| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
| 6 |
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| 7 |
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o pkg/ecco and several verification experiments: |
| 8 |
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Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F |
| 9 |
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from ecco package, and revert to unified routine in model/src/ |
| 10 |
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adjust verification experiments accordingly, especially gloal_oce_llc90 |
| 11 |
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Should conclude long-standing work by Gael to reconsile the_main_loop with ECCO |
| 12 |
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and will enable OpenAD's revolve loop in ECCO setup |
| 13 |
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o pkg/generic_advdiff: |
| 14 |
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- implement compressible flow method for multi-dim advection (similar to |
| 15 |
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gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since |
| 16 |
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TAF generates many recomputations) to use it; no yet coded with implicit |
| 17 |
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vertical advection. |
| 18 |
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- change experiment advect_cs (new output) and advect_xy (same output) |
| 19 |
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to test compressible flow multi-dim advection. |
| 20 |
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o pkg/generic_advdiff: |
| 21 |
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- fix SOM advection for unusual cases (linear Free-Surf in r*, other |
| 22 |
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cases where linear Free-Surf is not @ k=1, e.g., useShelfIce) |
| 23 |
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o pkg/seaice: |
| 24 |
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- fix bug in the no-slip implementation in seaice_calc_strainrates.F, this |
| 25 |
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bug affects two verification experiments (lab_sea and lab_sea.hb87), |
| 26 |
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recover old (wrong) results by setting noSlipFac = 2. in |
| 27 |
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seaice_calc_strainrates.F; |
| 28 |
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- add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0 |
| 29 |
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- add runtime parameter SEAICE_JFNKepsilon for that finite difference |
| 30 |
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gradient in the Jacobian times vector operation (s/r seaice_jacvec) |
| 31 |
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- fix line search in seaice_jfnk.F (s/r seaice_jfnk_update) |
| 32 |
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o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code: |
| 33 |
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- new subroutines seaice_lsr_tridiagu/v |
| 34 |
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- introduce loop bounds i/jmin/max to be able to use a restricted |
| 35 |
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additive Schwarz method, but not used for now. |
| 36 |
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- rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS |
| 37 |
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- use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner |
| 38 |
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o OpenAD support |
| 39 |
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Reorganize S/R call for overall time-stepping loop to facilitate |
| 40 |
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OpenAD revolve loop replacement |
| 41 |
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(new S/R main_do_loop.F) |
| 42 |
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o model/src: |
| 43 |
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- add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3; |
| 44 |
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- pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R |
| 45 |
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ADAMS_BASHFORTH2. |
| 46 |
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o pkg/cheapaml: |
| 47 |
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- add new parameter (default=F, same as before) to disable full domain |
| 48 |
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(including land) periodicity in X & Y dir. |
| 49 |
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- new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of |
| 50 |
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prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer |
| 51 |
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into single S/R CHEAPAML_TIMESTEP. |
| 52 |
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|
| 53 |
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checkpoint64d (2013/02/17) |
| 54 |
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o pkg/monitor (angular momentum): |
| 55 |
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- do not add Eta contribution to the total AM if using rigid-lid; |
| 56 |
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- correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta). |
| 57 |
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- horizontal discretisation: compute Zonal wind contribution separately for |
| 58 |
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each component (instead of from cell centered averaged) and use the 4 |
| 59 |
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grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part. |
| 60 |
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- Check that AM is conserved with linear dynamics (momAdvection=F and linear |
| 61 |
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FreeSurf) if using vectorInvariant momentum. |
| 62 |
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o model/src (horizontal grid): |
| 63 |
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- move initialisation of all horizontal grid arrays to null value |
| 64 |
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from specific horizontal grid S/R to main S/R INI_GRID; |
| 65 |
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- add 2 new arrays to project model C-grid velocity on to zonal direction |
| 66 |
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(similar to AngleCosC & -AngleSinC but at U and V point location) and |
| 67 |
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compute them in S/R CALC_GRID_ANGLES. |
| 68 |
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o pkg/seaice: replace a hard coded parameter by a runtime parameter |
| 69 |
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SEAICE_JFNK_tolIter |
| 70 |
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o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in |
| 71 |
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preconditioner for JFNK (run LSR into the overlaps as far as possible, |
| 72 |
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i.e OLx/y-2, but overwrite the solution in the overlaps) |
| 73 |
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- extend loop range in seaice_calc_viscosity |
| 74 |
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- add new parameters SEAICE_OLx/y (default = OLx/y-2) |
| 75 |
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- add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs |
| 76 |
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- slightly modify loops in tridiagonal solver lsr-preconditioner |
| 77 |
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- by default remove the extra exchange in seaice_preconditioner with a |
| 78 |
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replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE |
| 79 |
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- modify offline_exf_seaice so that old results without RAS are reproduced |
| 80 |
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for output.dyn_jfnk.txt |
| 81 |
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in seaice_fgmres.F (unrelated to RAS) |
| 82 |
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- add a cpp-flag option for a re-ordered mapping (potentially more |
| 83 |
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efficient), but because this changes the results, turn it off by |
| 84 |
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default |
| 85 |
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- replace the save statement by local common blocks |
| 86 |
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o utils/matlab: |
| 87 |
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- fix tile-offset in rdmnc.m when output was produced using EXCH2. |
| 88 |
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- update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab) |
| 89 |
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instead of local script "load_cs.m". |
| 90 |
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o pkg/seaice: |
| 91 |
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- fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected |
| 92 |
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to the scalarProductMetric and the unrolling. By chance this does not |
| 93 |
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change the verification experiment, because of the particular domain |
| 94 |
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decomposition |
| 95 |
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o pkg/diagnostics: |
| 96 |
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- change default missing_value from UNSET_RL to -999. |
| 97 |
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o pkg/layers: improve vectorization of layers_fluxcalc.F |
| 98 |
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- step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu |
| 99 |
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time spent in this routine by more than a factor of 3 on an NEC-SX8 |
| 100 |
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- step 2: replace search algorithm by a bisection algorithm found in |
| 101 |
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Press et al. Numerical Recipes in Fortran. This algorithm can be |
| 102 |
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vectorized and finds the correct bin in approx. log2(Nlayers) steps. |
| 103 |
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For now, use this algorithm only for TARGET_NEC_SX defined. |
| 104 |
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- moved the search algorithm into a separate subroutine, that is kept |
| 105 |
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within the same file for automatic inlining. |
| 106 |
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- modified catching potential errors |
| 107 |
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o pkg/ecco: |
| 108 |
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- add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY. |
| 109 |
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o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk : |
| 110 |
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- modifications for ALLOW_GENTIM2D_CONTROL |
| 111 |
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-- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes. |
| 112 |
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-- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid ) |
| 113 |
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-- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc |
| 114 |
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-- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F |
| 115 |
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o model/src: |
| 116 |
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- account for moist thermodynamics in (dry) potential temperature equation; |
| 117 |
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update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev) |
| 118 |
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and cpl_aim+ocn. |
| 119 |
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- also switch to standard compiler (gfortran, was using ifort previously) |
| 120 |
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for fizhi-cs experiments reference output. |
| 121 |
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o pkg/ctrl: |
| 122 |
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- 1st step toward generic time-varying control variable (2D) via CPP option |
| 123 |
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ALLOW_GENTIM2D_CONTROL |
| 124 |
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- note new namelist ctrl_nml_genarr in data.ctrl |
| 125 |
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o verification/global_ocean.cs32x15: |
| 126 |
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- switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new |
| 127 |
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thsice calling sequence and update "output.icedyn.txt" output file. |
| 128 |
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o pkg/ptracers: |
| 129 |
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- from Ryan A.: code to allow to restart a tracer at regular time interval |
| 130 |
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specifying a reset frequency and a reset-phase (for each tracers). |
| 131 |
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o pkg/thsice: |
| 132 |
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- implement new sequence of calls for thsice+seaice: |
| 133 |
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previously: ice-Dyn,ice-Advect,ice-Thermo(thsice) |
| 134 |
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new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect |
| 135 |
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- allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE" |
| 136 |
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in CPP_OPTIONS.h) to recover old sequence; |
| 137 |
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- update diagnostics for Intermediate State thsice diagnostics: now filled |
| 138 |
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just before advection (instead of just after advection in old sequence); |
| 139 |
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- update output of experiment offline_exf_seaice (standard test); |
| 140 |
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- in global_ocean.cs32x15 exp., postpone output.icedyn.txt update |
| 141 |
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by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h |
| 142 |
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o pkg/aim_v23: |
| 143 |
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- use tiled array for aim_CO2 and surface wind speed for export to coupler; |
| 144 |
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- use standard pkg/mdsio routines to read & write CO2 pickup file; |
| 145 |
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- in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F; |
| 146 |
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- Implement new sequence of calls for seaice advection (with thsice and |
| 147 |
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seaice diffusion): do ice advection after ice-Thermodynamic (previously |
| 148 |
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was done before); change aim_do_physics.F (split the bi,bj loops block); |
| 149 |
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- use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence; |
| 150 |
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o pkg/thsice: |
| 151 |
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- add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case |
| 152 |
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where just seaice diffusion is used without seaice-dynamics. |
| 153 |
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|
| 154 |
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checkpoint64c (2013/01/18) |
| 155 |
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o pkg/seaice: |
| 156 |
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- add a parameter JFNKres_tFac that can replace JFNKres_t |
| 157 |
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(= JFNKres_tFac*JFNKresidual before JFNK solver) |
| 158 |
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- add a line search option to the JFNK solver |
| 159 |
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- move update of u/vIce and computation of initial residual into a separate |
| 160 |
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routine (same file); makes the code a little easier to read (?) |
| 161 |
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- the line search requires computation of the residual and for some reason |
| 162 |
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I cannot do the update of u/vIce at the beginning of the Newton loop |
| 163 |
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without changing the results, so we move computation of the new residual |
| 164 |
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also to the end of the Newton loop, even without the line search |
| 165 |
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o pkg/mdsio: |
| 166 |
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- write missing value (corresponding to undefined array value) to meta files; |
| 167 |
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skip this if missing value is one (UNSET_RL would be a better value for the |
| 168 |
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case of undefined missing value but it's current the default missing-value); |
| 169 |
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Also update mdsio_read_meta.F (reading timeInterval & missing-value). |
| 170 |
|
o pkg/exf & thsice: |
| 171 |
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- for diagnostics purpose, fill-up and update Qsw array (+ fill the |
| 172 |
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diagnostics) even when SHORTWAVE_HEATING is #undef; |
| 173 |
|
o verification/cfc_example: |
| 174 |
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- turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to |
| 175 |
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illustrate how to use it). |
| 176 |
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o verification/offline_exf_seaice: |
| 177 |
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in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing |
| 178 |
|
files to only one time-record. |
| 179 |
|
in input.thermo: narrow the 2 bands of low initial ice-concentration near |
| 180 |
|
N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for |
| 181 |
|
snapshot output; same mcPheePiston value as in thsice with |
| 182 |
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surf-current=0.2m/s. |
| 183 |
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in input.thsice: similar set-up as in input.thermo (channel with same seaice |
| 184 |
|
initial conditions). |
| 185 |
|
o verification/cfc_example: |
| 186 |
|
- update file "data" with more standard choice (default rotationPeriod, |
| 187 |
|
exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F, |
| 188 |
|
set deltaTFreeSurf to deltaTtracer) and update the output. |
| 189 |
|
o pkg/layers: |
| 190 |
|
- fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC; |
| 191 |
|
- ensure that "layers_bolus" is switched to False when useGMRedi=False. |
| 192 |
|
o verification/offline_exf_seaice: |
| 193 |
|
- set all {field}period to zero for constant-in-time forcing (not tested |
| 194 |
|
anywhere else). |
| 195 |
|
o verification/offline_exf_seaice: |
| 196 |
|
- dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice; |
| 197 |
|
- dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice. |
| 198 |
|
o model/src: |
| 199 |
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- implement Finite-Volume method for (hydrostatic) presure gradient |
| 200 |
|
from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate. |
| 201 |
|
o pkg/seaice: implement EVP* by Lemieux et al. (2012). |
| 202 |
|
- In order to be compatible with the default EVP code, this requires changing |
| 203 |
|
the EVP code around a little; and because any small change immediately |
| 204 |
|
breaks the lab_sea.hb87 verification experiment, the reference output is |
| 205 |
|
updated two times (each time the remaining aggrement was only 2 digits): |
| 206 |
|
- after replacing 1/dt by 1*recip_dt with a precomputed recip_dt |
| 207 |
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- after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt |
| 208 |
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The adjoint test lab_sea.evp also needed to be updated. |
| 209 |
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- Turn on EVP* by setting SEAICE_deltaTevp as before, and setting |
| 210 |
|
SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be |
| 211 |
|
a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps |
| 212 |
|
explicitly with SEAICEnEVPstarSteps (thereby overriding the default of |
| 213 |
|
INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately |
| 214 |
|
kept obscure, because I need to test it a little more. |
| 215 |
|
o pkg/cheapaml: |
| 216 |
|
- fix few incorrect type (_RL/_RS) in subroutine calls. |
| 217 |
|
o pkg/seaice: |
| 218 |
|
- new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays |
| 219 |
|
to _RL vector; this fixes JFNK code when compiling with "-use_r4" option. |
| 220 |
|
o model/src: |
| 221 |
|
- add a warning if using select_rStar=2 with nonlinFreeSurf <> 4; |
| 222 |
|
change (in input_ad*/data) select_rStar from 2 to 1 for AD verification |
| 223 |
|
experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output) |
| 224 |
|
o pkg/cheapaml: |
| 225 |
|
- replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and |
| 226 |
|
update output of experiment cheapAML_box. |
| 227 |
|
- store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity, |
| 228 |
|
and set them only in one place (cheapaml_readparms.F). |
| 229 |
|
- replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI" |
| 230 |
|
- remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms) |
| 231 |
|
and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia). |
| 232 |
|
o model/src/the_main_loop.F: |
| 233 |
|
- fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION. |
| 234 |
|
o pkg/seaice: |
| 235 |
|
- remove legacy branch code. |
| 236 |
|
- retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly. |
| 237 |
|
o verification/*/code*/SEAICE_OPTIONS.h: |
| 238 |
|
- remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY, |
| 239 |
|
SEAICE_CAP_HEFF). |
| 240 |
|
o pkg/cheapaml: |
| 241 |
|
- use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time |
| 242 |
|
to load new forcing fields. |
| 243 |
|
- add missing "_d 0" where it's needed; + some editing (improve indentation). |
| 244 |
|
- remove switch to "-r8" compiler option (no longer needed) in verification |
| 245 |
|
cheapAML_box, keep same output (small trucation error differences). |
| 246 |
|
o verification/offline_exf_seaice: |
| 247 |
|
- add thermodynamics only test. |
| 248 |
|
o verification/cheapAML_box: |
| 249 |
|
- split the domain in 8 (2x4) tiles; add MPI and multi-threaded test; |
| 250 |
|
keep same output (same 14 digits for cg2d). |
| 251 |
|
- switch on "-r8" compiler option (some numerical values are missing |
| 252 |
|
the "_d 0") and update output (only 6 digits for cg2d were preserved). |
| 253 |
|
|
| 254 |
|
checkpoint64b (2012/12/24) |
| 255 |
|
o pkg/cheapaml: |
| 256 |
|
- remove un-used variables (Qnet,EmPmR) from pickup files. |
| 257 |
|
- store tendency of advected variables into cheapaml pickup file |
| 258 |
|
and fix the AB-2 restart. |
| 259 |
|
o verification/offline_exf_seaice and lab_sea adjoint: |
| 260 |
|
- switch to new code (#undef SEAICE_GROWTH_LEGACY). |
| 261 |
|
- switch to 4 time steps in offline, consistent with lab_sea. |
| 262 |
|
- match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice. |
| 263 |
|
- update results after change of experiment seaice. |
| 264 |
|
o pkg/seaice: |
| 265 |
|
- remove option SEAICE_MULTICATEGORY; has been replaced with run-time |
| 266 |
|
parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is |
| 267 |
|
still defined since SEAICE_multDim needs to be set to MULTDIM value (from |
| 268 |
|
SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default. |
| 269 |
|
o model/src: |
| 270 |
|
- add run-time parameter to select CG2D solver minimum-residual solution |
| 271 |
|
(in case of a poor convergence). |
| 272 |
|
o pkg/seaice/seaice_lsr.F |
| 273 |
|
- move calculation of matrix coefficients into new |
| 274 |
|
S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same |
| 275 |
|
file; the main purpose of this change is to be able to reuse the code |
| 276 |
|
in S/R SEAICE_PRECONDITIONER |
| 277 |
|
- modify the computation of the residual so that the mass of sea-ice |
| 278 |
|
is not used twice; this simplifies the calculations, but since |
| 279 |
|
the residual is never used except when LSR_mixIniGuess.ge.4---and this is |
| 280 |
|
not tested in testreport---this does not affect the testreport results. |
| 281 |
|
o verification/seaice_obcs: |
| 282 |
|
- disable SEAICE_GROWTH_LEGACY; reset input files to match those of |
| 283 |
|
verification/lab_sea/input.salt_plume; changes results/output.txt* |
| 284 |
o model/src: |
o model/src: |
| 285 |
- adapt quasi-hydrostatic formulation to work with p or p* coordinate. |
- adapt quasi-hydrostatic formulation to work with p or p* coordinate. |
| 286 |
o pkg/seaice: |
o pkg/seaice: |
| 309 |
- add a verification experiment for JFNK in offline_exf_seaice |
- add a verification experiment for JFNK in offline_exf_seaice |
| 310 |
o verification: |
o verification: |
| 311 |
- change (for now, only fwd test) offline_exf_seaice experiment: |
- change (for now, only fwd test) offline_exf_seaice experiment: |
| 312 |
use a re-entrant channel with idealized costline (trapezoidal shape) |
use a re-entrant channel with idealized coastline (trapezoidal shape) |
| 313 |
at southern boundary to explore seaice dynamics and thermodynamics |
at southern boundary to explore seaice dynamics and thermodynamics |
| 314 |
with simple forcing. Main set-up has dynamics+thermo and SST relaxation; |
with simple forcing. Main set-up has dynamics+thermo and SST relaxation; |
| 315 |
secondary test (input.thsice) use thermodynamics only with SST relaxation. |
secondary test (input.thsice) use thermodynamics only with SST relaxation. |
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