advection |
2153 |
on CS-grid: no longer loosing mass. |
2154 |
o exf & curvilinear-grid: no longer modify longitude xC & xG. |
2155 |
o pkg/ggl90: fix sloppy output and fix a bug |
2156 |
o pkg/seaice: added SEAICEuseEVPpickup parameter |
2157 |
- Set to false in order to start EVP solver with |
2158 |
non-EVP pickup files when using SEAICEuseEVP |
2159 |
- fix sign error in diffusion in seaice_calc_rhs |
2160 |
|
2161 |
checkpoint58h_post (2006/06/07) |
2162 |
* Modifications for bottom topography control |
2163 |
o replace hFacC by _hFacC at various places |
2164 |
o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL |
2165 |
o add non-self-adjoint cg2d_nsa |
2166 |
o update autodiff support routines |
2167 |
o re-initialise hfac after ctrl_depth_ini |
2168 |
o works for 5x5 box, doesnt work for global_ocean.90x40x15 |
2169 |
* Adding verification for 5x5 box (4-layer) bottom topography control |
2170 |
|
2171 |
checkpoint58g_post (2006/06/07) |
2172 |
o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., |
2173 |
used for mean seasonal cycle, mean diurnal cycle); add an example |
2174 |
in verification/global_ocean.cs32x15/input.thsice/data.diagnostics |
2175 |
o pkg/ggl90: |
2176 |
- add parameter (minimum surface kinetic energy) |
2177 |
- fix bug (avoiding division by zero) |
2178 |
o couple pkg/thsice to pkg/seaice: |
2179 |
- modify advection in seaice to accomodate new scalar fields to be advected |
2180 |
- only muliDimAdection scheme work with seaice/thsice |
2181 |
- mapping of thsice-variables to seaice-variables, back and forth |
2182 |
- does not break the verification experiments, but does not give the |
2183 |
desired results either |
2184 |
o pkg/seaice |
2185 |
- make (default) second order advection a bit less confusing? |
2186 |
|
2187 |
checkpoint58f_post (2006/06/05) |
2188 |
o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice |
2189 |
to pkg/seaice): |
2190 |
- new routines thsice_map_exf and thsice_get_exf provide the interface |
2191 |
- add an additional formal parameter to thsice_solve4temp |
2192 |
o pkg/exf: |
2193 |
- add new fields wspeed, snowprecip (to be able to couple to thsice) |
2194 |
- correct Stefan-Boltzmann constant |
2195 |
- new parameter for longwave surface emittance |
2196 |
- separate some stuff from exf_bulkformulae into new routines |
2197 |
exf_radiation, exf_wind |
2198 |
- add new parameters and constants: longwave emissivity for ocean, ice |
2199 |
and snow, evaporation parameters over ice |
2200 |
- decouple wind/stress computation from ALLOW_BULKFORMULA: always compute |
2201 |
either wind from stress or stress from wind |
2202 |
o pkg/thSIce: |
2203 |
- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F |
2204 |
- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND |
2205 |
and THSICE_CALC_THICKN |
2206 |
- for now, call to THSICE_GET_BULKF remains inside i,j loops. |
2207 |
- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h |
2208 |
to make debugging easier. |
2209 |
- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output |
2210 |
o pkg/bulk_force: |
2211 |
- clean-up comments and parameters ; |
2212 |
- add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; |
2213 |
o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; |
2214 |
generate new output for test-experiment: aim.5l_cs.thSI |
2215 |
o results_ad : rename "output.txt_adm" to "output_adm.txt" and change |
2216 |
testreport accordingly |
2217 |
|
2218 |
checkpoint58e_post (2006/05/17) |
2219 |
o SEAICE_CGRID adjoint done |
2220 |
o R_STAR adjoint implemented. |
2221 |
* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
2222 |
* need to sort out init. of h0facc, etc. |
2223 |
o Make pkg/profile fully independent of ecco,cost, etc. stuff |
2224 |
to be able to use it in pure forward. |
2225 |
|
2226 |
checkpoint58d_post (2006/04/21) |
2227 |
o upgrade simple test-experiment to tutorial example: |
2228 |
step.1: duplicate the experiment and (step.2) will remove the old copy. |
2229 |
tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
2230 |
tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) |
2231 |
tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
2232 |
tutorial_global_oce_biogeo <- copy of dic_example |
2233 |
tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
2234 |
tutorial_plume_on_slope <- copy of plume_on_slope |
2235 |
tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) |
2236 |
tutorial_global_oce_optim <- empty for now (David ?) |
2237 |
tutorial_global_oce_in_p <- copy of global_ocean_pressure |
2238 |
some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
2239 |
o correct a sign problem in cost_scat.F |
2240 |
o obcs and ptracers: fix boundary conditions for advections schemes |
2241 |
with larger stencil |
2242 |
o thsice adjoint: start |
2243 |
o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for |
2244 |
completeness |
2245 |
o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING |
2246 |
and COSINEMETH_III, add comments in default CPP_OPTIONS.h |
2247 |
o ptracers adjoint: |
2248 |
* avoid extensive recomputatations |
2249 |
* fix missing re-init. of gptr (missed by TAF) |
2250 |
o obcs: add a flag (OBCSprintDiags, defaults is true) that allows |
2251 |
me to turn off the excessive output to STDOUT that this package produces |
2252 |
o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common |
2253 |
and add those terms in Vector-Invariant formulation. |
2254 |
o in ctrl pkg, if ALLOW_CAL, use monthly mean controls |
2255 |
if the control period (xx_hfluxperiod etc) is 0 |
2256 |
o in profiles pkg, clean routines and fix details |
2257 |
o in ecco pkg, reading ssh data: |
2258 |
fix problem in case the model does not start at iter0=0 |
2259 |
o fix mnc-pickup/restart for ptracers |
2260 |
o new package prifiles: |
2261 |
code to compute profile-based cost by Gael Forget |
2262 |
(modifs in ecco, ctrl, autodiff) |
2263 |
o Benign bug fix in initialization (spotted by M. Mazloff) of |
2264 |
ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F |
2265 |
|
2266 |
checkpoint58c_post (2006/03/23) |
2267 |
o adjoint: finish NLFS adjoint and provide reference output in |
2268 |
verification/global_ocean.90x40x15/results_ad_nlfs |
2269 |
o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the |
2270 |
documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in |
2271 |
SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only |
2272 |
with SEAICE_CGRID defined. |
2273 |
o move calendarDumps from "data" to "data.cal" and clean-up the code |
2274 |
with a simple call to pkg/cal S/R: CAL_TIME2WRITE |
2275 |
o add useEXF & useCAL flags (for now, set in hard-coded way) |
2276 |
o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum |
2277 |
(were missing in NH mode, and wrong in quasihydrostatic mode). |
2278 |
waiting for Chris updated version of calc_gw to add those CALLs. |
2279 |
o fix bug in quasihydrostatic S/R ; |
2280 |
add a test for this option: global_ocean.90x40x15.qshyd |
2281 |
o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs. |
2282 |
(called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS) |
2283 |
o add on/off flag useOffLine for package OFFLINE |
2284 |
o seaice: |
2285 |
- modify advection so that it works also on the C-grid |
2286 |
- extend loop ranges in seaice_lsr and seaice_dynsolver; fixes |
2287 |
problem in multi-tile runs with C-grid |
2288 |
- add flags for clipping ice velocities and/or masking solver forcing |
2289 |
- fix drag (ocean on ice) formulation and a bug that caused noise in the |
2290 |
C-grid solver |
2291 |
- added a few comments to seaice_diffusion.F |
2292 |
- separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V |
2293 |
are now exclusive) |
2294 |
- add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which |
2295 |
required re-ordering the code a little: |
2296 |
+ make DAIRN global variable (defined in SEAICE) |
2297 |
+ move computation of the viscosities eta and zeta into a new separate |
2298 |
routine (because I need to recompute them in seaice_ocean_stress.F) |
2299 |
|
2300 |
checkpoint58b_post (2006/03/13) |
2301 |
o AIM+thSIce: fix sign of Short-Wave through the Ice ; |
2302 |
update output.txt of exp. aim.5l_cs.thSI |
2303 |
o various mnc cleanups and improvements: |
2304 |
+ shrink lookup tables by factor of ~4 |
2305 |
+ better error reporting when running out of lookup space |
2306 |
+ able to handle longer path/file names (up to 500 chars) |
2307 |
o adjoint: |
2308 |
- Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. |
2309 |
- TBD: "hidden" mom_vecinv recomp. in dynamics |
2310 |
o change forcing_In_AB to affects both T,S forcing and Momentum forcing |
2311 |
(allow to differentiate between forcing components using new integer flags: |
2312 |
momForcingOutAB=1/0 & tracForcingOutAB=1/0) |
2313 |
and add new flag to put Dissipation tendency out of Adams-Bashforth. |
2314 |
o ecco |
2315 |
- enable trend removal from SSH anomaly obs. |
2316 |
o adjoint |
2317 |
- a fix for PmEpR when #undef EXACT_CONSERV |
2318 |
- fix of "hidden" recomp. in thermodynamics (no TAF warnings) |
2319 |
- try to fix "hidden" recomp. in forward_step for NLFS |
2320 |
(NLFS seems broken sometimes after I checked it in) |
2321 |
o seaice: |
2322 |
- add c-grid version of the dynamic solver: |
2323 |
+ three new routines that are the c-grid substitute lsr, dynsolver |
2324 |
and ostres |
2325 |
+ put a few fields that were local to dynsolver into global common |
2326 |
blocks, so that I can move the computation of stresses etc into |
2327 |
seaice_lsr (saves coding but may break the adjoint). |
2328 |
- replace more hardwired parameters by runtime parameters |
2329 |
- add ice masks that mask the rhs of the implicit solvers where there |
2330 |
is no ice (commented out in seaice_dynsolver, because i am not sure |
2331 |
if this works properly), eventually this should replace the clipping |
2332 |
of ice velocities in seaice_dynsolver to +/-40cm/s. |
2333 |
o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly |
2334 |
include it only where its needed |
2335 |
o move balancing of fluxes before the call of external_forcing_surf |
2336 |
o seaice: |
2337 |
- correct units of turning angles (now they are really in degrees) |
2338 |
- move computation of GWATX/Y out of main routine into dynsolver |
2339 |
- initialize GWATX/Y in seaice_init |
2340 |
o Apply mask on Fresh-Water flux (needed for SSH forcing). |
2341 |
update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) |
2342 |
o seaice: add runtime flags for turning angles (default to zero) |
2343 |
o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean |
2344 |
and trend from exf forcing and ctrl control adjustments |
2345 |
o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF |
2346 |
(since checkpoint57x_post) |
2347 |
o change the default rotation period to 86164.s = the Earth rotation |
2348 |
o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) |
2349 |
and based on a reference stratification. Tested within hs94.cs-32x32x5. |
2350 |
o seaice advection: add code for choosing between the default (2nd order |
2351 |
central differences) and multiDim advection schemes provided by |
2352 |
pkg/generic_advdiff |
2353 |
o seaice: |
2354 |
- removed all references to SEAICE_GRID.h fields from |
2355 |
dynsolver, advect, diffus, lsr, without changing the results of lab_sea |
2356 |
(cubed-sphere configuration will change a little) |
2357 |
- grid computations in seaice_init are obsolete now. |
2358 |
- cleaned up code a little so that is easier to read (hopefully). |
2359 |
- added new (better?) discretizations of default advection and diffusion |
2360 |
(turn on with SEAICEuseFluxForm) |
2361 |
- replace 1 in 3d global fields by kSurface in growth.F |
2362 |
|
2363 |
checkpoint58a_post (2006/02/13) |
2364 |
o seaice: |
2365 |
- bug fix in advect.F |
2366 |
o shelfice: |
2367 |
- separate shelfice load anomaly from pload (breaks with time |
2368 |
dependent forcing), => introduce constant field shelficeLoadAnomaly. |
2369 |
Its default is 0., but it may be computed more cleverly from (unknown) |
2370 |
t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be |
2371 |
done offline. A good approximation of the pressure load anomaly is |
2372 |
necessary to avoid large initial adjustment processes underneath |
2373 |
deep-reaching shelfice. |
2374 |
- small fix in ISOMIP shelfice_thermodynamics |
2375 |
- add more sophisticated thermodynamics of Hellmer (1989), this is |
2376 |
now the default |
2377 |
- give a few constants more intuitive names |
2378 |
o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful |
2379 |
if bulk formulae are used in long integration (especially EmPmR). Turn |
2380 |
on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01 |
2381 |
if balancePrintMean, the imbalance that is substracted is printed to |
2382 |
STDOUT. |
2383 |
o fix bug (typo) in obcs_apply_eta.F |
2384 |
o add a new package shelfice which enables us to model the circulation |
2385 |
underneath shelf-ice with draughts of hundreds of meters. |
2386 |
- works |
2387 |
- to do: + include improved thermodynamics |
2388 |
+ check whether kSurfC (from model/inc/SURFACE.h) can be used |
2389 |
instead of new field kTopC |
2390 |
+ can we use topoFile, Ro_surf and existing code in ini_depth.F |
2391 |
instead of new field R_shelfIce and new code in ini_depth.F |
2392 |
and ini_mask_etc.F? |
2393 |
+ adjust vertical mixing schemes? |
2394 |
o seaice pkg: |
2395 |
- add a cpp-flag to include a simple formula for a salinity dependent |
2396 |
freezing point of sea water at the surface |
2397 |
- change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and |
2398 |
meridional stresses are now different (and hopefully correct) |
2399 |
o AIM pkg: change threshold on large-scale condensation to conserve Heat. |
2400 |
update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics |
2401 |
and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG) |
2402 |
o pkg/diagnostics: add options and parameters for regional-statistics |
2403 |
diagnostics ; define regions by reading a region-mask from a file |
2404 |
(might add other options later) |
2405 |
o pkg/bulk_force: |
2406 |
- add option and parameters to use AIM surface-flux formulae. |
2407 |
- Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ; |
2408 |
others forcing fields (defined in PARM05, parameter file "data") are loaded |
2409 |
from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F). |
2410 |
- initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F |
2411 |
- use the right EXCH call for uwind,vwind (to work on CS-grid). |
2412 |
- re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h) |
2413 |
and parameters (note: calcWindStress replaces .NOT.readwindstress). |
2414 |
- cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). |
2415 |
|
2416 |
checkpoint58 (2006/01/12) |
2417 |
o add "--embed-source" option to genmake2 which, when the supporting |
2418 |
tools can be compiled (as determined by genmake2) will turn on the |
2419 |
embed_files package which then embeds the entire MITgcm source code |
2420 |
(*.[fFhc] + Makefile) used for the build within the executable |
2421 |
- requested by CNH but off by default |
2422 |
- adds a paltry <9MB to the mitgcmuv executable in most cases |
2423 |
- only writes the output when useEMBEDSRC in eedata is true |
2424 |
o clean up 3-dim. relaxation codes: |
2425 |
* Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec |
2426 |
* Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) |
2427 |
* Thanks to Tom Haine for testing! |
2428 |
|
2429 |
checkpoint57z_post (2005/12/31) |
2430 |
o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): |
2431 |
affects output (@ truncation level) of exp. plume_on_slope ; updated. |
2432 |
o fix the pickup behavior for obcs in combination with ptracers |
2433 |
o fix a bug in ptracers_external_fields_load |
2434 |
o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...) |
2435 |
affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) |
2436 |
o transfered surface NH pressure to eta field (if exactConserv). |
2437 |
o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign) |
2438 |
and update lab_sea output.txt file. |
2439 |
o completing 3-dim. relaxation code: additional term |
2440 |
1/tau*( theta(i,j,k) - thetaStar(i,j,k) ) |
2441 |
in S/R EXTERNAL_FORCING_T (file external_forcing.F) |
2442 |
* At compile time, in "EXF_OPTIONS.h" set |
2443 |
#define ALLOW_CLIMTEMP_RELAXATION |
2444 |
#define ALLOW_CLIMSALT_RELAXATION |
2445 |
* At runtime in "data", under &PARM03 set (e.g., units in seconds) |
2446 |
tauThetaClimRelax3Dim = 15552000.0, |
2447 |
tauSaltClimRelax3Dim = 15552000.0, |
2448 |
* 3 cases: |
2449 |
1) Use a constant-in-time 3-dim. field |
2450 |
2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec. |
2451 |
3) Real-time relax. to time-evolving prescribed field |
2452 |
o Adding Laplacian-type smoothness constraint on |
2453 |
initial and boundary (forcing) controls (ic, bc) |
2454 |
* enable at compile-time via |
2455 |
ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION |
2456 |
* enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1 |
2457 |
* Absolute scale somewhat unclear so far |
2458 |
* no area weighting was included since no other cost term does so far |
2459 |
|
2460 |
checkpoint57y_post (2005/12/08) |
2461 |
First step for a NLFS adjoint |
2462 |
o initially suppress rStar (new flag DISABLE_RSTAR_CODE) |
2463 |
o new init. routines for calc_r_star, calc_surf_dr |
2464 |
o still need to deal with ini_masks_etc |
2465 |
o testreport seemed happy |
2466 |
checkpoint57y_pre (2005/12/08) |
2467 |
|
2468 |
o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
2469 |
o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) |
2470 |
o add new offset feature to offline pkg (plus minor cleanup) |
2471 |
o cfc fixes for final year of integration |
2472 |
o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should |
2473 |
be in GCHEM_OPTIONS). |
2474 |
|
2475 |
checkpoint57x_post (2005/12/04) |
2476 |
o fix testreport Pb in multiple test experiment. |
2477 |
o cleanup our namelist syntax in verification: |
2478 |
- make it more F95 standards compliant (some work still needed) |
2479 |
- allows the vast majority of our tests to work with gfortran |
2480 |
o Non-Hydrostatic: |
2481 |
- put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h |
2482 |
- fix exchange calls for CS-grid using the new EXCH_S3D_RL. |
2483 |
o Allow to apply AB on T,S rather than on AB(gT,gS): |
2484 |
- implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 |
2485 |
- use the same arrays (gtNm,gsNm) to hold tracer field at previous |
2486 |
time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). |
2487 |
- need a "clever" read_pickup to restart from the other AB formulation |
2488 |
o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h |
2489 |
o remove some unused variables (reduces number of compiler warnings) |
2490 |
o adjoint |
2491 |
* Disable useVariableViscosity for adjoint for time being |
2492 |
(there are a number of extensive recomputations) |
2493 |
* Initialize certain variables needed for adjoint |
2494 |
|
2495 |
checkpoint57w_post (2005/11/03) |
2496 |
o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names |
2497 |
fix the singleCpuIO RS version of MDSWRITEFIELD |
2498 |
and add a WARNING if using globalFiles=T with multi-processors. |
2499 |
o write grid-file(s) in only one format (MDS or MNC): default=MNC (if |
2500 |
using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc |
2501 |
o tracer advection scheme: |
2502 |
add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get |
2503 |
those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, |
2504 |
was not very convenient). |
2505 |
add implicit version for DST-3 & DST3_Flux_Limit vertical advection; |
2506 |
(further tests needed for the implicit DST & Flux-Limiter schemes). |
2507 |
o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef |
2508 |
and sRef for convenience, handy, when you want to initialize |
2509 |
ptracers in a large domain with a constant non-zero value. Also, |
2510 |
untangle ptracers_init.F a little. |
2511 |
|
2512 |
checkpoint57v_post (2005/10/13) |
2513 |
o change dome exp. to use variable viscosity in side-drag terms. |
2514 |
o remove all the files from the cfc_offline test since they are now |
2515 |
incorporated into tutorial_cfc_offline which has been producing |
2516 |
identical results for a few days of testing |
2517 |
o add new parameter: sideDragFactor to enable half-slip-side BC |
2518 |
and change side-drag S/R to use viscosity from mom_calc_visc |
2519 |
(can switch back by setting sideDragFactor=0.); affects results at |
2520 |
truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), |
2521 |
global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). |
2522 |
o vorticity & strain are now computed without masking, to account for |
2523 |
no-slip-side BC in variable viscosity calculation ; mask is applied |
2524 |
anyway later on, before computing advection/coriolis terms. |
2525 |
o modify exp4 to test new obcs support for reading from external files |
2526 |
and for passive tracers |
2527 |
o fix behavior of ptracers_monitor when monitor output is written to a |
2528 |
netcdf-file; still not independent of monitor.F (writes in the same |
2529 |
file). |
2530 |
o change default value of tRef (put a uniform, meaningful value for ocean |
2531 |
& atmos) and initialize sRef (was missing, as Martin mentioned). |
2532 |
o Redefine viscC?Leith*. Change the coefficients of Leith viscosity |
2533 |
to be proportional to enstrophy dissipation length. Thus, |
2534 |
viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) |
2535 |
This is now consistent with Smagorinsky and with the manual. |
2536 |
|
2537 |
checkpoint57u_post |
2538 |
o OBCS and PTRACERS: add open boundary support for passive tracers |
2539 |
- either use homogenous (pseudo) v.Neumann conditions or prescribe |
2540 |
OB-values from file; this is not different from the way theta and salinity |
2541 |
are treated |
2542 |
- however, Orlanski-radiation conditions are not supported, and the model |
2543 |
will stop if you use pTracers and Orlanski at the same time. |
2544 |
- beefed up the rountine obcs_external_fields_load: now only those open |
2545 |
boundary values are overwritten with values from files for which there |
2546 |
are really files, otherwise the OB-fields remain untouched. This makes |
2547 |
it possible to use different OBs at different ends of the domain (as |
2548 |
with EXF) |
2549 |
o reduce number of exch calls in shap_filt (s2). |
2550 |
o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ |
2551 |
truncation level) 4/5 MLAdjust test results (11&12 digits match). |
2552 |
|
2553 |
checkpoint57t_post (2005/10/03) |
2554 |
o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
2555 |
o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
2556 |
same truncation, independent of the face number: affects affects several |
2557 |
test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). |
2558 |
o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); |
2559 |
note that biharmonic viscosity + no-slip was not tested in any experiment. |
2560 |
o fix bug in non-linear free-surf side-drag ; generate new output for |
2561 |
global_ocean.cs32x15(+.thsice) & global_ocean_pressure. |
2562 |
o make mnc honor the writeBinaryPrec flag for most kinds of output |
2563 |
o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
2564 |
o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
2565 |
error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
2566 |
o add brackets in multi-terms sum to get same truncation, independent of |
2567 |
the face number (manage to get exactly same value of gU,gV at the cs-edge) |
2568 |
affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
2569 |
o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
2570 |
and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
2571 |
a maximum grid-scale Reynolds number. Also, changes all length calculations |
2572 |
in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
2573 |
Suggested values of viscosity parameters found in mom_calc_visc. |
2574 |
Many new viscosity diagnostics available. |
2575 |
|
2576 |
checkpoint57s_post (2005/09/20) |
2577 |
o Add clearing-house for viscosity calculations, mom_calc_visc and |
2578 |
correct numerous bugs in LeithD and Smagorinsky discretizations. |
2579 |
mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
2580 |
used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
2581 |
Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
2582 |
and with Strain-Tension viscous term calculation (mom_hdissip.F). |
2583 |
The Strain-Tension form is now called with useStrainTensonVisc=.true. |
2584 |
ViscAhStrain and viscAhTension are now retired. |
2585 |
o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
2586 |
o In response to JMC's bug report, genmake2 now ignores any soft-links |
2587 |
that it finds in the *current* directory when searching for files. |
2588 |
Soft-links found in any other source directories will still work as |
2589 |
they did before. |
2590 |
o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
2591 |
a C routine to unlimit the stack size |
2592 |
o mnc-ify pkg/aim snapshot vars |
2593 |
o mnc-ify pkg/land as requested by Daniel |
2594 |
o various changes to mnc including: |
2595 |
- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
2596 |
- output can now be grouped so that all files within a group |
2597 |
change the ITER portion of their names in lock-step together |
2598 |
- can now read ("global") PER-FACE (in addition to PER-TILE) files |
2599 |
and works with both EXCH1 and EXCH2 (but needs more testing) |
2600 |
- writing works for all verification test cases w/ g77 on Linux |
2601 |
|
2602 |
checkpoint57r_post (2005/09/07) |
2603 |
o make MNC variable initialization happen earlier |
2604 |
o add diagnostics for (almost) each term of the momentum Eq. |
2605 |
o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
2606 |
o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
2607 |
o remove MINIMAL_TAVE_OUTPUT option ; |
2608 |
add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
2609 |
o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
2610 |
allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
2611 |
o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
2612 |
o add time-dependent SST, SSS control |
2613 |
o cost terms in ecco/ modularized (new cost_generic.F) |
2614 |
o cost_averages routines are modularized (new cost_averagesgeneric.F) |
2615 |
o new infrastructure for seaice model vs. obs misfits in seaice/ |
2616 |
* driver from the_main_loop.F is seaice_cost_driver.F |
2617 |
* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
2618 |
* gradient check in Exp. 6a of natl_box_adjoint/ |
2619 |
o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
2620 |
(see README file) |
2621 |
|
2622 |
checkpoint57q_post (2005/08/19) |
2623 |
o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
2624 |
o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
2625 |
- bug was reported by Jean-Michel and Ian Fenty |
2626 |
o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
2627 |
update exp. cpl_aim+ocn output. |
2628 |
o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
2629 |
Needed for high-res. runs with large global files |
2630 |
to be able to limit tapelev size |
2631 |
o Changed some tests for adjoint: |
2632 |
* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
2633 |
* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
2634 |
* global_ocean.90x40x15/ back to default 3-level checkpointing |
2635 |
o Modifications to enable scripted COMMON to MODULE conversion |
2636 |
* verification/OpenAD/code/ has necessary scripts and description; |
2637 |
* converts, compiles and runs successfully; |
2638 |
|
2639 |
checkpoint57p_post (2005/08/01) |
2640 |
o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
2641 |
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
2642 |
(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
2643 |
o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
2644 |
o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
2645 |
(was already the case for dissipation with mom_vecinv, |
2646 |
and also the case for grad.PhiHyd when staggered-timeStep) |
2647 |
This will allow to put dissipation out-off the AB time-stepping. |
2648 |
Unfortunately, affects truncation error. Update output of exp. that "fails" |
2649 |
(cg2d matching number) and leave the others for later: front_relax(10), |
2650 |
global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
2651 |
matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
2652 |
|
2653 |
checkpoint57o_post (2005/07/30) |
2654 |
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
2655 |
(2) its ready to be documented during the 20050801 DocFest |
2656 |
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
2657 |
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
2658 |
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
2659 |
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
2660 |
(worth another tag) |
2661 |
|
2662 |
checkpoint57n_post (2005/07/29) |
2663 |
o adding precip control xx_precip 32 |
2664 |
o adding swflux control xx_swflux 33 |
2665 |
o Replacing 10 forcing penalty cost routines by 1 generic. |
2666 |
o Implementing partitioning in time-mean and variable adjustment |
2667 |
for atmos. state. |
2668 |
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
2669 |
o in natl_box_adjoint: |
2670 |
* updated exp 1 to 10 |
2671 |
(but does not have time-mean vs. variable split results yet) |
2672 |
o updated global1x1/*_seaice_adj/ |
2673 |
to incorporate latest changes |
2674 |
o enable useSingleCpuIO for mdsio vector routines |
2675 |
(applies in particular to tapelev I/O) |
2676 |
o removed inefficient K-loop in all active_file*control*.F |
2677 |
|
2678 |
checkpoint57m_post (2005/07/28) |
2679 |
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
2680 |
and advect_cs (use EXCH-2 and standard cs-32 grid files). |
2681 |
o pkg/exch2: filling of face-corner halo regions is optional |
2682 |
(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
2683 |
|
2684 |
checkpoint57l_post (2005/07/14) |
2685 |
tag before updating tutorials (pre-release-2) |
2686 |
o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
2687 |
for output and interpolation of input fields onto model grid) |
2688 |
o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
2689 |
Affects results of exp. rotating_tank ; update output.txt. |
2690 |
o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
2691 |
and taking the square quantity and/or using a fraction-weight field. |
2692 |
o fix aim_diagnostics_init.F mate numbers. |
2693 |
o add mnc output capability to diagnostics/diagstat and update |
2694 |
our cvsignore files for the ACSII output generated |
2695 |
|
2696 |
checkpoint57k_post (2005/07/02) |
2697 |
o lab_sea now uses diagnostics package and provides a suite of |
2698 |
new EXF diagnostics output. |
2699 |
|
2700 |
checkpoint57j_post (2005/06/30) |
2701 |
o exf |
2702 |
* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
2703 |
Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
2704 |
terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
2705 |
* extended diagnostics output |
2706 |
- now includes all EXF variables |
2707 |
- hs, hl moved to common block |
2708 |
- separate S/R for diagnostics, called after ctrl vector is added |
2709 |
- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
2710 |
- EXFqnet contains true Qnet (i.e. includes qsw) |
2711 |
* updated verif. lab_sea, global_with_exf |
2712 |
* Rearranging hflux (exf_mapfields -> exf_getforcing) |
2713 |
to ensure that diagnostics sees a true EXFqnet |
2714 |
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
2715 |
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
2716 |
several times with different frequencies. |
2717 |
o mnc-ify the thsice package as requested by Daniel Enderton |
2718 |
- the monitor--MNC output needs work |
2719 |
- many attributes need to be added (most are currently blank) |
2720 |
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
2721 |
- many attributes need to be added (most are currently blank) |
2722 |
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
2723 |
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
2724 |
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
2725 |
update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
2726 |
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
2727 |
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
2728 |
(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
2729 |
|
2730 |
checkpoint57i_post (2005/06/19) |
2731 |
o Diagnostics package was changed: diagnostic allocation is now deactivated |
2732 |
by setting an empty file name in the namelist (used to be by setting 0 frequency) |
2733 |
o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
2734 |
add 1rst Order upwind vertical Shear. |
2735 |
o add a quick fix for A/B checkpointing in OFFLINE mode |
2736 |
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
2737 |
end-run around the C/Fortran linking horror in eesup/src/timers.F |
2738 |
o added pkg/runclock: allows user to terminate run based on wall clock |
2739 |
o added non-hydrostatic scaling parameter: nh_am2 |
2740 |
o pkg/my82: futile attempt to make results compiler-independent by adding |
2741 |
some "_d 0", etc. no effect. |
2742 |
o for mnc output, fill the 'T' coordinate var with myTime and create a |
2743 |
separate 'iter' variable for iteration count |
2744 |
o pkg/diagnostics: |
2745 |
add new capability: output of Global/Regional & per-level statistics ; |
2746 |
tested against monitor output (including land & thSIce) on various exp. |
2747 |
o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
2748 |
|
2749 |
checkpoint57h_done (2005/05/19) |
2750 |
tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
2751 |
data.diagnostics, data.gchem, data.ptracers) is done. |
2752 |
|
2753 |
o pkg/diagnostics: prepare for Global/Regional statistics. |
2754 |
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
2755 |
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
2756 |
and rename it: DIFFERENT_MULTIPLE |
2757 |
|
2758 |
checkpoint57h_post (2005/05/14) |
2759 |
o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
2760 |
o pkg/diagnostics: change output frequency, now in seconds (instead |
2761 |
of Nb of iterations). This requires to change data.diagnostics. |
2762 |
checkpoint57h_pre (2005/05/12) |
2763 |
|
2764 |
o in mnc, let the user create the output dir if both mnc_outdir_date |
2765 |
and mnc_outdir_num are false |
2766 |
o add fflags() to pkg/diagnostics which allows one to specify, on a |
2767 |
per-file basis, the file precision [default behavior is unchanged] |
2768 |
o added diagnostics to pkg/kpp, including computation of mixed layer |
2769 |
depth based on a temperature/density criterion |
2770 |
o updated verification/natl_box to test the new pkg/kpp diagnostics |
2771 |
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
2772 |
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
2773 |
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
2774 |
not mnc -- this mistake was found by JMC and is now corrected |
2775 |
|
2776 |
checkpoint57g_post (2005/04/15) |
2777 |
o add Adams-Bashforth 3rd Order time stepping: |
2778 |
- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
2779 |
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
2780 |
checkpoint57g_pre (2005/04/15) |
2781 |
|
2782 |
o make lambda[Theta,Salt]ClimRelax spatially varying |
2783 |
(default remains spatially uniform constant based on tau) |
2784 |
o added new control variables |
2785 |
* init. uVel, vVel, etanN |
2786 |
* lambda[Theta,Salt]ClimRelax |
2787 |
o separate masks used for ctrl_pack/unpack 'from write_grid' output |
2788 |
(suggested by G. Forget) |
2789 |
|
2790 |
checkpoint57f_post (2005/04/06) |
2791 |
o add parameter "baseTime" = model base time = time at iteration zero |
2792 |
new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
2793 |
account for baseTime shift |
2794 |
o move Coriolis arrays from PARAMS.h to GRID.h |
2795 |
checkpoint57f_pre (2005/04/06) |
2796 |
|
2797 |
o mnc-ifying the seaice package |
2798 |
o introduced an alternative length scale calculation for use in the limiting |
2799 |
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
2800 |
o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
2801 |
o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
2802 |
as well as grad(vort3). Made it compatible with both approximate form |
2803 |
for the cubed sphere and full form of these gradients. Added flag |
2804 |
useFullLeith to select between approximate and full form. |
2805 |
o add "d0" in getcon.F to reduce differences between compilers/platforms |
2806 |
update output.txt of exp. fizhi-gridalt-hs |
2807 |
o change port_rand funtion to allow to set the seed. |
2808 |
o fix obscure MNC bug involving conversion between reals and integers |
2809 |
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
2810 |
new version is now more standards-compliant |
2811 |
o adjoint-related modifications |
2812 |
* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
2813 |
* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
2814 |
* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
2815 |
|
2816 |
checkpoint57e_post (2005/02/28) |
2817 |
o Adding eddy stress controls a la Ferreira et al. |
2818 |
checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
2819 |
|
2820 |
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
2821 |
update output.txt of exp. fizhi-gridalt-hs |
2822 |
o add more "Z" dimensions and associated coordinate vars to MNC |
2823 |
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
2824 |
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
2825 |
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
2826 |
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
2827 |
months and years. Requires pkg/cal. |
2828 |
o diagnostics: add pickup functionality |
2829 |
- off by default for backwards compatibility |
2830 |
- current version only uses MDSIO -- MNC will be added |
2831 |
o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
2832 |
o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
2833 |
|
2834 |
checkpoint57d_post (2005/02/11) |
2835 |
o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
2836 |
o modify verification/ideal_2D_oce so that it tests the creation of mnc |
2837 |
output from the diagnostics package |
2838 |
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
2839 |
o make genmake2 more portable by using ".$FS" instead of ".f" for more |
2840 |
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
2841 |
o add coordinate variables to the MNC output from the diagnostics package |
2842 |
o change MNC-flags default value: true when useMNC=TRUE |
2843 |
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
2844 |
the ability (off by default) to read the grid information using MNC |
2845 |
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
2846 |
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
2847 |
o do snap-shot diagnostics at the middle of the time-interval (instead of |
2848 |
at the end). |
2849 |
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
2850 |
new test for AIM with thSIce + slab-ocean |
2851 |
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
2852 |
o move state variable diagnostics to the beginning of the time step ; |
2853 |
(note: still needs some work specially for snap-shot diagnostics) |
2854 |
duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
2855 |
|
2856 |
checkpoint57c_post (2005/01/27) |
2857 |
o Change testing option (-ieee) to get closer agreement between g77 & ifort |
2858 |
o generate new output.txt files on faulks with g77 & the new -ieee option |
2859 |
checkpoint57c_pre (2005/01/27) |
2860 |
|
2861 |
o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
2862 |
update output.txt of exp. global_ocean.90x40x15 |
2863 |
o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
2864 |
results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
2865 |
o add saltFlux(+File) forcing capability with periodicExternalForcing |
2866 |
o allow to use pkg diagnostics for GM-Redi & ThSIce output |
2867 |
o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
2868 |
o improvements for the MNC output from DIAGNOSTICS: |
2869 |
- correct handling of the unlimitied dimension |
2870 |
- all dims now have associated coordinate variables |
2871 |
- variables located at U, V, and Corner ("Z") points are now written |
2872 |
with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
2873 |
*all* data points are output |
2874 |
o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
2875 |
o added pkg/seaice/seaice_monitor.F |
2876 |
o mdsio_readfield.F can now read files visible only to master MPI process. |
2877 |
o pkg/seaice: some test code for ice-modified ocean stress |
2878 |
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
2879 |
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
2880 |
spurious negative numbers for precipitation and humidity. Will cause |
2881 |
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
2882 |
o pkg/ctrl/ |
2883 |
* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
2884 |
May be enabled via doPackDiag |
2885 |
* introduce z-scaling of |
2886 |
+ gradient (doZscalePack) and |
2887 |
+ control (doZscaleUnpack) |
2888 |
o pkg/mdsio/ |
2889 |
* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
2890 |
* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
2891 |
|
2892 |
checkpoint57b_post (2004/12/20) |
2893 |
o simplify options in diagnostics_fill arguments (remove weird combinations) |
2894 |
o fix MNC coordinate variables so that they now contain per-face index |
2895 |
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
2896 |
general, EXCH2 grids are only aligned to a "local" coordinate system |
2897 |
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
2898 |
o Implement instantaneous output within pkg diagnostics: |
2899 |
setting a negative frequency in data.diagnostics produces |
2900 |
"snap-shot" output (as opposed to time-average if freq > 0) |
2901 |
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
2902 |
NOTE: change ptracer diagnostics name: use 2 characters to work with |
2903 |
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
2904 |
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
2905 |
becomes the coordinate variable for the 'T' dimension |
2906 |
o add CF-style coordinate variables to MNC |
2907 |
- just a first cut: numbers are meaningless on the cubesphere and |
2908 |
missing along the T axis but otherwise it works! |
2909 |
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
2910 |
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
2911 |
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
2912 |
this is based directly on what the model compute, so that the content of |
2913 |
each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
2914 |
o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
2915 |
o clean up build options files for SunOS, in particular |
2916 |
- remove -traditional from xmakedepend |
2917 |
- change -xarch=v9 to -xarch=native for f77 |
2918 |
- restore use of make (not gmake) |
2919 |
- add CC=gcc if using g77 |
2920 |
o changes per discussion of AM, JMC, & EH3 today: |
2921 |
- move redundant "grid" variables out of "state" -- in preparation of |
2922 |
creating proper CF-style coordinate variables and in recognition |
2923 |
that any/all grid variables can be easily copied (eg. w/NCO) from |
2924 |
the grid files into any of the other NetCDF files |
2925 |
- *always* output grid variables with MDSIO (this will eventually be |
2926 |
changed) |
2927 |
- output MNC grid file if useMNC is true |
2928 |
o every instance of _END_MASTER() has been found and replaced with |
2929 |
_END_MASTER( myThid ) in order to satisfy certain picky Sun |
2930 |
preprocessors |
2931 |
o re-arrange diagnostics pkg initialisation: |
2932 |
- allow each package to extend the available diagnostics list |
2933 |
- add some checking and fix small problems (multi-threaded, ...) |
2934 |
- new S/R diagnostics_fill (replace fill_diagnostics): |
2935 |
look through the short list of active diag. (instead of the long list) |
2936 |
create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
2937 |
|
2938 |
checkpoint57a_post (2004/12/10) |
2939 |
o this set of changes restores TAMC compatibility |
2940 |
tested for global_ocean.90x40x15 adjoint on trough |
2941 |
(what a pain) |
2942 |
|
2943 |
checkpoint57a_pre (2004/12/10) |
2944 |
o some modifs in tools/build_options for sunos |
2945 |
o call ctrl_pack for ctrl at end for optimcycle=0 |
2946 |
|
2947 |
checkpoint57 (2004/12/09) |
2948 |
o add horizontal bi-harmonic viscosity for vertical velocity |
2949 |
- new parameter viscA4W (defaults to viscA4) |
2950 |
- affects only non-hydrostatic code |
2951 |
- to be done: no-slip lateral boundary conditions |
2952 |
o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
2953 |
o implement Implicit Vertical advection for pTracers |
2954 |
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
2955 |
(implemented also for implicit vertical diffusion & advection) |
2956 |
o OBCS: extend application of tracer open boundary conditions |
2957 |
to a strip beyond the boundary of width Olx/Oly |
2958 |
o add call monitor to TAF set of required calls (flow directives) |
2959 |
and include in natl_box_adjoint |
2960 |
o untangle a few ifdefs related to cost, ctrl, autodiff |
2961 |
untangel a few ALLOW_ECCO_OPTIMIZATION |
2962 |
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
2963 |
(theta2, salt2 in ecco_cost_weights) |
2964 |
|
2965 |
checkpoint56c_post (2004/12/03) |
2966 |
o OBCS as control variables |
2967 |
- update ctrl_ad_diff.list, obcs_ad_diff.list |
2968 |
- remove balance of obcs controls from default |
2969 |
- fix index bug nobcs in ctrl_init |
2970 |
- fix dummy fields filen in ctrl_pack |
2971 |
- add dummy weights for obcs |
2972 |
o lsopt: comment out fort.94 output |
2973 |
o optim: |
2974 |
- remove unnecessary header files |
2975 |
- adjusted namelists |
2976 |
- add xerbla.F to Makefile |
2977 |
o exf: |
2978 |
- multiple modifications of exf_check_range |
2979 |
- unit change in exf_init_runoff from [m/year] to [m/s] |
2980 |
o mdsio: |
2981 |
- i/o-vector change debugLevel from debLevA to debLevB |
2982 |
|
2983 |
checkpoint56b_post (2004/12/01) |
2984 |
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
2985 |
is called from DO_THE_MODEL_IO |
2986 |
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
2987 |
- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
2988 |
- clean up PTRACERS_WRITE_TIMEAVE a little |
2989 |
o add another verification experiment that tests both the cfc-pkg and |
2990 |
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
2991 |
reactive tendencies treated inline with regular timestepping |
2992 |
o testreport previously did a lousy job of comparing small numbers, so |
2993 |
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
2994 |
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
2995 |
testreport. |
2996 |
o ptracers_monitor: bug fix for MPI |
2997 |
|
2998 |
checkpoint56a_post (2004/11/28) |
2999 |
o GCHEM: finish reorganizating the package |
3000 |
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
3001 |
(introduces another 3D-array for each passive tracer, but only if |
3002 |
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
3003 |
gchemTendency is not needed because the timestep is done separately) |
3004 |
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
3005 |
- GCHEM is now---more or less cleanly---separate from PTRACERS |
3006 |
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
3007 |
so clear to me how that should be done in a general way. |
3008 |
o CFC: improve formatting of output in CFC_ATMOS |
3009 |
o PTRACERS: |
3010 |
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
3011 |
that ALL experiments with ptracers enable can be checked. This makes |
3012 |
GCHEM_MONITOR obsolete. |
3013 |
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
3014 |
monitorFreq |
3015 |
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
3016 |
o add PTRACERS (PTR0[1-5]) to testreport output |
3017 |
o exf_check_range: |
3018 |
* default changed to .TRUE. |
3019 |
* will check values for niter0 if debLevA, every timestep if debLevB |
3020 |
* STOP in exf_check_range if 'out of range' |
3021 |
* range chosen generous to allow for potential extema |
3022 |
TBD: a version with stricter range |
3023 |
permitted range would be runtime parameters |
3024 |
o GMredi: |
3025 |
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
3026 |
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
3027 |
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
3028 |
o GCHEM: |
3029 |
- move call to GCHEM_FORCING_SEP, so that it is now called before |
3030 |
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
3031 |
- introduced a useGCHEM runtime flag and applied it everywhere. |
3032 |
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
3033 |
this flag is now only visible within GCHEM-pkg routines. |
3034 |
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
3035 |
be replaced by a 3D array that is computed before thermodynamics; for |
3036 |
this, the tracer ID iTracer had to be included into the parameter list |
3037 |
of ptracers_forcing |
3038 |
- set up forward_step to call gchem_forcing, that will replace |
3039 |
gchem_forcing_int in ptracers_forcing |
3040 |
- cleaning up |
3041 |
o small cleaning of exch2: remove files that are also in eesupp/src |
3042 |
|
3043 |
checkpoint56 (2004/11/17) |
3044 |
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
3045 |
o mnc: cleanup "full" files--fixes out-of-memory problem |
3046 |
o ECCO-GODAE |
3047 |
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
3048 |
* fully merged and updated from SIO code |
3049 |
windstress sign change affects |
3050 |
- exf_inscal_[u/v]stress |
3051 |
- sign of xx_tau[u/v] adjustments |
3052 |
- signs in cost_scat |
3053 |
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
3054 |
* natl_box_adjoint updated and compressed |
3055 |
* 2-level checkpoint switch added |
3056 |
(tested in EXP. 1 of natl_box_adjoint) |
3057 |
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
3058 |
o SVD |
3059 |
* first complete, non-hacked version for SVD calculations |
3060 |
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
3061 |
performed via direct access files admtlm_vector.it???? |
3062 |
(via ctrl_[un]pack) |
3063 |
* optimcycle is used for ARPACK iteration counter |
3064 |
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
3065 |
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
3066 |
and add linear transforms where necessary |
3067 |
* controls are initial/final SST, SSS (can be extended; need to check |
3068 |
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
3069 |
o mdsio: filename info to both stderr, stdout |
3070 |
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
3071 |
from sign change |
3072 |
|
3073 |
checkpoint55j_post (2004/11/10) |
3074 |
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
3075 |
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
3076 |
o add consistent build directories and .cvsignore files to verification |
3077 |
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
3078 |
o make all subroutines 30 or less characters in length for certain older |
3079 |
compilers to work (a thorough search only turns up two routines in |
3080 |
pkg/ptracers) |
3081 |
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
3082 |
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
3083 |
|
3084 |
checkpoint55i_post (2004/10/28) |
3085 |
o change arrays for total vertical diffusivity (2.D if explicit, |
3086 |
3.D if implicit) ; each ptracer uses its own background value. |
3087 |
o added mnc/NetCDF output capability to ocn_compon_interf |
3088 |
- added bits to verification/cpl_aim+ocn so that it can run on |
3089 |
ITRDA and other clusters without the mpirun "-wd" option |
3090 |
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
3091 |
configuration |
3092 |
o give MNC the ability to create additional files rather than |
3093 |
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
3094 |
- the default is just less than 2GB which is a practical limit |
3095 |
on many systems |
3096 |
o Compute the non-local term using either KPP vertical diffusivity (=default) |
3097 |
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
3098 |
|
3099 |
checkpoint55h_post (2004/10/20) |
3100 |
o add verification test "vermix" |
3101 |
o remove all the *_ioinc flags and replace with the single global |
3102 |
outputTypesInclusive flag |
3103 |
o allow to set a vertical profile of vertical diffusivity for T & S |
3104 |
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
3105 |
o useMNC moved from data.mnc to data.pkg |
3106 |
|
3107 |
checkpoint55g_post (2004/10/14) |
3108 |
o Renaming carbon AD experiments to comply with testreport conventions |
3109 |
o Updating adjoint of Held-Suarez hs94.1x64x5 |
3110 |
o Fixing directives for non-ECCO forward_step, after ECCO directives |
3111 |
have been fixed to avoid recomp. of do_oceanic_phys |
3112 |
Works well for global_ocean.90x40x15, |
3113 |
but recomp. issue remains for carbon |
3114 |
o Updating adjoint output for natl_box_adjoint after |
3115 |
pkg/ecco has been modified (see taga c55d_post) |
3116 |
|
3117 |
checkpoint55f_post (2004/10/13) |
3118 |
o rename to timeave_init_fixed |
3119 |
|
3120 |
checkpoint55e_post (2004/10/13) |
3121 |
o some delicate re-shuffle of store directives to avoid one |
3122 |
extra call of do_oceanic_physics |
3123 |
affects ecco_the_main_loop.F, do_oceanic_physics.F |
3124 |
checkpoint_lev1_directives.h |
3125 |
o NB: this may break global_ocean adjoint temporarily, |
3126 |
but it is clear how to fix it. Will do later, need this now. |
3127 |
|
3128 |
checkpoint55d_post (2004/10/11) |
3129 |
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
3130 |
o ecco_cost_weights is modified to 1x1 runs |
3131 |
o modifs to allow observations to be read in as |
3132 |
single file or yearly files |
3133 |
o enable to read exf forcing fields as either |
3134 |
single file or yearly files (flag useExfYearlyFields) |
3135 |
checkpoint55d_pre (2004/10/08) |
3136 |
|
3137 |
o switch between 2-level and 3-level checkpointing |
3138 |
o add ability of MNC to write local and "partial" (eg. 2D slices where |
3139 |
the full 3D field is never actually stored) arrays to NetCDF files |
3140 |
with the correct (that is, the complete multi-dimensional) set of |
3141 |
array indicies |
3142 |
- used in mom_vecinv() to write the diagFreq output |
3143 |
- tested (demonstrated) in verification/aim.5l_cs |
3144 |
o further mnc-ification |
3145 |
- add verification/lab_sea to the list with mnc setups |
3146 |
- fix undefined mnc v-names in cd_code |
3147 |
- add kpp to mnc output (both snapshot and timeave) |
3148 |
o non-hydrostatic code |
3149 |
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
3150 |
in calc_gw.F |
3151 |
- defaults to viscAh |
3152 |
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
3153 |
friction or Leith) in non-hydrostatic mode, as long as there is |
3154 |
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
3155 |
o pkg/cost |
3156 |
extend simple cost functions to treat time mean quantities |
3157 |
(T,U,V) via cost_accumulate_state from cost_tile |
3158 |
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
3159 |
be 2 times larger than the minimum size the advection scheme requires. |
3160 |
now get a perfect conservation of salt in advect_cs test-exp (updated) |
3161 |
o GGL90 (Gaspar's TKE mixed layer) |
3162 |
- add horizontal diffusion of TKE, requires exchanges in |
3163 |
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
3164 |
default. In OPA there is no horizontal diffusion of TKE but the |
3165 |
mixing coefficients are computed from a horizontal average of TKE of |
3166 |
6 points or so. I think that diffusion has a little more physical |
3167 |
justification. |
3168 |
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
3169 |
was in vain) |
3170 |
- mask tke-variable in ggl90_init |
3171 |
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
3172 |
o fix biharmonic diffusion on CS-grid. |
3173 |
o more obcs stuff |
3174 |
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
3175 |
for reading boundary values. This routine is called from |
3176 |
obcs_prescribe_read |
3177 |
- updated obcs_check |
3178 |
- changed sponge layer relaxation parameter units for days to seconds |
3179 |
- turned off sponge layer by default |
3180 |
- changed argument list of OBCS_CALC to myTime+deltaTclock |
3181 |
- fixed about 35 bugs in obcs_external_fields_load |
3182 |
|
3183 |
checkpoint55c_post (2004/09/23) |
3184 |
o obcs stuff |
3185 |
- new runtime flags useOBCSprescribe, useOBCSbalance |
3186 |
- re-arranged obcs_calc |
3187 |
- moved exf_getobcs to obcs_prescibe_read |
3188 |
obcs_prescibe_read is called after ORLANSKI stuff |
3189 |
and independent of it (executable can contain all). |
3190 |
- updated obcs_check |
3191 |
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
3192 |
These may be necessary only if tangential velocities are |
3193 |
prescribed at OB, not sure, needs testing. |
3194 |
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
3195 |
which simplifies the calls and passes the ifc check-bounds test |
3196 |
|
3197 |
checkpoint55b_post (2004/09/22) |
3198 |
o add a 2D scalar, Z location, exchange_2 routine. |
3199 |
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
3200 |
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
3201 |
affects advect_cs results (for the wrong reason): update output.txt |
3202 |
o use a more standard discretization for biharmonic viscosity ; |
3203 |
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
3204 |
affects results of dome set-up: update output.txt |
3205 |
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
3206 |
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
3207 |
|
3208 |
checkpoint55a_post (2004/09/20) |
3209 |
o merged code to |
3210 |
* prescribe/read time-dependent open boundaries |
3211 |
(works in conjunction with exf, cal) |
3212 |
* sponge layer code for open boundaries |
3213 |
* each boundary N/S/E/W now has its own CPP option |
3214 |
(healthy for the adjoint) |
3215 |
|
3216 |
checkpoint55 (2004/09/17) |
3217 |
o up-to-date adjoint of previous breaks |
3218 |
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
3219 |
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
3220 |
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
3221 |
- carbon: * remove tr1-related adjoint verification |
3222 |
* add ptracer as control variable |
3223 |
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
3224 |
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
3225 |
|
3226 |
checkpoint54f_post (2004/09/16) |
3227 |
o in verification/carbin/ remove experiment related to |
3228 |
ALLOW_PASSIVE_TRACER (array tr1 etc) |
3229 |
code_ad/ input_ad/ results_ad |
3230 |
|
3231 |
o add two new packages |
3232 |
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
3233 |
+ subject to optimization (memory) |
3234 |
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
3235 |
+ subject to reordering (many GOTOs in the original code) |
3236 |
+ so far opps is called for every (i,j) point, and then operates in |
3237 |
the vertical; one may want to reorder the scheme in order operate in |
3238 |
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
3239 |
fields) |
3240 |
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
3241 |
- all verification tests compile and run with linux_ia32_g77 |
3242 |
- defaults are compatible with current input files--nothing |
3243 |
should change if you were not previously using MNC |
3244 |
- MNC output has been added in numerous places (eg. timeave) |
3245 |
but there are still a few writes not yet do-able with MNC |
3246 |
(this is in progress) |
3247 |
- flags now allow for either/or/both use of MDSIO and MNC and |
3248 |
documentation will soon follow |
3249 |
- numerous small formatting cleanups for ProTeX |
3250 |
o add version info (via BUILD_INFO.h) to MNC and stdout |
3251 |
|
3252 |
checkpoint54e_post (2004/09/02) |
3253 |
o add two new packages |
3254 |
- pp81 (Packanowski and Philander, 1981), Richardson number and |
3255 |
stratification dependent mixing |
3256 |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
3257 |
- these scheme operate in a similar manner as KPP (without ghat, of |
3258 |
course), however there is only one diffusivity that is used for both |
3259 |
temperature and salinity (and passive tracers) |
3260 |
o add offline package |
3261 |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
3262 |
provided by Stephanie Dutkiewicz |
3263 |
o genmake2: add ability to search for C compilers and cleanup test output |
3264 |
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
3265 |
|
3266 |
checkpoint54d_post (2004/07/27) |
3267 |
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
3268 |
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
3269 |
leading to additional shift by 5 days each year of integration |
3270 |
(i.e. leading to considerable offset over the years) |
3271 |
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
3272 |
o start with no AB and no initial filtering (staggerTimeStep): |
3273 |
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
3274 |
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
3275 |
(external loading & cpl import/export stay in forward_step.F) |
3276 |
o update coupling interface to work with new staggerTimeStep |
3277 |
o change MDSIO ptracers_pickup. |
3278 |
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
3279 |
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
3280 |
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
3281 |
|
3282 |
checkpoint54c_post (2004/07/18) |
3283 |
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
3284 |
this affects (truncation error) output.txt of test-exp: |
3285 |
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
3286 |
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
3287 |
o change Qnet to always be the net heat flux, (+upward). |
3288 |
affects (truncation error) output of natl_box exp.: updated |
3289 |
o define the max number of passive tracers in PTRACERS_SIZE.h |
3290 |
o start to test mnc routinely in exp0 |
3291 |
o add sea-ice loading (sIceLoad) as a new forcing field. |
3292 |
|
3293 |
checkpoint54b_post (2004/07/08) |
3294 |
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
3295 |
impressive on Altix and Opteron systems) |
3296 |
o diagnostics can now write NetCDF files through the mnc package |
3297 |
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
3298 |
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
3299 |
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
3300 |
affects (truncation error) output of lab_sea & natl_box exp.: updated |
3301 |
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
3302 |
|
3303 |
checkpoint54a_post (2004/07/06) |
3304 |
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
3305 |
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
3306 |
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
3307 |
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
3308 |
+ internal_wave (shift in writing cg2d_ini_res) |
3309 |
checkpoint54a_pre (2004/07/05) |
3310 |
|
3311 |
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
3312 |
- modified verification/lab_sea and natl_box_adjoint accordingly |
3313 |
|
3314 |
checkpoint54 (2004/07/02) |
3315 |
checkpoint53g_post (2004/07/02) |
3316 |
o prepare splitting of thermodynamics: store convect.counter in common block |
3317 |
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
3318 |
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
3319 |
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
3320 |
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
3321 |
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
3322 |
o restore adjointability |
3323 |
|
3324 |
checkpoint53f_post (2004/06/25) |
3325 |
o modifications that affect AIM experiment results (update output.txt): |
3326 |
- no advection of S at top interface Nr (pkg/generic_advdiff) |
3327 |
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
3328 |
o AIM pkg: |
3329 |
- include stability function into surf.Flux derivative relative to Tsurf |
3330 |
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
3331 |
|
3332 |
checkpoint53e_post |
3333 |
o merged cylindrical coord configuration |
3334 |
o added rotating_tank experiment |
3335 |
checkpoint53e_pre |
3336 |
|
3337 |
checkpoint53d_post (2004/06/14) |
3338 |
o faulks upgraded: re-generate output.txt that have changed: |
3339 |
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
3340 |
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
3341 |
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
3342 |
o added Sadourny discretization of Coriolis |
3343 |
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
3344 |
- re-enabled use of omega3 (useAbsVorticity) |
3345 |
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
3346 |
vector-invariant equations |
3347 |
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
3348 |
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
3349 |
hopefully without new bugs |
3350 |
- still to do: biharmonic friction for non-hydrostatic w |
3351 |
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
3352 |
o regenerated output for global_ocean_ebm (using -ieee) |
3353 |
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
3354 |
of mom_common/ |
3355 |
- simple re-arrangement of instructions within computing loop |
3356 |
checkpoint53d_pre (2004/05/21) |
3357 |
|
3358 |
checkpoint53c_post (2004/05/21) |
3359 |
o new version of coupler for AIM+thSIce and Ocean models |
3360 |
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
3361 |
- land: change Evaporation of snow |
3362 |
- aim with thSIce: fix bug in snow-precip. |
3363 |
o changes to calc_gw.F |
3364 |
- bug fix for w^2 term near the bottom boundary |
3365 |
- (hopefully) improve the lateral slip boundary condtions for use with |
3366 |
partial/looped cells |
3367 |
- because the bug fix changes two verification experiments anyway (exp5 |
3368 |
and plume on slope), change the lateral boundary condition from half slip |
3369 |
to the value of no_slip_sides |
3370 |
o ebm package wasnt quite up to the parallel task. Fixed that. |
3371 |
o Adjoint of EBM package + verification |
3372 |
* TLM OK |
3373 |
* ADM not sufficient accuracy yet (needs further testing) |
3374 |
|
3375 |
checkpoint53b_post (2004/05/14) |
3376 |
o Commiting new energy balance model to repository |
3377 |
* package is pkg/ebm |
3378 |
* verif. is verification/global_ocean_ebm |
3379 |
* references are in ebm_driver.F |
3380 |
C * X. Wang, P. Stone and J. Marotzke, 1999: |
3381 |
C Global thermohaline circulation. Part I: |
3382 |
C Sensitivity to atmospheric moisture transport. |
3383 |
C J. Climate 12(1), 71-82 |
3384 |
C * X. Wang, P. Stone and J. Marotzke, 1999: |
3385 |
C Global thermohaline circulation. Part II: |
3386 |
C Sensitivity with interactive transport. |
3387 |
C J. Climate 12(1), 83-91 |
3388 |
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
3389 |
C Destabilization of the thermohaline circulation |
3390 |
C by atmospheric eddy transports. |
3391 |
C J. Climate 7(12), 1870-1882 |
3392 |
o Will need long integration testing. |
3393 |
checkpoint53b_pre (2004/05/14) |
3394 |
|
3395 |
o created pkg/mom_common in preparation for variable viscosity code |
3396 |
o renamed and split ini_mnc_io |
3397 |
o pkg/land: only liquid water can diffuse or run-off |
3398 |
o AIM using land: soil wetness availability account for snow |
3399 |
o added printMapIncludesZeros to EEPARMS namelist |
3400 |
|
3401 |
checkpoint53a_post (2004/05/11) |
3402 |
o restore TAMC compatiility for exf_constants.h |
3403 |
(no usage of _d in .h) |
3404 |
o Additional storing in KPP in an attempt to fix |
3405 |
TAMC problem with adjoint of KPP code. |
3406 |
(no success...) |
3407 |
Identical code works fine with TAF. |
3408 |
o Fixed verification/natl_box_adjoint experiments. |
3409 |
Initial conditions for Experiments 4 and 5 are now |
3410 |
set to "SEAICE_initialHEFF=0", which is more reasonable, |
3411 |
and hence gives results closer to that of Experiment 2. |
3412 |
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
3413 |
|
3414 |
checkpoint53 (2004/05/06) |
3415 |
o stable checkpoint with up to date adjoint |
3416 |
TLM tests only run for 1st grdchk at the moment. Its unclear if |
3417 |
this is a code problem or a problem with resetting code for g_ |
3418 |
variables that is being autogenerated wrong. |
3419 |
Otherwise: |
3420 |
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
3421 |
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
3422 |
are both still in chaos following their security messes. |
3423 |
|
3424 |
checkpoint52n_post (2004/05/06) |
3425 |
o various build (mostly genmake2) changes including: |
3426 |
- ability to build/run more easily within Cygwin and MacOS X |
3427 |
- more complicated Makefiles with a stronger dependence on Gnu Make |
3428 |
o pkg/seaice modifications |
3429 |
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
3430 |
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
3431 |
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
3432 |
- changed proxy for geostrophic velocity and updated |
3433 |
verification/lab_sea/results/* accordingly |
3434 |
- removed ADI dynamic solver from pkg/seaice |
3435 |
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
3436 |
they caused a segmentation fault under certain circumstances |
3437 |
- removed unused field WATR |
3438 |
o bug fix in exf-package: |
3439 |
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
3440 |
now reflect that. |
3441 |
o small fixes in the cal-package: |
3442 |
- set reference date to first of January for the 'model'-calendar |
3443 |
- failing of cal_CheckDate in cal_FullDate now actually results in a |
3444 |
warning |
3445 |
o small modifications in exf-package to increase flexibility: |
3446 |
- change climtempfreeze from a constant to a runtime parameter that |
3447 |
is specified in data.exf_clim (default = -1.9) |
3448 |
- introduce runtime parameter windstressmax (default = 2.0) that is |
3449 |
specified in data.exf |
3450 |
o fix in pkg/thsice: |
3451 |
- update Evap (Tsf changes) to be consistent with Latent heat flux |
3452 |
- maintain snow precipitation unchanged (even if Tsf >=0). |
3453 |
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
3454 |
|
3455 |
checkpoint52m_post (2004/04/18) |
3456 |
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
3457 |
this does not change any of the results, because myIter=0 in swfrac always |
3458 |
lead to jwtype=2 (the default anyway), but the call makes little sense |
3459 |
as a default |
3460 |
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
3461 |
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
3462 |
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
3463 |
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
3464 |
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
3465 |
o extending useSingleCpuIO option to work with new exch2 I/O format |
3466 |
- old-style, missing-tile I/O is still accessible by defining CPP |
3467 |
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
3468 |
o monitor package can write to NetCDF files and/or STDOUT |
3469 |
o fix re-definition bug in MNC_GRID_INIT_ALL() |
3470 |
o doc/api_reference added |
3471 |
- a framework for building an API Reference Manual using all |
3472 |
the "protex" comments embedded in the code |
3473 |
- see pkg/generic_advdiff, pkg/mnc for examples |
3474 |
o MNC: |
3475 |
- make myThid the last argument for all subroutines |
3476 |
- new default for the grid files: NO halos |
3477 |
- add useMNC and other run-time flags |
3478 |
- separate per-file-group handling of the unlimited dimension |
3479 |
- early initialization of MNC w/ flags read at the eeboot stage |
3480 |
and lookup tables set in initialize_fixed |
3481 |
- write all MNC output to a freshly-created directory |
3482 |
o thermodynamics sea-ice (thsice) is now tested with testreport. |
3483 |
o test exp. advect_cs: use the standard cs32 grid ; update output. |
3484 |
o Added functionality to grdchk: |
3485 |
pick global i,j,k position (or nearest wet) where to perform check. |
3486 |
|
3487 |
checkpoint52l_post (2004/03/11) |
3488 |
o new land formulation: |
3489 |
a) use ground enthalpy as prognostic variable to ensure exact |
3490 |
energy conservation. |
3491 |
b) account for water temperature and for latent heat of freezing |
3492 |
in all processes (rain, run-off, ground storage) |
3493 |
c) compute surface and ground temperature implicitly. |
3494 |
o aim_v23 modification for new land model: |
3495 |
a) Treat separately land / ocean / sea-ice surface fluxes |
3496 |
to allow implicit computation of land & sea-ice surface temp. |
3497 |
b) add snow precipitation. |
3498 |
checkpoint52l_pre (2004/03/11) |
3499 |
|
3500 |
o fix problem (when 1 tile is empty) in min/max monitor. |
3501 |
o fix bug in timeAve (u,vZetatave in common block) |
3502 |
o no restoring terms under ice for pkg/seaice |
3503 |
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
3504 |
o bug fix for pkg/seaice pickups |
3505 |
o change MNC call locations and add coordinate attributes |
3506 |
o mask vorticity at the corner ; affects global_ocean.cs output |
3507 |
o fix ini_curvilinear_grid ; test CS experiments with mpi |
3508 |
o aim.5l_cs: modify sea-ice fraction input file ; update output |
3509 |
o exf: Adding simple range check routine for exf fields after read |
3510 |
|
3511 |
checkpoint52k_post (2004/02/23) |
3512 |
o removed top-level directory "diags" |
3513 |
- we migrated these functions to pkg/timeave a long time ago |
3514 |
o fixed bug introduced in pkg/monitor |
3515 |
o accuracy ctrlprec = 32 insuffient for gradient checks using |
3516 |
averaged fields (I/O via cost_averages) |
3517 |
-> use ctrl.h in active_file*.F to control I/O precision. |
3518 |
o paramter list of CALL ADTHE_MAIN_LOOP |
3519 |
o added initial do_the_model_io to ecco |
3520 |
o set all ...Freq to zero after cost_final |
3521 |
taveFreq, dumpFreq, pChkptFreq |
3522 |
o MAIN and ECCO differentiability restored |
3523 |
|
3524 |
checkpoint52j_post (2004/02/18) |
3525 |
o fix nchklev in tamc.h for global_ocean... |
3526 |
o Bringing flow and store directives up-to-date |
3527 |
o Really weird thing! |
3528 |
call do_the_model_io from the_main_loop with parameters |
3529 |
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
3530 |
TAF places a faulty re-call of initialise_varia |
3531 |
after cost_final call which should not be there! |
3532 |
checkpoint52j_pre (2004/02/03) |
3533 |
|
3534 |
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
3535 |
error messages |
3536 |
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
3537 |
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
3538 |
debug output |
3539 |
o modfied mdsio_writefield.F to handle non-global files under exch2 |
3540 |
o update AIM Cubed-Sphere exp (aim.5l_cs): |
3541 |
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
3542 |
o update AIM Equatorial Channel exp: |
3543 |
use standard aim_v23 pkg and change the SST fields to be more realistic. |
3544 |
o globalFile now works with exch2 |
3545 |
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
3546 |
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
3547 |
o limit timeave output for hi-res integrations |
3548 |
|
3549 |
checkpoint52i_post (2004/01/21) |
3550 |
o removed CPP_EEOPTIONS.h from verification/*/code |
3551 |
o updated the tiling for global_ocean_pressure |
3552 |
checkpoint52i_pre (2004/01/20) |
3553 |
|
3554 |
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
3555 |
the old pkg/aim). |
3556 |
|
3557 |
checkpoint52h_pre (2004/01/20) |
3558 |
o shortened offending lines in exch2_send_rx?.template |
3559 |
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
3560 |
o genmake2: add build & execute test for NetCDF code |
3561 |
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
3562 |
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
3563 |
o added useSingleCPUIO flag to monitor.F and mon_out.F |
3564 |
o added temporary hack for sea-ice dynamics on the cube: |
3565 |
metric terms are ignored and it is assumed that |
3566 |
there is no sea-ice on cube faces 1, 2, 4, and 5. |
3567 |
|
3568 |
checkpoint52f_post (2004/01/09) |
3569 |
o added exch2 cube routines to pkg/exch2 |
3570 |
o modified hs94.cs-32x32x5 to use it |
3571 |
o added new grid files to hs94.cs-32x32x5 |
3572 |
checkpoint52f_pre (2004/01/07) |
3573 |
|
3574 |
checkpoint52e_post (2004/01/07) |
3575 |
o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
3576 |
for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
3577 |
o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
3578 |
to work with implicit vertical advection and AB ; |
3579 |
o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
3580 |
o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
3581 |
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
3582 |
checkpoint52e_pre (2004/01/02) |
3583 |
|
3584 |
o fix bug in impldiff when Nr=1 or Nr=2. |
3585 |
o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
3586 |
o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
3587 |
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
3588 |
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
3589 |
o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
3590 |
o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
3591 |
o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
3592 |
|
3593 |
checkpoint52d_post (2003/12/16) |
3594 |
o re-tiled many expts to allow comparison in multi-processor mode |
3595 |
- updated output accordingly |
3596 |
- changed hs94.128x64x5 to use intial T from file rather than use the |
3597 |
random number generator |
3598 |
o add infrastructure in model routines for fizhi and gridalt packages |
3599 |
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
3600 |
o changes to permit hi-res, cubed-sphere, configuration |
3601 |
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
3602 |
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
3603 |
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
3604 |
of surface winds for the cube |
3605 |
(A verification experiment, based on global_ocean.cs32x15, but with |
3606 |
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
3607 |
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
3608 |
complete with example surface forcing files and matlab scripts to look |
3609 |
at the output and compare it with that of global_ocean.cs32x15.) |
3610 |
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
3611 |
but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
3612 |
to conform to the common rule. |
3613 |
o check-in the first version of the coupler + interfaces for multi-components |
3614 |
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
3615 |
- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
3616 |
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
3617 |
- ocean and atmos. share the same horizontal grid (no interpolation). |
3618 |
- exchanges between component and coupler is done in forward_step |
3619 |
o new verification experiment, cpl_aim+ocn: |
3620 |
coupled ocean - AIM atmosphere on cs32 grid. |
3621 |
|
3622 |
checkpoint52d_pre (2003/12/06) |
3623 |
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
3624 |
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
3625 |
|
3626 |
checkpoint52c_post (2003/11/25) |
3627 |
o Fixing OPTIONS files for use of exf: |
3628 |
- ALLOW_ECCO not needed |
3629 |
- ECCO_CPPOPTIONS.h should not be included from |
3630 |
EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
3631 |
as has been the case in the past |
3632 |
- All cal/exf related options are currently set in |
3633 |
single header file. Should remain so until we |
3634 |
agree on a consistent new policy. |
3635 |
o Removed all CPP options for cal package. |
3636 |
cal has no more CPP options. |
3637 |
o modified STOREs in GAD_ADVECTION |
3638 |
o corrected key comp. for passkey |
3639 |
|
3640 |
checkpoint52b_post (2003/11/23) |
3641 |
o new version: "thsice" of thermodynamic sea-ice pkg: |
3642 |
- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
3643 |
- modify fluxes but do not change theta directly; |
3644 |
- light cleaning of bulk_force pkg (still needed with thsice). |
3645 |
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
3646 |
+ output_thsice.txt to test thsice & bulk_force pkgs. |
3647 |
o put back grid & coriolis monitor output. |
3648 |
checkpoint52b_pre (2003/11/23) |
3649 |
|
3650 |
o call "do_the_model_io" at the beginning (=> dump initial state) |
3651 |
o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
3652 |
o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
3653 |
(need info on NUMBER_OF_PTRACERS) |
3654 |
o missing PTRACERS headers in some routines |
3655 |
o default tamc.h in pkg/autodiff supposed to crash |
3656 |
to ensure proper customization |
3657 |
|
3658 |
checkpoint52a_post (2003/11/17) |
3659 |
o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
3660 |
- moved surfaceTendencyTice from pkg/seaice to main code |
3661 |
- subroutine FREEZE_SURFACE now limits only surface temperature |
3662 |
and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
3663 |
=> new output.txt for global_ocean.cs32x15 & global_with_exf |
3664 |
- keep the old version of FREEZE for backward compatibility; |
3665 |
global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
3666 |
- corresponding modifs for TAF directives |
3667 |
o added surface flux output variables to TIMEAVE_STATVARS |
3668 |
o time-averaged output for pkg/ptracers |
3669 |
o fix problem with ECCO-related divided adjoint |
3670 |
snapshot file was missing some ad-variables, |
3671 |
but no warning issued by TAF |
3672 |
|
3673 |
checkpoint52a_pre (2003/11/12) |
3674 |
o some bug fixes for #undef REAL4_IS_SLOW |
3675 |
|
3676 |
checkpoint52 = ecco_c52_e35 |
3677 |
o after testing adjoints of checkpoint51u_post |
3678 |
|
3679 |
checkpoint51u_post (2003/11/06) |
3680 |
o this is the post-merge tag of the ecco-branch |
3681 |
(needs another clean checkout and re-testing) |
3682 |
o various natl_box_adjoint configs and results |
3683 |
but no input fields |
3684 |
o obcs adjoint not yet merged! |
3685 |
o adding ECCO global 1x1 and 2x2 degree configs |
3686 |
o updated/extended some store directives for seaice |
3687 |
o pkg/ecco now containes ecco-specific part of cost function |
3688 |
o top level routines the_main_loop, forward_step |
3689 |
supersede those in model/src/ |
3690 |
previous input data.cost now in data.ecco |
3691 |
(new namelist ecco_cost_nml) |
3692 |
o in ctrl/ cleaned some cross-dependencies and updated CPP options |
3693 |
|
3694 |
checkpoint51t_post (2003/11/04) |
3695 |
o this is the pre-merge tag of the ecco-branch |
3696 |
|
3697 |
checkpoint51s_post (2003/11/04) |
3698 |
o cleanup: removed various obsolete #define-s |
3699 |
o pkg/grdchk |
3700 |
- renamed 'ph-grd 3' to 'grad-res' |
3701 |
- merged from ecco-branch |
3702 |
(remaining bug fixes for obcs gradient checks) |
3703 |
- additional high-precision output for testreport |
3704 |
(grep for 'precision_grdchk_result') |
3705 |
|
3706 |
checkpoint51r_post (2003/11/03) |
3707 |
o cleaned up or removed CPP_OPTIONS.h files |
3708 |
o updated results for some of the tests to reflect the new |
3709 |
optfiles (-ieee: -O0 instead of -O3) |
3710 |
|
3711 |
checkpoint51q_post (2003/10/30) |
3712 |
o cd_code: |
3713 |
- moved cd_scheme.F -> cd_code_scheme.F |
3714 |
- separate read_checkpoint from cd_code_ini_vars.F |
3715 |
- separated cd_code part from write_checkpoint |
3716 |
- updated AD_SOURCE, generated .flow |
3717 |
- added CD_CODE_VARS.h to the_main_loop |
3718 |
- Moving cd_code specific store dir.s to pkg/cd_code |
3719 |
o ctrl package totally restructured |
3720 |
- pack/unpack now optional and decoupled from |
3721 |
xx_/adxx_ I/O |
3722 |
- ctrl_pack/unpack cleaned |
3723 |
(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
3724 |
- confined inclusion of AD_CONFIG.h to where necessary. |
3725 |
o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
3726 |
|
3727 |
checkpoint51p_post (2003/10/30) |
3728 |
o create initial cd_code package |
3729 |
- WARNING: the initialization of fields within packages |
3730 |
is broken because INI_FIELDS (where READ_CHECKPOINT is |
3731 |
called) is called *before* PACKAGES_INIT_VARIABLES. |
3732 |
This seems to be backwards since |
3733 |
1) its important to initially zero the entire field including |
3734 |
the "halo" region |
3735 |
2) zeroing needs to be done *before* reading pickup info |
3736 |
and the pickup call might or might not happen in any |
3737 |
particular run |
3738 |
- this needs an overhaul for R2 |
3739 |
o cleanup verification/*/code/GMREDI_OPTIONS.h |
3740 |
o cleanup testreport |
3741 |
|
3742 |
checkpoint51o_post (2003/10/27) |
3743 |
o bringing AD-related verif's up to date with genmake2 |
3744 |
- carbon/ |
3745 |
- global_ocean.90x40x15/ |
3746 |
- hs.94.1x64x5/ |
3747 |
- (front_relax/ ) |
3748 |
o (more) consistent directory structure for AD-related verif.'s |
3749 |
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
3750 |
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
3751 |
o bug fix in find_alpha.F for MDJWF: |
3752 |
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
3753 |
change rho -> rho-rhoConst |
3754 |
- replace call find_rho to find_rhonum |
3755 |
o initialisation of rFlx extended to full array (required by TAF) |
3756 |
and shifted to thermodynamics |
3757 |
o removed PTRACERS.h in ptracers routine |
3758 |
o added surfacetendencyPtr to S/R parameter list pracers_forcing |
3759 |
o Correcting initialisations for fVerU, fVerV. |
3760 |
o helping TAF to recognize dependency on kUp for |
3761 |
fVerU, fVerV |
3762 |
o Replacing delZ by delR in pkg/ctrl/ |
3763 |
checkpoint51o_pre (2003/10/24) |
3764 |
|
3765 |
o undid all of cp51 pending some cleanups and discussion |
3766 |
o added the [#include "AD_CONFIG.h"] statement to all files that need |
3767 |
it for adjoint/tl #defines |
3768 |
o re-worked the build logic in genmake2 to support AD_CONFIG.h |
3769 |
o removed tools/genmake since it no longer works |
3770 |
|
3771 |
checkpoint51n_post (2003/10/23) |
3772 |
o modifications to make FREEZE flux visible to pkg/kpp |
3773 |
- moved surfaceTendencyTice from pkg/seaice to main code |
3774 |
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
3775 |
- subroutine FREEZE now limits only surface temperature |
3776 |
(this means new output.txt for global_ocean.90x40x15, |
3777 |
global_ocean.cs32x15, and global_with_exf) |
3778 |
o added surface flux output variables to TIMEAVE_STATVARS |
3779 |
|
3780 |
checkpoint51n_pre (2003/10/23) |
3781 |
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
3782 |
o added [#include "AD_CONFIG.h"] to all files that use the following |
3783 |
defines: |
3784 |
- ALLOW_ADJOINT_RUN |
3785 |
- ALLOW_TANGENTLINEAR_RUN |
3786 |
- ALLOW_ECCO_OPTIMIZATION |
3787 |
|
3788 |
checkpoint51m_post (2003/10/21) |
3789 |
o incorporating changes to get TAMC/TAF working in genmake2 |
3790 |
- added new TAMC/TAF targets to the Makefile |
3791 |
- various cleanups related to package handling |
3792 |
- these changes should have no impact on the forward model |
3793 |
|
3794 |
checkpoint51l_post (2003/10/20) |
3795 |
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
3796 |
- faster algorithm for cal_addtime.F |
3797 |
- higher precision arithmetic, where needed |
3798 |
- pkg/exf *startdate variables changed from calendar date to |
3799 |
model integration time |
3800 |
|
3801 |
checkpoint51l_pre (2003/10/17) |
3802 |
o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
3803 |
o enable to apply restoring on S & T only in a latitude band. |
3804 |
o update output (external_forcing_surf modif. change truncation errors) |
3805 |
global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
3806 |
|
3807 |
checkpoint51k_post (2003/10/16) |
3808 |
o change default to: useNHMTerms=.FALSE. |
3809 |
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
3810 |
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
3811 |
- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
3812 |
exp1, ideal_2D_oce |
3813 |
- change data file of oceanic exp (leave the results unchanged for now) |
3814 |
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
3815 |
o set gravitySign automatically according to the vertical coordinate used |
3816 |
(and change sign: back to "logical" value: +1 when R increases downward) |
3817 |
o added an include barrier to the default CPP_OPTIONS.h and |
3818 |
removed the #include "PACKAGES_CONFIG.h" from it |
3819 |
o fix a bug in mom_fluxform (from chk51j_post) |
3820 |
|
3821 |
checkpoint51j_post (2003/10/10) |
3822 |
o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
3823 |
o adjusted some flow directives (dynamics, thermodynamics) |
3824 |
o added cubed-sphere case to test cost function |
3825 |
o heckpoint_lev?_directives.h now include |
3826 |
pkg-specific directives, whenever those are enabled. |
3827 |
o Moving pkg-specific flow directives to corresponding pkg |
3828 |
Moving pkg-specific differentiation list to corresponding pkg |
3829 |
Moving pkg-specific checkpoint-lev storing to corresponding pkg |
3830 |
---> conventions are |
3831 |
- pkg_ad.flow |
3832 |
- pkg_ad_diff.list |
3833 |
- pkg_ad_check_lev?_dir.h |
3834 |
|
3835 |
checkpoint51i_post (2003/10/09) |
3836 |
o merge of the branch-genmake2 |
3837 |
- knowingly breaks the older genmake |
3838 |
- automatic generation of all ALLOW_${PKG_NAME} defines |
3839 |
- new testreport supersedes older testscript |
3840 |
o large number of package inclusion and header cleanups |
3841 |
checkpoint51i_pre (2003/10/08) |
3842 |
|
3843 |
o new output for adjoin of global ocean vector invariant |
3844 |
o fix for checkpoint of thermodynamic seaice and bulk_force |
3845 |
o Steph gchem various cleanups |
3846 |
|
3847 |
checkpoint 51h_pre |
3848 |
o fixed some single quotes |
3849 |
o modify gchem pkg to be more versatile |
3850 |
o modifications to clean up dic pkg |
3851 |
o add pkg/cfc |
3852 |
|
3853 |
checkpoint51g_post (2003/10/02) |
3854 |
o provide links for ARPACK and ADM*TLM |
3855 |
o start removing verification/vero/ |
3856 |
o update AD-related stuff |
3857 |
(in particular some IF-statements in model/src/ routines) |
3858 |
o adding to verification/global_ocean.90x40x15/ adjoint of |
3859 |
vector invariant setup |
3860 |
|
3861 |
checkpoint51f_post (2003/10/02) |
3862 |
o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
3863 |
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
3864 |
of tracer Green's fucntions for ocean inversion project. |
3865 |
|
3866 |
checkpoint51f_pre (2003/08/07) |
3867 |
o Added on-the-fly spatial interpolation capability |
3868 |
"USE_EXF_INTERPOLATION" to pkg/exf. |
3869 |
- This is a temporary Cartesian-grid hack until |
3870 |
the super-duper ESMF coupler becomes available. |
3871 |
- See verification/global_with_exf/README for usage example. |
3872 |
- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
3873 |
flags and modified pkg/seaice accordingly. |
3874 |
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
3875 |
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
3876 |
non-local transport term. |
3877 |
|
3878 |
checkpoint51e_post (2003/08/03) |
3879 |
o pkg/mom_vecinv: |
3880 |
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
3881 |
- add time-ave diagnostic of vorticity advection. |
3882 |
o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. |
3883 |
o atmospheric geopotential: - include water vapor effect; |
3884 |
- use p^kappa in p* scaling. |
3885 |
o land pkg: read initial state from files. |
3886 |
o AIM : add stratospheric drag in the upper level |
3887 |
|
3888 |
checkpoint51d_post (2003/07/18) |
3889 |
o change function ILNBLNK (=> last non-blank char.) to return zero |
3890 |
(instead of the string length) when the string. char is empty |
3891 |
o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) |
3892 |
o modif's to restore TAMC compatibility |
3893 |
- avoid "_d" constructs in PARAMETER declarations |
3894 |
- avoid interrupting lines by comment lines |
3895 |
o Use cluster local disks for purely local I/O |
3896 |
vs. globally visible disks needed for ctrl stuff |
3897 |
(merged from ecco-branch) |
3898 |
- new active_file_loc... and mdsio_..._loc routines |
3899 |
- affected packages: autodiff, ctrl, grdchk, mdsio |
3900 |
|
3901 |
checkpoint51c_post (2003/07/08) |
3902 |
o introducing integer flag debugLevel |
3903 |
- debLevZero: suppress all output |
3904 |
- debLevA: standard |
3905 |
- debLevB: equivalent to current debugMode=.TRUE. |
3906 |
o introducing pathname variable mdsioLocalDir for mdsio |
3907 |
that can be specified at runtime |
3908 |
(relevant for cluster I/O to local disk) |
3909 |
` |
3910 |
>>>checkpoint51b_post |
3911 |
adjoint of ptracers |
3912 |
o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
3913 |
o extended state in checkpoint_lev?, etc. |
3914 |
o alternative ctrl/cost with tr1 or ptracer |
3915 |
o new comlev1_bibj_ptracers |
3916 |
o new ptracers.flow |
3917 |
o made ptracers_forcing same as external_forcing_s |
3918 |
o added verification for adjoint with ptracers |
3919 |
- adm. grdchk fail so far |
3920 |
- tlm. grdchk OK |
3921 |
- checked tapelev/comlev recomputations: OK |
3922 |
<<<checkpoint51b_pre |
3923 |
|
3924 |
checkpoint51a_post (2003/06/25) |
3925 |
o added code for biogeochemistry package |
3926 |
- new pkgs: dic, gchem |
3927 |
- new subroutine in ptracers |
3928 |
o modify code for biogeo packages |
3929 |
- in model/src and pkg/ptracers |
3930 |
|
3931 |
checkpoint51 (2003/06/24) |
3932 |
o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN |
3933 |
- autodiff, ctrl, exf, grdchk, seaice |
3934 |
kept separate packages |
3935 |
- cost, ecco, obcs |
3936 |
o updating verification/internal_wave, verification/lab_sea |
3937 |
(all verif's pass on faulks.lcs.mit.edu RH7.3, g77) |
3938 |
|
3939 |
checkpoint50i_post (2003/06/23) |
3940 |
o Preparing next differentiable checkpoint and sync |
3941 |
of MAIN vs. ecco-branch |
3942 |
- 1st step: this one is differentiable |
3943 |
- 2nd step: next(! not this) checkpoint will have updated packages |
3944 |
from ecco-branch) |
3945 |
|
3946 |
checkpoint50h_post (2003/06/20) |
3947 |
o new package "land": provide surface BC for AIM. |
3948 |
o pkg/ptracers: apply exchange to all tracers after reading a pickup. |
3949 |
o AIM: use true log-P extrapolation for near surface temp (= as in |
3950 |
F.Molteni paper) ; update aim.5l_cs output. |
3951 |
o New variable in PARM03 for more flexible pickups |
3952 |
o somewhat cleaned package initialisation sequence for |
3953 |
ctrl/ cost/ ecco/ in packages_... routines |
3954 |
|
3955 |
checkpoint50g_post (2003/05/23) |
3956 |
o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
3957 |
- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
3958 |
- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
3959 |
made the default because of faster convergence than ADI |
3960 |
|
3961 |
checkpoint50f_post (2003/05/23) |
3962 |
o exf totally restructured |
3963 |
- replaced all exf_set_ routines by one generic exf_set_gen.F |
3964 |
and made sure it's still differentiable |
3965 |
- split exf_getffields.F into new exf_bulkformulae.F |
3966 |
- exf_inscal_/exf_outscal_ suffixes consistent with field names |
3967 |
- updated adjoint/makefile and relevant verif. accordingly |
3968 |
|
3969 |
checkpoint50f_pre (2003/05/23) |
3970 |
o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; |
3971 |
+ change Evap over land. (update aim.5l_cs output) |
3972 |
o added missing .cvsignores and made uniform across expts |
3973 |
o changed configuration of tidal_basin_2d expt |
3974 |
o added pkg/debug functions for tracing code in fatal crashes |
3975 |
o tidied pkg/monitor to use MONITOR_OPTIONS.h |
3976 |
o new fn in pkg/monitor to stop model if solution grows too big |
3977 |
o removed lots of single quotes from comments |
3978 |
|
3979 |
checkpoint50e_post (2003/05/14) |
3980 |
o make KPP work with PTRACERS |
3981 |
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
3982 |
nearly a copy of kpp_transport_s |
3983 |
- there is no analogue to SurfaceTendencyS, so I have to use |
3984 |
gPtr(of the surface layer) instead |
3985 |
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
3986 |
checkpoint50e_pre (2003/05/13) |
3987 |
|
3988 |
checkpoint50d_post (2003/05/13) |
3989 |
o change kpp output from multiple-record state files to single-record state |
3990 |
files analogous to write_state.F |
3991 |
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
3992 |
analogous to the cg2d-related output. |
3993 |
o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
3994 |
so that writing to internal file fn (with length 512) fails. |
3995 |
checkpoint50d_pre (2003/05/12) |
3996 |
|
3997 |
checkpoint50c_post (2003/05/12) |
3998 |
o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) |
3999 |
o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. |
4000 |
o add time-average diagnostic of U*V and vertical diffusive flux for theta. |
4001 |
o bug fixed in convective adjustment diagnostic (multi-tile set-up). |
4002 |
o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. |
4003 |
|
4004 |
checkpoint50c_pre (2003/04/30) |
4005 |
Merging from release1_p13: |
4006 |
o bug fix for pkg/seaice dynamic solver |
4007 |
o Added SEAICE_initialHEFF to pkg/seaice |
4008 |
|
4009 |
checkpoint50b_post (2003/04/17) |
4010 |
o store u*,v* in gU,V instead of in guNm1,gvNm1 |
4011 |
o in order to put the momForcing out of the Adams-Bashforth: |
4012 |
move forcing & CD-scheme calls from mom_fluxform & mom_vecinv |
4013 |
to timestep.F |
4014 |
o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays |
4015 |
o re-generate output for highly sensitive test-exp: |
4016 |
global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box |
4017 |
|
4018 |
checkpoint50b_pre (2003/04/17) |
4019 |
o restore the use of momAdvection & useCoriolis flags (mom_vecinv) |
4020 |
o corrected CPP option mismatch in exf_Bulk... functions for case |
4021 |
#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
4022 |
|
4023 |
checkpoint50a_post (2003/03/21) |
4024 |
o Bug fix for merging between c50 and KPP. |
4025 |
ikey was passed from thermodynamics to kpp_calc via |
4026 |
common block rather than being recomputed in kpp_calc, |
4027 |
in contradiction with new key itdkey. |
4028 |
New key ikppkey created, and tamc.h headers updated. |
4029 |
|
4030 |
checkpoint50 (2003/03/08) |
4031 |
- 2nd step of merge with ecco-branch: |
4032 |
merge changes in ecco-branch back into main trunk |
4033 |
- bug fix in find_alpha |
4034 |
- more storing in gmredi_calc_tensor.F, kpp_routines.F |
4035 |
- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
4036 |
- merged some sliced AD support routines |
4037 |
|
4038 |
checkpoint49 (2003/03/06) |
4039 |
merged from ecco-branch: |
4040 |
o exf: |
4041 |
- Enable initialisation of forcing fields to constant |
4042 |
(runtime) values. |
4043 |
- in exf_getffields.F |
4044 |
Reduce i-/j-loop to interior domain, discarding overlaps. |
4045 |
That also fixes wrong TAF-key computations for key_1, key_2 |
4046 |
with bulf formulae. |
4047 |
- exf_init.F modify #ifdef for exf_init_evap |
4048 |
- exf_getffieldrec.F, ctrl_getrec.F |
4049 |
The following INT-usages are not safe: |
4050 |
fldsecs = int(fldsecs/fldperiod)*fldperiod |
4051 |
fldcount = int(fldsecs/fldperiod) + 1 |
4052 |
and were modified. |
4053 |
o autodiff: checkpoint_lev... |
4054 |
- updated storing for bulk formulae (some arrays were missing) |
4055 |
- added state for seaice package |
4056 |
- synchronized with main branch |
4057 |
o DIVA: |
4058 |
Modif.s in |
4059 |
- the_main_loop.F |
4060 |
- the_model_main.F |
4061 |
and added cost_final_restore.F cost_final_store.F |
4062 |
o With these changes, it is possible to fully separate |
4063 |
the first forward run to compute the cost function (mdthe_main_loop) |
4064 |
and adjoint runs over individual DIVA intervals (adthe_main_loop) |
4065 |
into separate model executions. |
4066 |
This enables better tuning of DIVA to given queue sizes. |
4067 |
o Loss of cost function value in consecutive DIVA runs is |
4068 |
fixed by storing to 'costfinal' file. |
4069 |
o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
4070 |
beginning/end of adjoint integration is accounted for. |
4071 |
The current changes apply to TAF-1.4.26. |
4072 |
TAF has one remaining bug, requiring one manual change |
4073 |
(see MITgcm manual). |
4074 |
o cal: synchronized between MAIN and ecco-branch |
4075 |
|
4076 |
checkpoint48i_post (2003/03/05) |
4077 |
o Changes to restore differentiability of code w.r.t. previous tag |
4078 |
(mostly adding new routines to make list and replacing |
4079 |
pressure by totPhiHyd). |
4080 |
o Updated and merged grdchk package |
4081 |
- has both ADM and TLM checks |
4082 |
- works for single- and multi-proc. |
4083 |
- output cleaned |
4084 |
- worked successfully for parallel DIVA |
4085 |
o genmake: |
4086 |
- Adding -platform=SP4 |
4087 |
- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
4088 |
o Modif. for DIVA: |
4089 |
ctrl_unpack should not be called in intermediate DIVA interval. |
4090 |
(similar thing would apply for active files such as |
4091 |
tbar, sbar, psbar, which should not be reinitialised; |
4092 |
only relevant for ecco-branch) |
4093 |
|
4094 |
checkpoint48h_post (2003/02/28) |
4095 |
o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
4096 |
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
4097 |
o Added SEAICE_initialHEFF to pkg/seaice |
4098 |
o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
4099 |
|
4100 |
checkpoint48g_post (2003/02/18) |
4101 |
--- EOS: |
4102 |
o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
4103 |
store total Potential in totPhyHyd for diagnostics & EOS. |
4104 |
o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
4105 |
--- Pressure/geopotential gradient: |
4106 |
o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
4107 |
o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
4108 |
( changes results of global_ocean_pressure ) |
4109 |
o NLFS + z-coord.: add eta*Rho' contribution. |
4110 |
o accurate phiHyd when using interface-W at the middle between 2 centers |
4111 |
( changes results of ideal_2D_oce ) |
4112 |
o includes r* 2nd term in potential gradient. |
4113 |
|
4114 |
checkpoint48f_post (2003/02/18) |
4115 |
Merging from release1_p12: |
4116 |
o Modifications for using pkg/exf with pkg/seaice |
4117 |
- improved description of the various forcing configurations |
4118 |
- added basic radiation bulk formulae to pkg/exf |
4119 |
- units/sign fix for evap computation in exf_getffields.F |
4120 |
- updated verification/global_with_exf/results/output.txt |
4121 |
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
4122 |
(SBO) core products, including oceanic mass, center-of-mass, |
4123 |
angular, and bottom pressure (see pkg/sbo/README.sbo). |
4124 |
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
4125 |
to avoid negative values in shallow regions. |
4126 |
- updated verification/natl_box/results/output.txt |
4127 |
- updated verification/lab_sea/results/output.txt |
4128 |
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
4129 |
o Added useSingleCpuIO option (see PARAMS.h). |
4130 |
o Updated useSingleCpuIO option in mdsio_writefield.F to |
4131 |
work with multi-field files, e.g., for single-file pickup. |
4132 |
o pkg/seaice: |
4133 |
- bug fix in growth.F: QNET for no shortwave case |
4134 |
- added HeffFile for specifying initial sea-ice thickness |
4135 |
- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
4136 |
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
4137 |
kpp_transport_t.F, forward_step.F, and the_main_loop.F |
4138 |
o pkg/seaice: |
4139 |
- adjoint-friendly modifications |
4140 |
- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
4141 |
|
4142 |
checkpoint48e_post (2003/02/12) |
4143 |
o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) |
4144 |
o dynamics: change definition of computational domain & adapt mom_fluxform |
4145 |
accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. |
4146 |
o following exp works with Olx=Oly=2 (and pass through checkbounds option): |
4147 |
adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 |
4148 |
exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 |
4149 |
global_ocean.90x40x15 global_with_exf global_ocean_pressure |
4150 |
inverted_barometer solid-body.cs-32x32x1 |
4151 |
(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) |
4152 |
|
4153 |
checkpoint48d_post (2003/02/09) |
4154 |
o in preparation for r*: |
4155 |
a) use pre-computed gradient of hydrostatic potential: |
4156 |
changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce |
4157 |
b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: |
4158 |
=> affects results of glob_oce_pressure (different truncation error) |
4159 |
update output.txt of ideal_2D_oce & global_ocean_pressure |
4160 |
|
4161 |
checkpoint48d_pre (2003/02/08) |
4162 |
o in preparation for r*: |
4163 |
new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
4164 |
pass the 2 comp. of the grad. as arguments to momentum S/R. |
4165 |
but for the moment, only used if it does not change the results. |
4166 |
o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP |
4167 |
|
4168 |
checkpoint48c_post (2003/02/06) |
4169 |
Modifications in treatment of initial flux forcing controls |
4170 |
to avoid extra storing of flux fields. |
4171 |
|
4172 |
checkpoint48c_pre (2003/01/21) |
4173 |
o Added tidal_basin_2d experiment (currently 1D!) |
4174 |
o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) |
4175 |
|
4176 |
checkpoint48b_post (2003/01/27) |
4177 |
o r* coordinate added in #ifdef NONLIN_FRSURF block. |
4178 |
(modification to pressure gradient not yet implemented) |
4179 |
o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports |
4180 |
(for U & V) that are used for vertical advection of momentum. |
4181 |
|
4182 |
checkpoint48a_post (2003/01/24) |
4183 |
o In preparation for r*, use temp. array to compute vertical transport |
4184 |
in flux-form momentum pkg. => change results of few test-exp. |
4185 |
Update output of: exp4, exp5, front_relax, global_ocean_pressure, |
4186 |
lab_sea, natl_box & plume_on_slope |
4187 |
|
4188 |
checkpoint48 (2003/01/23) |
4189 |
o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') |
4190 |
|
4191 |
checkpoint47j_post (2003/01/21) |
4192 |
o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. |
4193 |
o moved adexch from forward_step to addummy_in_stepping |
4194 |
o added exch in ctrl_map_... |
4195 |
o aveFreq.=0. at end of cost_final to avoid overwrite in |
4196 |
reverse checkpointing loop |
4197 |
o Yet more changes in gmredi: |
4198 |
* adgmredi_calc_tensor |
4199 |
avoiding all recomputation of gmredi_slope_limit |
4200 |
* adgmredi_x/y/rtransport |
4201 |
added flag for excessive storing to avoid recomp. of |
4202 |
u/v/rtans, dTdx/y/z |
4203 |
-> this is not really necessary and very memory-consuming |
4204 |
* adgmredi_slope_psi: |
4205 |
consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff |
4206 |
* gmredi_slope_limit |
4207 |
re-activated full calculation of taperfct for case 'ac02' |
4208 |
o updating verification/ adjoints of carbon, global_ocean.90x40x15 |
4209 |
|
4210 |
checkpoint47i_post (2003/01/13) |
4211 |
o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. |
4212 |
o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) |
4213 |
default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) |
4214 |
o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) |
4215 |
o gmredi: fix few bugs. |
4216 |
|
4217 |
checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) |
4218 |
This will be a good checkpoint to plug into the ecco-branch. |
4219 |
o few modif.'s to get latest version adjointed |
4220 |
(mainly kick out code in ini_linear_phisurf) |
4221 |
o modif's to run adjoint with exactConserv |
4222 |
o case GM_BOLUS_ADVEC should be cleaned |
4223 |
S/R gmredi_slope_psi should be cleaned |
4224 |
o verification/carbon now has exactConserv=.TRUE. |
4225 |
|
4226 |
checkpoint47g_post (2003/01/10) |
4227 |
o time-average AIM output: becomes independent from statvars time-average |
4228 |
(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
4229 |
o After TAF bug fix: |
4230 |
Tested adjoint of gmredi package. |
4231 |
Tests were done with checkpoint47 rather than with latest |
4232 |
checkpoint47f_post since the latter is broken for the adjoint |
4233 |
verification/carbon/ contains both ADM and TLM gradient checks. |
4234 |
Here they are, before they get changed/lost/stolen. |
4235 |
Mostly modif.'s to fix numerical sensitivities. |
4236 |
Gradient checks OK for |
4237 |
- GM_taper_scheme: |
4238 |
* clipping |
4239 |
* ac02 |
4240 |
* linear |
4241 |
* glw91 |
4242 |
* dm95 |
4243 |
* ldd97 |
4244 |
- GMREDI_OPTIONS: |
4245 |
* GM_VISBECK_VARIABLE_K |
4246 |
* GM_NON_UNITY_DIAGONAL |
4247 |
* GM_EXTRA_DIAGONAL |
4248 |
* GM_BOLUS_ADVEC |
4249 |
in conjunction with data.gmredi parameters to be checked in |
4250 |
in a few minutes under verification/carbon/code/ |
4251 |
|
4252 |
checkpoint47f_post (2002/12/28) |
4253 |
Merging from release1_p10: |
4254 |
o modifications for using pkg/exf with pkg/seaice |
4255 |
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
4256 |
and SEAICE_EXTERNAL_FLUXES |
4257 |
- pkg/exf CPP options EXF_READ_EVAP and |
4258 |
EXF_NO_BULK_COMPUTATIONS |
4259 |
- usage examples are Experiments 8 and 9 in |
4260 |
verification/lab_sea/README |
4261 |
- verification/lab_sea default experiment now uses |
4262 |
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf |
4263 |
|
4264 |
checkpoint47e_post (2002/12/27) |
4265 |
o created a tag prior to creating a branch |
4266 |
|
4267 |
checkpoint47d_post (2002/12/16) |
4268 |
o fixed bug in the oceanic pressure coordinates code: vertical viscosity |
4269 |
at the bottom boundary had an erroneous half slip boundary condition |
4270 |
o added bottom drag and no slip boundary condition capabilities to |
4271 |
oceanic pressure coordinates code |
4272 |
o added new verification experiment global_ocean_pressure, this experiment is |
4273 |
also described in the tutorial section of the manual |
4274 |
checkpoint47d_pre (2002/12/16) |
4275 |
|
4276 |
checkpoint47c_post (2002/12/16) |
4277 |
o Added a verification experiment for a global cubed-sphere ocean run |
4278 |
- verification/global_ocean.cubed32x32x30 |
4279 |
- uses pkg/therm_seaice and pkg/bulk_forcing |
4280 |
|
4281 |
o allow to run AIM physics with SPEEDY input files (from Franco Molteni) |
4282 |
o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) |
4283 |
when using P-coordinate; only implemented for atmospheric config. |
4284 |
o OCEANICP & realFreshWater: include P-E direct effect on wVel ; |
4285 |
NOTES: requires option NONLIN_FRSURF to be "#define". |
4286 |
o update advect_xz/results/output.txt (left from checkpoint44g_post) |
4287 |
|
4288 |
checkpoint47b_post (2002/12/05) |
4289 |
Merging from release1_p9: |
4290 |
o pkg/seaice |
4291 |
- removed GOTO's and added taf directives |
4292 |
- double precision constants to reduce the g77 (Linux) |
4293 |
to F77 (SGI) differences reported in release1_p8 |
4294 |
o tools/genmake |
4295 |
- added SGI options |
4296 |
o verification/testscript |
4297 |
- updated to that of checkpoint47a_post |
4298 |
o verification/global_ocean.90x40x15/input/eedata |
4299 |
- modified for SGI f77 compatibility |
4300 |
o verification/lab_sea |
4301 |
- added description of sea-ice model |
4302 |
- added missing matlab routines |
4303 |
- added test of thermodynamics parallelization |
4304 |
|
4305 |
checkpoint47a_post (2002/11/23) |
4306 |
o new pkg: aim_v23 |
4307 |
= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
4308 |
for now, keep the same surface forcing as before. |
4309 |
- Part-Cell implemented into AIM; check that Heat & Water are conserved |
4310 |
- aim.5l_cs: use new aim pkg (run 10yr & get better results than before) |
4311 |
- aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg |
4312 |
o add diagnostic of surface correction term in monitor output |
4313 |
|
4314 |
o bulk_force and therm_seaice |
4315 |
- Two packages: bulk_force (Bulk forcing) |
4316 |
and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 |
4317 |
- Earlier integration from Stephaine Dutkiewicz |
4318 |
and Patrick Heimbach. |
4319 |
- Two ifdef statements for compile time, |
4320 |
ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE |
4321 |
|
4322 |
checkpoint47 (2002/11/15) |
4323 |
differentiable version of checkpoint46n_post |
4324 |
o bug fix in quasihydrostaticterms |
4325 |
o * "clean" adjoint code (in terms of extensive recomputations) |
4326 |
can now be obtained for all GMREDI options (i.e. for |
4327 |
- GM_VISBECK_VARIABLE_K |
4328 |
- GM_NON_UNITY_DIAGONAL |
4329 |
- GM_EXTRA_DIAGONAL |
4330 |
- GM_BOLUS_ADVEC ) |
4331 |
* However, wrong gradient check problem remains unsolved. |
4332 |
* New CPP options have been introduced for different |
4333 |
tapering schemes |
4334 |
o external_fields_load now part of differentiation list |
4335 |
o pressure needs multiple storing; |
4336 |
would be nice to have store_pressure at beginning or |
4337 |
end of forward_step, e.g. by having phiHyd global (5-dim.) |
4338 |
(NB: pressure is needed for certain cases in find_rho, |
4339 |
which is also invoked through convective_adjustment). |
4340 |
o recomputations in find_rho for cases |
4341 |
'JMD95'/'UNESCO' or 'MDJWF' are OK. |
4342 |
o #define ATMOSPHERIC_LOADING should be differentiable |
4343 |
o ini_forcing shifted to begining of initialise_varia |
4344 |
o Incorporating QNVS line search routines into MITgcm |
4345 |
(this is separate code, and therefore not under pkg) |
4346 |
lsopt/, optim/ |
4347 |
o Updated verification/carbon/ |
4348 |
- #define GM_VISBECK_VARIABLE_K |
4349 |
- GM_taper_scheme = 'ldd97' |
4350 |
|
4351 |
checkpoint46n_post (2002/11/12) |
4352 |
Merging from release1_p8: |
4353 |
o verification/natl_box: |
4354 |
updating new external_fields_load routine |
4355 |
o New package: pkg/seaice |
4356 |
Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). |
4357 |
The sea-ice code is based on Hibler (1979-1980). |
4358 |
Two sea-ice dynamic solvers, ADI and LSR, are included. |
4359 |
In addition to computing prognostic sea-ice variables and diagnosing |
4360 |
the forcing/external data fields that drive the ocean model, |
4361 |
SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
4362 |
The implied surface heat flux is then stored in variable |
4363 |
surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and |
4364 |
kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the |
4365 |
non-local transport term. Because this call precedes model |
4366 |
thermodynamics, temperature under sea-ice may not be "exactly" at |
4367 |
the freezing point by the time theta is dumped or time-averaged. |
4368 |
N.B.: fairly large differences in accuracy occur across |
4369 |
different platforms/compilers; comparison between |
4370 |
g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) |
4371 |
generated output gives: |
4372 |
T S U V |
4373 |
C D M c m s m s m s m s |
4374 |
n p a R g m m e . m m e . m m e . m m e . |
4375 |
f n k u 2 i a a d i a a d i a a d i a a d |
4376 |
g d e n d n x n . n x n . n x n . n x n . |
4377 |
|
4378 |
Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea |
4379 |
o GAD: |
4380 |
- generated new common blocks to account for call of |
4381 |
same gad routines with differing traceridentities |
4382 |
(needed to modify tracerIdentity indices in GAD.h) |
4383 |
- generated separate common blocks for case useCubedSphereExchange |
4384 |
(Department of Futurology) |
4385 |
- parameter lists to gmredi_?transport: added tracerIdentity |
4386 |
- added new key indices to tamc.h |
4387 |
o external_fields_load: |
4388 |
- added this routine to TAF list |
4389 |
- needed to make some common blocks global and additional storing |
4390 |
along the same lines as exf package (checkpoint_lev?_directives.h) |
4391 |
o exf: |
4392 |
updated external forcing package |
4393 |
- bug fixes carried over from ecco-branch |
4394 |
(missing OBCS_OPTIONS.h in two routines) |
4395 |
- enable easy to use "no forcing". |
4396 |
- added exf I/O for atmospheric loading |
4397 |
- added exf I/O for runoff data |
4398 |
- transfered scaling between exf <-> MITgcm to exf namelist |
4399 |
o Adding new verification experiment global_with_exf. |
4400 |
This verification experiment is almost identical to the |
4401 |
global_ocean.90x40x15 experiment, except that it uses |
4402 |
the exf (and cal) package instead of the |
4403 |
external_fields_load routine (cf README file). |
4404 |
|
4405 |
checkpoint46m_post (2002/11/07) |
4406 |
o modified testscript to return -- when there are no lines of "%MON" output |
4407 |
o added new flag "quasiHydrostatic" for QH mode |
4408 |
and new routine quasihydrostaticterms() |
4409 |
o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
4410 |
New routine: mom_u_coriolis_nh() |
4411 |
o fixed sign of non-hydrostatic metric terms in u and v equations. |
4412 |
Depend on correct sign of gravitySign. |
4413 |
o added work.pc* to .cvsignore in aim directories using ifc |
4414 |
o introduced flag for controllin non-hydrostatic metric terms |
4415 |
o removed gravitySign from PARM04 |
4416 |
o switched to g77/ifc from pgf77 in aim experiments |
4417 |
|
4418 |
checkpoint46l_post (2002/11/01) |
4419 |
o made convective adjustment work with pressure coordinates: |
4420 |
- changed the direction of k-loop in convective_adjustment.F for the |
4421 |
case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
4422 |
- adjusted the reference pressure k-index in convective_adjustment.F |
4423 |
- adjusted the convection condition in convect.F (in analogy to |
4424 |
calc_ivdc.F) |
4425 |
- convective_adjustment no longer computes anything on the halos |
4426 |
- removed the warnings about negative salinity from find_rho.F and |
4427 |
find_alpha.F; instead the new routine look_for_neg_salinity, called |
4428 |
at the beginning of find_rho, find_alpha, and find_beta, does a |
4429 |
check of the entire slice, if CPP-option |
4430 |
CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined |
4431 |
checkpoint46l_pre (2002/10/23) |
4432 |
|
4433 |
checkpoint46k_post (2002/10/23) |
4434 |
o fixed the verification/global_ocean.90x40x15 experiment: |
4435 |
- new bathymetry (the world according to A., JMC, and M.) |
4436 |
- new initial fields and forcing fields (*.bin files) |
4437 |
- new POLY3.COEFFS (for the next release one should switch to a full |
4438 |
equation of state: JMD95P or MDJWF) |
4439 |
- fixed several errors and redundancies in the data file |
4440 |
- experiment uses looped cells |
4441 |
- added matlab directory with diagnostic scripts for plotting of output |
4442 |
|
4443 |
o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
4444 |
- read AIM physics parameters from a file (data.aimphys) |
4445 |
- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
4446 |
|
4447 |
checkpoint46j_post (2002/10/07) |
4448 |
o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
4449 |
o move wVel computation at the end of the time step, in S/R integr_continuity |
4450 |
o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
4451 |
o update timeave pkg for wVel diagnostic. |
4452 |
checkpoint46j_pre (2002/09/27) |
4453 |
|
4454 |
checkpoint46i_post (2002/09/25) |
4455 |
o Clean up AIM package (and keep the results unchanged): |
4456 |
include CPP_OPTION and use IMPLICT NONE in all routines ; |
4457 |
declare all the variables _RL ; use _d 0 for all numerical constants. |
4458 |
use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
4459 |
|
4460 |
checkpoint46h_post (2002/09/25) |
4461 |
o cleaned up the use of rhoNil and rhoConst. |
4462 |
- rhoNil should only appear in the LINEAR equation of state, everywhere |
4463 |
else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
4464 |
and the dynamical equations are all divided by rhoConst |
4465 |
o introduced new parameter rhoConstFresh, a reference density of fresh |
4466 |
water, to remove the fresh water flux's dependence on rhoNil. The default |
4467 |
value is 999.8 kg/m^3 |
4468 |
o cleanup up external_forcing.F and external_forcing_surf.F |
4469 |
- can now be used by both OCEANIC and OCEANICP |
4470 |
checkpoint46h_pre (2002/09/18) |
4471 |
|
4472 |
Added code to convert surface volume flux (fresh water) into |
4473 |
a mass flux when using P coordinates in the ocean (OCEANICP). |
4474 |
Note: It assumes you have set rho0=rhoConst=density of fresh water. |
4475 |
|
4476 |
checkpoint46g_post (2002/09/18) |
4477 |
o Include a new diagnostic variable phiHydLow for the ocean model |
4478 |
- in z-coordinates, it is the bottom pressure anomaly |
4479 |
- in p-coordinates, it is the sea surface elevation |
4480 |
- in both cases, these variable have global drift, reflecting the mass |
4481 |
drift in z-coordinates and the volume drift in p-coordinates |
4482 |
- included time averaging for phiHydLow, be aware of the drift! |
4483 |
o depth-dependent computation of Bo_surf for pressure coordinates |
4484 |
in the ocean (buoyancyRelation='OCEANICP') |
4485 |
- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
4486 |
Theta, Salinity, and Pressure in the parameter list. This routine is |
4487 |
presently contained in find_rho.F. This routine does not give the |
4488 |
correct density for 'POLY3', which would be a z-dependent reference |
4489 |
density. |
4490 |
o cleaned up find_rho |
4491 |
- removed obsolete 'eqn' from the parameter list. |
4492 |
o added two new verification experiments: gop and goz |
4493 |
(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
4494 |
checkpoint46g_pre (2002/09/16) |
4495 |
|
4496 |
checkpoint46f_post (2002/09/16) |
4497 |
o Enable tangent linear (forward mode) gradient checks: |
4498 |
- extended active file handling to g_... files |
4499 |
- added TANGENT_SIMULATION to theSimulationMode |
4500 |
- extended grdchk package accordingly |
4501 |
o added tangent linear setup in verification/carbon/code_ftl |
4502 |
o added adjoint setup in verification/front_relax/code_ad |
4503 |
|
4504 |
checkpoint46e_post (2002/09/05) |
4505 |
o Added new equation of state -> MDJWF |
4506 |
- EOS of McDougall et al., 2002, JAOT, submitted |
4507 |
- caveat: the equation of state is only valid for a smaller (more |
4508 |
realistic?) range of values than JMD95P/Z and UNESCO |
4509 |
- added masks to the calculation of pressure in store_pressure |
4510 |
- added more check values for density in check_eos (ini_eos.F), some of |
4511 |
the old check values are out of the range of the MDJWF-eos, so don't |
4512 |
expect perfect matches for those |
4513 |
checkpoint46e_pre (2002/08/19) |
4514 |
|
4515 |
checkpoint46d_post (2002/08/19) |
4516 |
o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
4517 |
'OCEANICP', also initialised field pressure correctly in ini_eos in the |
4518 |
case of pressure coordinates. eosType='JMD95Z' in |
4519 |
combination with buoyancyRelation='OCEANICP' now causes an error. |
4520 |
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
4521 |
in find_alpha/beta. |
4522 |
checkpoint46d_pre (2002/08/15) |
4523 |
|
4524 |
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
4525 |
so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
4526 |
|
4527 |
checkpoint46c_post (2002/08/15) |
4528 |
o Changes necessary for ocean in p-coordinates |
4529 |
- Added new buoyancy relation = 'OCEANICP' |
4530 |
- Added new parameters = gravitySign (this used to be contained inside |
4531 |
the factor dRdZ which I added when we first switched to R coordinates). |
4532 |
X GM/Redi is not compatible (yet) |
4533 |
X bottom drag and no-slip need to be debugged. |
4534 |
checkpoint46c_pre (2002/08/07) |
4535 |
|
4536 |
checkpoint46b_post (2002/08/07) |
4537 |
o Added new equation of state -> JMD95Z and JMD95P |
4538 |
- EOS of Jackett and McDougall, 1995, JAOT |
4539 |
- moved all EOS parameters into EOS.h |
4540 |
- new routines ini_eos.F, store_pressure.F |
4541 |
o Added UNESCO EOS, but not recommended because it requires |
4542 |
in-situ temperature (see JMD95) |
4543 |
o Modified formatting for knudsen2.f in utils/knudsen2 and added |
4544 |
unesco.f to be used with POLY3 |
4545 |
checkpoint46b_pre (2002/07/31) |
4546 |
|
4547 |
checkpoint46a_post (2002/07/31) |
4548 |
o Added (atmospheric) pressure loading |
4549 |
- new field in FFIELDS.h, etc... |
4550 |
- new cpp flag ATMOSPHERIC_LOADING |
4551 |
o Changed hFacC to _hFacC in calc_phi_hyd.F |
4552 |
o Added SHORTWAVE_HEATING to some files for consistency |
4553 |
checkpoint46a_pre (2002/07/13) |
4554 |
|
4555 |
checkpoint46 (2002/07/13) |
4556 |
further merges from release1_p5 |
4557 |
o new ctrl package |
4558 |
- adopted from ECCO environment to enable optimization |
4559 |
- added Eliassen Palm fluxes to controls |
4560 |
o added Eliassen Palm flux controls to gradient check package |
4561 |
o cost package |
4562 |
- Compatible with new ctrl package |
4563 |
- added Eliassen Palm cost hooks |
4564 |
- modif's of existing cost functions |
4565 |
o Adjoint-related bug fixes in kpp: |
4566 |
- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
4567 |
- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
4568 |
o autodiff package |
4569 |
- flow directives: |
4570 |
+ new for S/R do_the_model_io |
4571 |
+ enhanced for S/R checkpoint |
4572 |
+ new gmredi.flow |
4573 |
- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
4574 |
disable adcommon.h/g_common.h by default. |
4575 |
- fixed problem for adjoint of global_max |
4576 |
o modified verification/carbon/ |
4577 |
o New setup for adjoint of global_ocean |
4578 |
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
4579 |
o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
4580 |
o incorporated hooks for sponge layer code (external_forcing.F) |
4581 |
|
4582 |
checkpoint45d_post (2002/07/12) |
4583 |
o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
4584 |
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
4585 |
(affects plume_on_slope "cg2d" output) |
4586 |
o add new parameter deltaTfreesurf for free-surface time stepping |
4587 |
o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
4588 |
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
4589 |
o change phiMin in exp1 (to agree with documentation) |
4590 |
o add new flags: |
4591 |
- T,S forcing inside/outside Adams-Bashforth |
4592 |
- turn off temp,salt advection and/or forcing |
4593 |
- for each tracer, define internal flag for multiDimAdvection & A-B |
4594 |
o monitor: change definition of KE to check conservation of Energy |
4595 |
|
4596 |
checkpoint45c_post (2002/05/30) |
4597 |
o Removed f90 comments ("!") |
4598 |
o Modified initialisations to enable exf package for MITgcm |
4599 |
(without invoking ECCO_PACKAGE). |
4600 |
o modifications to gradient check package (Martin Losch) |
4601 |
- enable centered differences |
4602 |
- modified format of standard output |
4603 |
|
4604 |
checkpoint45b_post (2002/05/30) |
4605 |
o cleaned exchange calls in cg2d |
4606 |
o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
4607 |
o included CPP option SINGLE_LAYER_MODE in thermodynamics |
4608 |
to configure barotropic setup (Martin Losch) |
4609 |
o moved some initialisations within bi,bj loop in dynamics |
4610 |
(TAF flow dependency) |
4611 |
o in initialise_varia, moved call packages_init_variables |
4612 |
before convective_adjustment_init |
4613 |
(corresponding adjustment of TAF tape initialisation). |
4614 |
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
4615 |
|
4616 |
checkpoint45a_post (2002/05/01) |
4617 |
o compute Rho over the whole domain (extend iMin,jMin indices) |
4618 |
o specific exchange for X-slice domain (case Ny=1) |
4619 |
o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
4620 |
o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
4621 |
|
4622 |
checkpoint44h_post = checkpoint45 |
4623 |
o Fix to restore differentiability: |
4624 |
place at which packages_init_variables is called in |
4625 |
initialise_varia is crucial for reverse control flow. |
4626 |
o modifications in GMRedi to enable stable adjoint |
4627 |
(corresponding modif's in thermodynamics, dynamics) |
4628 |
o added missing hook for sponge layer code in external_forcing |
4629 |
o modified test cost functions |
4630 |
o storing in gad_advection (plus removal of write(0,*)! |
4631 |
o missing headers TR1.h added in convective_adjustment routines |
4632 |
o errorMessageUnit set non-equal zero in eeboot |
4633 |
(conflict on some platforms, e.g. IBM SP3) |
4634 |
o modified carbon verif. |
4635 |
|
4636 |
checkpoint44h_pre (2002/03/14) |
4637 |
o vertical grid option: allow to put the Interface at the middle between |
4638 |
2 cell-centers ; replace delZ in pkg/kpp by drF. |
4639 |
o GM Advective form: Tracers are advected using the residual transport (= |
4640 |
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
4641 |
|
4642 |
checkpoint44g_post (2002/03/05) |
4643 |
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
4644 |
results) ; ifdef missing in thermodynamics.F |
4645 |
|
4646 |
checkpoint44f_pre,checkpoint44f_post |
4647 |
o added PTRACERS package |
4648 |
This allows an arbitrary number of passive tracers to be integrated |
4649 |
forward simultaneously with the dynamicaly model. |
4650 |
+ Implemented so far: |
4651 |
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
4652 |
- I/O and checkpointing |
4653 |
- GM/Redi *but* using the GM/Redi coefficient of Salt |
4654 |
+ Not implemented so far: |
4655 |
- KPP |
4656 |
- OBCS |
4657 |
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
4658 |
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
4659 |
line in data.pkg. |
4660 |
+ This package is disabled by default since it increases storage. |
4661 |
|
4662 |
|
4663 |
o testscript: added -cleanup option |
4664 |
o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
4665 |
b) enable to filter 2D fields. |
4666 |
|
4667 |
checkpoint44e_pre,post |
4668 |
o re-wrote convective adjustment to use pre-calculated weights |
4669 |
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
4670 |
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
4671 |
Original calls to convect() still in place. |
4672 |
|
4673 |
chkpt44d_pre,post |
4674 |
o added missing EXCLUDE_MONITOR flags |
4675 |
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
4676 |
(incompatible typ in MIN/MAX expressions caused problems |
4677 |
on IBM SP3) |
4678 |
o in genmake added variable MAKEDEPEND |
4679 |
plus resetting for case SunOS |
4680 |
o added timer_stats.c routine for IBM SP3 |
4681 |
o removed variables in dynamics |
4682 |
!!! I forgot to create tag chkpt44d_pre !!! |
4683 |
!!! But chkpt44d_pre = chkpt44c_post !!! |
4684 |
|
4685 |
o real fresh water flux implemented with non-linear free-surface. |
4686 |
|
4687 |
chkpt44c_pre,post |
4688 |
o few fix (mask in shap_s2, EmPmR in external_field_load, |
4689 |
USE_NATURAL_BCS in solve_for_P); |
4690 |
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
4691 |
|
4692 |
checkpoint44b_pre/_post |
4693 |
o merge of relevant stuff from the ecco-branch: |
4694 |
- genmake: removed $S64 overwrite for case SunOS |
4695 |
- pkg/exf: update and corrections for field swapping and obcs |
4696 |
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
4697 |
harmonized between ECCO and MITgcm |
4698 |
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
4699 |
updated checkpointing_lev... lists for obcs |
4700 |
- model/src: minor changes in forward_step, plot_field |
4701 |
added directive for divided adjoint in the_main_loop |
4702 |
- pkg/mdsio: added mdsio_gl_slice |
4703 |
|
4704 |
o check parameters & config (chkpt44a_pre,post) |
4705 |
o OBC and NonLin_FrSurf. |
4706 |
|
4707 |
checkpoint44 (2002/01/18) |
4708 |
o fix bug in mom_vi_del2uv |
4709 |
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
4710 |
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
4711 |
o update AIM experiments (NCEP input files) |
4712 |
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
4713 |
o added some stuff for AD |
4714 |
|
4715 |
checkpoint43 (2001/09/28) |
4716 |
o added two new advection tests |
4717 |
o added global 4x4 degree ocean test |
4718 |
o added test of H&S94 with free surface on cube |
4719 |
o some final mods for gradient check, adjoint,... |
4720 |
|
4721 |
checkpoint42 (2001/09/27) |
4722 |
Fixed AD-related problems: |
4723 |
o Store directives up-to-date with re-arranged Adams-Bashforth |
4724 |
(mainly thermodynamics.F) |
4725 |
o New store directives for multi-dim. advection schemes |
4726 |
* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
4727 |
* new common block and key passkey |
4728 |
(mainly gad_advection.F) |
4729 |
o Modified store directives for split of dynamics/thermodynamics |
4730 |
for the case ALLOW_KPP |
4731 |
o Cleaned argument list for timestep_tracer.F |
4732 |
|
4733 |
checkpoint41 (2001/09/27) |
4734 |
o re-formatted/added comments in prologues of key subroutines |
4735 |
to work with protex |
4736 |
|
4737 |
checkpoint40 (2001/09/27) |
4738 |
o moved calc_gs, calc_gt and calc_tr1 back to model/src |
4739 |
o added FLT (floats) package from Arne along with demo. experiment |
4740 |
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
4741 |
implementation of forward-in-time forcing terms |
4742 |
o more mods for non-linear free-surface including new variable |
4743 |
o modified multi-dim method to work on cube |
4744 |
o bug fix in KPP (from DM) |
4745 |
|
4746 |
checkpoint40pre9 (2001/09/27) |
4747 |
o added DST advection schemes |
4748 |
o fix MPI bug on SGI's |
4749 |
o modifications for non-linear free-surface |
4750 |
o fixed conditionals for fixed flow/passive tracer only mode |
4751 |
o added tension/strain form of stress tensor |
4752 |
o changes to commenting of arguments for TAF/TAMC |
4753 |
o added/updated many matlab scripts |
4754 |
o added multi-dimensional advection method for tracers |
4755 |
|
4756 |
checkpoint40pre8 (2001/09/05) |
4757 |
o new package rw/ |
4758 |
Added method for dumping intermediate local arrays: |
4759 |
mdsio_writetile - same as mdsio_writefield except works from inside |
4760 |
bi,bj loop |
4761 |
mdsio_writelocal - same as mdsio_writetile except works for local |
4762 |
arrays |
4763 |
write_local_r? - higher-level wrapper for mdsio_writelocal |
4764 |
Controlled by diagFreq. Defaults to zero (ie. no dumps) |
4765 |
Example given at end of mom_vecinv.F that dumps some local arrays. |
4766 |
o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
4767 |
control flux-form versus vector invariant code. |
4768 |
Switch is runtime flag vectorInvariantMomentum (defaults to false) |
4769 |
or genmake -DISABLE ... |
4770 |
o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
4771 |
(additional storing is now needed for case vecinv; |
4772 |
currently nothing implemented to switch this storing off |
4773 |
in case fluxform is used since no CPP flag available). |
4774 |
|
4775 |
checkpoint40pre7 (2001/08/14) |
4776 |
o bug fix in dynamics.F |
4777 |
calc_viscosity called before k=1,Nr loop. |
4778 |
o added some #ifdef's ALLOW_PASSIVE_TRACER |
4779 |
o cleaned initialisations in ctrl_map_ini |
4780 |
related to TAF |
4781 |
|
4782 |
checkpoint40pre6 (2001/08/13) |
4783 |
o split dynamics into thermodynamics & dynamics |
4784 |
o corresponding split of calc_diffusivity into |
4785 |
calc_diffusivity, calc_viscosity |
4786 |
(kpp_calc_diff, kpp_calc_visc). |
4787 |
o Added diffkr, kapgm to control variables |
4788 |
o bug fix in gmredi_slope_limit for ldd97 |
4789 |
|
4790 |
checkpoint40pre5 (2001/07/31) |
4791 |
o proper initialization of Adams-Bashforth time stepping |
4792 |
+ uses forward step for very first step of model (iter=0) |
4793 |
o re-generated *all* output since almost all output is modified by this |
4794 |
change (sorry but we've been putting this one off for about 2 years) |
4795 |
+ natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were |
4796 |
*not* regenerated since they are already out of date and I don't |
4797 |
want to create the impression that they are suddenly working. |
4798 |
o removed KAP stuff for DEC's |
4799 |
o modified/added many .cvsignore files in */code and */input |
4800 |
o added new expt "solid-body.cs-32x32x1" |
4801 |
+ this uses an alternative form of ini_curvilinear_grid.F which |
4802 |
is not necessarily any better than the current one... |
4803 |
|
4804 |
checkpoint40pre4 (2001/07/30) |
4805 |
o added re-initialisations of utrans,vtrans,rtrans in |
4806 |
calc_common_factors which are crucial for TAF. |
4807 |
o extended iMin,jMin range for calc_common_factors, |
4808 |
calc_diffusivity |
4809 |
o added option ALLOW_PASSIVE_TRACER |
4810 |
o a few minor updates and fixes |
4811 |
|
4812 |
checkpoint40pre3 (2001/07/13) |
4813 |
o created calc_gtr1.F for gad package |
4814 |
o split the_main_loop and re-introduced forward_step |
4815 |
o some recomputations of nIter0 for TAMC |
4816 |
|
4817 |
checkpoint40pre2 (2001/07/13) |
4818 |
o Updated to latest branch of AJA, JMC |
4819 |
o Added gradient check package |
4820 |
o Added routines for passive tracer handling |
4821 |
o Added carbon sequestration sensitivity experiment |
4822 |
|
4823 |
checkpoint39 (2001/05/14) |
4824 |
o Modifications and fixes to support TAMC |
4825 |
(mainly missing or wrong directives) |
4826 |
o Corrected common blocks when fooling TAMC to produce adjoint I/O |
4827 |
in addummy_in_stepping |
4828 |
o Updated verification/vero/ (bug fixes in code/, correct pickups in input/) |
4829 |
o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs. |
4830 |
o Included following packages: |
4831 |
cal: calendar |
4832 |
exf: external forcing |
4833 |
ecco: essential routines to control use of cal, exf |
4834 |
(NB: this is not the full ECCO environment) |
4835 |
o disabled some packages by default in genmake |
4836 |
|
4837 |
checkpoint38 (2001/04/10) |
4838 |
o see notes_c37_adj.txt |
4839 |
o corrected wrong layer index in external_forcing_t |
4840 |
o replaced the_main_loop/forward_step by the_main_loop |
4841 |
o removed forceoutput from write_state |
4842 |
(replaced criteria for initial/final state) |
4843 |
o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
4844 |
|
4845 |
checkpoint37 (2001/03/13) |
4846 |
o mdsio.F routine split and packaged in pkg/mdsio |
4847 |
(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
4848 |
used unless genmake -disable=mdsio) |
4849 |
o allow a more precise surface-geopotential gradient for the atmosphere |
4850 |
taking into account the change in space of Alpha (=1/rho) at the surface. |
4851 |
o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit] |
4852 |
(ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa]) |
4853 |
o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and |
4854 |
Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential |
4855 |
[m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere). |
4856 |
o Time-Average diagnostics defined as a pseudo package "timeave". |
4857 |
o pickup files : old pickup (before c35) did not work with new code (c35 |
4858 |
and after) unless activating 2 commented lines in initialise-varia. |
4859 |
o Non-Hydrostatic pickup file Pb fixed. |
4860 |
o bug with Rigid-lid version (since c35) fixed. |
4861 |
|
4862 |
checkpoint36 (2001/02/20) |
4863 |
o implement Crank-Nickelson barotropic time-stepping |
4864 |
o recover Time-Average diagnostics |
4865 |
o fix Pb in checkpoint (PR#19) |
4866 |
o AIM become a standard package ; clean unused CPP_kees |
4867 |
|
4868 |
checkpoint35 (2001/02/08) |
4869 |
o subtantial rewrite of dynamics.f |
4870 |
o allows staggered time-stepping |
4871 |
o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
4872 |
o added bottom drag (linear + quadratic) |
4873 |
|
4874 |
checkpoint34 (2001/01/30) |
4875 |
o Modified exchange routines for correct reverse simulation. |
4876 |
o Added verification output to comply with bug fix in impldiff.F |
4877 |
as of c33 (exp2, natl_box). |
4878 |
o Corrected store directives in dynamics.F |
4879 |
o Corrected array boundaries in impldiff.F |
4880 |
o Corrected array dimensions in gmredi. |
4881 |
Added temporary scalars to avoid storage by TAMC (gmredi, kpp). |
4882 |
o Added routine GLOBAL_SUM_INT to global_sum.F |
4883 |
o Added mdsio_gl.F for ECCO purposes. |
4884 |
|
4885 |
checkpoint33 (2000/11/30) |
4886 |
o Fixed bug in lower BC in impldiff.F |
4887 |
o Fixed confusion about units of forcing arrays in FFIELDS.h |
4888 |
namely Fu,Fv,Qnet,Qsw,EmPmR: |
4889 |
- Removed verification/natl_box/code/external_fields_scale.F |
4890 |
(did not differ from that in model/src) |
4891 |
- Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units |
4892 |
(see FFIELDS.h for description) |
4893 |
- Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F, |
4894 |
kpp_calc.F and kpp_transport_t.F |
4895 |
- Removed model/src/external_fields_scale.F and calls to it |
4896 |
- verification/natl_box uses flux data with "atmospheric" sign so |
4897 |
a special version of external_fields_load.F is used to |
4898 |
change the data as it's read in. This way, the arrays |
4899 |
have the right units and signs at all times tha a user could |
4900 |
possibly use them. |
4901 |
o Corrected genmake to delete a temporary file during configuration |
4902 |
|
4903 |
checkpoint32 (2000/11/13) |
4904 |
o Scaling of forcing fields moved from external_forcing.F to |
4905 |
external_fields_scale.F, called directly after loading fields. |
4906 |
o Surface relaxation terms added to surface tendency fields in |
4907 |
extra subroutine. |
4908 |
o impldiff.F changed to avoid storing by TAMC of huge intermediate |
4909 |
fields. |
4910 |
o Changes in GMRedi to comply with packaging structure. |
4911 |
o Modifications and bug fixes in KPP package. |
4912 |
o Verification experiment for KPP added (verification/nat_box/) |
4913 |
|
4914 |
checkpoint31 (2000/09/11) |
4915 |
o Packages interface brought in line with defined standard |
4916 |
-> new routines packages_...F |
4917 |
-> changes in initialise_fixed.F, initialise_varia.F |
4918 |
-> enables initialisation interface for ECCO package |
4919 |
o Rescaling of external forcing fields immediately after read |
4920 |
(removed from external_forcing.F) |
4921 |
-> new: surface_fields_scale.F |
4922 |
-> affects ini_foorcing.F, external_fields_load.F |
4923 |
o Computation of surface tendencies before tendency updates. |
4924 |
-> new: external_forcing_surf.F |
4925 |
o Change of variable names useGMRedi, useKPP, useECCO |
4926 |
o Further changes in dynamics.F, impldiff.F for TAMC |
4927 |
o Tested for experiments 0, 2, 4. |
4928 |
- not yet tested for GMRedi. |
4929 |
- not yet tested for KPP. |
4930 |
|
4931 |
checkpoint30 (2000/07/13) |
4932 |
o Updates for OBCs |
4933 |
o New experiment for test OBCs (internal_wave) |
4934 |
o New output.txt in verification/exp4/results/ |
4935 |
o Updates for KPP: calculation of viscosity corrected, new variables |
4936 |
kpp_dumpFreq and kpp_taveFreq |
4937 |
o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) |
4938 |
and entry for T90 in genmake |
4939 |
|
4940 |
checkpoint29 (2000/06/21) |
4941 |
o packaged KPP and GM/Redi |
4942 |
|
4943 |
checkpoint28 (2000/06/09) |
4944 |
o Corrected initialization of hFacMin for difference vertical coordinates |
4945 |
o Modified calculation of partial cell thickness to more robust algorithm |
4946 |
o config_summary.F: replaced write_1D_... by write_0D_... |
4947 |
read_write.F: added subroutines write_0D_... |
4948 |
o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho: |
4949 |
included some initialisations required for TAMC. |
4950 |
o routine calc_isoslopes: modified sqrt computation to make it |
4951 |
differentiable for zero argument. |
4952 |
o routines dynamics, impldiff: |
4953 |
included store directives and tape key computations required for TAMC. |
4954 |
o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC |
4955 |
|
4956 |
checkpoint27 (2000/04/10) |
4957 |
o fixed calc_isoslopes() to so that cancellation of terms in tensor |
4958 |
formulation works properly with variable resolution. |
4959 |
o restructured the calling tree between the_model_main() and dynamics() |
4960 |
o split initialise() into initialise_fixed() and initialise_varia() |
4961 |
o introduced initialization file pSurfInitFile for free surface (cg2d_x) |
4962 |
in new routine ini_psurf() |
4963 |
|
4964 |
checkpoint26 (2000/04/05) |
4965 |
o moved some #ifdef in optional routines to encompass everything |
4966 |
except the argument declarations. This was using up some memory. |
4967 |
o fixed macros like _ADT to work with both versions of Linux cpp |
4968 |
o cleaned up some unused and uninitialized variables |
4969 |
(helps when debugging with strict compile options) |
4970 |
o split up CPP_EEOPTIONS.h into options and macros |
4971 |
(macros are now in eesupp/inc/CPP_EEMACROS.h) |
4972 |
o patch for 2 processor JAM mode |
4973 |
|
4974 |
checkpoint25 (2000/03/15) |
4975 |
o updates for OBCs and NH |
4976 |
o dramatically reduced memory usage |
4977 |
o added "JAM" routines for use on Artic network |
4978 |
o parameterization of convection by implicit vertical diffusion |
4979 |
o added a diagnostic of convective index |
4980 |
o moved call to calc_divg_hat() from dynamics() to solve_for_pressure() |
4981 |
(this is was partly for OBCs and NH but also in anticipation of |
4982 |
an explicit free-surface option) |
4983 |
o initial state input files for U and V |
4984 |
|
4985 |
checkpoint24 (1999/08/02) |
4986 |
o Removed some spurious "REAL"s |
4987 |
o Updated KPP to latest version from JPL |
4988 |
o Added a COS(latitude) in horizontal viscosity |
4989 |
|
4990 |
checkpoint23 (1999/05/26) |
4991 |
o Added del^4 diffusion for salt and temperature |
4992 |
o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) |
4993 |
|
4994 |
checkpoint22 (1999/05/18) |
4995 |
o Made many small changes: implicit none, format(i5), etc... |
4996 |
o Introduced KPP mixing scheme (compiles and runs but *not* tested) |
4997 |
|
4998 |
checkpoint21 (1999/05/18) |
4999 |
o Introduced new I/O package that supports direct-access records (mdsio.F) |
5000 |
o Split-up mid-level I/O routines |
5001 |
o Updated input data for experiments 0,1,2,4 and 5 |
5002 |
o Finally removed the genmake.* scripts (everyone seems happy with genmake) |
5003 |
|
5004 |
checkpoint20 (1999/03/22) |
5005 |
o Tidied up open-boundaries some more |
5006 |
o Added non-hydrostatic code |
5007 |
o Fixed some input data |
5008 |
o Modified MPI start-up to work in "coupled" context. |
5009 |
|
5010 |
checkpoint19 (1998/12/15) |
5011 |
o Tidied up directory structure for verification experiments. |
5012 |
o Added new code for open boundaries. |
5013 |
o Corrected advective terms near boundaries. |
5014 |
o Added CPP flag for "old UV" geometry and corrected spherical geometry. |
5015 |
o Implemented free-slip/no-slip BCs and del^4 dissipation. |
5016 |
o Split default parameters out of ini_parms.F into set_defaults.F. |
5017 |
|
5018 |
checkpoint18 (1998/11/30) |
5019 |
o Further changes for optional code generation with |
5020 |
CPP - ugh! |
5021 |
|
5022 |
checkpoint17 (1998/11/03) |
5023 |
o Beginning to incorporating modularity |
5024 |
for supporting atmos. and ocean configs. |
5025 |
o Small changes for TAMC complinace |
5026 |
o New ultra simple test case. Barotropic box |
5027 |
configuration "exp0". |
5028 |
|
5029 |
checkpoint16 (1998/10/28) |
5030 |
o Minor changes to exchange routines to support |
5031 |
accumulation in reverse mode. Adjoint of an |
5032 |
assignment is an addition. |
5033 |
o Changes to support compilation by TAMC (LR(1) |
5034 |
syntax) and by g77 under Linux ( 72 character |
5035 |
limit ). |
5036 |
|
5037 |
checkpoint15 (1998/09/29) |
5038 |
Rewrote exchange routines to allow |
5039 |
o General tile <-> tile connectivity. |
5040 |
o TAMC reverse mode flag ( is this really needed? ) |
5041 |
o Variable width overlap and exchange region widths. |
5042 |
o Hooks for sharing data via DMA, Arctic, Memory Channel, |
5043 |
shmput/shmget, VIA, SYSV shmem and every other cool |
5044 |
communication method. |
5045 |
|
5046 |
checkpoint14 (1998/09/09) |
5047 |
Consistent isomorphism chages made. These allow dynamical core |
5048 |
to support both pressure and meters as a vertical coordinate. |
5049 |
|
5050 |
checkpoint13 (1998/07/17) |
5051 |
Release which corrects global_max problem and a couple |
5052 |
of KGM time-averaging diagnostic errors. Also contains |
5053 |
a double-gyre experiment setup as well as the baseline |
5054 |
4 degree global template. The double gyre template is |
5055 |
organised to allow it to be applied automatically to |
5056 |
the baseline configuration. |
5057 |
|
5058 |
branch-point-rdot |
5059 |
A few tidy-ups have been made bt the real point of this |
5060 |
check-point (excuse the pun) is to allow a branch to be |
5061 |
made for the purposes of adding the rDot alterations. |
5062 |
I don't want to commit the rDot to the main-trunk until |
5063 |
we've actually tested it... |
5064 |
|
5065 |
checkpoint12 (1998/07/08) |
5066 |
Tidy up and added generic genmake script (formerly |
5067 |
configure script). |
5068 |
Released to testers. |
5069 |
|
5070 |
checkpoint11 (1998/07/02) |
5071 |
Re-arranged initialise() and introduced ini_vertical_grid() |
5072 |
and ini_masks_etc(). |
5073 |
|
5074 |
checkpoint10 (1998/07/01) |
5075 |
Introduced the configure script. |
5076 |
Separated out the diags package. |
5077 |
Added template for writing time-averages of tile/intermediate quantities. |
5078 |
Updated SIZE.h in exp2 and made the data big-endian. |
5079 |
|
5080 |
checkpoint9 (1998/06/22) |
5081 |
MPI fix. Filename changes (meta/data). salbin*y stuff. |
5082 |
General tidy-up. |
5083 |
SST.bin SSS.bin added to verification/exp2 |
5084 |
|
5085 |
checkpoint8 (1998/06/22) |
5086 |
Inludes time-dependant forcing and time-averaging. |
5087 |
Works at 4x4 and 2.8125x2.8125 global |
5088 |
|
5089 |
checkpoint7-4degree-ref |
5090 |
Branch from checkpoint7. Released for application to |
5091 |
global modeling and general modeling - process studies, regional |
5092 |
model etc.. |
5093 |
Configured for verification/exp2 - 4 degree global, two process. |
5094 |
|
5095 |
checkpoint7 (1998/06/15) |
5096 |
Created by cnh |
5097 |
Simple 4 degree global simulation |
5098 |
configuration. |
5099 |
Includes climatological wind, |
5100 |
hydrography, bathymetry etc |
5101 |
Does not include Heat Flux and E-P |
5102 |
|
5103 |
checkpoint6 (1998/06/08) |
5104 |
Created by cnh |
5105 |
merged checkpoint5 with CD and |
5106 |
spherical polar code. |
5107 |
Still some problems with GM Redi |
5108 |
abd full topography. |
5109 |
|
5110 |
checkpoint5 (1998/06/08) |
5111 |
Created by AJA |
5112 |
contains updates to GM Redi |
5113 |
and reordered timestepping loop |
5114 |
for Implicit Diffusion. |
5115 |
|
5116 |
checkpoint4 (1998/05/30) |
5117 |
Created by cnh |
5118 |
Contains memory saving macros ( _rdxc etc..) for when |
5119 |
grid variations are limited. |
5120 |
Contains polynomial coeffs for EOS and knudsen program |
5121 |
for generation. |
5122 |
|
5123 |
checkpoint3 (1998/05/26) |
5124 |
Created by cnh |
5125 |
Added extra flags for runtime options |
5126 |
Added this file |
5127 |
Added implicit free-surface |
5128 |
Added pre-conditioner |
5129 |
Put compare01 into repository ( compare01/... ) |
5130 |
Put data and eedata into repository ( verification/exp1 ) |
5131 |
|
5132 |
checkpoint2 |
5133 |
Created by AJA |
5134 |
Added GM/Redi |
5135 |
|
5136 |
checkpoint1 |
5137 |
Created by AJA |
5138 |
Restructured kloop in dynamics.F |
5139 |
Added non-linear EOS |
5140 |
|
5141 |
baseline |
5142 |
Original checked in code |