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$Header$ |
$Header$ |
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$Name$ |
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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o pkg obcs: |
| 8 |
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- go through NH code only if nonHydrostatic=T |
| 9 |
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- fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart) |
| 10 |
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o pkg ctrl |
| 11 |
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- make obcs as control parameter work also with useSingleCPUio |
| 12 |
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- replace a few sny and snx by Ny and Nx to be consistent with |
| 13 |
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ctrl_set_globfld_x/yz.F |
| 14 |
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o pkg seaice |
| 15 |
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- re-introduce global field frWtrAtm for the case of |
| 16 |
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ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F) |
| 17 |
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- catch the case of an empty filename in seaice_cost_init_fixed.F |
| 18 |
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o pkg ecco: |
| 19 |
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- small bug fixes in the_main_loop |
| 20 |
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. fix order of monitor arguments |
| 21 |
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. change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY |
| 22 |
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. move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so |
| 23 |
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that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF |
| 24 |
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- replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the |
| 25 |
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imbalance diagnostics for wmean_h/sflux = 0 |
| 26 |
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- add actual values to f_obcsn/s/w/e in ecco_cost_final.F |
| 27 |
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- catch the case of empty filenames in ecco_cost_init_fixed.F |
| 28 |
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and ecco_readparms.F |
| 29 |
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- fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta) |
| 30 |
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to make this statement meaningfull in ecco_cost_weights.F |
| 31 |
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o pkg zonal_filt: |
| 32 |
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- change ZONAL_FILTER S/R interface (allows to filter 2-D fields) |
| 33 |
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- when using rStar, filter uVel*hFacW instead of uVel |
| 34 |
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(tested without topography: fix a Pb of growing instability with NLFS) |
| 35 |
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o pkg/aim/thsice: |
| 36 |
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-Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F |
| 37 |
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(works as SST restoring) |
| 38 |
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o pkg/thsice: |
| 39 |
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-add specific parameter for salt restoring in slab mixed-layer |
| 40 |
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(by default equal to the temperature restoring) |
| 41 |
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|
| 42 |
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checkpoint61v |
| 43 |
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o pkg/kpp: |
| 44 |
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-add double diffusive contributions as a hack, turned off by default |
| 45 |
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for now, and the code can be excluded with a CPP-flag |
| 46 |
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EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX |
| 47 |
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-add a verification experiments to "vermix" to test this code |
| 48 |
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o pkg/mom_common: |
| 49 |
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Move computation of length scales to mom_init_fixed.F (avoid recomputation |
| 50 |
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at each time-steps*levels). |
| 51 |
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o pkg/layers: |
| 52 |
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Created a new package for computing volume fluxes in temperature or |
| 53 |
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[not yet implemented] density layers, e.g. for calculating residual |
| 54 |
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overturning circulations. |
| 55 |
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o pkg/diagnostics: |
| 56 |
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implement a RS type version for the set of DIAGNOSTICS-FILL subroutines |
| 57 |
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o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option) |
| 58 |
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o pkg/mdsio (& pkg/rw): rework high level S/R interface: |
| 59 |
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To avoid mixing type (RS/RL) of input/output array argument, |
| 60 |
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replace single mixed-type array with a pair from each type (RS/RL). |
| 61 |
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o setting pickupSuff force to start from a pickup (even if nIter0=0): this |
| 62 |
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is now implemented for all pkgs (previously only done for the main pickup) |
| 63 |
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|
| 64 |
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checkpoint61u |
| 65 |
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o pkg/obcs: |
| 66 |
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- change OB?eta from _RS to _RL and put them into a separate commen block |
| 67 |
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- add code to read OB?eta from a file via obcs_prescribe_read: the code |
| 68 |
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compiles and does not destroy any other experiments, the data is read |
| 69 |
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properly, but the code is not tested in actual applications |
| 70 |
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o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to |
| 71 |
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create a meaningful unit attribute for the time coordinate variable |
| 72 |
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o pkg/ebm: add plenty of missing "_d 0" ; |
| 73 |
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update results of experiment global_ocean_ebm (fwd + adjoint tests) |
| 74 |
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Notes: several pieces of code only works for (very) specific set up |
| 75 |
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(domain size, lat range, etc ...); should be documented & stop if one |
| 76 |
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of those assumptions is not meet. |
| 77 |
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o pkg/seaice: add missing "_d 0" in HSNOW initialisation |
| 78 |
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update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests) |
| 79 |
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and offline_exf_seaice (seaicetd + adjoint). |
| 80 |
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o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC): |
| 81 |
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update results of experiments: lab_sea (4 fwd tests + 3 adjoint), |
| 82 |
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seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2). |
| 83 |
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o few changes to pass when compiling with strick checking of arguments |
| 84 |
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across S/R (allow to find few bugs in S/R calls). |
| 85 |
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o pkg/seaice: |
| 86 |
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- seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new |
| 87 |
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2d-fields, for slightly better performance |
| 88 |
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|
| 89 |
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checkpoint61t |
| 90 |
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o pkg/seaice: |
| 91 |
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- remove unused variables in seaice_evp |
| 92 |
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- reduce number of SQRT in seaice_evp and seaice_calc_viscosities |
| 93 |
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o eeset_parms.F, open_copy_data_file.F & ini_parms.F: |
| 94 |
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named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT): |
| 95 |
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each processor opens a different file (a fix from Matt). |
| 96 |
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o cg2d: |
| 97 |
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use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F : |
| 98 |
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this reduces number of EXCH calls by 2 when using exch2. |
| 99 |
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For now, keep previous size array for gc2d_nsa.F to avoid Pb with store |
| 100 |
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directives and missing simple EXCH (exch_s3d_rx) adjoint code. |
| 101 |
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o pkg/thsice: |
| 102 |
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add code for Near Infra-Red albedo (from Jeff) |
| 103 |
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(turned on with run-time flag: thSIce_calc_albNIR, in data.ice). |
| 104 |
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o ini_model_io: |
| 105 |
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move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F |
| 106 |
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MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F |
| 107 |
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to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice. |
| 108 |
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|
| 109 |
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checkpoint61s |
| 110 |
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o pkg/exch2 (exch2_rxN_cube*): |
| 111 |
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remove last BARRIER (no need to synchronise after getting data from shared |
| 112 |
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buffer (get) as long as any change to buffer (put,recv) is between BARRIER) |
| 113 |
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o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH |
| 114 |
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and generate new output (for the 2 tests) using default rotationPeriod. |
| 115 |
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o pkg/exch2: |
| 116 |
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- always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F |
| 117 |
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(was already the case with AUTODIFF_EXCH2 defined) |
| 118 |
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- add bj in exch2 arrays and S/R. |
| 119 |
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- can now use pkg/exch2 for regular (non CS) set-up; switch test experiment |
| 120 |
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MLAdjust to exch2 (identical results except with MPI -> truncation diff); |
| 121 |
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o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep |
| 122 |
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- adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY |
| 123 |
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GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT |
| 124 |
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- verification experiment natl_box.longstep |
| 125 |
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o build_options: ifort+mpi_aces optfile (following Constantinos advise): |
| 126 |
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allow different versions of ifort (8 or 9) and different versions |
| 127 |
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of mpi (mpich or mpich2) to be used with the same optfile. |
| 128 |
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requires to load a netcdf module and set MPI_INC_DIR (see comments inside |
| 129 |
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optfile). Change testing scripts (example_scripts/ACESgrid) accordingly. |
| 130 |
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o pkg/seaice: |
| 131 |
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fix previous modif (3-level field removed) for old-pickup reading |
| 132 |
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|
| 133 |
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checkpoint61r |
| 134 |
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o pkg/seaice: |
| 135 |
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- clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps: |
| 136 |
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1. introduce fields for time step (N-1) |
| 137 |
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2. do not use levels 2 and 3 anymore (but keep them) |
| 138 |
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3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This |
| 139 |
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includes changes to pkg/thsice/thsice_get_velocity.F, |
| 140 |
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model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and |
| 141 |
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pkg/obcs/obcs_apply_uvice.F. |
| 142 |
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- completely remove code for leap-frog time stepping for second order |
| 143 |
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advection |
| 144 |
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- adjusted adjoint accordingly; |
| 145 |
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gradient checks have improved by an order of magnitude! |
| 146 |
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|
| 147 |
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checkpoint61q |
| 148 |
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o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver |
| 149 |
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- the boundary conditions along open boundaries are unclear, because the |
| 150 |
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associated masks are set to zero and are thus treated as closed when |
| 151 |
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applying the slip-boundary conditions. |
| 152 |
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- move initialisation of grid variables from seaice_init_varia to _fixed |
| 153 |
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o adding doc/diags_changes.txt |
| 154 |
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o model/src: |
| 155 |
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do_the_model_io: rename few pkg S/R which are called from do_the_model_io, |
| 156 |
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to avoid "_diags" naming if no relation to pkg/diagnostics. |
| 157 |
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ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF |
| 158 |
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file and only call PLOT_FIELD_XYZ if debugMode=T. |
| 159 |
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remove few PLOT_FIELD_XY calls outside initialisation. |
| 160 |
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remove few unnecessary BARRIER. |
| 161 |
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o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling |
| 162 |
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of salt_plume package in Southern Ocean |
| 163 |
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o pkg/thsice: |
| 164 |
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- fix hOceMxL in overlap (needed for sea-ice advection); |
| 165 |
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update output of experiment global_ocean.cs32x15.icedyn. |
| 166 |
|
o pkg/seaice: |
| 167 |
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- make the (placeholder-)tracer IceAge a little more meaningful |
| 168 |
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by avoiding ridging of age due to convergent ice flow |
| 169 |
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- add diagnostics for surface temperature, atmospheric and oceanic |
| 170 |
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heat flux, and atmospheric and oceanic ice growth |
| 171 |
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|
| 172 |
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checkpoint61p |
| 173 |
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o eesupp (global_max & global_sum): |
| 174 |
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- add one more element to buffer (start at index 0) for GL_MAX/SUM output; |
| 175 |
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- remove starting & endding barrier (no longer needed) |
| 176 |
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o pkg/mdsio, writelocal: |
| 177 |
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works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined |
| 178 |
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(remove the STOP): uses shared buffer IO to store data from all threads |
| 179 |
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and then let master-thread write nThreads tiles. |
| 180 |
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o pkg/mdsio (read/write field): |
| 181 |
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- tiled IO done in 1 piece (all levels at a time); |
| 182 |
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- new header file "MDSIO_BUFF_3D.h" with 3-D buffers. |
| 183 |
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- multi-threaded: allow to read/write local (non-shared) array |
| 184 |
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(was already working with singleCpuIO ; now works also without); |
| 185 |
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=> no longer needs barrier call after reading a file (added inside |
| 186 |
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mds_read/write field). |
| 187 |
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- move barrier calls outside gather/scatter_2d to mds_read/write_field |
| 188 |
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o pkg/obcs/exf |
| 189 |
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- exf_getffieldrec.F: add a few ". _d 0" and |
| 190 |
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add code to catch the case fldperiod = 0. |
| 191 |
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- obcs_precribe_read.F: change if statements so that they match |
| 192 |
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the variable type (_RL) |
| 193 |
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- add a separate exf_iprec_obcs to exf_set_obcs (by default equal to |
| 194 |
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exf_iprec) as part of namelist EXF_NML_01 |
| 195 |
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o pkg/mdsio: |
| 196 |
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- read/write tiled (local) files: read/write 1-level tile chunk at a time |
| 197 |
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(instead of segment of length sNx); expected to speed up tiled IO. |
| 198 |
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o pkg/exch2: |
| 199 |
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- take buffer copy from/to array out of S/R exch2_send/recv into new |
| 200 |
|
S/R exch2_put/get ; Exch of local variable now works with MPI+MTH |
| 201 |
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(tested by removing commom block statement in SOLVE_FOR_PRESSURE.h). |
| 202 |
|
- ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get) |
| 203 |
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- simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds |
| 204 |
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(which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by |
| 205 |
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including Topology header file (and common blocks). |
| 206 |
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- implement EXCH_IGNORE_CORNERS in scalar exchange (rx1); |
| 207 |
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remove 2nd exch call in exch2_s3d_rx (no longer needed). |
| 208 |
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- document S/R arg. list (+ update some comments) |
| 209 |
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o pkg/seaice: |
| 210 |
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- added SEAICE_CLIM_AIR code, which permits modulation of surface air |
| 211 |
|
temperature and humidity over sea ice based on climatological values. |
| 212 |
|
- clean up computation of Hibler+Bryan (1987) stress coupling for the case |
| 213 |
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of LSR (this change is expected to change the results slightly because now |
| 214 |
|
it uses slightly difference moduli from the second last LSR solution, but |
| 215 |
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that is more consistent with the stress computations; this part of the code |
| 216 |
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is not tested in the verification experiments) |
| 217 |
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- fix diagnostics for flux of ice in case of B-grid |
| 218 |
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- turn strain rates eij and press into global fields within global |
| 219 |
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common block in SEAICE.h for more straighforward diagnostics |
| 220 |
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- fix diagnostics for principal stress components, press, zeta, eta |
| 221 |
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to give something meaning full |
| 222 |
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o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate |
| 223 |
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new output (all 4 tests) using default rotationPeriod. |
| 224 |
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o pkg KPP: |
| 225 |
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- add flag (LimitHblStable) to avoid limiting BL depth under stable conditions |
| 226 |
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- fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1 |
| 227 |
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and normal grid from 1 to Nr) |
| 228 |
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o Fix computations of L4rdt in mom_calc_visc.F |
| 229 |
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o eesupp: |
| 230 |
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new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg): |
| 231 |
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should be called before a "stop" if we know that all process are going |
| 232 |
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to stop; if one Proc does call this S/R, will hang in MPI_FINALISE. |
| 233 |
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|
| 234 |
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checkpoint61o |
| 235 |
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o pkg/exch2: change check_depths to issue just a warning (instead of error+stop) |
| 236 |
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o model/src/ini_curvilinear_grid.F: |
| 237 |
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compute angleSin/CosC when they are not read from a file |
| 238 |
|
o pkg/seaice: |
| 239 |
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add pseudo time stepping for LSOR |
| 240 |
|
o pkg/exch2: |
| 241 |
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temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW |
| 242 |
|
o pkg/seaice: |
| 243 |
|
Adding separate sea ice albedo, drag coefficients, and HO in Southern |
| 244 |
|
Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h |
| 245 |
|
o SingleCpuIO: |
| 246 |
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fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used. |
| 247 |
|
o pkg/seaice: |
| 248 |
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put exchanged variable in (local) common block for MPI+Multi-Threads |
| 249 |
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to work (necessary with exch1, and for now with exch2 too). |
| 250 |
|
o verification: to get more experiments tested with mpi, mth and mpi+mth, |
| 251 |
|
change tiling of: |
| 252 |
|
aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15, |
| 253 |
|
hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope |
| 254 |
|
update output of exp: |
| 255 |
|
exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5), |
| 256 |
|
tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod) |
| 257 |
|
+ ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU |
| 258 |
|
(note: output.txt generated on faulks using only 1 tile) |
| 259 |
|
o eesupp & mdsio (SingleCpuIO): |
| 260 |
|
- remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time |
| 261 |
|
parameter "W2_useE2ioLayOut" (read from file "data.exch2"). |
| 262 |
|
Note: was not effective for globalFile & useSingleCpuIO=F; now fixed. |
| 263 |
|
- move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc). |
| 264 |
|
- fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same |
| 265 |
|
gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array). |
| 266 |
|
o pkg/exch2: |
| 267 |
|
- new code to set-up W2-Exch2 topology (replace matlab-topology-generator): |
| 268 |
|
read parameter file "data.exch2" if it exists; otherwise try default regular |
| 269 |
|
cube without blank-tile; new header file "W2_EXCH2_SIZE.h"; |
| 270 |
|
- update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible |
| 271 |
|
with new code (not to be used, just as a backup solution). |
| 272 |
|
- add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2" |
| 273 |
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in utils/exch2/input. |
| 274 |
|
|
| 275 |
|
checkpoint61n |
| 276 |
|
o eesupp & mdsio (SingleCpuIO): |
| 277 |
|
- move mapping to global io-buffer inside gather_2d/scater_2d: this save |
| 278 |
|
memory (1 less 2D global RL array); skip 1 buffer copy; and only send/ |
| 279 |
|
receive real*4 array (instead of real*8) to read/write 32.bit files. |
| 280 |
|
(new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S |
| 281 |
|
and remove new mapping S/R) |
| 282 |
|
o pkg/mdsio: in preparation for topology-generator within pkg/exch2: |
| 283 |
|
- Change declaration of SingleCpuIO buffer, reduced to only 1 dim.: |
| 284 |
|
xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h |
| 285 |
|
when using exch2. Add S/R to map global io-buffer to global model array. |
| 286 |
|
- uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt. |
| 287 |
|
|
| 288 |
|
checkpoint61m |
| 289 |
|
o write_utils : change WRITE_1D_R8 to WRITE_1D_RL |
| 290 |
|
and add 3 other S/R for other types (R4,R8,RS). |
| 291 |
|
Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument. |
| 292 |
|
o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros): |
| 293 |
|
- ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ; |
| 294 |
|
- reduce number of macro definitions (keep only those which are used); |
| 295 |
|
can always call directly the corrresponding S/R if needed. |
| 296 |
|
- everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix |
| 297 |
|
_R4/_R8 to _RS/_RL when applied to _RS/_RL variable. |
| 298 |
|
Fixed wrong type of arg in: |
| 299 |
|
atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F |
| 300 |
|
ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F |
| 301 |
|
To fix: global_sum of var in common block is wrong (multi-threaded) in: |
| 302 |
|
dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F |
| 303 |
|
To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops) |
| 304 |
|
o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd |
| 305 |
|
"nlfs" mpi test is going to stop when checking for unconnected tile egdes. |
| 306 |
|
o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error |
| 307 |
|
o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile |
| 308 |
|
edges are closed (zero depth); might happen with "blank tiles"; |
| 309 |
|
for now, disabled if using OBCS. |
| 310 |
|
o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi": |
| 311 |
|
link *_mpi files from "MODS" dir) to return to a strait-forward behavior. |
| 312 |
|
o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D) |
| 313 |
|
to reduce length of 1.D array print in STDOUT. |
| 314 |
|
o adjustment.cs-32x32x1: changed to oceanic test with 1 continent |
| 315 |
|
+ use 48 tiles (16x8): this will allow to test "blank tiles". |
| 316 |
|
o start to test MPI + multi-threaded (change testreport to skip tests |
| 317 |
|
where number of tiles do not match). |
| 318 |
|
o genmake2: add option "-omp" to turn on Open-MP ; |
| 319 |
|
passed to testreport (if using -mth) ; merge few (*+mth) optfiles. |
| 320 |
|
o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them) |
| 321 |
|
and keep the original tile numbering. Note: compatible with old |
| 322 |
|
W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files. |
| 323 |
|
|
| 324 |
|
checkpoint61l |
| 325 |
|
o Overlaps had been forgotten in calculating ijk keys : fixed |
| 326 |
|
o fix cyrus makedepend for gcc 4.4 |
| 327 |
|
o experiment fizhi-cs-aqualev20: |
| 328 |
|
switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE) |
| 329 |
|
and generate new output. Note: new output is much closer to the old |
| 330 |
|
one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from |
| 331 |
|
the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007. |
| 332 |
|
o pkg/fizhi: |
| 333 |
|
- change to avoid indices going deliberately over array-bounds |
| 334 |
|
- remove unnecessary MPI stuff |
| 335 |
|
- perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY" |
| 336 |
|
- new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE: |
| 337 |
|
does not go over array-bounds and therefore returns reliable output. |
| 338 |
|
- in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls: |
| 339 |
|
this S/R has 4 output arguments, which are used inside "get_alarm"; |
| 340 |
|
when it is called with the same variable "ndum" in place of several |
| 341 |
|
output arguments, this produces weird side effect inside "get_alarm" |
| 342 |
|
(e.g., datein=dates(n) is overwritten by timein=times(n) since both |
| 343 |
|
datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum" |
| 344 |
|
address) and produces error. |
| 345 |
|
o tools/gemake2: (March 27-29 2009) |
| 346 |
|
with option "-mpi": link *_mpi files from "MODS" dir (this is what |
| 347 |
|
testreport does). |
| 348 |
|
o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output |
| 349 |
|
o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F: |
| 350 |
|
update lab_sea.lsr & lab_sea.salt_plume results |
| 351 |
|
o pkg/seaice: |
| 352 |
|
Major overhaul of the LSOR solver: change discretization from original |
| 353 |
|
finite differences to finite volume. The old routine is still in the |
| 354 |
|
file seaice_lsr.F and can be turned on with the CPP-flag |
| 355 |
|
SEAICE_OLD_AND_BAD_DISCRETIZATION |
| 356 |
|
Along with this change, the discretization of the strain rates is changed. |
| 357 |
|
The same flag turns on the old discretization in seaice_calc_strainrates.F |
| 358 |
|
All verification experiments with seaice are affected (except for |
| 359 |
|
seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old |
| 360 |
|
results by setting the above flag. |
| 361 |
|
Further changes involve changes in defaults: |
| 362 |
|
- ALLOW_FLOODING is defined and turned on by default |
| 363 |
|
- SEAICEadvSnow = .true. is now the default |
| 364 |
|
- SEAICEadvSalt = .true. is now the default |
| 365 |
|
- SEAICEadvAge = .true. is now the default |
| 366 |
|
- SEAICE_clipVelocities = .false. is now the default |
| 367 |
|
(as per J. Zhang's recommendation) |
| 368 |
|
- B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE |
| 369 |
|
is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS |
| 370 |
|
- seaice_growth: replace computation of UG by a simple copy from wspeed |
| 371 |
|
|
| 372 |
|
checkpoint61k |
| 373 |
|
o pkg/seaice: a few bug fixes mostly concerning the metric terms: |
| 374 |
|
seaice_lsr: fixed a few metric terms, |
| 375 |
|
affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs |
| 376 |
|
add more debugging diagnostics |
| 377 |
|
seaice_evp: removed superfluous many metric terms of FV discretization |
| 378 |
|
of stress divergence |
| 379 |
|
affects lab_sea, lab_sea.hb87 |
| 380 |
|
seaice_ocean_stress: removed superfluous many metric terms of FV discretization |
| 381 |
|
of stress divergence for non-evp solver |
| 382 |
|
(this part is not tested anywhere) |
| 383 |
|
seaice_calc_strainrates: fixed a bug in no-slip boundary conditions, |
| 384 |
|
they were effectively only half slip |
| 385 |
|
affects lab_sea.hb87 |
| 386 |
|
updated all relevant verification experiments (except lab_sea//output_adm.txt |
| 387 |
|
which was left over, but fails at level 7 & 6) |
| 388 |
|
|
| 389 |
|
checkpoint61j |
| 390 |
|
o pkg/seaice: turn a few hard wired parameters into run time parameters |
| 391 |
|
o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model |
| 392 |
|
time in seconds as promised by the usints in seaice_monitor and exf_monitor |
| 393 |
|
o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids |
| 394 |
|
that are not cubed-sphere grids |
| 395 |
|
o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR |
| 396 |
|
o pkg/ctrl: |
| 397 |
|
fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low) |
| 398 |
|
o non-hydrostatic (calc_gw.F): |
| 399 |
|
fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec |
| 400 |
|
update output of exp. global_ocean.cs32x15.viscA4 |
| 401 |
|
o remove backward compatibility for thetaMin,phiMin |
| 402 |
|
(replaced by xgOrigin,ygOrigin on Jan 27, 2009) |
| 403 |
|
o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the |
| 404 |
|
interpolated wind field not only for curvilineargrid=.true., but also |
| 405 |
|
for a rotated grid (rotateGrid=.true.) |
| 406 |
|
o pkg/exf: add capability to bypass interpolation for runoff |
| 407 |
|
by setting yet another CPP-flag |
| 408 |
|
o eesupp/src, B-grid exchange: |
| 409 |
|
add simple (6 tiles, non MPI) CS exch + standard interface S/R. |
| 410 |
|
o autodiff |
| 411 |
|
new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV |
| 412 |
|
allows to switch to single-prec common blocks; |
| 413 |
|
corresponding switch occurs in tamc.h, integer isbyte |
| 414 |
|
TAF store directivs "byte" and "kind" seem equivalent; |
| 415 |
|
Most tamc.h have been updated correspondingly. |
| 416 |
|
|
| 417 |
|
checkpoint61i |
| 418 |
|
o autodiff: |
| 419 |
|
fix autodiff_sore/_restore indices for obcs |
| 420 |
|
(spotted by I. Hoteit, M. Mazloff) |
| 421 |
|
o pkg/autodiff, pkg/ctrl: |
| 422 |
|
Add flag to reduce all tapelev I/O to single-prec. |
| 423 |
|
In data.ctrl set |
| 424 |
|
doSinglePrecTapelev = .TRUE. |
| 425 |
|
o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2: |
| 426 |
|
check in hack for SX8 compiler (for dxV, dyU); remove it afterwards. |
| 427 |
|
o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for |
| 428 |
|
real fresh water flux (not yet) |
| 429 |
|
o pkg/mdsio & rw: |
| 430 |
|
- add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta) |
| 431 |
|
- add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX. |
| 432 |
|
o pkg/flt: |
| 433 |
|
- replace FLT_INIT by 3-steps standard initialization S/R: readparms, |
| 434 |
|
init_fixed & ini_varia. |
| 435 |
|
- clean-up & simplify linear interpolation S/R: |
| 436 |
|
move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid. |
| 437 |
|
- fix some indices (mainly vertical index) ; add IMPLICIT NONE. |
| 438 |
|
- more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R. |
| 439 |
|
- add vert. coordinate & horiz. indices to output files. |
| 440 |
|
- change vertical position in initial condition, from index to depth [m]. |
| 441 |
|
- store horizontal (decimal) indices i,j in common block (instead of coord. x,y) |
| 442 |
|
(easier to get to a curvilinear grid) ; delX,delY no longer used. |
| 443 |
|
o pkg/ggl90: a few modifications: |
| 444 |
|
- fix bottom boundary condition, and interpolation of KappaE |
| 445 |
|
near top and bottom |
| 446 |
|
- use same set of viscosity/diffusivity for TKE/momnetum/tracer |
| 447 |
|
- add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH) |
| 448 |
|
- add a few options for mixing-length upper limit (--> mxlMaxFlag) |
| 449 |
|
o rename thetaMin,phiMin -> xgOrigin,ygOrigin |
| 450 |
|
(maintain temporary backward compatibility, until next checkpoint) |
| 451 |
|
|
| 452 |
|
checkpoint61h |
| 453 |
|
o pkg/diagnostics with "periodic averaging diagnostics": |
| 454 |
|
fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. |
| 455 |
|
o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82 |
| 456 |
|
o pkg/obcs: fix loop ranges for balancing code |
| 457 |
|
o pkg/flt: |
| 458 |
|
- improve criteria for finding which tile owns a float. |
| 459 |
|
- fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case. |
| 460 |
|
o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg |
| 461 |
|
aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling |
| 462 |
|
with ocean biogeo) |
| 463 |
|
o pkg/flt: |
| 464 |
|
- do some cleaning and fix the restart ; |
| 465 |
|
- add output.txt in flt_example/results to get this pkg tested. |
| 466 |
|
o genmake2: add an EXTENDED_SRC option and flag. |
| 467 |
|
for now, cannot be turned on on command line (only through genmake_local) |
| 468 |
|
o pkg/mdsio: read/write vector: |
| 469 |
|
- singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS |
| 470 |
|
- singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR |
| 471 |
|
& MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. |
| 472 |
|
- affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) |
| 473 |
|
(drop to 4 digits matching for grad). But this test does not look very |
| 474 |
|
reliable (was already failling on eddy, fc5, at 6.digits). Update output. |
| 475 |
|
|
| 476 |
|
checkpoint61g |
| 477 |
|
o pkg/flt: |
| 478 |
|
- move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) |
| 479 |
|
+ make OPTIONS file more standard. |
| 480 |
|
- rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) |
| 481 |
|
- fix _BYTESWAPIO CPP-Flag |
| 482 |
|
- standard reading of file-parameter "data.flt" |
| 483 |
|
- fix argument list of S/R FLT_RESTART |
| 484 |
|
still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F |
| 485 |
|
o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell |
| 486 |
|
o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to |
| 487 |
|
a still unfixed compiler/optimization bug |
| 488 |
|
|
| 489 |
|
checkpoint61f |
| 490 |
|
o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; |
| 491 |
|
update results of global_ocean.cs32x15.icedyn test. |
| 492 |
|
o move getcon.F from model/src to pkg/fizhi. |
| 493 |
|
o pkg/exf: add parameter for extrapolation of temp up to the surface |
| 494 |
|
and option to prevent negative evap (in bulk_largeyeager04 only). |
| 495 |
|
o Prather Advection scheme: fix tracer conservation for divergent flow |
| 496 |
|
(e.g., when using NonLin Free-Surface). |
| 497 |
|
o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead |
| 498 |
|
o gmredi (Visbeck-variable-K): |
| 499 |
|
- add more parameters to Visbeck-variable-K. |
| 500 |
|
- use a 5 points average for dSigmaR in Visbeck-K calculation |
| 501 |
|
(more "homogenous": same stencil and same weights as in dSigmaH) |
| 502 |
|
- update output of ideal_2D_oce experiment. |
| 503 |
|
o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 |
| 504 |
|
(#undef REAL4_IS_SLOW) |
| 505 |
|
- pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 |
| 506 |
|
coordinate variable |
| 507 |
|
- pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables |
| 508 |
|
(surface forcing fields), removes some of the functionality |
| 509 |
|
- model/src/write_grid.F: write _RS variables as RS-netcdf variables |
| 510 |
|
- model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but |
| 511 |
|
probably not all: copy _RS surface flux fields to RL field before |
| 512 |
|
calling DIAGNOSTICS_FILL |
| 513 |
|
- model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into |
| 514 |
|
real*4 (CALL EXCH_*_RS) versions. |
| 515 |
|
- tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 |
| 516 |
|
(generate new output). |
| 517 |
|
|
| 518 |
|
checkpoint61e |
| 519 |
|
o gmredi (Visbeck-variable-K): |
| 520 |
|
- fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h |
| 521 |
|
- change computation of Visbeck-K where Slope > Smax : |
| 522 |
|
now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct) |
| 523 |
|
previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output. |
| 524 |
|
o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic |
| 525 |
|
to be the same as with Z-coord. (i.e., m/s & no-units respectively). |
| 526 |
|
o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc) |
| 527 |
|
o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz |
| 528 |
|
does not become too large (to avoid precision problems in implicit-diffusion |
| 529 |
|
solver); update ideal_2D_oce output. |
| 530 |
|
o pkg ggl90: |
| 531 |
|
- in ggl90_cal.F: compute only one set of visc/diff, used to |
| 532 |
|
step forward TKE/T/S/momentum |
| 533 |
|
- default value of GGL90viscMax/GGL90diffMax larger and equal (to |
| 534 |
|
have Prandlt =1) |
| 535 |
|
o gmredi (fm07): |
| 536 |
|
- add lower limit on Transition layer thickness + lower limit on 1/lambda |
| 537 |
|
- allow to set few more params from data.gmredi |
| 538 |
|
o pkg ggl90: |
| 539 |
|
- add missing sqrt(2) factor in computation of mixing length |
| 540 |
|
scale in ggl90_calc.F |
| 541 |
|
(see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) |
| 542 |
|
|
| 543 |
|
checkpoint61d |
| 544 |
|
o adjoint modifs |
| 545 |
|
- adapt to new field rhoInSitu |
| 546 |
|
- allow to revert from StoreDynVars2D, StoreDynVars3D |
| 547 |
|
to individual fields |
| 548 |
|
(switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) |
| 549 |
|
o store 3-D (in-situ) density in commom block (DYNVARS.h) |
| 550 |
|
- save 1 rho computation. |
| 551 |
|
- no longer modify T & S inland when using down_slope pkg. |
| 552 |
|
o gad_som : allow to switch to SOM advection for T & S without corresponding |
| 553 |
|
pickup files (using new S/R: MDS_CHECK4FILE). |
| 554 |
|
o keep removing _BEGIN/_END_MASTER between MDSIO S/R call |
| 555 |
|
(for useSingleCpuIO to work in multi-threaded) |
| 556 |
|
o pkg/shelfice: |
| 557 |
|
- disentangle parameters: retire shelfIceFile in data/PARM05 and substitute |
| 558 |
|
with SHELFICEtopoFile in data.shelfice |
| 559 |
|
- move code for reading ice shelf topography and modifying hFacC into separate |
| 560 |
|
subroutines of the shelfice package |
| 561 |
|
- separate initialisation of "fixed" and "variable" variables |
| 562 |
|
- kTopC is not (yet) replaced by kSurfC, although this is possible |
| 563 |
|
o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
| 564 |
|
o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
| 565 |
|
and rename: |
| 566 |
|
ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
| 567 |
|
ini_reference_state.F --> load_ref_files.F (- set anelastic factors) |
| 568 |
|
o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) |
| 569 |
|
|
| 570 |
|
checkpoint61c |
| 571 |
|
o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" |
| 572 |
|
to add mass source/sink of fluid in the interior (3-D generalisation |
| 573 |
|
of oceanic real-fresh water flux). |
| 574 |
|
o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) |
| 575 |
|
o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) |
| 576 |
|
o new pkg: down_slope |
| 577 |
|
density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). |
| 578 |
|
- presently, modify T & S inland (dwnslp_calc_rho.F). |
| 579 |
|
can be avoided if rho was stored in common bloc and used in calc_phi_hyd. |
| 580 |
|
- implementation for ocean in P-coords not tested. |
| 581 |
|
- add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. |
| 582 |
|
o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) |
| 583 |
|
(to facilitate conversion of oceanic pkg to p-coordinate). |
| 584 |
|
o change FIND_RHO to FIND_RHO_2D : |
| 585 |
|
pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. |
| 586 |
|
o new pkg: cheapaml |
| 587 |
|
|
| 588 |
|
checkpoint61b |
| 589 |
|
o exch2: |
| 590 |
|
change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) |
| 591 |
|
- no longer depend on the order sequence (N,S,E,W). |
| 592 |
|
- 3rd exchange no longer needed (tested with 24 tiles). |
| 593 |
|
- same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) |
| 594 |
|
- exch_UV_A-grid readily available (but not yet tested). |
| 595 |
|
comment out 3rd exch call and remove copy of V to U at SE & NE face-corners |
| 596 |
|
(both are no longer needed) in exch_uv: no effect in forward run; but |
| 597 |
|
get truncation error differences with adjoint exch. |
| 598 |
|
o exch2: |
| 599 |
|
- change index-bounds storage (moved from target to local tile, |
| 600 |
|
more intuitive this way) ; rename/remove some variables. |
| 601 |
|
- change utils/exch2/matlab-topology-generator & code_mods accordingly. |
| 602 |
|
|
| 603 |
|
checkpoint61a |
| 604 |
|
o exch2/matlab-topology-generator: |
| 605 |
|
fix bug in index bounds for N-S internal exchange (hard to tell if this |
| 606 |
|
had any effect on the solution). |
| 607 |
|
o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf |
| 608 |
|
is exceeded |
| 609 |
|
o testreport: modify syntax of awk, so that it works also with |
| 610 |
|
awk, and not only with nawk and gawk |
| 611 |
|
|
| 612 |
|
checkpoint61 |
| 613 |
|
o autodiff |
| 614 |
|
Change default for TAF usage by removing argument '-nonew_arg' |
| 615 |
|
This changes TAF subroutine argument list (ordering of active var.) |
| 616 |
|
Omission of this flag leads to incompatibility w.r.t. TAMC |
| 617 |
|
To restore TAMC-compatibility, need following modifs: |
| 618 |
|
* use adoptfile tools/adjoint_options/adjoint_tamc_compatibility |
| 619 |
|
* use CPP option #define AUTODIFF_TAMC_COMPATIBILITY |
| 620 |
|
Tested TAF version is 1.9.22 |
| 621 |
|
N.B.: exch2 hand-written adjoint code currently not TAMC compatible |
| 622 |
|
|
| 623 |
|
checkpoint60 |
| 624 |
|
--->>> This is the last checkpoint for which generating the adjoint |
| 625 |
|
--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" |
| 626 |
|
--->>> by default. |
| 627 |
|
--->>> Future checkpoints will ommit this flag by default. |
| 628 |
|
o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. |
| 629 |
|
o pkg/grdchk: Add gradient check to etan0 perturbations. |
| 630 |
|
o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). |
| 631 |
|
o pkg/autodiff: more flexibility in zeroadj. |
| 632 |
|
model/src: modifying do_oceanic_phys.F accordingly. |
| 633 |
|
o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. |
| 634 |
|
o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option |
| 635 |
|
special setup of gmredi for which the adjoint is stable |
| 636 |
|
enough for parameter optimization. |
| 637 |
|
o bridging the gap between eddy stress and GM. |
| 638 |
|
-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) |
| 639 |
|
along with a change in CPP option (now ALLOW_EDDYPSI). |
| 640 |
|
-> when using GM w/ GM_AdvForm: |
| 641 |
|
The total eddy streamfunction (Psi = eddyPsi + K x Slope) |
| 642 |
|
is applied either in the tracer Eq. or in momentum Eq. |
| 643 |
|
depending on data.gmredi (intro. GM_InMomAsStress). |
| 644 |
|
-> ALLOW_EDDYPSI_CONTROL for estimation purpose. |
| 645 |
|
The key modifications are in model/src/taueddy_external_forcing.F |
| 646 |
|
pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F |
| 647 |
|
|
| 648 |
|
checkpoint59r |
| 649 |
|
o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array |
| 650 |
|
from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); |
| 651 |
|
fix option to read coriolis(@ cell-corner) from files with CS-grid. |
| 652 |
|
o pkg/mnc: add some attributes to standard 1D-coordinate variables |
| 653 |
|
o pkg/diagnostics: enforce missing_value attribute for scalar variables at |
| 654 |
|
mass points, when using mnc for output |
| 655 |
|
- add runtime parameter (missing_value, missing_value_int) to override |
| 656 |
|
default (which is the value of getcon('UNDEF')) |
| 657 |
|
o pkg/mnc: prepare mnc for the actual use of missing values with the |
| 658 |
|
diagnostics package: small fix in mnc_cw_readwrite.template and more |
| 659 |
|
initialisation of never used fields |
| 660 |
|
- replace mnc_common.h and mnc_id_header.h with corresponding upper case |
| 661 |
|
versions |
| 662 |
|
o pkg/thsice/thsice_ini_vars.F added default initial values so that |
| 663 |
|
thermodynamics sea ice solver does not blow up when some initial fields |
| 664 |
|
are missing. |
| 665 |
|
o move from external_forcing_surf.F to ini_forcing.F |
| 666 |
|
the p-coord. hack consisting in using pLoad to set phi0surf ; |
| 667 |
|
update output of tutorial_global_oce_in_p (affected @ truncation level). |
| 668 |
|
o Freshen up a bit hs94.1x64x5, notably: |
| 669 |
|
remove rotationPeriod and tRef=5*0. (adjoint only), and add |
| 670 |
|
exactConserv=.TRUE. |
| 671 |
|
o pkg/generic_advdiff: |
| 672 |
|
change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
| 673 |
|
applies to files where Temperature & Salinity 2nd Order moments are used. |
| 674 |
|
o pkg/ptracers: add second-order moment advection schemes (80 and 81); |
| 675 |
|
this uses a dynamically allocated internal state data structure |
| 676 |
|
(#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) |
| 677 |
|
and requires a fortran 90 compiler |
| 678 |
|
|
| 679 |
|
checkpoint59q |
| 680 |
|
o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) |
| 681 |
|
(from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) |
| 682 |
|
o Refresh tutorial_global_oce_biogeo, notably: |
| 683 |
|
- change bathymetry (put back seamounts in ACC, use hFacs) |
| 684 |
|
- change EOS (POLY3 --> JMD95Z) |
| 685 |
|
- use Bryan-Lewis vertical diffusivity |
| 686 |
|
- use multidimensional advection |
| 687 |
|
- remove old virtual virtual in dic pkg, now done through ptracer pkg |
| 688 |
|
- change a couple of parameters in dic pkg |
| 689 |
|
o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F |
| 690 |
|
o pkg/obcs: change default to OBCSfixTopo = .true., |
| 691 |
|
- set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result |
| 692 |
|
- replace "debugMode" with "debugLevel .GE. debLevB" |
| 693 |
|
o implementation of TAF directives for gchem,cfc,dic |
| 694 |
|
o remove "exp5" (replaced by tutorial_deep_convection). |
| 695 |
|
o pkg/obcs: add code to fix topography gradients normal to open boundaries; |
| 696 |
|
this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; |
| 697 |
|
the code can be turned on by setting OBCSfixTopo = .true. in data.obcs |
| 698 |
|
--> changes results in exp4, seaice_obcs |
| 699 |
|
o tutorial_deep_convection : |
| 700 |
|
update the set-up and increase resolution and domain size ; start |
| 701 |
|
from pseudo initial conditions = output at t=120mn in order to see |
| 702 |
|
something happening when running testreport. |
| 703 |
|
o pkg/seaice: add os7mp as an advection scheme |
| 704 |
|
add check for advection schemes |
| 705 |
|
add a flag for restoring T and S underneath sea ice |
| 706 |
|
o pkg/my82: add netcdf-support and diagnostics |
| 707 |
|
o thsice pkg: |
| 708 |
|
- Now hsMax limits snow height by turning it into ice following |
| 709 |
|
flooding scheme (and now conserving energy) |
| 710 |
|
- Slight rewriting of the formula in thsice_calc_thick.F |
| 711 |
|
- Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos |
| 712 |
|
--> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice |
| 713 |
|
|
| 714 |
|
checkpoint59p |
| 715 |
|
o gchem / dic / cfc : |
| 716 |
|
- add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); |
| 717 |
|
- add new parameter files: "data.dic" & "data.cfc" ; |
| 718 |
|
- various re-arrangement in initialisation & header file ; |
| 719 |
|
- fix tutorial_global_oce_biogeo for multi-threaded test. |
| 720 |
|
o pkg/dic: test for "pickup_dic" file when restarting ; |
| 721 |
|
if no pickup-file, can restart with a re-initialised pH (same as it did |
| 722 |
|
before) providing pickupStrictlyMatch is set to False. |
| 723 |
|
o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP |
| 724 |
|
+ fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP |
| 725 |
|
o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2 |
| 726 |
|
and staggerTimeStep is off (needed for stability of Internal-wave dynamics). |
| 727 |
|
o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax, |
| 728 |
|
& lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers |
| 729 |
|
(note: not clear to me what lambdaTr1ClimRelax is still used for ...) |
| 730 |
|
o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which |
| 731 |
|
scheme to use for vorticty-term ; |
| 732 |
|
- compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F |
| 733 |
|
(with default selectVortScheme, return to original discretisation) |
| 734 |
|
- remove weird combination (e.g.: upwindVorticity & highOrderVorticity) |
| 735 |
|
o pkg/seaice: add a line to the summary to indicate grid type (B/C) |
| 736 |
|
o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the |
| 737 |
|
bottom ; only used with variable horizontal viscosity and non-hydrostatic. |
| 738 |
|
also fix diagnostics VISCAHW & VISCA4W. |
| 739 |
|
|
| 740 |
|
checkpoint59o |
| 741 |
|
o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). |
| 742 |
|
o change the loop ordering in most gad_*_adv_x.F to improve vectorization: |
| 743 |
|
move a few statemens out the main loop into separate loops |
| 744 |
|
o pkg/shelfice: |
| 745 |
|
- sort out freshwater flux; convert freshwater fluxes to mass fluxes |
| 746 |
|
(kg/m^2/s), does not break tests, because in verification/isomip, |
| 747 |
|
rhoConstFresh=rhoConst (by accident) |
| 748 |
|
- rearrange computation of tLoc, sLoc, pLoc to make code more efficient |
| 749 |
|
- move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into |
| 750 |
|
new file model/src/seawater.F, so that they are available for all pkgs. |
| 751 |
|
- convert potential temperature into in-situ temperature. This changes the |
| 752 |
|
isomip tests => update tests |
| 753 |
|
o add a flag writePickupAtEnd (default=true) to be able to suppress |
| 754 |
|
writing a pickup at the last timestep |
| 755 |
|
o tools/mpack-1.6 : |
| 756 |
|
- disable automake (not working) and autoconf (not needed). |
| 757 |
|
- update to version 1.6.4 which fix MD5 code on some 64 bits platforms |
| 758 |
|
also cleaner with much less compilation warnings. |
| 759 |
|
o pkg/profiles: |
| 760 |
|
rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg |
| 761 |
|
(for "less than 32 characters name" compiler requirement) |
| 762 |
|
o pkg/obcs and pkg/exf: added capability to specify seaice open boundary |
| 763 |
|
conditions that have a different sampling frequency than S/T/U/V obcs |
| 764 |
|
o pkg/diagnostics (stats-diags): |
| 765 |
|
- fix global Min/Max in case 1 processor get only empty tiles |
| 766 |
|
o genmake2: replace (4 times) |
| 767 |
|
make genmake_tc_1.o >> genmake_warnings 2>&1 |
| 768 |
|
with |
| 769 |
|
COMM="$CC $CFLAGS -c genmake_tc_1.c" |
| 770 |
|
echo $COMM >> genmake_warnings |
| 771 |
|
$COMM >> genmake_warnings 2>&1 |
| 772 |
|
to make genmake2 always see the value of CC as specified in the optfile. |
| 773 |
|
o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid. |
| 774 |
|
- add diagnostics for 1srt & 2nd Order moments and sub-grid variance. |
| 775 |
|
- modify verification advect_cs test to test SOM-advection on CS-grid. |
| 776 |
|
o pkg/ctrl: |
| 777 |
|
- Rewrite of ctrl_map_ini_ecco.F, |
| 778 |
|
introducing a generic routine (ctrl_map_ini_gen.F). |
| 779 |
|
- Modification of ctrl_bound/adctrl_bound handling control vector bounds. |
| 780 |
|
|
| 781 |
|
checkpoint59n |
| 782 |
|
o pkg/diagnostics: for large number of diagnostics, store diagnostic mate |
| 783 |
|
number in dedicate array "hdiag": |
| 784 |
|
- new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST |
| 785 |
|
with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST. |
| 786 |
|
- many small changes (integer format) for large number of diagnostics |
| 787 |
|
- start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with |
| 788 |
|
a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23. |
| 789 |
|
o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For |
| 790 |
|
usingSphericalGrid, this allows to define the rotated grid coordinates |
| 791 |
|
via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the |
| 792 |
|
geographical coordinates according to the inverse of the rotation defined |
| 793 |
|
by the Euler angles, so that Coriolis parameter and online-interpolation by |
| 794 |
|
exf works with the geographical coordinates on XC/YC/XG/YG. |
| 795 |
|
Naturally, this feature does not work with all packages, so some |
| 796 |
|
combinations are prohibited in config_summary (flt, flt_zonal, ecco, |
| 797 |
|
profiles), because there the coordinates are assumed to be regular |
| 798 |
|
spherical grid coordinates. |
| 799 |
|
o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc: |
| 800 |
|
- introduce isopycnal diffusion coefficient control. |
| 801 |
|
o tools/adjoint_options: |
| 802 |
|
- additional control vector components. |
| 803 |
|
o pkg/mnc: have mnc create marginally meaning full coordinate variables |
| 804 |
|
(that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 |
| 805 |
|
o pkg/mypackage: |
| 806 |
|
- add example of read/write pickup for state-var ; |
| 807 |
|
- add entry points to the main code for state-vars diags & write-pickup. |
| 808 |
|
o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year |
| 809 |
|
transitions for useExfYearlyFields |
| 810 |
|
- add new subroutine that determines the file to read from for |
| 811 |
|
use*YearlyFields = .TRUE. and .FALSE. |
| 812 |
|
- add a verification experiment to global_with_exf that tests |
| 813 |
|
useExfYearlyFields with USE_EXF_INTERPOLATION defined |
| 814 |
|
o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in |
| 815 |
|
analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new |
| 816 |
|
subroutines (which could be generated from a template, because they are |
| 817 |
|
almost identical), for now they are included in obcs_prescribe_read.F for |
| 818 |
|
simplicity |
| 819 |
|
o pkg/exf: |
| 820 |
|
- add a little more diagnostic to exf_interp_read (in analogy to |
| 821 |
|
mds_read_field, can be turned off with debugLevel < debugLevA=1) |
| 822 |
|
- improve vectorizability of exf_interp for TARGET_NEC_SX, makes code |
| 823 |
|
ugly but fast by unrolling short inner loops, inserting a unroll=8 |
| 824 |
|
directive in routine lagran, and splitting a loop and making do while the |
| 825 |
|
outermost loop (the latter requires the intoduction of index arrays) |
| 826 |
|
o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice |
| 827 |
|
o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver |
| 828 |
|
http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html |
| 829 |
|
o verification/seaice_obcs: updated for restart test and latest options |
| 830 |
|
o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different |
| 831 |
|
ice rheology (so-called truncated ellipse, that gets rid of tensile stress); |
| 832 |
|
for now this is only available for the C-grid code and also within |
| 833 |
|
#ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code |
| 834 |
|
|
| 835 |
|
checkpoint59m |
| 836 |
|
o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) |
| 837 |
|
and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature |
| 838 |
|
o gad_som : fix flux output (& diagnostics) to have same units as other |
| 839 |
|
advection scheme fluxes (was previously multiplied by deltaT). |
| 840 |
|
o added verification/seaice_obcs both to test seaice open boundaries |
| 841 |
|
and to provide an example matlab scrpt for generating them |
| 842 |
|
o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume |
| 843 |
|
o pkg/salt_plume: clean up salt_plume_frac.F to |
| 844 |
|
remove redundancy in PlumeMethod 1 and 4 |
| 845 |
|
o pkg/kpp: added saltplume diagnostics |
| 846 |
|
o pkg/obcs and pkg/seaice: |
| 847 |
|
- do not set uice and vice to zero when OB*icefile are unspecified |
| 848 |
|
- OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default |
| 849 |
|
- moved seaice tracer obcs after call to seaice_growth |
| 850 |
|
o pkg/salt_plume: added various options for salt plume depth |
| 851 |
|
criterion and for vertical distribution of the salt |
| 852 |
|
|
| 853 |
|
checkpoint59l |
| 854 |
|
o pkg/ptracers: new version of ptracers pickup: |
| 855 |
|
read meta file and write only fields which are needed to restart. |
| 856 |
|
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
| 857 |
|
o pkg/seaice: |
| 858 |
|
- add timescale for melting due to warm mixed layer as a means of |
| 859 |
|
setting SEAICE_availHeatFrac more conveniently |
| 860 |
|
- add a CPP-flag/runtime parameter check for flooding algorithm |
| 861 |
|
- reformulated availHeat in seaice_growth.F to be independent of AREA |
| 862 |
|
o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent |
| 863 |
|
unit changes |
| 864 |
|
o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint |
| 865 |
|
o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC |
| 866 |
|
SX vector computer. |
| 867 |
|
o pkg/seaice: |
| 868 |
|
- removed SEAICE_FFIELDS.h and seaice_get_forcing.F |
| 869 |
|
seaice forcing fields can now be read only through pkg/exf |
| 870 |
|
- removed some unused halos |
| 871 |
|
o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP |
| 872 |
|
o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL |
| 873 |
|
or U/VICE from U/VWIND before computing U/VSTRESS |
| 874 |
|
|
| 875 |
|
checkpoint59k |
| 876 |
|
o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between |
| 877 |
|
dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. |
| 878 |
|
o fix un-initialised variable problem (in mom_vecinv & shap_filt): |
| 879 |
|
all experiments pass when compile with un-initialised var. checking option. |
| 880 |
|
o added pkg/salt_plume |
| 881 |
|
o script to test restart (for now, in MITgcm_contrib/jmc_script) |
| 882 |
|
o pkg/seaice: new read/write pickup version. |
| 883 |
|
read meta file and write only fields which are needed to restart. |
| 884 |
|
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
| 885 |
|
o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) |
| 886 |
|
o lab_sea.hb87: modify the domain & update output.hb87.txt : |
| 887 |
|
lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 |
| 888 |
|
at j=1 & j=Ny+1 : this case is not treated correctly in the restart |
| 889 |
|
process. Fixed here by closing the domain at the Northern boundary. |
| 890 |
|
o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. |
| 891 |
|
o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing |
| 892 |
|
a set of consecutive levels in/from a 3-D array. |
| 893 |
|
o pkg/ptracers: |
| 894 |
|
use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). |
| 895 |
|
to-do: fix pkg/diagnostics when large number of diagnostics are defined. |
| 896 |
|
|
| 897 |
|
checkpoint59j |
| 898 |
|
o in pkgs: dic, obcs, offline, rbcs: |
| 899 |
|
standard way to compute coeff. for time interpolation between 2 time reccords |
| 900 |
|
which retains full precision (& make results less dependent on compiler). |
| 901 |
|
update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. |
| 902 |
|
o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those |
| 903 |
|
packages instead of reading ice cover and wind speed separately |
| 904 |
|
o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h |
| 905 |
|
(keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad |
| 906 |
|
to allow to compile customized code before the update) |
| 907 |
|
o cleaning-up: |
| 908 |
|
- fix CPP instruction syntax in pkg/obcs |
| 909 |
|
- replace (some) call to MDSIO S/R with call to RW interface S/R ; and |
| 910 |
|
add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio) |
| 911 |
|
- fix some threads issue in IO parts. |
| 912 |
|
o pkg/dic: |
| 913 |
|
- add tons of "_d 0" (--> much better testreports !) |
| 914 |
|
and then update outputs of tutorial_global_oce_biogeo |
| 915 |
|
o pkg/mom_fluxform: |
| 916 |
|
add a special version of momentum advection intended to conserve momentum |
| 917 |
|
next to a bathymetry step or a coastline edge. (default = off = #undef) |
| 918 |
|
o new read/write pickup version: |
| 919 |
|
- for now, only implemented for main (mdsio) pickup file. |
| 920 |
|
- write out only what is needed to restart; merge pickup_nh , pickup_ph |
| 921 |
|
and main pickup together. |
| 922 |
|
- read meta file; read only what is needed to restart; stop if a field |
| 923 |
|
is missing (if pickupStrictlyMatch=T, = the default) or try to restart |
| 924 |
|
if it make sense (even if the restart is not perfect). |
| 925 |
|
- if no meta file, assume that pickup to read corresponds exactly to |
| 926 |
|
a pickup that would currently be written. |
| 927 |
|
- read pickup written in the old format (until checkpoint59i) if it |
| 928 |
|
recognizes an old meta file (no field-list). |
| 929 |
|
- add a meta file in exp. which starts from a pickup: 2 cases: |
| 930 |
|
a) minimal meta file (with just file precision) + pickupStrictlyMatch=F |
| 931 |
|
e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta |
| 932 |
|
b) a meta file describing the content of the associated pickup file |
| 933 |
|
e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta |
| 934 |
|
o pkg/mdsio & pkg/rw: |
| 935 |
|
- new routine to read a meta file ; new set of routine to read |
| 936 |
|
Multiple-fields file (with meta file). |
| 937 |
|
o added open boundary conditions capability for seaice |
| 938 |
|
HSNOW, HSALT, UICE, and VICE |
| 939 |
|
|
| 940 |
|
checkpoint59i |
| 941 |
|
o adjoint: |
| 942 |
|
* fix multiDimAdvection adjoint |
| 943 |
|
(partial recomputation problem by TAF for fVerT(:,:,kDown) |
| 944 |
|
and comlev1 size definition (maxpass vs. max. number of tracers) |
| 945 |
|
* verification/global_ocean.90x45x15 adjoint now tests |
| 946 |
|
NLFS and multiDimAdvection using DST3 (=30) |
| 947 |
|
* verification/lab_sea now tests multiDimAdvection using DST3 (=30) |
| 948 |
|
o pkg/kpp: add "_d 0" to real constant (if missing); |
| 949 |
|
update output of exp: natl_box (10.digits); vermix (std, 7.digits) |
| 950 |
|
and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). |
| 951 |
|
o prepare for "clever pickup" implementation: add new header file "RESTART.h" |
| 952 |
|
for internal parameters related to restart process (formerly from PARAMS.h) |
| 953 |
|
and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. |
| 954 |
|
o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed |
| 955 |
|
as argument. (only atm2d & obcs write_pickup have not yet been updated) |
| 956 |
|
o pkg/monitor: |
| 957 |
|
- use GLOBAL_SUM_TILE instead of _GLOBAL_SUM |
| 958 |
|
- fix mon_stats_rs (statistics over the full domain, even where field is zero) |
| 959 |
|
- account for deep Atmosphere factor and density factor (anelastic) |
| 960 |
|
o added open boundary conditions capability for seaice HEFF and AREA |
| 961 |
|
o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) |
| 962 |
|
thermodynamics |
| 963 |
|
- requires a little reorganization, which affects the testreport results |
| 964 |
|
of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, |
| 965 |
|
so that now the conservative form is tested |
| 966 |
|
- add a few comments |
| 967 |
|
o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* |
| 968 |
|
o add a little bit of code to gad_os7mp_adv_?.F to help vectorization |
| 969 |
|
o add new diagnostics to seaice: advective, diffusive fluxes (only for |
| 970 |
|
multidim-advection, for scheme 2 they are not filled) and transports, |
| 971 |
|
thermodynamic growth rates |
| 972 |
|
o change units of EmPmR (inside the code, + within coupling interface) |
| 973 |
|
from m/s to kg/m2/s (mass flux) but leave input file unchanged. |
| 974 |
|
Affects results @ truncation level (cg2d match) and update output of |
| 975 |
|
experiments: lab_sea(6), global_ocean.90x40x15(10), |
| 976 |
|
global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) |
| 977 |
|
+ adjoint results: global_ocean_ebm(11) and lab_sea (12). |
| 978 |
|
Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). |
| 979 |
|
Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). |
| 980 |
|
|
| 981 |
|
checkpoint59h |
| 982 |
|
o pkg/exf: |
| 983 |
|
- improve vectorization by moving if-statement out of loops in |
| 984 |
|
exf_mapfields, exf_radiation |
| 985 |
|
- exf_bulkformulae.F: introduce 2D fields and vectorize code |
| 986 |
|
o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package |
| 987 |
|
o testreport: |
| 988 |
|
- allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE |
| 989 |
|
monitor & update offline_exf_seaice exp. output. |
| 990 |
|
- AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) |
| 991 |
|
o pkg/seaice: |
| 992 |
|
- bug fix in the evp solver: boundary conditions were affected be |
| 993 |
|
masking of zMax/zMin (changes results) |
| 994 |
|
- minor bug fix in boundary conditions in seaice_calc_strainrates |
| 995 |
|
(changes results for no_slip) |
| 996 |
|
- seaice_lsr.F: make interpolation of eta dependent on boundaries |
| 997 |
|
- replace hardcoded lower limit for zeta (zMin) by runtime parameter |
| 998 |
|
- add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean |
| 999 |
|
stress formulation and no-slip boundary conditions |
| 1000 |
|
o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP |
| 1001 |
|
in gad_calc_rhs.F ; add few safety stops in initialisation phase. |
| 1002 |
|
o pkg/seaice: a first HSALT time stepping equation has been checked in |
| 1003 |
|
o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV |
| 1004 |
|
in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem |
| 1005 |
|
without requiring DO-IF statements |
| 1006 |
|
o pkg/thsice: |
| 1007 |
|
use continuous power-law function for partition of energy between lateral |
| 1008 |
|
melting/freezing and thinning/thickening ; old code using step function |
| 1009 |
|
still available with #undef THSICE_FRACEN_POWERLAW |
| 1010 |
|
update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice |
| 1011 |
|
o testreport: change AD testing : check against results/output_adm.txt |
| 1012 |
|
using same scripts as for forward test. |
| 1013 |
|
|
| 1014 |
|
checkpoint59g |
| 1015 |
|
o adjoint testing: in preparation for changing testreport: |
| 1016 |
|
- output format: cost and grad written on separated lines |
| 1017 |
|
- ad output results in directory "results" (instead of "results_ad") |
| 1018 |
|
o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
| 1019 |
|
o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
| 1020 |
|
o pkg/ecco: allow user defined cost function contributions |
| 1021 |
|
o testreport: |
| 1022 |
|
Allow to choose (per experiment) the list of tested output variables |
| 1023 |
|
and the main variable (used to issue a pass/FAIL ) ; |
| 1024 |
|
- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
| 1025 |
|
- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
| 1026 |
|
Also modify printing of summary: |
| 1027 |
|
a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
| 1028 |
|
b) echo the list of tested variables in the individual summary.txt of |
| 1029 |
|
each experiment. |
| 1030 |
|
o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
| 1031 |
|
threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
| 1032 |
|
(but still depend on the tile decompostion of the domain). |
| 1033 |
|
o pkg/seaice: change a discretization detail to make the B-grid code |
| 1034 |
|
"more symmetric". This change is likely to remove all "ridges/leads" that |
| 1035 |
|
where quasi-aligned with the grid in B-grid solutions. It may also be |
| 1036 |
|
the solution to the stress coupling issues with the B-grid. |
| 1037 |
|
o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
| 1038 |
|
remove .cvsignore from input dir. (since testreport no longer run here). |
| 1039 |
|
o pkg/thsice: |
| 1040 |
|
- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
| 1041 |
|
- fix reshaping of sea-ice just after advection: |
| 1042 |
|
melt all the ice only if ice-volume is too small. |
| 1043 |
|
- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
| 1044 |
|
prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
| 1045 |
|
and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
| 1046 |
|
o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
| 1047 |
|
tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
| 1048 |
|
o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
| 1049 |
|
forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
| 1050 |
|
(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
| 1051 |
|
and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
| 1052 |
|
of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
| 1053 |
|
-> update output.txt |
| 1054 |
|
o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
| 1055 |
|
this affects truncation error: -> update output.txt of exp: |
| 1056 |
|
global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
| 1057 |
|
ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
| 1058 |
|
|
| 1059 |
|
checkpoint59f |
| 1060 |
|
o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
| 1061 |
|
o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
| 1062 |
|
a bounded range (in forward mode) |
| 1063 |
|
o pkg/ecco, ctrl, autodiff and mom_common: |
| 1064 |
|
internal parameter controls, completements of implementations |
| 1065 |
|
o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
| 1066 |
|
o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
| 1067 |
|
(not seem any difference in testing results). |
| 1068 |
|
o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
| 1069 |
|
at face corners. |
| 1070 |
|
o pkg/generic_advdiff: |
| 1071 |
|
- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
| 1072 |
|
loop range indices for computing vertical advection tendency |
| 1073 |
|
and do the calculation in the interior only (no overlap) ; |
| 1074 |
|
for now, only implemented for SOM advection (to save CPU time). |
| 1075 |
|
- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
| 1076 |
|
o exch2 adjoint |
| 1077 |
|
First set of changes: |
| 1078 |
|
- add exch2 hand-written adjoint templates |
| 1079 |
|
- exch2 hand-written no longer use TAF-flag 'nownew_arg' |
| 1080 |
|
This will require cleanup in pkg/autodiff/*.F |
| 1081 |
|
(changed routines currently kept separate in verif. code/) |
| 1082 |
|
- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
| 1083 |
|
that used to hide exch2 or cubed-sphere specific code |
| 1084 |
|
(commented via 'cph-exch2') |
| 1085 |
|
o pkg/seaice |
| 1086 |
|
- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
| 1087 |
|
o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
| 1088 |
|
output of global_ocean.cs32x15.thsice . |
| 1089 |
|
|
| 1090 |
|
checkpoint59e |
| 1091 |
|
o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
| 1092 |
|
for B-grid vector (not yet tested) and C-grid vector (<- only used |
| 1093 |
|
when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). |
| 1094 |
|
o starting implementation of Duffy et al. (GRL 1999) salt plume scheme |
| 1095 |
|
(#ifdef ALLOW_SALT_PLUME) |
| 1096 |
|
o gather_2d/scatter_2d: removed halo regions |
| 1097 |
|
o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
| 1098 |
|
scheme and the corresponding test case (under front_relax dir). For now, |
| 1099 |
|
only available with Skew-flux form and not yet tested in realistic set-up. |
| 1100 |
|
adjoint: store directives updated, but gradient checks deteriorated, |
| 1101 |
|
so maybe GM/Redi adjoint is now broken. |
| 1102 |
|
o seaice adjoint |
| 1103 |
|
* add AREA, HEFF, HSNOW as control variable |
| 1104 |
|
(should not change lab_sea results) |
| 1105 |
|
* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
| 1106 |
|
o pkg/seaice: |
| 1107 |
|
* added computation of saltFlux in seaice_growth; |
| 1108 |
|
For time being, sea ice salinity is assumed constant |
| 1109 |
|
contribution of snow flooding to freshening of sea ice is neglected. |
| 1110 |
|
SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
| 1111 |
|
defaults to 0.0 in order to maintain backward compatibility. |
| 1112 |
|
Typical values for SEAICE_salinity are 4 to 10 g/kg. |
| 1113 |
|
* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
| 1114 |
|
* added SEAICE_availHeatFrac, which specifies fraction of surface level |
| 1115 |
|
heat content used to melt or grow ice |
| 1116 |
|
* commented out cap of HICE: it helps keep ice thinner |
| 1117 |
|
* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
| 1118 |
|
* applied OBCS T/S mask to HEFFM sea ice mask |
| 1119 |
|
|
| 1120 |
|
checkpoint59d |
| 1121 |
|
o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
| 1122 |
|
for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
| 1123 |
|
(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
| 1124 |
|
o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
| 1125 |
|
and change default value of parameter "GM_Small_Number"; |
| 1126 |
|
update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
| 1127 |
|
global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
| 1128 |
|
tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
| 1129 |
|
o pkg/ecco: cost function when applying pkg/smooth to controls |
| 1130 |
|
o pkg/ctrl: add forcingPrecond run time parameter |
| 1131 |
|
o pkg/seaice: |
| 1132 |
|
- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
| 1133 |
|
- fix bug in metric terms of u-equation in LSR solver (implicit part), |
| 1134 |
|
changes verification/lab_sea |
| 1135 |
|
- rearrange implicit part of u-equation in LSR solver to make it easier to |
| 1136 |
|
read, understand, and debug. This causes changes at the truncation level. |
| 1137 |
|
- fix (serious) bug in the boundary conditions (sign error in the implicit |
| 1138 |
|
part) of the LSR solver. Changes all LSR results. |
| 1139 |
|
- fixed problem with HSNOW initialization to avoid thick snow when AREA |
| 1140 |
|
is initilized with small values - does not change lab_sea results. |
| 1141 |
|
- added HsnowFile initialization capability |
| 1142 |
|
o pkg/smooth: addition to model/src and pkg/ctrl so allow |
| 1143 |
|
initialization of pkg/smooth and application to control vector |
| 1144 |
|
o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
| 1145 |
|
o dependencies: pkg/profiles requires pkg/cal |
| 1146 |
|
o pkg/profiles: |
| 1147 |
|
- added option ALLOW_PROFILES_GENERICGRID |
| 1148 |
|
-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
| 1149 |
|
that interpolation information (grid points and coefficients) is provided |
| 1150 |
|
within the netcdf input files. |
| 1151 |
|
-> sample matlab scripts can be found in MITgcm_contrib/gael |
| 1152 |
|
that allow you to prepare netcdf input files. |
| 1153 |
|
- also modified: cleaner include statements, cleaner error print statements, |
| 1154 |
|
cleaner stops when error, and more tests of the netcdf input files consistency. |
| 1155 |
|
o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
| 1156 |
|
o pkg/seaice: |
| 1157 |
|
- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
| 1158 |
|
requires a new routine: seaice_diagnostics_fill.F |
| 1159 |
|
- make sure that seaice does not move if not forced (pressure replacement |
| 1160 |
|
method, Hibler and Ip, 1995), changes results |
| 1161 |
|
- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
| 1162 |
|
- SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). |
| 1163 |
|
It is turned off by default (=-1.), because it changes the results. |
| 1164 |
|
- make it possible to read AREA from a file, too. |
| 1165 |
|
|
| 1166 |
|
checkpoint59c |
| 1167 |
|
o add S/R and diagnostics for oceanic mixed-layer depth |
| 1168 |
|
o move GMRedi call after all vertical mixing schemes (including KPP) |
| 1169 |
|
o pkg/thsice: |
| 1170 |
|
- ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs |
| 1171 |
|
(melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice |
| 1172 |
|
o pkg/obcs: |
| 1173 |
|
- bug fix for balance code |
| 1174 |
|
o pkg/seaice: |
| 1175 |
|
- allow values of SEAICE_elasticParm > 1 |
| 1176 |
|
- add new parameter SEAICE_evpTauRelax as an alternative |
| 1177 |
|
to SEAICE_elasticParm |
| 1178 |
|
- make lsr boundary conditions free slip (by default), changes result |
| 1179 |
|
- add code for no slip boundary conditions for lsr |
| 1180 |
|
- set minimum of zeta to zero (and not 4e8) (changes results) |
| 1181 |
|
- add a cap on AREA after advecting AREA if seaice_growth is not called |
| 1182 |
|
o change calculation of Visbeck K: |
| 1183 |
|
- no longer depend on tapering scheme; instead, compute slope (limited |
| 1184 |
|
by GM_maxSlope). this is equivalent to what was comuted before with |
| 1185 |
|
clipping or linear tappering. |
| 1186 |
|
- fix vertical averaging (wrong by 1/2 level) |
| 1187 |
|
- leave the old version (but will not be maintained) within |
| 1188 |
|
#ifdef OLD_VISBECK_CALC / #endif |
| 1189 |
|
- update output of exp. ideal_2D_oce |
| 1190 |
|
o change error catch in calc_r_star to improve vectorization |
| 1191 |
|
o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
| 1192 |
|
add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
| 1193 |
|
o adjoint: |
| 1194 |
|
Re-organized adjoint checkpointing according to Matt Mazloff |
| 1195 |
|
(but with modifs/completions/cleanups) |
| 1196 |
|
Storing is now bundled into large arrays to optimized I/O |
| 1197 |
|
(and second step in cleanup of the_main_loop) |
| 1198 |
|
|
| 1199 |
|
checkpoint59b |
| 1200 |
|
o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
| 1201 |
|
- export/import (between ocean & coupler) fields needed for ocean DIC. |
| 1202 |
|
o pkg/seaice: |
| 1203 |
|
- get rid of three more exchanges seaice_calc_viscosities (required |
| 1204 |
|
different loop boundaries in seaice_lsr and seaice_ocean_stress) |
| 1205 |
|
- bug fix in seaice_ocean_stress (update of lab_sea required) |
| 1206 |
|
- reduce loop boundaries to necessary minimum also in seaice_evp |
| 1207 |
|
- go back to the old way of computing deltaC/Z as the adjoint likes that |
| 1208 |
|
better |
| 1209 |
|
o Refresh of tutorial_global_oce_latlon (includes changing salinity-like |
| 1210 |
|
passive tracer to an Age Tracer) + update output.txt |
| 1211 |
|
o pkg/exf: |
| 1212 |
|
- implement A-grid / C-grid selection for wind-stress input files. |
| 1213 |
|
- clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) |
| 1214 |
|
for now, in exf_bulk_largeyeager04.F only : |
| 1215 |
|
- change implementation for case where windspeed + 2. components wind-stress |
| 1216 |
|
are read-in. AND use rhoConstFresh to convert evap. |
| 1217 |
|
o pkg/seaice: |
| 1218 |
|
- use correct EXCH_UV for wind-forcing (on A-grid). |
| 1219 |
|
- change SEAICE_OPTIONS.h to limit the number of option combinations (regarding |
| 1220 |
|
SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops. |
| 1221 |
|
o pkg/exf: |
| 1222 |
|
- default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC) |
| 1223 |
|
EXF_INTERPOLATION: |
| 1224 |
|
- merge global_with_exf/code version of exf_interp_read.F |
| 1225 |
|
to the main code ; |
| 1226 |
|
- Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when |
| 1227 |
|
reading the file ; Important: This options needs to be defined to recover |
| 1228 |
|
previous code. |
| 1229 |
|
otherwise, use fixed size array to read in (size=exf_interp_bufferSize). |
| 1230 |
|
- no longer loose real*8 precision along the way when using exf_iprec=64. |
| 1231 |
|
o pkg/seaice: rearrangement of common blocks (really needs more cleaning up) |
| 1232 |
|
- change discretisation of evp-solver in order to avoid another exchange |
| 1233 |
|
(changes lab_sea) and clean up a little |
| 1234 |
|
- replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS) |
| 1235 |
|
help the adjoint (this also changes the results slightly) |
| 1236 |
|
- add a few "_d 0" where they had been missing in seaice_evp.F |
| 1237 |
|
- cleaning up: remove unused seaice_calc_rhs.F |
| 1238 |
|
o pkg/exf: some cleaning-up: |
| 1239 |
|
- change various "constants" into runtime parameters |
| 1240 |
|
- cleaned-up Large&Yeager04 routine which should eventually |
| 1241 |
|
replace exf_bulkformulae.F (changed names of S/R and CPP) |
| 1242 |
|
and merged various ALLOW_ATM_WIND options |
| 1243 |
|
only used with thsice pkg (in thsice_get_exf.F): |
| 1244 |
|
- implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04) |
| 1245 |
|
which are used when useStabilityFct_overIce=TRUE (= the default) |
| 1246 |
|
- change default values of ice & snow emissivity and scale downward LW |
| 1247 |
|
by ice & snow emissivity. |
| 1248 |
|
o pkg/thsice: |
| 1249 |
|
fix few little problems, in thsice_calc_thickn.F: |
| 1250 |
|
- growth vertically (and not laterally) if iceFrac == iceMaskMax |
| 1251 |
|
- melt only laterally if hIce < hThinIce (as the comments say) |
| 1252 |
|
and in thsice_extend.F: |
| 1253 |
|
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
| 1254 |
|
- start to form ice as soon as the minimum ice-volume is reachable. |
| 1255 |
|
update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice), |
| 1256 |
|
and cpl_aim+ocn |
| 1257 |
|
o pkg/kpp |
| 1258 |
|
- move computation of surface related input fields to KPP into a new |
| 1259 |
|
subroutine kpp_forcing_surf.F |
| 1260 |
|
- remove wrong (within bi,bj loops) EXCH calls. |
| 1261 |
|
- little cleaning (add argument myThid in last position, cvs header ...) |
| 1262 |
|
- for now, fix conservation problem by exchanging KPPviscAz (may not |
| 1263 |
|
be the best fix) |
| 1264 |
|
o pkg/seaice |
| 1265 |
|
- check for inconsistent evp parameter/cpp-flag combination |
| 1266 |
|
- remove leftover errIO flat for obsolete name list error handling |
| 1267 |
|
o OpenAD |
| 1268 |
|
- changed verification/OpenAD to full baroclinic setup (including GM/Redi) |
| 1269 |
|
|
| 1270 |
|
checkpoint59a |
| 1271 |
|
o pkg/seaice: some parameter clarifications and a little bit of clean up |
| 1272 |
|
o pkg/thsice: rename run-time parameters: |
| 1273 |
|
himin -> hIceMin |
| 1274 |
|
himin0 -> hThinIce |
| 1275 |
|
hihig -> hThickIce |
| 1276 |
|
i0 -> i0swFrac |
| 1277 |
|
transCoef -> bMeltCoef |
| 1278 |
|
frac_energy -> fracMelting |
| 1279 |
|
add new parameters: hNewIceMax, fracFreezing, dhSnowLin |
| 1280 |
|
with default values (for now) that do not change the results. |
| 1281 |
|
remove old version of thsice vars advection in pkg/seaice. |
| 1282 |
|
o in FFIELDS.h: |
| 1283 |
|
- replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD |
| 1284 |
|
- make pLoad & sIceLoad always available (but still only used if |
| 1285 |
|
ATMOSPHERIC_LOADING is #define). |
| 1286 |
|
o pkg/kpp: replaced _KPP_RL with _RL |
| 1287 |
|
o bug fixes for vertical diffusivity computations when both KPP and |
| 1288 |
|
3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F |
| 1289 |
|
are no longer updating the vertical diffusivity array |
| 1290 |
|
(passed as argument) but are (re-) setting those arrays. |
| 1291 |
|
o pkg/seaice: fix bug in evp solver, while doing that |
| 1292 |
|
- change (improve?) discretization of stress computations for both |
| 1293 |
|
cgrid-lsr and evp solver |
| 1294 |
|
- add a new routine to compute strain rates |
| 1295 |
|
- the above changes lab_sea results |
| 1296 |
|
- add no slip conditions for evp solver (off by default), lsr-version |
| 1297 |
|
may follow |
| 1298 |
|
- fix exchange for shear at Z-points (does not change lab_sea) |
| 1299 |
|
- retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp |
| 1300 |
|
(to force the user to pick a time step since there is not "safe" way |
| 1301 |
|
of choosing it) |
| 1302 |
|
- add principal stress diagnostics |
| 1303 |
|
- rearrange fields for evp a little to avoid having to call a: too many |
| 1304 |
|
exchanges and b: exchanges for stress trensor components which we do |
| 1305 |
|
not have. |
| 1306 |
|
- modify Hibler+Bryan (1987) stress coupling so that it reuses information |
| 1307 |
|
of evp, complete rewrite for lsr case (latter is does not yet work |
| 1308 |
|
in all cases) |
| 1309 |
|
o pkg/kpp: add code to have mixing in shelf ice caverns |
| 1310 |
|
- add myThid to all kpp routines (long overdue) |
| 1311 |
|
|
| 1312 |
|
checkpoint59 |
| 1313 |
|
o pkg/exf: |
| 1314 |
|
- fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND & |
| 1315 |
|
ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid |
| 1316 |
|
- move exf header files from lower_case.h to UPPER_CASE.h ; |
| 1317 |
|
add missing cvs Header & Name |
| 1318 |
|
- add adjoint routines and flow dirs for newly used exch_uv_agrid routines |
| 1319 |
|
- add namelist param. selectStressGridPosition, exf_monFreq |
| 1320 |
|
- retire many _CLIM routines, and remove data.exf_clim |
| 1321 |
|
+ params moved to data.exf |
| 1322 |
|
+ climsst, climsss now handled by exf_set_gen, i.e. |
| 1323 |
|
climss?period=0 refers to constant field, |
| 1324 |
|
climss?period=-12 to monthly forcing |
| 1325 |
|
- split up namelists in data.exf |
| 1326 |
|
o pkg/seaice: |
| 1327 |
|
- remove seaice_exch and seaice_exch_uv |
| 1328 |
|
- remove superfluous exchange of theta |
| 1329 |
|
- add myThid to seaice_budget_ocean/ice |
| 1330 |
|
- add new interface for atmospheric wind forcing (C-grid only) |
| 1331 |
|
+ new routine |
| 1332 |
|
+ two new field (taux, tauy for stress over ice) |
| 1333 |
|
+ removed one global field (DAIRN) for C-grid case only |
| 1334 |
|
o pkg/thsise |
| 1335 |
|
- 2nd set of modifs for thsice adjoint in conjunction with exf |
| 1336 |
|
o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.) |
| 1337 |
|
|
| 1338 |
|
checkpoint58y_post |
| 1339 |
|
o Added capability for latitudinal dependence of Bryan and Lewis, 1979 |
| 1340 |
|
vertical diffusivity, similar to that in MOM4; turned on using |
| 1341 |
|
#define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using |
| 1342 |
|
diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file. |
| 1343 |
|
o Added capability for 3D specification of background vertical diffusion |
| 1344 |
|
coefficient. This is done by (i) #define ALLOW_3D_DIFFKR |
| 1345 |
|
in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime |
| 1346 |
|
"data" file that contains the 3D vertical diffusivity coefficients. |
| 1347 |
|
o ice dynamics (pkg/seaice) with thsice thermodynamics: |
| 1348 |
|
- add code within pkg thsice to advect & diffuse sea-ice fields |
| 1349 |
|
similar to (and will replace) what has been added in seaice_advdiff.F, |
| 1350 |
|
but: - conserving Mass, Heat & Salt. |
| 1351 |
|
- better when using non-linear advection scheme (not yet fully tested) |
| 1352 |
|
- can also be used in atmospheric set-up (for now, only the diffusion). |
| 1353 |
|
|
| 1354 |
|
checkpoint58x_post |
| 1355 |
|
o IO option for global-file compact format: |
| 1356 |
|
- add options when generating topology (utils/exch2/matlab-topology-generator) |
| 1357 |
|
- add I/O capability (pkg/mdsio). |
| 1358 |
|
- adapt utils/matlab/rdmds.m to read this format. |
| 1359 |
|
for now long-line format not yet supported by pkg/mdsio (& exch2). |
| 1360 |
|
o shelfice: add a few diagnostics |
| 1361 |
|
|
| 1362 |
|
checkpoint58w_post |
| 1363 |
|
o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: |
| 1364 |
|
rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref |
| 1365 |
|
(and replace horiVertRatio in NH code). |
| 1366 |
|
Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) |
| 1367 |
|
and tutorial_plume_on_slope (sensitive to truncation) |
| 1368 |
|
o seaice: if ALLOW_ATM_WIND is undefined use wind stress |
| 1369 |
|
directly to drive seaice model (C-grid only) |
| 1370 |
|
o exf: when input wind-stress (#undef ALLOW_ATM_WIND): |
| 1371 |
|
- reintroduce computation of wind from stress, |
| 1372 |
|
- compute tau (in exf_bulkformulae.F) from windstress averaged to |
| 1373 |
|
mass points to avoid tau = 0 |
| 1374 |
|
- fix serious bug: (1/3) in Fortran is not the same as (1./3.) |
| 1375 |
|
o rdmnc.m: make it work with "global" files created with gluemnc |
| 1376 |
|
o rdmnc.m : some improvements in dealing with singleton dimension |
| 1377 |
|
(tested on all testreport mnc output files). |
| 1378 |
|
o genmake2: disable pkg/profiles if netcdf test fails. |
| 1379 |
|
o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output. |
| 1380 |
|
o move call to cal_readparms up to make calendar parameters/variable available |
| 1381 |
|
to all packages |
| 1382 |
|
|
| 1383 |
|
checkpoint58v_post |
| 1384 |
|
o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get |
| 1385 |
|
useDynP_inEos_Zc tested. |
| 1386 |
|
o pkg/exf: changes to properly interpolate/mask/scale initial fields |
| 1387 |
|
o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields |
| 1388 |
|
and portions thereof. See read_cs.txt for description and examples. |
| 1389 |
|
o utils/matlab/cs_grid/bk_line: to compute transport through passages, |
| 1390 |
|
add a script (grt_circ_bkl.m) to generate broken-line between 2 points, |
| 1391 |
|
following the great-circle arc between those 2 points. |
| 1392 |
|
o trap un-initialized variable with pathscale compiler on weddell.mit.edu |
| 1393 |
|
(thanks to Constantinos): fix few problems and get (almost) all exp to pass. |
| 1394 |
|
o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in |
| 1395 |
|
- enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) |
| 1396 |
|
- used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81) |
| 1397 |
|
- still needs work (not working with some options ; efficiency to improve) |
| 1398 |
|
and serious testing. |
| 1399 |
|
- use this scheme for temperature & salinity in 2 advection test exp.: |
| 1400 |
|
advect_xy & advect_xz, respectively. |
| 1401 |
|
|
| 1402 |
|
checkpoint58u_post |
| 1403 |
|
o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. |
| 1404 |
|
o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. |
| 1405 |
|
o testreport: add option "-skipdir" to skip some test. |
| 1406 |
|
o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent |
| 1407 |
|
momentum calculation. |
| 1408 |
|
o gad_advection: fix vertAdvecScheme (if different from advectionScheme) |
| 1409 |
|
o some cleaning: usePickupBeforeC35 no longer supported ; remove this option. |
| 1410 |
|
remove checkpoint.F and the_correction_step.F (no longer used); |
| 1411 |
|
do the k loop inside CYCLE_TRACER (supposed to be more efficient). |
| 1412 |
|
o add option (linFSConserveTr) to correct for tracer source/sink due to |
| 1413 |
|
Linear Free surface |
| 1414 |
|
o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine |
| 1415 |
|
o pkg/thsice: fix reading mnc-pickups |
| 1416 |
|
|
| 1417 |
|
checkpoint58t_post |
| 1418 |
|
o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) |
| 1419 |
|
o pkg/mdsio: |
| 1420 |
|
- clean-up mdsio_readfield.F & mdsio_writefield_new.F and |
| 1421 |
|
move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & |
| 1422 |
|
mdsio_write_field.F (S/R MDS_WRITE_FIELD); |
| 1423 |
|
- fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD |
| 1424 |
|
- collect old S/R in one file: mdsio_rw_field.F (now just a call to |
| 1425 |
|
either MDS_READ_FIELD or MDS_WRITE_FIELD ) |
| 1426 |
|
- new S/R (to replace MDSWRITEMETA), which allows to write more |
| 1427 |
|
informations (variable names, time ...) to meta files. |
| 1428 |
|
- modify rdmds.m to give back the meta file content. |
| 1429 |
|
o pkg/diagnostics: change vertical interpolation to be safer, and more |
| 1430 |
|
flexible (define p-levels to interpolate to in data.diagnostics); |
| 1431 |
|
add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right |
| 1432 |
|
diagnostic pointer. |
| 1433 |
|
o pkg/seaice: more cleaning up of seaice_growth, added many comments |
| 1434 |
|
o pkg/exf: put runoff0 and runoff1 into the appropriate common block |
| 1435 |
|
o fix multi-category seaice: |
| 1436 |
|
- change cpp flag SEAICE_MULTILEVEL to more meaningful name: |
| 1437 |
|
SEAICE_MULTICATEGORY |
| 1438 |
|
- fix short wave heat flux |
| 1439 |
|
o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics |
| 1440 |
|
and allow to use EVP solver. Change forward lab_sea: test both EVP |
| 1441 |
|
solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) |
| 1442 |
|
o Initial check-in of lab_sea adjoint |
| 1443 |
|
(very similar to natl_box_adjoint/code_seaice) |
| 1444 |
|
* used C-grid and EVP solver |
| 1445 |
|
* used KPP, GM/Redi |
| 1446 |
|
* uses inAdExact=.TRUE. |
| 1447 |
|
* gradient checks fail for both ADM and TLM |
| 1448 |
|
due to sensitive snow melt code in seaice_grwoth (look for "JZ") |
| 1449 |
|
f.d. gradients actually seem more problematic than ADM, TLM gradients; |
| 1450 |
|
issue is related to forward mismatch between g77 an ifort |
| 1451 |
|
o pkg/seaice: overhaul of thermodynamics |
| 1452 |
|
- growth.F and groatb.F are replaced by new routine seaice_growth.F |
| 1453 |
|
- budget.F is replaced by two new routines seaice_budget_ocean/ice.F |
| 1454 |
|
- move a few global fields out of SEAICE.h into seaice_growth.F and |
| 1455 |
|
make them 2D (FICE/QNETO/ ...) |
| 1456 |
|
- remove FO (it is the same as QNETO) |
| 1457 |
|
- introduce a few local fields to avoid modifying external fields such |
| 1458 |
|
as atemp, etc. |
| 1459 |
|
|
| 1460 |
|
checkpoint58s_post |
| 1461 |
|
o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F |
| 1462 |
|
changed exf_set_gen.F so that |
| 1463 |
|
genperiod=0 means input file is one time-constant field and |
| 1464 |
|
genperiod=-12 means input file contains 12 monthly means |
| 1465 |
|
o CG2D: use pre-computed solver main-diagonal (stored in common block); |
| 1466 |
|
this affects truncation error ; generate new output file for exp. which |
| 1467 |
|
fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), |
| 1468 |
|
global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), |
| 1469 |
|
ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), |
| 1470 |
|
MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), |
| 1471 |
|
tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), |
| 1472 |
|
vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) |
| 1473 |
|
o start implementation of deep-atmosphere and anelastic formulation |
| 1474 |
|
o verification: remove 2nd copy of input files and use script "prepare_run" |
| 1475 |
|
to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) |
| 1476 |
|
o mom_common/vecinv/fluxform: fix a few initialisation isssues |
| 1477 |
|
o profiles: fix for multithreaded case |
| 1478 |
|
|
| 1479 |
|
o diagnostics: rename few diags: |
| 1480 |
|
s/'PRESSURE'/'RCENTER '/g |
| 1481 |
|
s/'TICE '/'oceFreez'/g |
| 1482 |
|
s/'TAUX '/'oceTAUX '/g |
| 1483 |
|
s/'TAUY '/'oceTAUY '/g |
| 1484 |
|
s/'SWFLUX '/'oceQsw '/g |
| 1485 |
|
s/DIFx/DFxE/g |
| 1486 |
|
s/DIFy/DFyE/g |
| 1487 |
|
and add few ocean-forcing diagnostics: |
| 1488 |
|
atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS |
| 1489 |
|
o modifications to pkg/seaice/growth.F and budget.F, which change results of |
| 1490 |
|
lab_sea experiment: HSNOW was sometimes treated as effective and sometimes |
| 1491 |
|
as actual snow thickness. It now refers everywhere to effective snow |
| 1492 |
|
thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. |
| 1493 |
|
|
| 1494 |
|
checkpoint58r_post |
| 1495 |
|
o modifications to pkg/seaice/growth.F, which change results of |
| 1496 |
|
lab_sea experiment: fixes pertain to melting snow over open water, to |
| 1497 |
|
masking EVAP under sea ice, and to using the correct AREA variable for |
| 1498 |
|
computations of EVAP, PRECIP, HSNOW, and GHEFF |
| 1499 |
|
o add ability to read bathy, salt, and theta using MNC (off by def) |
| 1500 |
|
o add flooding algorithm and advection of HSNOW for pkg/seaice; |
| 1501 |
|
both are turned off by default and do no change any results |
| 1502 |
|
o seaice advection with pkg/thsice: a step toward the use of non-linear |
| 1503 |
|
advection scheme, but #ifdef or commented out for now (requires more EXCH). |
| 1504 |
|
o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens |
| 1505 |
|
(identical results) and the standard version of EXTERNAL_FIELDS_LOAD |
| 1506 |
|
in natl_box (affects results @ truncation level: update output.txt) |
| 1507 |
|
o multi-threading and IO: |
| 1508 |
|
- replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. |
| 1509 |
|
- remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls |
| 1510 |
|
(needed to work with SingleCpuIO): tested in all verif. exp. |
| 1511 |
|
o GAD: use simpler DST3 formulation as default (old version left within #ifdef) |
| 1512 |
|
affects the results (but none of the verification test uses this scheme). |
| 1513 |
|
o Adding some pkg/diagnostics capability to pkg/seaice |
| 1514 |
|
(will certainly be subject to changes) |
| 1515 |
|
o ctrl: adding new control variables: |
| 1516 |
|
lwflux, lwdown, evap, snowprecip, apressure, runoff |
| 1517 |
|
|
| 1518 |
|
checkpoint58q_post |
| 1519 |
|
o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up |
| 1520 |
|
1/6-deg Southern Ocean configuration by 8% on IBM Datastar and |
| 1521 |
|
high_res_cube configuration by 4% on Columbia. |
| 1522 |
|
o clean-up multi-threaded problems (reported by debugger tcheck on ACES); |
| 1523 |
|
add (in global_with_exf/code) a version of EXF_INTERP_READ without |
| 1524 |
|
dynamical allocation (seems to work in multi-threaded). |
| 1525 |
|
o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using |
| 1526 |
|
single CPU io) so that TAF does not have to see EESUPPORT.h |
| 1527 |
|
o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
| 1528 |
|
|
| 1529 |
|
checkpoint58p_post |
| 1530 |
|
o obcs: stop if obcs is used with useCDscheme = .true. |
| 1531 |
|
o shelfice: |
| 1532 |
|
- fix a sign error so that no slip at shelfice interface works |
| 1533 |
|
- remove stop for combination non-hydrostatic code and shelfice. That does |
| 1534 |
|
not mean, that the results are correct, but at least they are numerically |
| 1535 |
|
stable |
| 1536 |
|
o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) |
| 1537 |
|
o added adjoint exch routined for all exch*3d* routines |
| 1538 |
|
and updated flow directives |
| 1539 |
|
|
| 1540 |
|
checkpoint58o_post |
| 1541 |
|
o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; |
| 1542 |
|
remove old subroutines (_XY_ & _XYZ_); update the adjoint version. |
| 1543 |
|
o change controling S/R for writing pickup file (new S/R do_write_pickup) |
| 1544 |
|
and clean-up reading/writing of pickup files. |
| 1545 |
|
o fix local version of read/write pickup (NH part) in rotating_tank/code |
| 1546 |
|
o simplify EXCH interface: |
| 1547 |
|
- change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) |
| 1548 |
|
- not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version |
| 1549 |
|
o added the regrid package |
| 1550 |
|
o shelfice: |
| 1551 |
|
- add a simple boundary layer scheme to reduce noise |
| 1552 |
|
- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
| 1553 |
|
|
| 1554 |
|
checkpoint58n_post |
| 1555 |
|
o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
| 1556 |
|
local variable (not in common block). |
| 1557 |
|
o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
| 1558 |
|
- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
| 1559 |
|
- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
| 1560 |
|
to work with SingleCpuIO. |
| 1561 |
|
o add "_d 0" to real constant of pkg/cfc subroutines ; |
| 1562 |
|
update exp. cfc_exemple & tutorial_cfc_offline output files. |
| 1563 |
|
o multi-threading and IO: |
| 1564 |
|
- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
| 1565 |
|
(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
| 1566 |
|
- barrier before and after reading. |
| 1567 |
|
- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
| 1568 |
|
- avoid using MDS_WRITELOCAL for LAND pkg output. |
| 1569 |
|
- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
| 1570 |
|
common-block variables ; Allows multi-threading with master-thread IO. |
| 1571 |
|
o change default MAX_NO_THREADS from 32 to 4 ; |
| 1572 |
|
and stop cleanly when MAX_NO_THREADS is too small. |
| 1573 |
|
o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
| 1574 |
|
|
| 1575 |
|
checkpoint58m_post |
| 1576 |
|
o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
| 1577 |
|
and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
| 1578 |
|
o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
| 1579 |
|
keep global_ocean.90x40x15 (for AD testing) with former secondary test |
| 1580 |
|
(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
| 1581 |
|
o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
| 1582 |
|
add MITgcm_tutorials (= code + all the tutorials) |
| 1583 |
|
o ecco, option to compute cost for total ssh (mean+anom) |
| 1584 |
|
o consistent with addition of ptracer and ssh in pkg/profiles |
| 1585 |
|
o profiles: adding ptracer and ssh |
| 1586 |
|
o testreport: change multi-test output-file name |
| 1587 |
|
(from output.txt.{name} to output.{name}.txt) |
| 1588 |
|
o profiles: now ok for mutli-tiles case |
| 1589 |
|
o seaice: add 4 parameters for different advection schemes for area, |
| 1590 |
|
(effective) seaice thickness, enthalphy, and snow height. Their default |
| 1591 |
|
is the standard parameter SEAICEadvScheme |
| 1592 |
|
o calc_gw: |
| 1593 |
|
- add cosFacU in zonal viscous flux (harmonic.visc.). |
| 1594 |
|
- put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. |
| 1595 |
|
of tutorial_plume_on_slope. |
| 1596 |
|
o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). |
| 1597 |
|
o calc_gw: true flux-form, account for horizontal grid spacing. |
| 1598 |
|
update rotating_tank results, but not plume_on_slope (affected at |
| 1599 |
|
truncation level, 11 digits). |
| 1600 |
|
|
| 1601 |
|
checkpoint58l_post |
| 1602 |
|
o calc_gw: |
| 1603 |
|
- take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V |
| 1604 |
|
- remove side-drag for now (need to fix it); update plume_on_slope results. |
| 1605 |
|
- fix for partial-cell & non-uniform dz; update plume_on_slope results. |
| 1606 |
|
o commit code to make SST/SSS weights spatially variable |
| 1607 |
|
(based on either variable in-situ or variable initial T/S weights) |
| 1608 |
|
o pkg/ecco: |
| 1609 |
|
* commit code to relax deviations of xx_theta, xx_salt to 5*sigma, |
| 1610 |
|
now based on horizontally varying weights wthetaLev, wsaltLev |
| 1611 |
|
* cost_averagesflags now returns year indices in addition to day, month |
| 1612 |
|
* sflux balance is performed on annual basis |
| 1613 |
|
(sflxumm, sfluxmm2, bal_sfluxmm) |
| 1614 |
|
* for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, |
| 1615 |
|
including separate counting and multipliers |
| 1616 |
|
o pkg/rbcs |
| 1617 |
|
* add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing |
| 1618 |
|
|
| 1619 |
|
checkpoint58k_post |
| 1620 |
|
o testreport: |
| 1621 |
|
- always build in dir. "build" (if not there, mkdir build instead of building |
| 1622 |
|
& running in input) |
| 1623 |
|
- run in dir run (if it exists), in build otherwise. |
| 1624 |
|
- call prepare_run (if input/prepare_run exists) |
| 1625 |
|
- run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. |
| 1626 |
|
o pkg/exf modifications to interpolation and rotation routines for more |
| 1627 |
|
reasonable treatment of North Pole singularity: for tracers North Pole |
| 1628 |
|
value is set to northernmost zonal-mean value, for zonal velocity it is |
| 1629 |
|
set to zero, and for meridional velocity it is set to northernmost value. |
| 1630 |
|
o pkg/exf/exf_check_range.F |
| 1631 |
|
- add tile index to diagnostics and move stop statement to the very |
| 1632 |
|
end of the routine. |
| 1633 |
|
o pkg/diagnostics: (diagnostics_main_init.F) |
| 1634 |
|
define title of isomorphic variables according to the current config. |
| 1635 |
|
o pkg/thsice with pkg/seaice dynamics: |
| 1636 |
|
- fix domain of computation (interior only, required for exf) and do exchanges |
| 1637 |
|
- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient |
| 1638 |
|
o towards a standard way of dealing with multi-threading in MONITOR |
| 1639 |
|
and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. |
| 1640 |
|
o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) |
| 1641 |
|
to W momentum equation in nonhydrostatic and quasihydrostatic runs. |
| 1642 |
|
o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. |
| 1643 |
|
o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) |
| 1644 |
|
o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL |
| 1645 |
|
(problems ? with gradient check in bottom_ctrl_5x5 adjoint test) |
| 1646 |
|
o tracer advection: |
| 1647 |
|
- clean-up and simplify calc_common_factors.F |
| 1648 |
|
- make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer |
| 1649 |
|
advection subroutine (but still not used within DST advection S/R) |
| 1650 |
|
o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
| 1651 |
|
|
| 1652 |
|
checkpoint58j_post |
| 1653 |
|
o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
| 1654 |
|
from file (collects calls previously in FORWARD_STEP) |
| 1655 |
|
o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS |
| 1656 |
|
o adjoint store dir. adjusted accordingly |
| 1657 |
|
o genmake2 |
| 1658 |
|
replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. |
| 1659 |
|
|
| 1660 |
|
checkpoint58i_post |
| 1661 |
|
o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
| 1662 |
|
on wind stress (SEAICEstressFactor defaults to 1.) |
| 1663 |
|
o Total number of Timers is finite (<=40): comment out 2 non-essential one |
| 1664 |
|
in the_main_loop.F to avoid Pb (e.g., when running fizhi test) |
| 1665 |
|
o vector_invariant: fix highOrderVorticity(=4.th.Order) advection |
| 1666 |
|
on CS-grid: no longer loosing mass. |
| 1667 |
|
o exf & curvilinear-grid: no longer modify longitude xC & xG. |
| 1668 |
|
o pkg/ggl90: fix sloppy output and fix a bug |
| 1669 |
|
o pkg/seaice: added SEAICEuseEVPpickup parameter |
| 1670 |
|
- Set to false in order to start EVP solver with |
| 1671 |
|
non-EVP pickup files when using SEAICEuseEVP |
| 1672 |
|
- fix sign error in diffusion in seaice_calc_rhs |
| 1673 |
|
|
| 1674 |
|
checkpoint58h_post |
| 1675 |
|
* Modifications for bottom topography control |
| 1676 |
|
o replace hFacC by _hFacC at various places |
| 1677 |
|
o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL |
| 1678 |
|
o add non-self-adjoint cg2d_nsa |
| 1679 |
|
o update autodiff support routines |
| 1680 |
|
o re-initialise hfac after ctrl_depth_ini |
| 1681 |
|
o works for 5x5 box, doesnt work for global_ocean.90x40x15 |
| 1682 |
|
* Adding verification for 5x5 box (4-layer) bottom topography control |
| 1683 |
|
|
| 1684 |
|
checkpoint58g_post |
| 1685 |
|
o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., |
| 1686 |
|
used for mean seasonal cycle, mean diurnal cycle); add an example |
| 1687 |
|
in verification/global_ocean.cs32x15/input.thsice/data.diagnostics |
| 1688 |
|
o pkg/ggl90: |
| 1689 |
|
- add parameter (minimum surface kinetic energy) |
| 1690 |
|
- fix bug (avoiding division by zero) |
| 1691 |
|
o couple pkg/thsice to pkg/seaice: |
| 1692 |
|
- modify advection in seaice to accomodate new scalar fields to be advected |
| 1693 |
|
- only muliDimAdection scheme work with seaice/thsice |
| 1694 |
|
- mapping of thsice-variables to seaice-variables, back and forth |
| 1695 |
|
- does not break the verification experiments, but does not give the |
| 1696 |
|
desired results either |
| 1697 |
|
o pkg/seaice |
| 1698 |
|
- make (default) second order advection a bit less confusing? |
| 1699 |
|
|
| 1700 |
|
checkpoint58f_post |
| 1701 |
|
o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice |
| 1702 |
|
to pkg/seaice): |
| 1703 |
|
- new routines thsice_map_exf and thsice_get_exf provide the interface |
| 1704 |
|
- add an additional formal parameter to thsice_solve4temp |
| 1705 |
|
o pkg/exf: |
| 1706 |
|
- add new fields wspeed, snowprecip (to be able to couple to thsice) |
| 1707 |
|
- correct Stefan-Boltzmann constant |
| 1708 |
|
- new parameter for longwave surface emittance |
| 1709 |
|
- separate some stuff from exf_bulkformulae into new routines |
| 1710 |
|
exf_radiation, exf_wind |
| 1711 |
|
- add new parameters and constants: longwave emissivity for ocean, ice |
| 1712 |
|
and snow, evaporation parameters over ice |
| 1713 |
|
- decouple wind/stress computation from ALLOW_BULKFORMULA: always compute |
| 1714 |
|
either wind from stress or stress from wind |
| 1715 |
|
o pkg/thSIce: |
| 1716 |
|
- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F |
| 1717 |
|
- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND |
| 1718 |
|
and THSICE_CALC_THICKN |
| 1719 |
|
- for now, call to THSICE_GET_BULKF remains inside i,j loops. |
| 1720 |
|
- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h |
| 1721 |
|
to make debugging easier. |
| 1722 |
|
- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output |
| 1723 |
|
o pkg/bulk_force: |
| 1724 |
|
- clean-up comments and parameters ; |
| 1725 |
|
- add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; |
| 1726 |
|
o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; |
| 1727 |
|
generate new output for test-experiment: aim.5l_cs.thSI |
| 1728 |
|
o results_ad : rename "output.txt_adm" to "output_adm.txt" and change |
| 1729 |
|
testreport accordingly |
| 1730 |
|
|
| 1731 |
|
checkpoint58e_post |
| 1732 |
|
o SEAICE_CGRID adjoint done |
| 1733 |
|
o R_STAR adjoint implemented. |
| 1734 |
|
* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
| 1735 |
|
* need to sort out init. of h0facc, etc. |
| 1736 |
|
o Make pkg/profile fully independent of ecco,cost, etc. stuff |
| 1737 |
|
to be able to use it in pure forward. |
| 1738 |
|
|
| 1739 |
|
checkpoint58d_post |
| 1740 |
|
o upgrade simple test-experiment to tutorial example: |
| 1741 |
|
step.1: duplicate the experiment and (step.2) will remove the old copy. |
| 1742 |
|
tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
| 1743 |
|
tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) |
| 1744 |
|
tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
| 1745 |
|
tutorial_global_oce_biogeo <- copy of dic_example |
| 1746 |
|
tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
| 1747 |
|
tutorial_plume_on_slope <- copy of plume_on_slope |
| 1748 |
|
tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) |
| 1749 |
|
tutorial_global_oce_optim <- empty for now (David ?) |
| 1750 |
|
tutorial_global_oce_in_p <- copy of global_ocean_pressure |
| 1751 |
|
some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
| 1752 |
|
o correct a sign problem in cost_scat.F |
| 1753 |
|
o obcs and ptracers: fix boundary conditions for advections schemes |
| 1754 |
|
with larger stencil |
| 1755 |
|
o thsice adjoint: start |
| 1756 |
|
o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for |
| 1757 |
|
completeness |
| 1758 |
|
o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING |
| 1759 |
|
and COSINEMETH_III, add comments in default CPP_OPTIONS.h |
| 1760 |
|
o ptracers adjoint: |
| 1761 |
|
* avoid extensive recomputatations |
| 1762 |
|
* fix missing re-init. of gptr (missed by TAF) |
| 1763 |
|
o obcs: add a flag (OBCSprintDiags, defaults is true) that allows |
| 1764 |
|
me to turn off the excessive output to STDOUT that this package produces |
| 1765 |
|
o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common |
| 1766 |
|
and add those terms in Vector-Invariant formulation. |
| 1767 |
|
o in ctrl pkg, if ALLOW_CAL, use monthly mean controls |
| 1768 |
|
if the control period (xx_hfluxperiod etc) is 0 |
| 1769 |
|
o in profiles pkg, clean routines and fix details |
| 1770 |
|
o in ecco pkg, reading ssh data: |
| 1771 |
|
fix problem in case the model does not start at iter0=0 |
| 1772 |
|
o fix mnc-pickup/restart for ptracers |
| 1773 |
|
o new package prifiles: |
| 1774 |
|
code to compute profile-based cost by Gael Forget |
| 1775 |
|
(modifs in ecco, ctrl, autodiff) |
| 1776 |
|
o Benign bug fix in initialization (spotted by M. Mazloff) of |
| 1777 |
|
ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F |
| 1778 |
|
|
| 1779 |
|
checkpoint58c_post |
| 1780 |
|
o adjoint: finish NLFS adjoint and provide reference output in |
| 1781 |
|
verification/global_ocean.90x40x15/results_ad_nlfs |
| 1782 |
|
o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the |
| 1783 |
|
documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in |
| 1784 |
|
SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only |
| 1785 |
|
with SEAICE_CGRID defined. |
| 1786 |
|
o move calendarDumps from "data" to "data.cal" and clean-up the code |
| 1787 |
|
with a simple call to pkg/cal S/R: CAL_TIME2WRITE |
| 1788 |
|
o add useEXF & useCAL flags (for now, set in hard-coded way) |
| 1789 |
|
o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum |
| 1790 |
|
(were missing in NH mode, and wrong in quasihydrostatic mode). |
| 1791 |
|
waiting for Chris updated version of calc_gw to add those CALLs. |
| 1792 |
|
o fix bug in quasihydrostatic S/R ; |
| 1793 |
|
add a test for this option: global_ocean.90x40x15.qshyd |
| 1794 |
|
o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs. |
| 1795 |
|
(called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS) |
| 1796 |
|
o add on/off flag useOffLine for package OFFLINE |
| 1797 |
|
o seaice: |
| 1798 |
|
- modify advection so that it works also on the C-grid |
| 1799 |
|
- extend loop ranges in seaice_lsr and seaice_dynsolver; fixes |
| 1800 |
|
problem in multi-tile runs with C-grid |
| 1801 |
|
- add flags for clipping ice velocities and/or masking solver forcing |
| 1802 |
|
- fix drag (ocean on ice) formulation and a bug that caused noise in the |
| 1803 |
|
C-grid solver |
| 1804 |
|
- added a few comments to seaice_diffusion.F |
| 1805 |
|
- separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V |
| 1806 |
|
are now exclusive) |
| 1807 |
|
- add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which |
| 1808 |
|
required re-ordering the code a little: |
| 1809 |
|
+ make DAIRN global variable (defined in SEAICE) |
| 1810 |
|
+ move computation of the viscosities eta and zeta into a new separate |
| 1811 |
|
routine (because I need to recompute them in seaice_ocean_stress.F) |
| 1812 |
|
|
| 1813 |
|
checkpoint58b_post |
| 1814 |
|
o AIM+thSIce: fix sign of Short-Wave through the Ice ; |
| 1815 |
|
update output.txt of exp. aim.5l_cs.thSI |
| 1816 |
|
o various mnc cleanups and improvements: |
| 1817 |
|
+ shrink lookup tables by factor of ~4 |
| 1818 |
|
+ better error reporting when running out of lookup space |
| 1819 |
|
+ able to handle longer path/file names (up to 500 chars) |
| 1820 |
|
o adjoint: |
| 1821 |
|
- Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. |
| 1822 |
|
- TBD: "hidden" mom_vecinv recomp. in dynamics |
| 1823 |
|
o change forcing_In_AB to affects both T,S forcing and Momentum forcing |
| 1824 |
|
(allow to differentiate between forcing components using new integer flags: |
| 1825 |
|
momForcingOutAB=1/0 & tracForcingOutAB=1/0) |
| 1826 |
|
and add new flag to put Dissipation tendency out of Adams-Bashforth. |
| 1827 |
|
o ecco |
| 1828 |
|
- enable trend removal from SSH anomaly obs. |
| 1829 |
|
o adjoint |
| 1830 |
|
- a fix for PmEpR when #undef EXACT_CONSERV |
| 1831 |
|
- fix of "hidden" recomp. in thermodynamics (no TAF warnings) |
| 1832 |
|
- try to fix "hidden" recomp. in forward_step for NLFS |
| 1833 |
|
(NLFS seems broken sometimes after I checked it in) |
| 1834 |
|
o seaice: |
| 1835 |
|
- add c-grid version of the dynamic solver: |
| 1836 |
|
+ three new routines that are the c-grid substitute lsr, dynsolver |
| 1837 |
|
and ostres |
| 1838 |
|
+ put a few fields that were local to dynsolver into global common |
| 1839 |
|
blocks, so that I can move the computation of stresses etc into |
| 1840 |
|
seaice_lsr (saves coding but may break the adjoint). |
| 1841 |
|
- replace more hardwired parameters by runtime parameters |
| 1842 |
|
- add ice masks that mask the rhs of the implicit solvers where there |
| 1843 |
|
is no ice (commented out in seaice_dynsolver, because i am not sure |
| 1844 |
|
if this works properly), eventually this should replace the clipping |
| 1845 |
|
of ice velocities in seaice_dynsolver to +/-40cm/s. |
| 1846 |
|
o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly |
| 1847 |
|
include it only where its needed |
| 1848 |
|
o move balancing of fluxes before the call of external_forcing_surf |
| 1849 |
|
o seaice: |
| 1850 |
|
- correct units of turning angles (now they are really in degrees) |
| 1851 |
|
- move computation of GWATX/Y out of main routine into dynsolver |
| 1852 |
|
- initialize GWATX/Y in seaice_init |
| 1853 |
|
o Apply mask on Fresh-Water flux (needed for SSH forcing). |
| 1854 |
|
update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) |
| 1855 |
|
o seaice: add runtime flags for turning angles (default to zero) |
| 1856 |
|
o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean |
| 1857 |
|
and trend from exf forcing and ctrl control adjustments |
| 1858 |
|
o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF |
| 1859 |
|
(since checkpoint57x_post) |
| 1860 |
|
o change the default rotation period to 86164.s = the Earth rotation |
| 1861 |
|
o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) |
| 1862 |
|
and based on a reference stratification. Tested within hs94.cs-32x32x5. |
| 1863 |
|
o seaice advection: add code for choosing between the default (2nd order |
| 1864 |
|
central differences) and multiDim advection schemes provided by |
| 1865 |
|
pkg/generic_advdiff |
| 1866 |
|
o seaice: |
| 1867 |
|
- removed all references to SEAICE_GRID.h fields from |
| 1868 |
|
dynsolver, advect, diffus, lsr, without changing the results of lab_sea |
| 1869 |
|
(cubed-sphere configuration will change a little) |
| 1870 |
|
- grid computations in seaice_init are obsolete now. |
| 1871 |
|
- cleaned up code a little so that is easier to read (hopefully). |
| 1872 |
|
- added new (better?) discretizations of default advection and diffusion |
| 1873 |
|
(turn on with SEAICEuseFluxForm) |
| 1874 |
|
- replace 1 in 3d global fields by kSurface in growth.F |
| 1875 |
|
|
| 1876 |
|
checkpoint58a_post |
| 1877 |
|
o seaice: |
| 1878 |
|
- bug fix in advect.F |
| 1879 |
|
o shelfice: |
| 1880 |
|
- separate shelfice load anomaly from pload (breaks with time |
| 1881 |
|
dependent forcing), => introduce constant field shelficeLoadAnomaly. |
| 1882 |
|
Its default is 0., but it may be computed more cleverly from (unknown) |
| 1883 |
|
t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be |
| 1884 |
|
done offline. A good approximation of the pressure load anomaly is |
| 1885 |
|
necessary to avoid large initial adjustment processes underneath |
| 1886 |
|
deep-reaching shelfice. |
| 1887 |
|
- small fix in ISOMIP shelfice_thermodynamics |
| 1888 |
|
- add more sophisticated thermodynamics of Hellmer (1989), this is |
| 1889 |
|
now the default |
| 1890 |
|
- give a few constants more intuitive names |
| 1891 |
|
o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful |
| 1892 |
|
if bulk formulae are used in long integration (especially EmPmR). Turn |
| 1893 |
|
on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01 |
| 1894 |
|
if balancePrintMean, the imbalance that is substracted is printed to |
| 1895 |
|
STDOUT. |
| 1896 |
|
o fix bug (typo) in obcs_apply_eta.F |
| 1897 |
|
o add a new package shelfice which enables us to model the circulation |
| 1898 |
|
underneath shelf-ice with draughts of hundreds of meters. |
| 1899 |
|
- works |
| 1900 |
|
- to do: + include improved thermodynamics |
| 1901 |
|
+ check whether kSurfC (from model/inc/SURFACE.h) can be used |
| 1902 |
|
instead of new field kTopC |
| 1903 |
|
+ can we use topoFile, Ro_surf and existing code in ini_depth.F |
| 1904 |
|
instead of new field R_shelfIce and new code in ini_depth.F |
| 1905 |
|
and ini_mask_etc.F? |
| 1906 |
|
+ adjust vertical mixing schemes? |
| 1907 |
|
o seaice pkg: |
| 1908 |
|
- add a cpp-flag to include a simple formula for a salinity dependent |
| 1909 |
|
freezing point of sea water at the surface |
| 1910 |
|
- change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and |
| 1911 |
|
meridional stresses are now different (and hopefully correct) |
| 1912 |
|
o AIM pkg: change threshold on large-scale condensation to conserve Heat. |
| 1913 |
|
update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics |
| 1914 |
|
and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG) |
| 1915 |
|
o pkg/diagnostics: add options and parameters for regional-statistics |
| 1916 |
|
diagnostics ; define regions by reading a region-mask from a file |
| 1917 |
|
(might add other options later) |
| 1918 |
|
o pkg/bulk_force: |
| 1919 |
|
- add option and parameters to use AIM surface-flux formulae. |
| 1920 |
|
- Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ; |
| 1921 |
|
others forcing fields (defined in PARM05, parameter file "data") are loaded |
| 1922 |
|
from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F). |
| 1923 |
|
- initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F |
| 1924 |
|
- use the right EXCH call for uwind,vwind (to work on CS-grid). |
| 1925 |
|
- re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h) |
| 1926 |
|
and parameters (note: calcWindStress replaces .NOT.readwindstress). |
| 1927 |
|
- cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). |
| 1928 |
|
|
| 1929 |
|
checkpoint58 |
| 1930 |
|
o add "--embed-source" option to genmake2 which, when the supporting |
| 1931 |
|
tools can be compiled (as determined by genmake2) will turn on the |
| 1932 |
|
embed_files package which then embeds the entire MITgcm source code |
| 1933 |
|
(*.[fFhc] + Makefile) used for the build within the executable |
| 1934 |
|
- requested by CNH but off by default |
| 1935 |
|
- adds a paltry <9MB to the mitgcmuv executable in most cases |
| 1936 |
|
- only writes the output when useEMBEDSRC in eedata is true |
| 1937 |
|
o clean up 3-dim. relaxation codes: |
| 1938 |
|
* Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec |
| 1939 |
|
* Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) |
| 1940 |
|
* Thanks to Tom Haine for testing! |
| 1941 |
|
|
| 1942 |
|
checkpoint57z_post |
| 1943 |
|
o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): |
| 1944 |
|
affects output (@ truncation level) of exp. plume_on_slope ; updated. |
| 1945 |
|
o fix the pickup behavior for obcs in combination with ptracers |
| 1946 |
|
o fix a bug in ptracers_external_fields_load |
| 1947 |
|
o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...) |
| 1948 |
|
affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) |
| 1949 |
|
o transfered surface NH pressure to eta field (if exactConserv). |
| 1950 |
|
o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign) |
| 1951 |
|
and update lab_sea output.txt file. |
| 1952 |
|
o completing 3-dim. relaxation code: additional term |
| 1953 |
|
1/tau*( theta(i,j,k) - thetaStar(i,j,k) ) |
| 1954 |
|
in S/R EXTERNAL_FORCING_T (file external_forcing.F) |
| 1955 |
|
* At compile time, in "EXF_OPTIONS.h" set |
| 1956 |
|
#define ALLOW_CLIMTEMP_RELAXATION |
| 1957 |
|
#define ALLOW_CLIMSALT_RELAXATION |
| 1958 |
|
* At runtime in "data", under &PARM03 set (e.g., units in seconds) |
| 1959 |
|
tauThetaClimRelax3Dim = 15552000.0, |
| 1960 |
|
tauSaltClimRelax3Dim = 15552000.0, |
| 1961 |
|
* 3 cases: |
| 1962 |
|
1) Use a constant-in-time 3-dim. field |
| 1963 |
|
2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec. |
| 1964 |
|
3) Real-time relax. to time-evolving prescribed field |
| 1965 |
|
o Adding Laplacian-type smoothness constraint on |
| 1966 |
|
initial and boundary (forcing) controls (ic, bc) |
| 1967 |
|
* enable at compile-time via |
| 1968 |
|
ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION |
| 1969 |
|
* enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1 |
| 1970 |
|
* Absolute scale somewhat unclear so far |
| 1971 |
|
* no area weighting was included since no other cost term does so far |
| 1972 |
|
|
| 1973 |
|
checkpoint57y_post |
| 1974 |
|
First step for a NLFS adjoint |
| 1975 |
|
o initially suppress rStar (new flag DISABLE_RSTAR_CODE) |
| 1976 |
|
o new init. routines for calc_r_star, calc_surf_dr |
| 1977 |
|
o still need to deal with ini_masks_etc |
| 1978 |
|
o testreport seemed happy |
| 1979 |
|
checkpoint57y_pre |
| 1980 |
|
|
| 1981 |
|
o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
| 1982 |
|
o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) |
| 1983 |
|
o add new offset feature to offline pkg (plus minor cleanup) |
| 1984 |
|
o cfc fixes for final year of integration |
| 1985 |
|
o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should |
| 1986 |
|
be in GCHEM_OPTIONS). |
| 1987 |
|
|
| 1988 |
|
checkpoint57x_post |
| 1989 |
|
o fix testreport Pb in multiple test experiment. |
| 1990 |
|
o cleanup our namelist syntax in verification: |
| 1991 |
|
- make it more F95 standards compliant (some work still needed) |
| 1992 |
|
- allows the vast majority of our tests to work with gfortran |
| 1993 |
|
o Non-Hydrostatic: |
| 1994 |
|
- put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h |
| 1995 |
|
- fix exchange calls for CS-grid using the new EXCH_S3D_RL. |
| 1996 |
|
o Allow to apply AB on T,S rather than on AB(gT,gS): |
| 1997 |
|
- implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 |
| 1998 |
|
- use the same arrays (gtNm,gsNm) to hold tracer field at previous |
| 1999 |
|
time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). |
| 2000 |
|
- need a "clever" read_pickup to restart from the other AB formulation |
| 2001 |
|
o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h |
| 2002 |
|
o remove some unused variables (reduces number of compiler warnings) |
| 2003 |
|
o adjoint |
| 2004 |
|
* Disable useVariableViscosity for adjoint for time being |
| 2005 |
|
(there are a number of extensive recomputations) |
| 2006 |
|
* Initialize certain variables needed for adjoint |
| 2007 |
|
|
| 2008 |
|
checkpoint57w_post |
| 2009 |
|
o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names |
| 2010 |
|
fix the singleCpuIO RS version of MDSWRITEFIELD |
| 2011 |
|
and add a WARNING if using globalFiles=T with multi-processors. |
| 2012 |
|
o write grid-file(s) in only one format (MDS or MNC): default=MNC (if |
| 2013 |
|
using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc |
| 2014 |
|
o tracer advection scheme: |
| 2015 |
|
add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get |
| 2016 |
|
those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, |
| 2017 |
|
was not very convenient). |
| 2018 |
|
add implicit version for DST-3 & DST3_Flux_Limit vertical advection; |
| 2019 |
|
(further tests needed for the implicit DST & Flux-Limiter schemes). |
| 2020 |
|
o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef |
| 2021 |
|
and sRef for convenience, handy, when you want to initialize |
| 2022 |
|
ptracers in a large domain with a constant non-zero value. Also, |
| 2023 |
|
untangle ptracers_init.F a little. |
| 2024 |
|
|
| 2025 |
|
checkpoint57v_post |
| 2026 |
|
o change dome exp. to use variable viscosity in side-drag terms. |
| 2027 |
|
o remove all the files from the cfc_offline test since they are now |
| 2028 |
|
incorporated into tutorial_cfc_offline which has been producing |
| 2029 |
|
identical results for a few days of testing |
| 2030 |
|
o add new parameter: sideDragFactor to enable half-slip-side BC |
| 2031 |
|
and change side-drag S/R to use viscosity from mom_calc_visc |
| 2032 |
|
(can switch back by setting sideDragFactor=0.); affects results at |
| 2033 |
|
truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), |
| 2034 |
|
global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). |
| 2035 |
|
o vorticity & strain are now computed without masking, to account for |
| 2036 |
|
no-slip-side BC in variable viscosity calculation ; mask is applied |
| 2037 |
|
anyway later on, before computing advection/coriolis terms. |
| 2038 |
|
o modify exp4 to test new obcs support for reading from external files |
| 2039 |
|
and for passive tracers |
| 2040 |
|
o fix behavior of ptracers_monitor when monitor output is written to a |
| 2041 |
|
netcdf-file; still not independent of monitor.F (writes in the same |
| 2042 |
|
file). |
| 2043 |
|
o change default value of tRef (put a uniform, meaningful value for ocean |
| 2044 |
|
& atmos) and initialize sRef (was missing, as Martin mentioned). |
| 2045 |
|
o Redefine viscC?Leith*. Change the coefficients of Leith viscosity |
| 2046 |
|
to be proportional to enstrophy dissipation length. Thus, |
| 2047 |
|
viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) |
| 2048 |
|
This is now consistent with Smagorinsky and with the manual. |
| 2049 |
|
|
| 2050 |
|
checkpoint57u_post |
| 2051 |
|
o OBCS and PTRACERS: add open boundary support for passive tracers |
| 2052 |
|
- either use homogenous (pseudo) v.Neumann conditions or prescribe |
| 2053 |
|
OB-values from file; this is not different from the way theta and salinity |
| 2054 |
|
are treated |
| 2055 |
|
- however, Orlanski-radiation conditions are not supported, and the model |
| 2056 |
|
will stop if you use pTracers and Orlanski at the same time. |
| 2057 |
|
- beefed up the rountine obcs_external_fields_load: now only those open |
| 2058 |
|
boundary values are overwritten with values from files for which there |
| 2059 |
|
are really files, otherwise the OB-fields remain untouched. This makes |
| 2060 |
|
it possible to use different OBs at different ends of the domain (as |
| 2061 |
|
with EXF) |
| 2062 |
|
o reduce number of exch calls in shap_filt (s2). |
| 2063 |
|
o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ |
| 2064 |
|
truncation level) 4/5 MLAdjust test results (11&12 digits match). |
| 2065 |
|
|
| 2066 |
|
checkpoint57t_post |
| 2067 |
|
o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
| 2068 |
|
o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
| 2069 |
|
same truncation, independent of the face number: affects affects several |
| 2070 |
|
test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). |
| 2071 |
|
o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); |
| 2072 |
|
note that biharmonic viscosity + no-slip was not tested in any experiment. |
| 2073 |
|
o fix bug in non-linear free-surf side-drag ; generate new output for |
| 2074 |
|
global_ocean.cs32x15(+.thsice) & global_ocean_pressure. |
| 2075 |
|
o make mnc honor the writeBinaryPrec flag for most kinds of output |
| 2076 |
|
o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
| 2077 |
|
o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
| 2078 |
|
error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
| 2079 |
|
o add brackets in multi-terms sum to get same truncation, independent of |
| 2080 |
|
the face number (manage to get exactly same value of gU,gV at the cs-edge) |
| 2081 |
|
affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
| 2082 |
|
o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
| 2083 |
|
and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
| 2084 |
|
a maximum grid-scale Reynolds number. Also, changes all length calculations |
| 2085 |
|
in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
| 2086 |
|
Suggested values of viscosity parameters found in mom_calc_visc. |
| 2087 |
|
Many new viscosity diagnostics available. |
| 2088 |
|
|
| 2089 |
|
checkpoint57s_post |
| 2090 |
|
o Add clearing-house for viscosity calculations, mom_calc_visc and |
| 2091 |
|
correct numerous bugs in LeithD and Smagorinsky discretizations. |
| 2092 |
|
mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
| 2093 |
|
used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
| 2094 |
|
Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
| 2095 |
|
and with Strain-Tension viscous term calculation (mom_hdissip.F). |
| 2096 |
|
The Strain-Tension form is now called with useStrainTensonVisc=.true. |
| 2097 |
|
ViscAhStrain and viscAhTension are now retired. |
| 2098 |
|
o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
| 2099 |
|
o In response to JMC's bug report, genmake2 now ignores any soft-links |
| 2100 |
|
that it finds in the *current* directory when searching for files. |
| 2101 |
|
Soft-links found in any other source directories will still work as |
| 2102 |
|
they did before. |
| 2103 |
|
o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
| 2104 |
|
a C routine to unlimit the stack size |
| 2105 |
|
o mnc-ify pkg/aim snapshot vars |
| 2106 |
|
o mnc-ify pkg/land as requested by Daniel |
| 2107 |
|
o various changes to mnc including: |
| 2108 |
|
- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
| 2109 |
|
- output can now be grouped so that all files within a group |
| 2110 |
|
change the ITER portion of their names in lock-step together |
| 2111 |
|
- can now read ("global") PER-FACE (in addition to PER-TILE) files |
| 2112 |
|
and works with both EXCH1 and EXCH2 (but needs more testing) |
| 2113 |
|
- writing works for all verification test cases w/ g77 on Linux |
| 2114 |
|
|
| 2115 |
|
checkpoint57r_post |
| 2116 |
|
o make MNC variable initialization happen earlier |
| 2117 |
|
o add diagnostics for (almost) each term of the momentum Eq. |
| 2118 |
|
o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
| 2119 |
|
o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
| 2120 |
|
o remove MINIMAL_TAVE_OUTPUT option ; |
| 2121 |
|
add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
| 2122 |
|
o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
| 2123 |
|
allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
| 2124 |
|
o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
| 2125 |
|
o add time-dependent SST, SSS control |
| 2126 |
|
o cost terms in ecco/ modularized (new cost_generic.F) |
| 2127 |
|
o cost_averages routines are modularized (new cost_averagesgeneric.F) |
| 2128 |
|
o new infrastructure for seaice model vs. obs misfits in seaice/ |
| 2129 |
|
* driver from the_main_loop.F is seaice_cost_driver.F |
| 2130 |
|
* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
| 2131 |
|
* gradient check in Exp. 6a of natl_box_adjoint/ |
| 2132 |
|
o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
| 2133 |
|
(see README file) |
| 2134 |
|
|
| 2135 |
|
checkpoint57q_post |
| 2136 |
|
o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
| 2137 |
|
o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
| 2138 |
|
- bug was reported by Jean-Michel and Ian Fenty |
| 2139 |
|
o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
| 2140 |
|
update exp. cpl_aim+ocn output. |
| 2141 |
|
o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
| 2142 |
|
Needed for high-res. runs with large global files |
| 2143 |
|
to be able to limit tapelev size |
| 2144 |
|
o Changed some tests for adjoint: |
| 2145 |
|
* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
| 2146 |
|
* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
| 2147 |
|
* global_ocean.90x40x15/ back to default 3-level checkpointing |
| 2148 |
|
o Modifications to enable scripted COMMON to MODULE conversion |
| 2149 |
|
* verification/OpenAD/code/ has necessary scripts and description; |
| 2150 |
|
* converts, compiles and runs successfully; |
| 2151 |
|
|
| 2152 |
|
checkpoint57p_post |
| 2153 |
|
o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
| 2154 |
|
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
| 2155 |
|
(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
| 2156 |
|
o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
| 2157 |
|
o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
| 2158 |
|
(was already the case for dissipation with mom_vecinv, |
| 2159 |
|
and also the case for grad.PhiHyd when staggered-timeStep) |
| 2160 |
|
This will allow to put dissipation out-off the AB time-stepping. |
| 2161 |
|
Unfortunately, affects truncation error. Update output of exp. that "fails" |
| 2162 |
|
(cg2d matching number) and leave the others for later: front_relax(10), |
| 2163 |
|
global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
| 2164 |
|
matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
| 2165 |
|
|
| 2166 |
|
checkpoint57o_post |
| 2167 |
|
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
| 2168 |
|
(2) its ready to be documented during the 20050801 DocFest |
| 2169 |
|
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
| 2170 |
|
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
| 2171 |
|
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
| 2172 |
|
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
| 2173 |
|
(worth another tag) |
| 2174 |
|
|
| 2175 |
|
checkpoint57n_post |
| 2176 |
|
o adding precip control xx_precip 32 |
| 2177 |
|
o adding swflux control xx_swflux 33 |
| 2178 |
|
o Replacing 10 forcing penalty cost routines by 1 generic. |
| 2179 |
|
o Implementing partitioning in time-mean and variable adjustment |
| 2180 |
|
for atmos. state. |
| 2181 |
|
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
| 2182 |
|
o in natl_box_adjoint: |
| 2183 |
|
* updated exp 1 to 10 |
| 2184 |
|
(but does not have time-mean vs. variable split results yet) |
| 2185 |
|
o updated global1x1/*_seaice_adj/ |
| 2186 |
|
to incorporate latest changes |
| 2187 |
|
o enable useSingleCpuIO for mdsio vector routines |
| 2188 |
|
(applies in particular to tapelev I/O) |
| 2189 |
|
o removed inefficient K-loop in all active_file*control*.F |
| 2190 |
|
|
| 2191 |
|
checkpoint57m_post |
| 2192 |
|
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
| 2193 |
|
and advect_cs (use EXCH-2 and standard cs-32 grid files). |
| 2194 |
|
o pkg/exch2: filling of face-corner halo regions is optional |
| 2195 |
|
(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
| 2196 |
|
|
| 2197 |
|
checkpoint57l_post |
| 2198 |
|
tag before updating tutorials (pre-release-2) |
| 2199 |
|
o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
| 2200 |
|
for output and interpolation of input fields onto model grid) |
| 2201 |
|
o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
| 2202 |
|
Affects results of exp. rotating_tank ; update output.txt. |
| 2203 |
|
o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
| 2204 |
|
and taking the square quantity and/or using a fraction-weight field. |
| 2205 |
|
o fix aim_diagnostics_init.F mate numbers. |
| 2206 |
|
o add mnc output capability to diagnostics/diagstat and update |
| 2207 |
|
our cvsignore files for the ACSII output generated |
| 2208 |
|
|
| 2209 |
|
checkpoint57k_post |
| 2210 |
|
o lab_sea now uses diagnostics package and provides a suite of |
| 2211 |
|
new EXF diagnostics output. |
| 2212 |
|
|
| 2213 |
|
checkpoint57j_post |
| 2214 |
|
o exf |
| 2215 |
|
* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
| 2216 |
|
Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
| 2217 |
|
terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
| 2218 |
|
* extended diagnostics output |
| 2219 |
|
- now includes all EXF variables |
| 2220 |
|
- hs, hl moved to common block |
| 2221 |
|
- separate S/R for diagnostics, called after ctrl vector is added |
| 2222 |
|
- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
| 2223 |
|
- EXFqnet contains true Qnet (i.e. includes qsw) |
| 2224 |
|
* updated verif. lab_sea, global_with_exf |
| 2225 |
|
* Rearranging hflux (exf_mapfields -> exf_getforcing) |
| 2226 |
|
to ensure that diagnostics sees a true EXFqnet |
| 2227 |
|
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
| 2228 |
|
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
| 2229 |
|
several times with different frequencies. |
| 2230 |
|
o mnc-ify the thsice package as requested by Daniel Enderton |
| 2231 |
|
- the monitor--MNC output needs work |
| 2232 |
|
- many attributes need to be added (most are currently blank) |
| 2233 |
|
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
| 2234 |
|
- many attributes need to be added (most are currently blank) |
| 2235 |
|
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
| 2236 |
|
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
| 2237 |
|
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
| 2238 |
|
update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
| 2239 |
|
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
| 2240 |
|
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
| 2241 |
|
(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
| 2242 |
|
|
| 2243 |
|
checkpoint57i_post |
| 2244 |
|
o Diagnostics package was changed: diagnostic allocation is now deactivated |
| 2245 |
|
by setting an empty file name in the namelist (used to be by setting 0 frequency) |
| 2246 |
|
o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
| 2247 |
|
add 1rst Order upwind vertical Shear. |
| 2248 |
|
o add a quick fix for A/B checkpointing in OFFLINE mode |
| 2249 |
|
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
| 2250 |
|
end-run around the C/Fortran linking horror in eesup/src/timers.F |
| 2251 |
|
o added pkg/runclock: allows user to terminate run based on wall clock |
| 2252 |
|
o added non-hydrostatic scaling parameter: nh_am2 |
| 2253 |
|
o pkg/my82: futile attempt to make results compiler-independent by adding |
| 2254 |
|
some "_d 0", etc. no effect. |
| 2255 |
|
o for mnc output, fill the 'T' coordinate var with myTime and create a |
| 2256 |
|
separate 'iter' variable for iteration count |
| 2257 |
|
o pkg/diagnostics: |
| 2258 |
|
add new capability: output of Global/Regional & per-level statistics ; |
| 2259 |
|
tested against monitor output (including land & thSIce) on various exp. |
| 2260 |
|
o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
| 2261 |
|
|
| 2262 |
|
checkpoint57h_done |
| 2263 |
|
tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
| 2264 |
|
data.diagnostics, data.gchem, data.ptracers) is done. |
| 2265 |
|
|
| 2266 |
|
o pkg/diagnostics: prepare for Global/Regional statistics. |
| 2267 |
|
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
| 2268 |
|
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
| 2269 |
|
and rename it: DIFFERENT_MULTIPLE |
| 2270 |
|
|
| 2271 |
|
checkpoint57h_post |
| 2272 |
|
o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
| 2273 |
|
o pkg/diagnostics: change output frequency, now in seconds (instead |
| 2274 |
|
of Nb of iterations). This requires to change data.diagnostics. |
| 2275 |
|
checkpoint57h_pre |
| 2276 |
|
|
| 2277 |
|
o in mnc, let the user create the output dir if both mnc_outdir_date |
| 2278 |
|
and mnc_outdir_num are false |
| 2279 |
|
o add fflags() to pkg/diagnostics which allows one to specify, on a |
| 2280 |
|
per-file basis, the file precision [default behavior is unchanged] |
| 2281 |
|
o added diagnostics to pkg/kpp, including computation of mixed layer |
| 2282 |
|
depth based on a temperature/density criterion |
| 2283 |
|
o updated verification/natl_box to test the new pkg/kpp diagnostics |
| 2284 |
|
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
| 2285 |
|
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
| 2286 |
|
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
| 2287 |
|
not mnc -- this mistake was found by JMC and is now corrected |
| 2288 |
|
|
| 2289 |
|
checkpoint57g_post |
| 2290 |
|
o add Adams-Bashforth 3rd Order time stepping: |
| 2291 |
|
- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
| 2292 |
|
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
| 2293 |
|
checkpoint57g_pre |
| 2294 |
|
|
| 2295 |
|
o make lambda[Theta,Salt]ClimRelax spatially varying |
| 2296 |
|
(default remains spatially uniform constant based on tau) |
| 2297 |
|
o added new control variables |
| 2298 |
|
* init. uVel, vVel, etanN |
| 2299 |
|
* lambda[Theta,Salt]ClimRelax |
| 2300 |
|
o separate masks used for ctrl_pack/unpack 'from write_grid' output |
| 2301 |
|
(suggested by G. Forget) |
| 2302 |
|
|
| 2303 |
|
checkpoint57f_post |
| 2304 |
|
o add parameter "baseTime" = model base time = time at iteration zero |
| 2305 |
|
new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
| 2306 |
|
account for baseTime shift |
| 2307 |
|
o move Coriolis arrays from PARAMS.h to GRID.h |
| 2308 |
|
checkpoint57f_pre |
| 2309 |
|
|
| 2310 |
|
o mnc-ifying the seaice package |
| 2311 |
|
o introduced an alternative length scale calculation for use in the limiting |
| 2312 |
|
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
| 2313 |
|
o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
| 2314 |
|
o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
| 2315 |
|
as well as grad(vort3). Made it compatible with both approximate form |
| 2316 |
|
for the cubed sphere and full form of these gradients. Added flag |
| 2317 |
|
useFullLeith to select between approximate and full form. |
| 2318 |
|
o add "d0" in getcon.F to reduce differences between compilers/platforms |
| 2319 |
|
update output.txt of exp. fizhi-gridalt-hs |
| 2320 |
|
o change port_rand funtion to allow to set the seed. |
| 2321 |
|
o fix obscure MNC bug involving conversion between reals and integers |
| 2322 |
|
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
| 2323 |
|
new version is now more standards-compliant |
| 2324 |
|
o adjoint-related modifications |
| 2325 |
|
* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
| 2326 |
|
* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
| 2327 |
|
* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
| 2328 |
|
|
| 2329 |
|
checkpoint57e_post |
| 2330 |
|
o Adding eddy stress controls a la Ferreira et al. |
| 2331 |
|
checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
| 2332 |
|
|
| 2333 |
|
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
| 2334 |
|
update output.txt of exp. fizhi-gridalt-hs |
| 2335 |
|
o add more "Z" dimensions and associated coordinate vars to MNC |
| 2336 |
|
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
| 2337 |
|
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
| 2338 |
|
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
| 2339 |
|
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
| 2340 |
|
months and years. Requires pkg/cal. |
| 2341 |
|
o diagnostics: add pickup functionality |
| 2342 |
|
- off by default for backwards compatibility |
| 2343 |
|
- current version only uses MDSIO -- MNC will be added |
| 2344 |
|
o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
| 2345 |
|
o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
| 2346 |
|
|
| 2347 |
|
checkpoint57d_post |
| 2348 |
|
o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
| 2349 |
|
o modify verification/ideal_2D_oce so that it tests the creation of mnc |
| 2350 |
|
output from the diagnostics package |
| 2351 |
|
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
| 2352 |
|
o make genmake2 more portable by using ".$FS" instead of ".f" for more |
| 2353 |
|
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
| 2354 |
|
o add coordinate variables to the MNC output from the diagnostics package |
| 2355 |
|
o change MNC-flags default value: true when useMNC=TRUE |
| 2356 |
|
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
| 2357 |
|
the ability (off by default) to read the grid information using MNC |
| 2358 |
|
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
| 2359 |
|
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
| 2360 |
|
o do snap-shot diagnostics at the middle of the time-interval (instead of |
| 2361 |
|
at the end). |
| 2362 |
|
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
| 2363 |
|
new test for AIM with thSIce + slab-ocean |
| 2364 |
|
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
| 2365 |
|
o move state variable diagnostics to the beginning of the time step ; |
| 2366 |
|
(note: still needs some work specially for snap-shot diagnostics) |
| 2367 |
|
duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
| 2368 |
|
|
| 2369 |
|
checkpoint57c_post |
| 2370 |
|
o Change testing option (-ieee) to get closer agreement between g77 & ifort |
| 2371 |
|
o generate new output.txt files on faulks with g77 & the new -ieee option |
| 2372 |
|
checkpoint57c_pre |
| 2373 |
|
|
| 2374 |
|
o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
| 2375 |
|
update output.txt of exp. global_ocean.90x40x15 |
| 2376 |
|
o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
| 2377 |
|
results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
| 2378 |
|
o add saltFlux(+File) forcing capability with periodicExternalForcing |
| 2379 |
|
o allow to use pkg diagnostics for GM-Redi & ThSIce output |
| 2380 |
|
o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
| 2381 |
|
o improvements for the MNC output from DIAGNOSTICS: |
| 2382 |
|
- correct handling of the unlimitied dimension |
| 2383 |
|
- all dims now have associated coordinate variables |
| 2384 |
|
- variables located at U, V, and Corner ("Z") points are now written |
| 2385 |
|
with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
| 2386 |
|
*all* data points are output |
| 2387 |
|
o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
| 2388 |
|
o added pkg/seaice/seaice_monitor.F |
| 2389 |
|
o mdsio_readfield.F can now read files visible only to master MPI process. |
| 2390 |
|
o pkg/seaice: some test code for ice-modified ocean stress |
| 2391 |
|
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
| 2392 |
|
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
| 2393 |
|
spurious negative numbers for precipitation and humidity. Will cause |
| 2394 |
|
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
| 2395 |
|
o pkg/ctrl/ |
| 2396 |
|
* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
| 2397 |
|
May be enabled via doPackDiag |
| 2398 |
|
* introduce z-scaling of |
| 2399 |
|
+ gradient (doZscalePack) and |
| 2400 |
|
+ control (doZscaleUnpack) |
| 2401 |
|
o pkg/mdsio/ |
| 2402 |
|
* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
| 2403 |
|
* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
| 2404 |
|
|
| 2405 |
|
checkpoint57b_post |
| 2406 |
|
o simplify options in diagnostics_fill arguments (remove weird combinations) |
| 2407 |
|
o fix MNC coordinate variables so that they now contain per-face index |
| 2408 |
|
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
| 2409 |
|
general, EXCH2 grids are only aligned to a "local" coordinate system |
| 2410 |
|
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
| 2411 |
|
o Implement instantaneous output within pkg diagnostics: |
| 2412 |
|
setting a negative frequency in data.diagnostics produces |
| 2413 |
|
"snap-shot" output (as opposed to time-average if freq > 0) |
| 2414 |
|
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
| 2415 |
|
NOTE: change ptracer diagnostics name: use 2 characters to work with |
| 2416 |
|
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
| 2417 |
|
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
| 2418 |
|
becomes the coordinate variable for the 'T' dimension |
| 2419 |
|
o add CF-style coordinate variables to MNC |
| 2420 |
|
- just a first cut: numbers are meaningless on the cubesphere and |
| 2421 |
|
missing along the T axis but otherwise it works! |
| 2422 |
|
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
| 2423 |
|
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
| 2424 |
|
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
| 2425 |
|
this is based directly on what the model compute, so that the content of |
| 2426 |
|
each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
| 2427 |
|
o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
| 2428 |
|
o clean up build options files for SunOS, in particular |
| 2429 |
|
- remove -traditional from xmakedepend |
| 2430 |
|
- change -xarch=v9 to -xarch=native for f77 |
| 2431 |
|
- restore use of make (not gmake) |
| 2432 |
|
- add CC=gcc if using g77 |
| 2433 |
|
o changes per discussion of AM, JMC, & EH3 today: |
| 2434 |
|
- move redundant "grid" variables out of "state" -- in preparation of |
| 2435 |
|
creating proper CF-style coordinate variables and in recognition |
| 2436 |
|
that any/all grid variables can be easily copied (eg. w/NCO) from |
| 2437 |
|
the grid files into any of the other NetCDF files |
| 2438 |
|
- *always* output grid variables with MDSIO (this will eventually be |
| 2439 |
|
changed) |
| 2440 |
|
- output MNC grid file if useMNC is true |
| 2441 |
|
o every instance of _END_MASTER() has been found and replaced with |
| 2442 |
|
_END_MASTER( myThid ) in order to satisfy certain picky Sun |
| 2443 |
|
preprocessors |
| 2444 |
|
o re-arrange diagnostics pkg initialisation: |
| 2445 |
|
- allow each package to extend the available diagnostics list |
| 2446 |
|
- add some checking and fix small problems (multi-threaded, ...) |
| 2447 |
|
- new S/R diagnostics_fill (replace fill_diagnostics): |
| 2448 |
|
look through the short list of active diag. (instead of the long list) |
| 2449 |
|
create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
| 2450 |
|
|
| 2451 |
|
checkpoint57a_post |
| 2452 |
|
o this set of changes restores TAMC compatibility |
| 2453 |
|
tested for global_ocean.90x40x15 adjoint on trough |
| 2454 |
|
(what a pain) |
| 2455 |
|
|
| 2456 |
|
checkpoint57a_pre |
| 2457 |
|
o some modifs in tools/build_options for sunos |
| 2458 |
|
o call ctrl_pack for ctrl at end for optimcycle=0 |
| 2459 |
|
|
| 2460 |
|
checkpoint57 |
| 2461 |
|
o add horizontal bi-harmonic viscosity for vertical velocity |
| 2462 |
|
- new parameter viscA4W (defaults to viscA4) |
| 2463 |
|
- affects only non-hydrostatic code |
| 2464 |
|
- to be done: no-slip lateral boundary conditions |
| 2465 |
|
o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
| 2466 |
|
o implement Implicit Vertical advection for pTracers |
| 2467 |
|
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
| 2468 |
|
(implemented also for implicit vertical diffusion & advection) |
| 2469 |
|
o OBCS: extend application of tracer open boundary conditions |
| 2470 |
|
to a strip beyond the boundary of width Olx/Oly |
| 2471 |
|
o add call monitor to TAF set of required calls (flow directives) |
| 2472 |
|
and include in natl_box_adjoint |
| 2473 |
|
o untangle a few ifdefs related to cost, ctrl, autodiff |
| 2474 |
|
untangel a few ALLOW_ECCO_OPTIMIZATION |
| 2475 |
|
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
| 2476 |
|
(theta2, salt2 in ecco_cost_weights) |
| 2477 |
|
|
| 2478 |
|
checkpoint56c_post |
| 2479 |
|
o OBCS as control variables |
| 2480 |
|
- update ctrl_ad_diff.list, obcs_ad_diff.list |
| 2481 |
|
- remove balance of obcs controls from default |
| 2482 |
|
- fix index bug nobcs in ctrl_init |
| 2483 |
|
- fix dummy fields filen in ctrl_pack |
| 2484 |
|
- add dummy weights for obcs |
| 2485 |
|
o lsopt: comment out fort.94 output |
| 2486 |
|
o optim: |
| 2487 |
|
- remove unnecessary header files |
| 2488 |
|
- adjusted namelists |
| 2489 |
|
- add xerbla.F to Makefile |
| 2490 |
|
o exf: |
| 2491 |
|
- multiple modifications of exf_check_range |
| 2492 |
|
- unit change in exf_init_runoff from [m/year] to [m/s] |
| 2493 |
|
o mdsio: |
| 2494 |
|
- i/o-vector change debugLevel from debLevA to debLevB |
| 2495 |
|
|
| 2496 |
|
checkpoint56b_post |
| 2497 |
|
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
| 2498 |
|
is called from DO_THE_MODEL_IO |
| 2499 |
|
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
| 2500 |
|
- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
| 2501 |
|
- clean up PTRACERS_WRITE_TIMEAVE a little |
| 2502 |
|
o add another verification experiment that tests both the cfc-pkg and |
| 2503 |
|
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
| 2504 |
|
reactive tendencies treated inline with regular timestepping |
| 2505 |
|
o testreport previously did a lousy job of comparing small numbers, so |
| 2506 |
|
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
| 2507 |
|
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
| 2508 |
|
testreport. |
| 2509 |
|
o ptracers_monitor: bug fix for MPI |
| 2510 |
|
|
| 2511 |
|
checkpoint56a_post |
| 2512 |
|
o GCHEM: finish reorganizating the package |
| 2513 |
|
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
| 2514 |
|
(introduces another 3D-array for each passive tracer, but only if |
| 2515 |
|
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
| 2516 |
|
gchemTendency is not needed because the timestep is done separately) |
| 2517 |
|
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
| 2518 |
|
- GCHEM is now---more or less cleanly---separate from PTRACERS |
| 2519 |
|
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
| 2520 |
|
so clear to me how that should be done in a general way. |
| 2521 |
|
o CFC: improve formatting of output in CFC_ATMOS |
| 2522 |
|
o PTRACERS: |
| 2523 |
|
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
| 2524 |
|
that ALL experiments with ptracers enable can be checked. This makes |
| 2525 |
|
GCHEM_MONITOR obsolete. |
| 2526 |
|
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
| 2527 |
|
monitorFreq |
| 2528 |
|
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
| 2529 |
|
o add PTRACERS (PTR0[1-5]) to testreport output |
| 2530 |
|
o exf_check_range: |
| 2531 |
|
* default changed to .TRUE. |
| 2532 |
|
* will check values for niter0 if debLevA, every timestep if debLevB |
| 2533 |
|
* STOP in exf_check_range if 'out of range' |
| 2534 |
|
* range chosen generous to allow for potential extema |
| 2535 |
|
TBD: a version with stricter range |
| 2536 |
|
permitted range would be runtime parameters |
| 2537 |
|
o GMredi: |
| 2538 |
|
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
| 2539 |
|
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
| 2540 |
|
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
| 2541 |
|
o GCHEM: |
| 2542 |
|
- move call to GCHEM_FORCING_SEP, so that it is now called before |
| 2543 |
|
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
| 2544 |
|
- introduced a useGCHEM runtime flag and applied it everywhere. |
| 2545 |
|
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
| 2546 |
|
this flag is now only visible within GCHEM-pkg routines. |
| 2547 |
|
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
| 2548 |
|
be replaced by a 3D array that is computed before thermodynamics; for |
| 2549 |
|
this, the tracer ID iTracer had to be included into the parameter list |
| 2550 |
|
of ptracers_forcing |
| 2551 |
|
- set up forward_step to call gchem_forcing, that will replace |
| 2552 |
|
gchem_forcing_int in ptracers_forcing |
| 2553 |
|
- cleaning up |
| 2554 |
|
o small cleaning of exch2: remove files that are also in eesupp/src |
| 2555 |
|
|
| 2556 |
|
checkpoint56 |
| 2557 |
|
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
| 2558 |
|
o mnc: cleanup "full" files--fixes out-of-memory problem |
| 2559 |
|
o ECCO-GODAE |
| 2560 |
|
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
| 2561 |
|
* fully merged and updated from SIO code |
| 2562 |
|
windstress sign change affects |
| 2563 |
|
- exf_inscal_[u/v]stress |
| 2564 |
|
- sign of xx_tau[u/v] adjustments |
| 2565 |
|
- signs in cost_scat |
| 2566 |
|
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
| 2567 |
|
* natl_box_adjoint updated and compressed |
| 2568 |
|
* 2-level checkpoint switch added |
| 2569 |
|
(tested in EXP. 1 of natl_box_adjoint) |
| 2570 |
|
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
| 2571 |
|
o SVD |
| 2572 |
|
* first complete, non-hacked version for SVD calculations |
| 2573 |
|
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
| 2574 |
|
performed via direct access files admtlm_vector.it???? |
| 2575 |
|
(via ctrl_[un]pack) |
| 2576 |
|
* optimcycle is used for ARPACK iteration counter |
| 2577 |
|
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
| 2578 |
|
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
| 2579 |
|
and add linear transforms where necessary |
| 2580 |
|
* controls are initial/final SST, SSS (can be extended; need to check |
| 2581 |
|
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
| 2582 |
|
o mdsio: filename info to both stderr, stdout |
| 2583 |
|
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
| 2584 |
|
from sign change |
| 2585 |
|
|
| 2586 |
|
checkpoint55j_post |
| 2587 |
|
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
| 2588 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 2589 |
|
o add consistent build directories and .cvsignore files to verification |
| 2590 |
|
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
| 2591 |
|
o make all subroutines 30 or less characters in length for certain older |
| 2592 |
|
compilers to work (a thorough search only turns up two routines in |
| 2593 |
|
pkg/ptracers) |
| 2594 |
|
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
| 2595 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 2596 |
|
|
| 2597 |
|
checkpoint55i_post |
| 2598 |
|
o change arrays for total vertical diffusivity (2.D if explicit, |
| 2599 |
|
3.D if implicit) ; each ptracer uses its own background value. |
| 2600 |
|
o added mnc/NetCDF output capability to ocn_compon_interf |
| 2601 |
|
- added bits to verification/cpl_aim+ocn so that it can run on |
| 2602 |
|
ITRDA and other clusters without the mpirun "-wd" option |
| 2603 |
|
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
| 2604 |
|
configuration |
| 2605 |
|
o give MNC the ability to create additional files rather than |
| 2606 |
|
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
| 2607 |
|
- the default is just less than 2GB which is a practical limit |
| 2608 |
|
on many systems |
| 2609 |
|
o Compute the non-local term using either KPP vertical diffusivity (=default) |
| 2610 |
|
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
| 2611 |
|
|
| 2612 |
|
checkpoint55h_post |
| 2613 |
|
o add verification test "vermix" |
| 2614 |
|
o remove all the *_ioinc flags and replace with the single global |
| 2615 |
|
outputTypesInclusive flag |
| 2616 |
|
o allow to set a vertical profile of vertical diffusivity for T & S |
| 2617 |
|
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
| 2618 |
|
o useMNC moved from data.mnc to data.pkg |
| 2619 |
|
|
| 2620 |
|
checkpoint55g_post |
| 2621 |
|
o Renaming carbon AD experiments to comply with testreport conventions |
| 2622 |
|
o Updating adjoint of Held-Suarez hs94.1x64x5 |
| 2623 |
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
| 2624 |
|
have been fixed to avoid recomp. of do_oceanic_phys |
| 2625 |
|
Works well for global_ocean.90x40x15, |
| 2626 |
|
but recomp. issue remains for carbon |
| 2627 |
|
o Updating adjoint output for natl_box_adjoint after |
| 2628 |
|
pkg/ecco has been modified (see taga c55d_post) |
| 2629 |
|
|
| 2630 |
|
checkpoint55f_post |
| 2631 |
|
o rename to timeave_init_fixed |
| 2632 |
|
|
| 2633 |
|
checkpoint55e_post |
| 2634 |
|
o some delicate re-shuffle of store directives to avoid one |
| 2635 |
|
extra call of do_oceanic_physics |
| 2636 |
|
affects ecco_the_main_loop.F, do_oceanic_physics.F |
| 2637 |
|
checkpoint_lev1_directives.h |
| 2638 |
|
o NB: this may break global_ocean adjoint temporarily, |
| 2639 |
|
but it is clear how to fix it. Will do later, need this now. |
| 2640 |
|
|
| 2641 |
|
checkpoint55d_post |
| 2642 |
|
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
| 2643 |
|
o ecco_cost_weights is modified to 1x1 runs |
| 2644 |
|
o modifs to allow observations to be read in as |
| 2645 |
|
single file or yearly files |
| 2646 |
|
o enable to read exf forcing fields as either |
| 2647 |
|
single file or yearly files (flag useExfYearlyFields) |
| 2648 |
|
checkpoint55d_pre |
| 2649 |
|
|
| 2650 |
|
o switch between 2-level and 3-level checkpointing |
| 2651 |
|
o add ability of MNC to write local and "partial" (eg. 2D slices where |
| 2652 |
|
the full 3D field is never actually stored) arrays to NetCDF files |
| 2653 |
|
with the correct (that is, the complete multi-dimensional) set of |
| 2654 |
|
array indicies |
| 2655 |
|
- used in mom_vecinv() to write the diagFreq output |
| 2656 |
|
- tested (demonstrated) in verification/aim.5l_cs |
| 2657 |
|
o further mnc-ification |
| 2658 |
|
- add verification/lab_sea to the list with mnc setups |
| 2659 |
|
- fix undefined mnc v-names in cd_code |
| 2660 |
|
- add kpp to mnc output (both snapshot and timeave) |
| 2661 |
|
o non-hydrostatic code |
| 2662 |
|
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
| 2663 |
|
in calc_gw.F |
| 2664 |
|
- defaults to viscAh |
| 2665 |
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
| 2666 |
|
friction or Leith) in non-hydrostatic mode, as long as there is |
| 2667 |
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
| 2668 |
|
o pkg/cost |
| 2669 |
|
extend simple cost functions to treat time mean quantities |
| 2670 |
|
(T,U,V) via cost_accumulate_state from cost_tile |
| 2671 |
|
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
| 2672 |
|
be 2 times larger than the minimum size the advection scheme requires. |
| 2673 |
|
now get a perfect conservation of salt in advect_cs test-exp (updated) |
| 2674 |
|
o GGL90 (Gaspar's TKE mixed layer) |
| 2675 |
|
- add horizontal diffusion of TKE, requires exchanges in |
| 2676 |
|
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
| 2677 |
|
default. In OPA there is no horizontal diffusion of TKE but the |
| 2678 |
|
mixing coefficients are computed from a horizontal average of TKE of |
| 2679 |
|
6 points or so. I think that diffusion has a little more physical |
| 2680 |
|
justification. |
| 2681 |
|
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
| 2682 |
|
was in vain) |
| 2683 |
|
- mask tke-variable in ggl90_init |
| 2684 |
|
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
| 2685 |
|
o fix biharmonic diffusion on CS-grid. |
| 2686 |
|
o more obcs stuff |
| 2687 |
|
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
| 2688 |
|
for reading boundary values. This routine is called from |
| 2689 |
|
obcs_prescribe_read |
| 2690 |
|
- updated obcs_check |
| 2691 |
|
- changed sponge layer relaxation parameter units for days to seconds |
| 2692 |
|
- turned off sponge layer by default |
| 2693 |
|
- changed argument list of OBCS_CALC to myTime+deltaTclock |
| 2694 |
|
- fixed about 35 bugs in obcs_external_fields_load |
| 2695 |
|
|
| 2696 |
|
checkpoint55c_post |
| 2697 |
|
o obcs stuff |
| 2698 |
|
- new runtime flags useOBCSprescribe, useOBCSbalance |
| 2699 |
|
- re-arranged obcs_calc |
| 2700 |
|
- moved exf_getobcs to obcs_prescibe_read |
| 2701 |
|
obcs_prescibe_read is called after ORLANSKI stuff |
| 2702 |
|
and independent of it (executable can contain all). |
| 2703 |
|
- updated obcs_check |
| 2704 |
|
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
| 2705 |
|
These may be necessary only if tangential velocities are |
| 2706 |
|
prescribed at OB, not sure, needs testing. |
| 2707 |
|
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
| 2708 |
|
which simplifies the calls and passes the ifc check-bounds test |
| 2709 |
|
|
| 2710 |
|
checkpoint55b_post |
| 2711 |
|
o add a 2D scalar, Z location, exchange_2 routine. |
| 2712 |
|
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
| 2713 |
|
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
| 2714 |
|
affects advect_cs results (for the wrong reason): update output.txt |
| 2715 |
|
o use a more standard discretization for biharmonic viscosity ; |
| 2716 |
|
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
| 2717 |
|
affects results of dome set-up: update output.txt |
| 2718 |
|
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
| 2719 |
|
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
| 2720 |
|
|
| 2721 |
|
checkpoint55a_post |
| 2722 |
|
o merged code to |
| 2723 |
|
* prescribe/read time-dependent open boundaries |
| 2724 |
|
(works in conjunction with exf, cal) |
| 2725 |
|
* sponge layer code for open boundaries |
| 2726 |
|
* each boundary N/S/E/W now has its own CPP option |
| 2727 |
|
(healthy for the adjoint) |
| 2728 |
|
|
| 2729 |
|
checkpoint55 |
| 2730 |
|
o up-to-date adjoint of previous breaks |
| 2731 |
|
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
| 2732 |
|
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
| 2733 |
|
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
| 2734 |
|
- carbon: * remove tr1-related adjoint verification |
| 2735 |
|
* add ptracer as control variable |
| 2736 |
|
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
| 2737 |
|
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
| 2738 |
|
|
| 2739 |
|
checkpoint54f_post |
| 2740 |
|
o in verification/carbin/ remove experiment related to |
| 2741 |
|
ALLOW_PASSIVE_TRACER (array tr1 etc) |
| 2742 |
|
code_ad/ input_ad/ results_ad |
| 2743 |
|
|
| 2744 |
|
o add two new packages |
| 2745 |
|
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
| 2746 |
|
+ subject to optimization (memory) |
| 2747 |
|
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
| 2748 |
|
+ subject to reordering (many GOTOs in the original code) |
| 2749 |
|
+ so far opps is called for every (i,j) point, and then operates in |
| 2750 |
|
the vertical; one may want to reorder the scheme in order operate in |
| 2751 |
|
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
| 2752 |
|
fields) |
| 2753 |
|
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
| 2754 |
|
- all verification tests compile and run with linux_ia32_g77 |
| 2755 |
|
- defaults are compatible with current input files--nothing |
| 2756 |
|
should change if you were not previously using MNC |
| 2757 |
|
- MNC output has been added in numerous places (eg. timeave) |
| 2758 |
|
but there are still a few writes not yet do-able with MNC |
| 2759 |
|
(this is in progress) |
| 2760 |
|
- flags now allow for either/or/both use of MDSIO and MNC and |
| 2761 |
|
documentation will soon follow |
| 2762 |
|
- numerous small formatting cleanups for ProTeX |
| 2763 |
|
o add version info (via BUILD_INFO.h) to MNC and stdout |
| 2764 |
|
|
| 2765 |
checkpoint54e_post |
checkpoint54e_post |
| 2766 |
o add two new packages |
o add two new packages |
| 2767 |
- pp81 (Packanowski and Philander, 1981), Richardson number and |
- pp81 (Packanowski and Philander, 1981), Richardson number and |
| 2769 |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
| 2770 |
- these scheme operate in a similar manner as KPP (without ghat, of |
- these scheme operate in a similar manner as KPP (without ghat, of |
| 2771 |
course), however there is only one diffusivity that is used for both |
course), however there is only one diffusivity that is used for both |
| 2772 |
temperature and salinity (and passive tracers)ç |
temperature and salinity (and passive tracers) |
| 2773 |
o add offline package |
o add offline package |
| 2774 |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
| 2775 |
provided by Stephanie Dutkiewicz |
provided by Stephanie Dutkiewicz |
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