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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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checkpoint59f |
| 8 |
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o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
| 9 |
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o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
| 10 |
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a bounded range (in forward mode) |
| 11 |
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o pkg/ecco, ctrl, autodiff and mom_common: |
| 12 |
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internal parameter controls, completements of implementations |
| 13 |
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o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
| 14 |
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o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
| 15 |
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(not seem any difference in testing results). |
| 16 |
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o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
| 17 |
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at face corners. |
| 18 |
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o pkg/generic_advdiff: |
| 19 |
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- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
| 20 |
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loop range indices for computing vertical advection tendency |
| 21 |
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and do the calculation in the interior only (no overlap) ; |
| 22 |
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for now, only implemented for SOM advection (to save CPU time). |
| 23 |
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- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
| 24 |
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o exch2 adjoint |
| 25 |
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First set of changes: |
| 26 |
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- add exch2 hand-written adjoint templates |
| 27 |
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- exch2 hand-written no longer use TAF-flag 'nownew_arg' |
| 28 |
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This will require cleanup in pkg/autodiff/*.F |
| 29 |
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(changed routines currently kept separate in verif. code/) |
| 30 |
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- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
| 31 |
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that used to hide exch2 or cubed-sphere specific code |
| 32 |
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(commented via 'cph-exch2') |
| 33 |
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o pkg/seaice |
| 34 |
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- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
| 35 |
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o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
| 36 |
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output of global_ocean.cs32x15.thsice . |
| 37 |
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|
| 38 |
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checkpoint59e |
| 39 |
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o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
| 40 |
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for B-grid vector (not yet tested) and C-grid vector (<- only used |
| 41 |
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when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). |
| 42 |
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o starting implementation of Duffy et al. (GRL 1999) salt plume scheme |
| 43 |
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(#ifdef ALLOW_SALT_PLUME) |
| 44 |
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o gather_2d/scatter_2d: removed halo regions |
| 45 |
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o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
| 46 |
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scheme and the corresponding test case (under front_relax dir). For now, |
| 47 |
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only available with Skew-flux form and not yet tested in realistic set-up. |
| 48 |
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adjoint: store directives updated, but gradient checks deteriorated, |
| 49 |
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so maybe GM/Redi adjoint is now broken. |
| 50 |
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o seaice adjoint |
| 51 |
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* add AREA, HEFF, HSNOW as control variable |
| 52 |
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(should not change lab_sea results) |
| 53 |
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* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
| 54 |
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o pkg/seaice: |
| 55 |
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* added computation of saltFlux in seaice_growth; |
| 56 |
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For time being, sea ice salinity is assumed constant |
| 57 |
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contribution of snow flooding to freshening of sea ice is neglected. |
| 58 |
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SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
| 59 |
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defaults to 0.0 in order to maintain backward compatibility. |
| 60 |
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Typical values for SEAICE_salinity are 4 to 10 g/kg. |
| 61 |
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* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
| 62 |
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* added SEAICE_availHeatFrac, which specifies fraction of surface level |
| 63 |
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heat content used to melt or grow ice |
| 64 |
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* commented out cap of HICE: it helps keep ice thinner |
| 65 |
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* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
| 66 |
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* applied OBCS T/S mask to HEFFM sea ice mask |
| 67 |
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|
| 68 |
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checkpoint59d |
| 69 |
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o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
| 70 |
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for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
| 71 |
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(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
| 72 |
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o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
| 73 |
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and change default value of parameter "GM_Small_Number"; |
| 74 |
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update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
| 75 |
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global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
| 76 |
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tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
| 77 |
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o pkg/ecco: cost function when applying pkg/smooth to controls |
| 78 |
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o pkg/ctrl: add forcingPrecond run time parameter |
| 79 |
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o pkg/seaice: |
| 80 |
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- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
| 81 |
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- fix bug in metric terms of u-equation in LSR solver (implicit part), |
| 82 |
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changes verification/lab_sea |
| 83 |
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- rearrange implicit part of u-equation in LSR solver to make it easier to |
| 84 |
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read, understand, and debug. This causes changes at the truncation level. |
| 85 |
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- fix (serious) bug in the boundary conditions (sign error in the implicit |
| 86 |
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part) of the LSR solver. Changes all LSR results. |
| 87 |
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- fixed problem with HSNOW initialization to avoid thick snow when AREA |
| 88 |
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is initilized with small values - does not change lab_sea results. |
| 89 |
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- added HsnowFile initialization capability |
| 90 |
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o pkg/smooth: addition to model/src and pkg/ctrl so allow |
| 91 |
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initialization of pkg/smooth and application to control vector |
| 92 |
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o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
| 93 |
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o dependencies: pkg/profiles requires pkg/cal |
| 94 |
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o pkg/profiles: |
| 95 |
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- added option ALLOW_PROFILES_GENERICGRID |
| 96 |
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-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
| 97 |
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that interpolation information (grid points and coefficients) is provided |
| 98 |
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within the netcdf input files. |
| 99 |
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-> sample matlab scripts can be found in MITgcm_contrib/gael |
| 100 |
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that allow you to prepare netcdf input files. |
| 101 |
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- also modified: cleaner include statements, cleaner error print statements, |
| 102 |
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cleaner stops when error, and more tests of the netcdf input files consistency. |
| 103 |
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o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
| 104 |
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o pkg/seaice: |
| 105 |
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- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
| 106 |
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requires a new routine: seaice_diagnostics_fill.F |
| 107 |
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- make sure that seaice does not move if not forced (pressure replacement |
| 108 |
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method, Hibler and Ip, 1995), changes results |
| 109 |
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- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
| 110 |
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- SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). |
| 111 |
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It is turned off by default (=-1.), because it changes the results. |
| 112 |
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- make it possible to read AREA from a file, too. |
| 113 |
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|
| 114 |
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checkpoint59c |
| 115 |
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o add S/R and diagnostics for oceanic mixed-layer depth |
| 116 |
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o move GMRedi call after all vertical mixing schemes (including KPP) |
| 117 |
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o pkg/thsice: |
| 118 |
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- ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs |
| 119 |
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(melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice |
| 120 |
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o pkg/obcs: |
| 121 |
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- bug fix for balance code |
| 122 |
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o pkg/seaice: |
| 123 |
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- allow values of SEAICE_elasticParm > 1 |
| 124 |
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- add new parameter SEAICE_evpTauRelax as an alternative |
| 125 |
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to SEAICE_elasticParm |
| 126 |
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- make lsr boundary conditions free slip (by default), changes result |
| 127 |
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- add code for no slip boundary conditions for lsr |
| 128 |
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- set minimum of zeta to zero (and not 4e8) (changes results) |
| 129 |
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- add a cap on AREA after advecting AREA if seaice_growth is not called |
| 130 |
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o change calculation of Visbeck K: |
| 131 |
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- no longer depend on tapering scheme; instead, compute slope (limited |
| 132 |
|
by GM_maxSlope). this is equivalent to what was comuted before with |
| 133 |
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clipping or linear tappering. |
| 134 |
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- fix vertical averaging (wrong by 1/2 level) |
| 135 |
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- leave the old version (but will not be maintained) within |
| 136 |
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#ifdef OLD_VISBECK_CALC / #endif |
| 137 |
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- update output of exp. ideal_2D_oce |
| 138 |
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o change error catch in calc_r_star to improve vectorization |
| 139 |
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o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
| 140 |
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add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
| 141 |
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o adjoint: |
| 142 |
|
Re-organized adjoint checkpointing according to Matt Mazloff |
| 143 |
|
(but with modifs/completions/cleanups) |
| 144 |
|
Storing is now bundled into large arrays to optimized I/O |
| 145 |
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(and second step in cleanup of the_main_loop) |
| 146 |
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|
| 147 |
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checkpoint59b |
| 148 |
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o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
| 149 |
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- export/import (between ocean & coupler) fields needed for ocean DIC. |
| 150 |
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o pkg/seaice: |
| 151 |
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- get rid of three more exchanges seaice_calc_viscosities (required |
| 152 |
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different loop boundaries in seaice_lsr and seaice_ocean_stress) |
| 153 |
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- bug fix in seaice_ocean_stress (update of lab_sea required) |
| 154 |
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- reduce loop boundaries to necessary minimum also in seaice_evp |
| 155 |
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- go back to the old way of computing deltaC/Z as the adjoint likes that |
| 156 |
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better |
| 157 |
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o Refresh of tutorial_global_oce_latlon (includes changing salinity-like |
| 158 |
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passive tracer to an Age Tracer) + update output.txt |
| 159 |
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o pkg/exf: |
| 160 |
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- implement A-grid / C-grid selection for wind-stress input files. |
| 161 |
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- clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) |
| 162 |
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for now, in exf_bulk_largeyeager04.F only : |
| 163 |
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- change implementation for case where windspeed + 2. components wind-stress |
| 164 |
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are read-in. AND use rhoConstFresh to convert evap. |
| 165 |
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o pkg/seaice: |
| 166 |
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- use correct EXCH_UV for wind-forcing (on A-grid). |
| 167 |
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- change SEAICE_OPTIONS.h to limit the number of option combinations (regarding |
| 168 |
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SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops. |
| 169 |
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o pkg/exf: |
| 170 |
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- default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC) |
| 171 |
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EXF_INTERPOLATION: |
| 172 |
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- merge global_with_exf/code version of exf_interp_read.F |
| 173 |
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to the main code ; |
| 174 |
|
- Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when |
| 175 |
|
reading the file ; Important: This options needs to be defined to recover |
| 176 |
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previous code. |
| 177 |
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otherwise, use fixed size array to read in (size=exf_interp_bufferSize). |
| 178 |
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- no longer loose real*8 precision along the way when using exf_iprec=64. |
| 179 |
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o pkg/seaice: rearrangement of common blocks (really needs more cleaning up) |
| 180 |
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- change discretisation of evp-solver in order to avoid another exchange |
| 181 |
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(changes lab_sea) and clean up a little |
| 182 |
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- replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS) |
| 183 |
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help the adjoint (this also changes the results slightly) |
| 184 |
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- add a few "_d 0" where they had been missing in seaice_evp.F |
| 185 |
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- cleaning up: remove unused seaice_calc_rhs.F |
| 186 |
|
o pkg/exf: some cleaning-up: |
| 187 |
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- change various "constants" into runtime parameters |
| 188 |
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- cleaned-up Large&Yeager04 routine which should eventually |
| 189 |
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replace exf_bulkformulae.F (changed names of S/R and CPP) |
| 190 |
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and merged various ALLOW_ATM_WIND options |
| 191 |
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only used with thsice pkg (in thsice_get_exf.F): |
| 192 |
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- implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04) |
| 193 |
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which are used when useStabilityFct_overIce=TRUE (= the default) |
| 194 |
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- change default values of ice & snow emissivity and scale downward LW |
| 195 |
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by ice & snow emissivity. |
| 196 |
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o pkg/thsice: |
| 197 |
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fix few little problems, in thsice_calc_thickn.F: |
| 198 |
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- growth vertically (and not laterally) if iceFrac == iceMaskMax |
| 199 |
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- melt only laterally if hIce < hThinIce (as the comments say) |
| 200 |
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and in thsice_extend.F: |
| 201 |
|
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
| 202 |
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- start to form ice as soon as the minimum ice-volume is reachable. |
| 203 |
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update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice), |
| 204 |
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and cpl_aim+ocn |
| 205 |
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o pkg/kpp |
| 206 |
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- move computation of surface related input fields to KPP into a new |
| 207 |
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subroutine kpp_forcing_surf.F |
| 208 |
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- remove wrong (within bi,bj loops) EXCH calls. |
| 209 |
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- little cleaning (add argument myThid in last position, cvs header ...) |
| 210 |
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- for now, fix conservation problem by exchanging KPPviscAz (may not |
| 211 |
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be the best fix) |
| 212 |
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o pkg/seaice |
| 213 |
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- check for inconsistent evp parameter/cpp-flag combination |
| 214 |
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- remove leftover errIO flat for obsolete name list error handling |
| 215 |
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o OpenAD |
| 216 |
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- changed verification/OpenAD to full baroclinic setup (including GM/Redi) |
| 217 |
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|
| 218 |
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checkpoint59a |
| 219 |
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o pkg/seaice: some parameter clarifications and a little bit of clean up |
| 220 |
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o pkg/thsice: rename run-time parameters: |
| 221 |
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himin -> hIceMin |
| 222 |
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himin0 -> hThinIce |
| 223 |
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hihig -> hThickIce |
| 224 |
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i0 -> i0swFrac |
| 225 |
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transCoef -> bMeltCoef |
| 226 |
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frac_energy -> fracMelting |
| 227 |
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add new parameters: hNewIceMax, fracFreezing, dhSnowLin |
| 228 |
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with default values (for now) that do not change the results. |
| 229 |
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remove old version of thsice vars advection in pkg/seaice. |
| 230 |
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o in FFIELDS.h: |
| 231 |
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- replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD |
| 232 |
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- make pLoad & sIceLoad always available (but still only used if |
| 233 |
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ATMOSPHERIC_LOADING is #define). |
| 234 |
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o pkg/kpp: replaced _KPP_RL with _RL |
| 235 |
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o bug fixes for vertical diffusivity computations when both KPP and |
| 236 |
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3D diffusivity arrays are used. |
| 237 |
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o pkg/seaice: fix bug in evp solver, while doing that |
| 238 |
|
- change (improve?) discretization of stress computations for both |
| 239 |
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cgrid-lsr and evp solver |
| 240 |
|
- add a new routine to compute strain rates |
| 241 |
|
- the above changes lab_sea results |
| 242 |
|
- add no slip conditions for evp solver (off by default), lsr-version |
| 243 |
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may follow |
| 244 |
|
- fix exchange for shear at Z-points (does not change lab_sea) |
| 245 |
|
- retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp |
| 246 |
|
(to force the user to pick a time step since there is not "safe" way |
| 247 |
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of choosing it) |
| 248 |
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- add principal stress diagnostics |
| 249 |
|
- rearrange fields for evp a little to avoid having to call a: too many |
| 250 |
|
exchanges and b: exchanges for stress trensor components which we do |
| 251 |
|
not have. |
| 252 |
|
- modify Hibler+Bryan (1987) stress coupling so that it reuses information |
| 253 |
|
of evp, complete rewrite for lsr case (latter is does not yet work |
| 254 |
|
in all cases) |
| 255 |
|
o pkg/kpp: add code to have mixing in shelf ice caverns |
| 256 |
|
- add myThid to all kpp routines (long overdue) |
| 257 |
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|
| 258 |
|
checkpoint59 |
| 259 |
|
o pkg/exf: |
| 260 |
|
- fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND & |
| 261 |
|
ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid |
| 262 |
|
- move exf header files from lower_case.h to UPPER_CASE.h ; |
| 263 |
|
add missing cvs Header & Name |
| 264 |
|
- add adjoint routines and flow dirs for newly used exch_uv_agrid routines |
| 265 |
|
- add namelist param. selectStressGridPosition, exf_monFreq |
| 266 |
|
- retire many _CLIM routines, and remove data.exf_clim |
| 267 |
|
+ params moved to data.exf |
| 268 |
|
+ climsst, climsss now handled by exf_set_gen, i.e. |
| 269 |
|
climss?period=0 refers to constant field, |
| 270 |
|
climss?period=-12 to monthly forcing |
| 271 |
|
- split up namelists in data.exf |
| 272 |
|
o pkg/seaice: |
| 273 |
|
- remove seaice_exch and seaice_exch_uv |
| 274 |
|
- remove superfluous exchange of theta |
| 275 |
|
- add myThid to seaice_budget_ocean/ice |
| 276 |
|
- add new interface for atmospheric wind forcing (C-grid only) |
| 277 |
|
+ new routine |
| 278 |
|
+ two new field (taux, tauy for stress over ice) |
| 279 |
|
+ removed one global field (DAIRN) for C-grid case only |
| 280 |
|
o pkg/thsise |
| 281 |
|
- 2nd set of modifs for thsice adjoint in conjunction with exf |
| 282 |
|
o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.) |
| 283 |
|
|
| 284 |
|
checkpoint58y_post |
| 285 |
|
o Added capability for latitudinal dependence of Bryan and Lewis, 1979 |
| 286 |
|
vertical diffusivity, similar to that in MOM4; turned on using |
| 287 |
|
#define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using |
| 288 |
|
diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file. |
| 289 |
|
o Added capability for 3D specification of background vertical diffusion |
| 290 |
|
coefficient. This is done by (i) #define ALLOW_3D_DIFFKR |
| 291 |
|
in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime |
| 292 |
|
"data" file that contains the 3D vertical diffusivity coefficients. |
| 293 |
|
o ice dynamics (pkg/seaice) with thsice thermodynamics: |
| 294 |
|
- add code within pkg thsice to advect & diffuse sea-ice fields |
| 295 |
|
similar to (and will replace) what has been added in seaice_advdiff.F, |
| 296 |
|
but: - conserving Mass, Heat & Salt. |
| 297 |
|
- better when using non-linear advection scheme (not yet fully tested) |
| 298 |
|
- can also be used in atmospheric set-up (for now, only the diffusion). |
| 299 |
|
|
| 300 |
|
checkpoint58x_post |
| 301 |
|
o IO option for global-file compact format: |
| 302 |
|
- add options when generating topology (utils/exch2/matlab-topology-generator) |
| 303 |
|
- add I/O capability (pkg/mdsio). |
| 304 |
|
- adapt utils/matlab/rdmds.m to read this format. |
| 305 |
|
for now long-line format not yet supported by pkg/mdsio (& exch2). |
| 306 |
|
o shelfice: add a few diagnostics |
| 307 |
|
|
| 308 |
|
checkpoint58w_post |
| 309 |
|
o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: |
| 310 |
|
rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref |
| 311 |
|
(and replace horiVertRatio in NH code). |
| 312 |
|
Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) |
| 313 |
|
and tutorial_plume_on_slope (sensitive to truncation) |
| 314 |
|
o seaice: if ALLOW_ATM_WIND is undefined use wind stress |
| 315 |
|
directly to drive seaice model (C-grid only) |
| 316 |
|
o exf: when input wind-stress (#undef ALLOW_ATM_WIND): |
| 317 |
|
- reintroduce computation of wind from stress, |
| 318 |
|
- compute tau (in exf_bulkformulae.F) from windstress averaged to |
| 319 |
|
mass points to avoid tau = 0 |
| 320 |
|
- fix serious bug: (1/3) in Fortran is not the same as (1./3.) |
| 321 |
|
o rdmnc.m: make it work with "global" files created with gluemnc |
| 322 |
|
o rdmnc.m : some improvements in dealing with singleton dimension |
| 323 |
|
(tested on all testreport mnc output files). |
| 324 |
|
o genmake2: disable pkg/profiles if netcdf test fails. |
| 325 |
|
o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output. |
| 326 |
|
o move call to cal_readparms up to make calendar parameters/variable available |
| 327 |
|
to all packages |
| 328 |
|
|
| 329 |
|
checkpoint58v_post |
| 330 |
|
o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get |
| 331 |
|
useDynP_inEos_Zc tested. |
| 332 |
|
o pkg/exf: changes to properly interpolate/mask/scale initial fields |
| 333 |
|
o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields |
| 334 |
|
and portions thereof. See read_cs.txt for description and examples. |
| 335 |
|
o utils/matlab/cs_grid/bk_line: to compute transport through passages, |
| 336 |
|
add a script (grt_circ_bkl.m) to generate broken-line between 2 points, |
| 337 |
|
following the great-circle arc between those 2 points. |
| 338 |
|
o trap un-initialized variable with pathscale compiler on weddell.mit.edu |
| 339 |
|
(thanks to Constantinos): fix few problems and get (almost) all exp to pass. |
| 340 |
|
o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in |
| 341 |
|
- enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) |
| 342 |
|
- used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81) |
| 343 |
|
- still needs work (not working with some options ; efficiency to improve) |
| 344 |
|
and serious testing. |
| 345 |
|
- use this scheme for temperature & salinity in 2 advection test exp.: |
| 346 |
|
advect_xy & advect_xz, respectively. |
| 347 |
|
|
| 348 |
|
checkpoint58u_post |
| 349 |
|
o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. |
| 350 |
|
o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. |
| 351 |
|
o testreport: add option "-skipdir" to skip some test. |
| 352 |
|
o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent |
| 353 |
|
momentum calculation. |
| 354 |
|
o gad_advection: fix vertAdvecScheme (if different from advectionScheme) |
| 355 |
|
o some cleaning: usePickupBeforeC35 no longer supported ; remove this option. |
| 356 |
|
remove checkpoint.F and the_correction_step.F (no longer used); |
| 357 |
|
do the k loop inside CYCLE_TRACER (supposed to be more efficient). |
| 358 |
|
o add option (linFSConserveTr) to correct for tracer source/sink due to |
| 359 |
|
Linear Free surface |
| 360 |
|
o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine |
| 361 |
|
o pkg/thsice: fix reading mnc-pickups |
| 362 |
|
|
| 363 |
|
checkpoint58t_post |
| 364 |
|
o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) |
| 365 |
|
o pkg/mdsio: |
| 366 |
|
- clean-up mdsio_readfield.F & mdsio_writefield_new.F and |
| 367 |
|
move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & |
| 368 |
|
mdsio_write_field.F (S/R MDS_WRITE_FIELD); |
| 369 |
|
- fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD |
| 370 |
|
- collect old S/R in one file: mdsio_rw_field.F (now just a call to |
| 371 |
|
either MDS_READ_FIELD or MDS_WRITE_FIELD ) |
| 372 |
|
- new S/R (to replace MDSWRITEMETA), which allows to write more |
| 373 |
|
informations (variable names, time ...) to meta files. |
| 374 |
|
- modify rdmds.m to give back the meta file content. |
| 375 |
|
o pkg/diagnostics: change vertical interpolation to be safer, and more |
| 376 |
|
flexible (define p-levels to interpolate to in data.diagnostics); |
| 377 |
|
add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right |
| 378 |
|
diagnostic pointer. |
| 379 |
|
o pkg/seaice: more cleaning up of seaice_growth, added many comments |
| 380 |
|
o pkg/exf: put runoff0 and runoff1 into the appropriate common block |
| 381 |
|
o fix multi-category seaice: |
| 382 |
|
- change cpp flag SEAICE_MULTILEVEL to more meaningful name: |
| 383 |
|
SEAICE_MULTICATEGORY |
| 384 |
|
- fix short wave heat flux |
| 385 |
|
o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics |
| 386 |
|
and allow to use EVP solver. Change forward lab_sea: test both EVP |
| 387 |
|
solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) |
| 388 |
|
o Initial check-in of lab_sea adjoint |
| 389 |
|
(very similar to natl_box_adjoint/code_seaice) |
| 390 |
|
* used C-grid and EVP solver |
| 391 |
|
* used KPP, GM/Redi |
| 392 |
|
* uses inAdExact=.TRUE. |
| 393 |
|
* gradient checks fail for both ADM and TLM |
| 394 |
|
due to sensitive snow melt code in seaice_grwoth (look for "JZ") |
| 395 |
|
f.d. gradients actually seem more problematic than ADM, TLM gradients; |
| 396 |
|
issue is related to forward mismatch between g77 an ifort |
| 397 |
|
o pkg/seaice: overhaul of thermodynamics |
| 398 |
|
- growth.F and groatb.F are replaced by new routine seaice_growth.F |
| 399 |
|
- budget.F is replaced by two new routines seaice_budget_ocean/ice.F |
| 400 |
|
- move a few global fields out of SEAICE.h into seaice_growth.F and |
| 401 |
|
make them 2D (FICE/QNETO/ ...) |
| 402 |
|
- remove FO (it is the same as QNETO) |
| 403 |
|
- introduce a few local fields to avoid modifying external fields such |
| 404 |
|
as atemp, etc. |
| 405 |
|
|
| 406 |
|
checkpoint58s_post |
| 407 |
|
o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F |
| 408 |
|
changed exf_set_gen.F so that |
| 409 |
|
genperiod=0 means input file is one time-constant field and |
| 410 |
|
genperiod=-12 means input file contains 12 monthly means |
| 411 |
|
o CG2D: use pre-computed solver main-diagonal (stored in common block); |
| 412 |
|
this affects truncation error ; generate new output file for exp. which |
| 413 |
|
fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), |
| 414 |
|
global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), |
| 415 |
|
ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), |
| 416 |
|
MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), |
| 417 |
|
tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), |
| 418 |
|
vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) |
| 419 |
|
o start implementation of deep-atmosphere and anelastic formulation |
| 420 |
|
o verification: remove 2nd copy of input files and use script "prepare_run" |
| 421 |
|
to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) |
| 422 |
|
o mom_common/vecinv/fluxform: fix a few initialisation isssues |
| 423 |
|
o profiles: fix for multithreaded case |
| 424 |
|
|
| 425 |
|
o diagnostics: rename few diags: |
| 426 |
|
s/'PRESSURE'/'RCENTER '/g |
| 427 |
|
s/'TICE '/'oceFreez'/g |
| 428 |
|
s/'TAUX '/'oceTAUX '/g |
| 429 |
|
s/'TAUY '/'oceTAUY '/g |
| 430 |
|
s/'SWFLUX '/'oceQsw '/g |
| 431 |
|
s/DIFx/DFxE/g |
| 432 |
|
s/DIFy/DFyE/g |
| 433 |
|
and add few ocean-forcing diagnostics: |
| 434 |
|
atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS |
| 435 |
|
o modifications to pkg/seaice/growth.F and budget.F, which change results of |
| 436 |
|
lab_sea experiment: HSNOW was sometimes treated as effective and sometimes |
| 437 |
|
as actual snow thickness. It now refers everywhere to effective snow |
| 438 |
|
thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. |
| 439 |
|
|
| 440 |
|
checkpoint58r_post |
| 441 |
|
o modifications to pkg/seaice/growth.F, which change results of |
| 442 |
|
lab_sea experiment: fixes pertain to melting snow over open water, to |
| 443 |
|
masking EVAP under sea ice, and to using the correct AREA variable for |
| 444 |
|
computations of EVAP, PRECIP, HSNOW, and GHEFF |
| 445 |
|
o add ability to read bathy, salt, and theta using MNC (off by def) |
| 446 |
|
o add flooding algorithm and advection of HSNOW for pkg/seaice; |
| 447 |
|
both are turned off by default and do no change any results |
| 448 |
|
o seaice advection with pkg/thsice: a step toward the use of non-linear |
| 449 |
|
advection scheme, but #ifdef or commented out for now (requires more EXCH). |
| 450 |
|
o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens |
| 451 |
|
(identical results) and the standard version of EXTERNAL_FIELDS_LOAD |
| 452 |
|
in natl_box (affects results @ truncation level: update output.txt) |
| 453 |
|
o multi-threading and IO: |
| 454 |
|
- replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. |
| 455 |
|
- remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls |
| 456 |
|
(needed to work with SingleCpuIO): tested in all verif. exp. |
| 457 |
|
o GAD: use simpler DST3 formulation as default (old version left within #ifdef) |
| 458 |
|
affects the results (but none of the verification test uses this scheme). |
| 459 |
|
o Adding some pkg/diagnostics capability to pkg/seaice |
| 460 |
|
(will certainly be subject to changes) |
| 461 |
|
o ctrl: adding new control variables: |
| 462 |
|
lwflux, lwdown, evap, snowprecip, apressure, runoff |
| 463 |
|
|
| 464 |
|
checkpoint58q_post |
| 465 |
|
o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up |
| 466 |
|
1/6-deg Southern Ocean configuration by 8% on IBM Datastar and |
| 467 |
|
high_res_cube configuration by 4% on Columbia. |
| 468 |
|
o clean-up multi-threaded problems (reported by debugger tcheck on ACES); |
| 469 |
|
add (in global_with_exf/code) a version of EXF_INTERP_READ without |
| 470 |
|
dynamical allocation (seems to work in multi-threaded). |
| 471 |
|
o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using |
| 472 |
|
single CPU io) so that TAF does not have to see EESUPPORT.h |
| 473 |
|
o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
| 474 |
|
|
| 475 |
|
checkpoint58p_post |
| 476 |
|
o obcs: stop if obcs is used with useCDscheme = .true. |
| 477 |
|
o shelfice: |
| 478 |
|
- fix a sign error so that no slip at shelfice interface works |
| 479 |
|
- remove stop for combination non-hydrostatic code and shelfice. That does |
| 480 |
|
not mean, that the results are correct, but at least they are numerically |
| 481 |
|
stable |
| 482 |
|
o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) |
| 483 |
|
o added adjoint exch routined for all exch*3d* routines |
| 484 |
|
and updated flow directives |
| 485 |
|
|
| 486 |
|
checkpoint58o_post |
| 487 |
|
o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; |
| 488 |
|
remove old subroutines (_XY_ & _XYZ_); update the adjoint version. |
| 489 |
|
o change controling S/R for writing pickup file (new S/R do_write_pickup) |
| 490 |
|
and clean-up reading/writing of pickup files. |
| 491 |
|
o fix local version of read/write pickup (NH part) in rotating_tank/code |
| 492 |
|
o simplify EXCH interface: |
| 493 |
|
- change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) |
| 494 |
|
- not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version |
| 495 |
|
o added the regrid package |
| 496 |
|
o shelfice: |
| 497 |
|
- add a simple boundary layer scheme to reduce noise |
| 498 |
|
- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
| 499 |
|
|
| 500 |
|
checkpoint58n_post |
| 501 |
|
o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
| 502 |
|
local variable (not in common block). |
| 503 |
|
o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
| 504 |
|
- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
| 505 |
|
- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
| 506 |
|
to work with SingleCpuIO. |
| 507 |
|
o add "_d 0" to real constant of pkg/cfc subroutines ; |
| 508 |
|
update exp. cfc_exemple & tutorial_cfc_offline output files. |
| 509 |
|
o multi-threading and IO: |
| 510 |
|
- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
| 511 |
|
(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
| 512 |
|
- barrier before and after reading. |
| 513 |
|
- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
| 514 |
|
- avoid using MDS_WRITELOCAL for LAND pkg output. |
| 515 |
|
- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
| 516 |
|
common-block variables ; Allows multi-threading with master-thread IO. |
| 517 |
|
o change default MAX_NO_THREADS from 32 to 4 ; |
| 518 |
|
and stop cleanly when MAX_NO_THREADS is too small. |
| 519 |
|
o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
| 520 |
|
|
| 521 |
|
checkpoint58m_post |
| 522 |
|
o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
| 523 |
|
and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
| 524 |
|
o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
| 525 |
|
keep global_ocean.90x40x15 (for AD testing) with former secondary test |
| 526 |
|
(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
| 527 |
|
o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
| 528 |
|
add MITgcm_tutorials (= code + all the tutorials) |
| 529 |
|
o ecco, option to compute cost for total ssh (mean+anom) |
| 530 |
|
o consistent with addition of ptracer and ssh in pkg/profiles |
| 531 |
|
o profiles: adding ptracer and ssh |
| 532 |
|
o testreport: change multi-test output-file name |
| 533 |
|
(from output.txt.{name} to output.{name}.txt) |
| 534 |
|
o profiles: now ok for mutli-tiles case |
| 535 |
|
o seaice: add 4 parameters for different advection schemes for area, |
| 536 |
|
(effective) seaice thickness, enthalphy, and snow height. Their default |
| 537 |
|
is the standard parameter SEAICEadvScheme |
| 538 |
|
o calc_gw: |
| 539 |
|
- add cosFacU in zonal viscous flux (harmonic.visc.). |
| 540 |
|
- put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. |
| 541 |
|
of tutorial_plume_on_slope. |
| 542 |
|
o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). |
| 543 |
|
o calc_gw: true flux-form, account for horizontal grid spacing. |
| 544 |
|
update rotating_tank results, but not plume_on_slope (affected at |
| 545 |
|
truncation level, 11 digits). |
| 546 |
|
|
| 547 |
|
checkpoint58l_post |
| 548 |
|
o calc_gw: |
| 549 |
|
- take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V |
| 550 |
|
- remove side-drag for now (need to fix it); update plume_on_slope results. |
| 551 |
|
- fix for partial-cell & non-uniform dz; update plume_on_slope results. |
| 552 |
|
o commit code to make SST/SSS weights spatially variable |
| 553 |
|
(based on either variable in-situ or variable initial T/S weights) |
| 554 |
|
o pkg/ecco: |
| 555 |
|
* commit code to relax deviations of xx_theta, xx_salt to 5*sigma, |
| 556 |
|
now based on horizontally varying weights wthetaLev, wsaltLev |
| 557 |
|
* cost_averagesflags now returns year indices in addition to day, month |
| 558 |
|
* sflux balance is performed on annual basis |
| 559 |
|
(sflxumm, sfluxmm2, bal_sfluxmm) |
| 560 |
|
* for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, |
| 561 |
|
including separate counting and multipliers |
| 562 |
|
o pkg/rbcs |
| 563 |
|
* add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing |
| 564 |
|
|
| 565 |
|
checkpoint58k_post |
| 566 |
|
o testreport: |
| 567 |
|
- always build in dir. "build" (if not there, mkdir build instead of building |
| 568 |
|
& running in input) |
| 569 |
|
- run in dir run (if it exists), in build otherwise. |
| 570 |
|
- call prepare_run (if input/prepare_run exists) |
| 571 |
|
- run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. |
| 572 |
|
o pkg/exf modifications to interpolation and rotation routines for more |
| 573 |
|
reasonable treatment of North Pole singularity: for tracers North Pole |
| 574 |
|
value is set to northernmost zonal-mean value, for zonal velocity it is |
| 575 |
|
set to zero, and for meridional velocity it is set to northernmost value. |
| 576 |
|
o pkg/exf/exf_check_range.F |
| 577 |
|
- add tile index to diagnostics and move stop statement to the very |
| 578 |
|
end of the routine. |
| 579 |
|
o pkg/diagnostics: (diagnostics_main_init.F) |
| 580 |
|
define title of isomorphic variables according to the current config. |
| 581 |
|
o pkg/thsice with pkg/seaice dynamics: |
| 582 |
|
- fix domain of computation (interior only, required for exf) and do exchanges |
| 583 |
|
- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient |
| 584 |
|
o towards a standard way of dealing with multi-threading in MONITOR |
| 585 |
|
and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. |
| 586 |
|
o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) |
| 587 |
|
to W momentum equation in nonhydrostatic and quasihydrostatic runs. |
| 588 |
|
o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. |
| 589 |
|
o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) |
| 590 |
|
o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL |
| 591 |
|
(problems ? with gradient check in bottom_ctrl_5x5 adjoint test) |
| 592 |
|
o tracer advection: |
| 593 |
|
- clean-up and simplify calc_common_factors.F |
| 594 |
|
- make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer |
| 595 |
|
advection subroutine (but still not used within DST advection S/R) |
| 596 |
|
o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
| 597 |
|
|
| 598 |
|
checkpoint58j_post |
| 599 |
|
o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
| 600 |
|
from file (collects calls previously in FORWARD_STEP) |
| 601 |
|
o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS |
| 602 |
|
o adjoint store dir. adjusted accordingly |
| 603 |
|
o genmake2 |
| 604 |
|
replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. |
| 605 |
|
|
| 606 |
|
checkpoint58i_post |
| 607 |
|
o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
| 608 |
|
on wind stress (SEAICEstressFactor defaults to 1.) |
| 609 |
|
o Total number of Timers is finite (<=40): comment out 2 non-essential one |
| 610 |
|
in the_main_loop.F to avoid Pb (e.g., when running fizhi test) |
| 611 |
|
o vector_invariant: fix highOrderVorticity(=4.th.Order) advection |
| 612 |
|
on CS-grid: no longer loosing mass. |
| 613 |
|
o exf & curvilinear-grid: no longer modify longitude xC & xG. |
| 614 |
|
o pkg/ggl90: fix sloppy output and fix a bug |
| 615 |
|
o pkg/seaice: added SEAICEuseEVPpickup parameter |
| 616 |
|
- Set to false in order to start EVP solver with |
| 617 |
|
non-EVP pickup files when using SEAICEuseEVP |
| 618 |
|
- fix sign error in diffusion in seaice_calc_rhs |
| 619 |
|
|
| 620 |
|
checkpoint58h_post |
| 621 |
|
* Modifications for bottom topography control |
| 622 |
|
o replace hFacC by _hFacC at various places |
| 623 |
|
o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL |
| 624 |
|
o add non-self-adjoint cg2d_nsa |
| 625 |
|
o update autodiff support routines |
| 626 |
|
o re-initialise hfac after ctrl_depth_ini |
| 627 |
|
o works for 5x5 box, doesnt work for global_ocean.90x40x15 |
| 628 |
|
* Adding verification for 5x5 box (4-layer) bottom topography control |
| 629 |
|
|
| 630 |
|
checkpoint58g_post |
| 631 |
|
o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., |
| 632 |
|
used for mean seasonal cycle, mean diurnal cycle); add an example |
| 633 |
|
in verification/global_ocean.cs32x15/input.thsice/data.diagnostics |
| 634 |
|
o pkg/ggl90: |
| 635 |
|
- add parameter (minimum surface kinetic energy) |
| 636 |
|
- fix bug (avoiding division by zero) |
| 637 |
|
o couple pkg/thsice to pkg/seaice: |
| 638 |
|
- modify advection in seaice to accomodate new scalar fields to be advected |
| 639 |
|
- only muliDimAdection scheme work with seaice/thsice |
| 640 |
|
- mapping of thsice-variables to seaice-variables, back and forth |
| 641 |
|
- does not break the verification experiments, but does not give the |
| 642 |
|
desired results either |
| 643 |
|
o pkg/seaice |
| 644 |
|
- make (default) second order advection a bit less confusing? |
| 645 |
|
|
| 646 |
|
checkpoint58f_post |
| 647 |
|
o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice |
| 648 |
|
to pkg/seaice): |
| 649 |
|
- new routines thsice_map_exf and thsice_get_exf provide the interface |
| 650 |
|
- add an additional formal parameter to thsice_solve4temp |
| 651 |
|
o pkg/exf: |
| 652 |
|
- add new fields wspeed, snowprecip (to be able to couple to thsice) |
| 653 |
|
- correct Stefan-Boltzmann constant |
| 654 |
|
- new parameter for longwave surface emittance |
| 655 |
|
- separate some stuff from exf_bulkformulae into new routines |
| 656 |
|
exf_radiation, exf_wind |
| 657 |
|
- add new parameters and constants: longwave emissivity for ocean, ice |
| 658 |
|
and snow, evaporation parameters over ice |
| 659 |
|
- decouple wind/stress computation from ALLOW_BULKFORMULA: always compute |
| 660 |
|
either wind from stress or stress from wind |
| 661 |
|
o pkg/thSIce: |
| 662 |
|
- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F |
| 663 |
|
- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND |
| 664 |
|
and THSICE_CALC_THICKN |
| 665 |
|
- for now, call to THSICE_GET_BULKF remains inside i,j loops. |
| 666 |
|
- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h |
| 667 |
|
to make debugging easier. |
| 668 |
|
- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output |
| 669 |
|
o pkg/bulk_force: |
| 670 |
|
- clean-up comments and parameters ; |
| 671 |
|
- add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; |
| 672 |
|
o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; |
| 673 |
|
generate new output for test-experiment: aim.5l_cs.thSI |
| 674 |
|
o results_ad : rename "output.txt_adm" to "output_adm.txt" and change |
| 675 |
|
testreport accordingly |
| 676 |
|
|
| 677 |
|
checkpoint58e_post |
| 678 |
|
o SEAICE_CGRID adjoint done |
| 679 |
|
o R_STAR adjoint implemented. |
| 680 |
|
* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
| 681 |
|
* need to sort out init. of h0facc, etc. |
| 682 |
|
o Make pkg/profile fully independent of ecco,cost, etc. stuff |
| 683 |
|
to be able to use it in pure forward. |
| 684 |
|
|
| 685 |
|
checkpoint58d_post |
| 686 |
|
o upgrade simple test-experiment to tutorial example: |
| 687 |
|
step.1: duplicate the experiment and (step.2) will remove the old copy. |
| 688 |
|
tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
| 689 |
|
tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) |
| 690 |
|
tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
| 691 |
|
tutorial_global_oce_biogeo <- copy of dic_example |
| 692 |
|
tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
| 693 |
|
tutorial_plume_on_slope <- copy of plume_on_slope |
| 694 |
|
tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) |
| 695 |
|
tutorial_global_oce_optim <- empty for now (David ?) |
| 696 |
|
tutorial_global_oce_in_p <- copy of global_ocean_pressure |
| 697 |
|
some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
| 698 |
|
o correct a sign problem in cost_scat.F |
| 699 |
|
o obcs and ptracers: fix boundary conditions for advections schemes |
| 700 |
|
with larger stencil |
| 701 |
|
o thsice adjoint: start |
| 702 |
|
o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for |
| 703 |
|
completeness |
| 704 |
|
o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING |
| 705 |
|
and COSINEMETH_III, add comments in default CPP_OPTIONS.h |
| 706 |
|
o ptracers adjoint: |
| 707 |
|
* avoid extensive recomputatations |
| 708 |
|
* fix missing re-init. of gptr (missed by TAF) |
| 709 |
|
o obcs: add a flag (OBCSprintDiags, defaults is true) that allows |
| 710 |
|
me to turn off the excessive output to STDOUT that this package produces |
| 711 |
|
o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common |
| 712 |
|
and add those terms in Vector-Invariant formulation. |
| 713 |
|
o in ctrl pkg, if ALLOW_CAL, use monthly mean controls |
| 714 |
|
if the control period (xx_hfluxperiod etc) is 0 |
| 715 |
|
o in profiles pkg, clean routines and fix details |
| 716 |
|
o in ecco pkg, reading ssh data: |
| 717 |
|
fix problem in case the model does not start at iter0=0 |
| 718 |
|
o fix mnc-pickup/restart for ptracers |
| 719 |
|
o new package prifiles: |
| 720 |
|
code to compute profile-based cost by Gael Forget |
| 721 |
|
(modifs in ecco, ctrl, autodiff) |
| 722 |
|
o Benign bug fix in initialization (spotted by M. Mazloff) of |
| 723 |
|
ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F |
| 724 |
|
|
| 725 |
|
checkpoint58c_post |
| 726 |
|
o adjoint: finish NLFS adjoint and provide reference output in |
| 727 |
|
verification/global_ocean.90x40x15/results_ad_nlfs |
| 728 |
|
o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the |
| 729 |
|
documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in |
| 730 |
|
SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only |
| 731 |
|
with SEAICE_CGRID defined. |
| 732 |
|
o move calendarDumps from "data" to "data.cal" and clean-up the code |
| 733 |
|
with a simple call to pkg/cal S/R: CAL_TIME2WRITE |
| 734 |
|
o add useEXF & useCAL flags (for now, set in hard-coded way) |
| 735 |
|
o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum |
| 736 |
|
(were missing in NH mode, and wrong in quasihydrostatic mode). |
| 737 |
|
waiting for Chris updated version of calc_gw to add those CALLs. |
| 738 |
|
o fix bug in quasihydrostatic S/R ; |
| 739 |
|
add a test for this option: global_ocean.90x40x15.qshyd |
| 740 |
|
o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs. |
| 741 |
|
(called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS) |
| 742 |
|
o add on/off flag useOffLine for package OFFLINE |
| 743 |
|
o seaice: |
| 744 |
|
- modify advection so that it works also on the C-grid |
| 745 |
|
- extend loop ranges in seaice_lsr and seaice_dynsolver; fixes |
| 746 |
|
problem in multi-tile runs with C-grid |
| 747 |
|
- add flags for clipping ice velocities and/or masking solver forcing |
| 748 |
|
- fix drag (ocean on ice) formulation and a bug that caused noise in the |
| 749 |
|
C-grid solver |
| 750 |
|
- added a few comments to seaice_diffusion.F |
| 751 |
|
- separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V |
| 752 |
|
are now exclusive) |
| 753 |
|
- add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which |
| 754 |
|
required re-ordering the code a little: |
| 755 |
|
+ make DAIRN global variable (defined in SEAICE) |
| 756 |
|
+ move computation of the viscosities eta and zeta into a new separate |
| 757 |
|
routine (because I need to recompute them in seaice_ocean_stress.F) |
| 758 |
|
|
| 759 |
|
checkpoint58b_post |
| 760 |
|
o AIM+thSIce: fix sign of Short-Wave through the Ice ; |
| 761 |
|
update output.txt of exp. aim.5l_cs.thSI |
| 762 |
|
o various mnc cleanups and improvements: |
| 763 |
|
+ shrink lookup tables by factor of ~4 |
| 764 |
|
+ better error reporting when running out of lookup space |
| 765 |
|
+ able to handle longer path/file names (up to 500 chars) |
| 766 |
|
o adjoint: |
| 767 |
|
- Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. |
| 768 |
|
- TBD: "hidden" mom_vecinv recomp. in dynamics |
| 769 |
|
o change forcing_In_AB to affects both T,S forcing and Momentum forcing |
| 770 |
|
(allow to differentiate between forcing components using new integer flags: |
| 771 |
|
momForcingOutAB=1/0 & tracForcingOutAB=1/0) |
| 772 |
|
and add new flag to put Dissipation tendency out of Adams-Bashforth. |
| 773 |
|
o ecco |
| 774 |
|
- enable trend removal from SSH anomaly obs. |
| 775 |
|
o adjoint |
| 776 |
|
- a fix for PmEpR when #undef EXACT_CONSERV |
| 777 |
|
- fix of "hidden" recomp. in thermodynamics (no TAF warnings) |
| 778 |
|
- try to fix "hidden" recomp. in forward_step for NLFS |
| 779 |
|
(NLFS seems broken sometimes after I checked it in) |
| 780 |
|
o seaice: |
| 781 |
|
- add c-grid version of the dynamic solver: |
| 782 |
|
+ three new routines that are the c-grid substitute lsr, dynsolver |
| 783 |
|
and ostres |
| 784 |
|
+ put a few fields that were local to dynsolver into global common |
| 785 |
|
blocks, so that I can move the computation of stresses etc into |
| 786 |
|
seaice_lsr (saves coding but may break the adjoint). |
| 787 |
|
- replace more hardwired parameters by runtime parameters |
| 788 |
|
- add ice masks that mask the rhs of the implicit solvers where there |
| 789 |
|
is no ice (commented out in seaice_dynsolver, because i am not sure |
| 790 |
|
if this works properly), eventually this should replace the clipping |
| 791 |
|
of ice velocities in seaice_dynsolver to +/-40cm/s. |
| 792 |
|
o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly |
| 793 |
|
include it only where its needed |
| 794 |
|
o move balancing of fluxes before the call of external_forcing_surf |
| 795 |
|
o seaice: |
| 796 |
|
- correct units of turning angles (now they are really in degrees) |
| 797 |
|
- move computation of GWATX/Y out of main routine into dynsolver |
| 798 |
|
- initialize GWATX/Y in seaice_init |
| 799 |
|
o Apply mask on Fresh-Water flux (needed for SSH forcing). |
| 800 |
|
update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) |
| 801 |
|
o seaice: add runtime flags for turning angles (default to zero) |
| 802 |
|
o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean |
| 803 |
|
and trend from exf forcing and ctrl control adjustments |
| 804 |
|
o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF |
| 805 |
|
(since checkpoint57x_post) |
| 806 |
|
o change the default rotation period to 86164.s = the Earth rotation |
| 807 |
|
o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) |
| 808 |
|
and based on a reference stratification. Tested within hs94.cs-32x32x5. |
| 809 |
|
o seaice advection: add code for choosing between the default (2nd order |
| 810 |
|
central differences) and multiDim advection schemes provided by |
| 811 |
|
pkg/generic_advdiff |
| 812 |
|
o seaice: |
| 813 |
|
- removed all references to SEAICE_GRID.h fields from |
| 814 |
|
dynsolver, advect, diffus, lsr, without changing the results of lab_sea |
| 815 |
|
(cubed-sphere configuration will change a little) |
| 816 |
|
- grid computations in seaice_init are obsolete now. |
| 817 |
|
- cleaned up code a little so that is easier to read (hopefully). |
| 818 |
|
- added new (better?) discretizations of default advection and diffusion |
| 819 |
|
(turn on with SEAICEuseFluxForm) |
| 820 |
|
- replace 1 in 3d global fields by kSurface in growth.F |
| 821 |
|
|
| 822 |
|
checkpoint58a_post |
| 823 |
|
o seaice: |
| 824 |
|
- bug fix in advect.F |
| 825 |
|
o shelfice: |
| 826 |
|
- separate shelfice load anomaly from pload (breaks with time |
| 827 |
|
dependent forcing), => introduce constant field shelficeLoadAnomaly. |
| 828 |
|
Its default is 0., but it may be computed more cleverly from (unknown) |
| 829 |
|
t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be |
| 830 |
|
done offline. A good approximation of the pressure load anomaly is |
| 831 |
|
necessary to avoid large initial adjustment processes underneath |
| 832 |
|
deep-reaching shelfice. |
| 833 |
|
- small fix in ISOMIP shelfice_thermodynamics |
| 834 |
|
- add more sophisticated thermodynamics of Hellmer (1989), this is |
| 835 |
|
now the default |
| 836 |
|
- give a few constants more intuitive names |
| 837 |
|
o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful |
| 838 |
|
if bulk formulae are used in long integration (especially EmPmR). Turn |
| 839 |
|
on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01 |
| 840 |
|
if balancePrintMean, the imbalance that is substracted is printed to |
| 841 |
|
STDOUT. |
| 842 |
|
o fix bug (typo) in obcs_apply_eta.F |
| 843 |
|
o add a new package shelfice which enables us to model the circulation |
| 844 |
|
underneath shelf-ice with draughts of hundreds of meters. |
| 845 |
|
- works |
| 846 |
|
- to do: + include improved thermodynamics |
| 847 |
|
+ check whether kSurfC (from model/inc/SURFACE.h) can be used |
| 848 |
|
instead of new field kTopC |
| 849 |
|
+ can we use topoFile, Ro_surf and existing code in ini_depth.F |
| 850 |
|
instead of new field R_shelfIce and new code in ini_depth.F |
| 851 |
|
and ini_mask_etc.F? |
| 852 |
|
+ adjust vertical mixing schemes? |
| 853 |
|
o seaice pkg: |
| 854 |
|
- add a cpp-flag to include a simple formula for a salinity dependent |
| 855 |
|
freezing point of sea water at the surface |
| 856 |
|
- change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and |
| 857 |
|
meridional stresses are now different (and hopefully correct) |
| 858 |
|
o AIM pkg: change threshold on large-scale condensation to conserve Heat. |
| 859 |
|
update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics |
| 860 |
|
and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG) |
| 861 |
|
o pkg/diagnostics: add options and parameters for regional-statistics |
| 862 |
|
diagnostics ; define regions by reading a region-mask from a file |
| 863 |
|
(might add other options later) |
| 864 |
|
o pkg/bulk_force: |
| 865 |
|
- add option and parameters to use AIM surface-flux formulae. |
| 866 |
|
- Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ; |
| 867 |
|
others forcing fields (defined in PARM05, parameter file "data") are loaded |
| 868 |
|
from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F). |
| 869 |
|
- initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F |
| 870 |
|
- use the right EXCH call for uwind,vwind (to work on CS-grid). |
| 871 |
|
- re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h) |
| 872 |
|
and parameters (note: calcWindStress replaces .NOT.readwindstress). |
| 873 |
|
- cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). |
| 874 |
|
|
| 875 |
|
checkpoint58 |
| 876 |
|
o add "--embed-source" option to genmake2 which, when the supporting |
| 877 |
|
tools can be compiled (as determined by genmake2) will turn on the |
| 878 |
|
embed_files package which then embeds the entire MITgcm source code |
| 879 |
|
(*.[fFhc] + Makefile) used for the build within the executable |
| 880 |
|
- requested by CNH but off by default |
| 881 |
|
- adds a paltry <9MB to the mitgcmuv executable in most cases |
| 882 |
|
- only writes the output when useEMBEDSRC in eedata is true |
| 883 |
|
o clean up 3-dim. relaxation codes: |
| 884 |
|
* Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec |
| 885 |
|
* Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) |
| 886 |
|
* Thanks to Tom Haine for testing! |
| 887 |
|
|
| 888 |
|
checkpoint57z_post |
| 889 |
|
o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): |
| 890 |
|
affects output (@ truncation level) of exp. plume_on_slope ; updated. |
| 891 |
|
o fix the pickup behavior for obcs in combination with ptracers |
| 892 |
|
o fix a bug in ptracers_external_fields_load |
| 893 |
|
o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...) |
| 894 |
|
affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) |
| 895 |
|
o transfered surface NH pressure to eta field (if exactConserv). |
| 896 |
|
o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign) |
| 897 |
|
and update lab_sea output.txt file. |
| 898 |
|
o completing 3-dim. relaxation code: additional term |
| 899 |
|
1/tau*( theta(i,j,k) - thetaStar(i,j,k) ) |
| 900 |
|
in S/R EXTERNAL_FORCING_T (file external_forcing.F) |
| 901 |
|
* At compile time, in "EXF_OPTIONS.h" set |
| 902 |
|
#define ALLOW_CLIMTEMP_RELAXATION |
| 903 |
|
#define ALLOW_CLIMSALT_RELAXATION |
| 904 |
|
* At runtime in "data", under &PARM03 set (e.g., units in seconds) |
| 905 |
|
tauThetaClimRelax3Dim = 15552000.0, |
| 906 |
|
tauSaltClimRelax3Dim = 15552000.0, |
| 907 |
|
* 3 cases: |
| 908 |
|
1) Use a constant-in-time 3-dim. field |
| 909 |
|
2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec. |
| 910 |
|
3) Real-time relax. to time-evolving prescribed field |
| 911 |
|
o Adding Laplacian-type smoothness constraint on |
| 912 |
|
initial and boundary (forcing) controls (ic, bc) |
| 913 |
|
* enable at compile-time via |
| 914 |
|
ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION |
| 915 |
|
* enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1 |
| 916 |
|
* Absolute scale somewhat unclear so far |
| 917 |
|
* no area weighting was included since no other cost term does so far |
| 918 |
|
|
| 919 |
|
checkpoint57y_post |
| 920 |
|
First step for a NLFS adjoint |
| 921 |
|
o initially suppress rStar (new flag DISABLE_RSTAR_CODE) |
| 922 |
|
o new init. routines for calc_r_star, calc_surf_dr |
| 923 |
|
o still need to deal with ini_masks_etc |
| 924 |
|
o testreport seemed happy |
| 925 |
|
checkpoint57y_pre |
| 926 |
|
|
| 927 |
|
o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
| 928 |
|
o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) |
| 929 |
|
o add new offset feature to offline pkg (plus minor cleanup) |
| 930 |
|
o cfc fixes for final year of integration |
| 931 |
|
o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should |
| 932 |
|
be in GCHEM_OPTIONS). |
| 933 |
|
|
| 934 |
|
checkpoint57x_post |
| 935 |
|
o fix testreport Pb in multiple test experiment. |
| 936 |
|
o cleanup our namelist syntax in verification: |
| 937 |
|
- make it more F95 standards compliant (some work still needed) |
| 938 |
|
- allows the vast majority of our tests to work with gfortran |
| 939 |
|
o Non-Hydrostatic: |
| 940 |
|
- put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h |
| 941 |
|
- fix exchange calls for CS-grid using the new EXCH_S3D_RL. |
| 942 |
|
o Allow to apply AB on T,S rather than on AB(gT,gS): |
| 943 |
|
- implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 |
| 944 |
|
- use the same arrays (gtNm,gsNm) to hold tracer field at previous |
| 945 |
|
time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). |
| 946 |
|
- need a "clever" read_pickup to restart from the other AB formulation |
| 947 |
|
o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h |
| 948 |
|
o remove some unused variables (reduces number of compiler warnings) |
| 949 |
|
o adjoint |
| 950 |
|
* Disable useVariableViscosity for adjoint for time being |
| 951 |
|
(there are a number of extensive recomputations) |
| 952 |
|
* Initialize certain variables needed for adjoint |
| 953 |
|
|
| 954 |
|
checkpoint57w_post |
| 955 |
|
o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names |
| 956 |
|
fix the singleCpuIO RS version of MDSWRITEFIELD |
| 957 |
|
and add a WARNING if using globalFiles=T with multi-processors. |
| 958 |
|
o write grid-file(s) in only one format (MDS or MNC): default=MNC (if |
| 959 |
|
using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc |
| 960 |
|
o tracer advection scheme: |
| 961 |
|
add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get |
| 962 |
|
those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, |
| 963 |
|
was not very convenient). |
| 964 |
|
add implicit version for DST-3 & DST3_Flux_Limit vertical advection; |
| 965 |
|
(further tests needed for the implicit DST & Flux-Limiter schemes). |
| 966 |
|
o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef |
| 967 |
|
and sRef for convenience, handy, when you want to initialize |
| 968 |
|
ptracers in a large domain with a constant non-zero value. Also, |
| 969 |
|
untangle ptracers_init.F a little. |
| 970 |
|
|
| 971 |
|
checkpoint57v_post |
| 972 |
|
o change dome exp. to use variable viscosity in side-drag terms. |
| 973 |
|
o remove all the files from the cfc_offline test since they are now |
| 974 |
|
incorporated into tutorial_cfc_offline which has been producing |
| 975 |
|
identical results for a few days of testing |
| 976 |
|
o add new parameter: sideDragFactor to enable half-slip-side BC |
| 977 |
|
and change side-drag S/R to use viscosity from mom_calc_visc |
| 978 |
|
(can switch back by setting sideDragFactor=0.); affects results at |
| 979 |
|
truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), |
| 980 |
|
global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). |
| 981 |
|
o vorticity & strain are now computed without masking, to account for |
| 982 |
|
no-slip-side BC in variable viscosity calculation ; mask is applied |
| 983 |
|
anyway later on, before computing advection/coriolis terms. |
| 984 |
|
o modify exp4 to test new obcs support for reading from external files |
| 985 |
|
and for passive tracers |
| 986 |
|
o fix behavior of ptracers_monitor when monitor output is written to a |
| 987 |
|
netcdf-file; still not independent of monitor.F (writes in the same |
| 988 |
|
file). |
| 989 |
|
o change default value of tRef (put a uniform, meaningful value for ocean |
| 990 |
|
& atmos) and initialize sRef (was missing, as Martin mentioned). |
| 991 |
|
o Redefine viscC?Leith*. Change the coefficients of Leith viscosity |
| 992 |
|
to be proportional to enstrophy dissipation length. Thus, |
| 993 |
|
viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) |
| 994 |
|
This is now consistent with Smagorinsky and with the manual. |
| 995 |
|
|
| 996 |
|
checkpoint57u_post |
| 997 |
|
o OBCS and PTRACERS: add open boundary support for passive tracers |
| 998 |
|
- either use homogenous (pseudo) v.Neumann conditions or prescribe |
| 999 |
|
OB-values from file; this is not different from the way theta and salinity |
| 1000 |
|
are treated |
| 1001 |
|
- however, Orlanski-radiation conditions are not supported, and the model |
| 1002 |
|
will stop if you use pTracers and Orlanski at the same time. |
| 1003 |
|
- beefed up the rountine obcs_external_fields_load: now only those open |
| 1004 |
|
boundary values are overwritten with values from files for which there |
| 1005 |
|
are really files, otherwise the OB-fields remain untouched. This makes |
| 1006 |
|
it possible to use different OBs at different ends of the domain (as |
| 1007 |
|
with EXF) |
| 1008 |
|
o reduce number of exch calls in shap_filt (s2). |
| 1009 |
|
o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ |
| 1010 |
|
truncation level) 4/5 MLAdjust test results (11&12 digits match). |
| 1011 |
|
|
| 1012 |
|
checkpoint57t_post |
| 1013 |
|
o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
| 1014 |
|
o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
| 1015 |
|
same truncation, independent of the face number: affects affects several |
| 1016 |
|
test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). |
| 1017 |
|
o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); |
| 1018 |
|
note that biharmonic viscosity + no-slip was not tested in any experiment. |
| 1019 |
|
o fix bug in non-linear free-surf side-drag ; generate new output for |
| 1020 |
|
global_ocean.cs32x15(+.thsice) & global_ocean_pressure. |
| 1021 |
|
o make mnc honor the writeBinaryPrec flag for most kinds of output |
| 1022 |
|
o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
| 1023 |
|
o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
| 1024 |
|
error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
| 1025 |
|
o add brackets in multi-terms sum to get same truncation, independent of |
| 1026 |
|
the face number (manage to get exactly same value of gU,gV at the cs-edge) |
| 1027 |
|
affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
| 1028 |
|
o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
| 1029 |
|
and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
| 1030 |
|
a maximum grid-scale Reynolds number. Also, changes all length calculations |
| 1031 |
|
in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
| 1032 |
|
Suggested values of viscosity parameters found in mom_calc_visc. |
| 1033 |
|
Many new viscosity diagnostics available. |
| 1034 |
|
|
| 1035 |
|
checkpoint57s_post |
| 1036 |
|
o Add clearing-house for viscosity calculations, mom_calc_visc and |
| 1037 |
|
correct numerous bugs in LeithD and Smagorinsky discretizations. |
| 1038 |
|
mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
| 1039 |
|
used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
| 1040 |
|
Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
| 1041 |
|
and with Strain-Tension viscous term calculation (mom_hdissip.F). |
| 1042 |
|
The Strain-Tension form is now called with useStrainTensonVisc=.true. |
| 1043 |
|
ViscAhStrain and viscAhTension are now retired. |
| 1044 |
|
o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
| 1045 |
|
o In response to JMC's bug report, genmake2 now ignores any soft-links |
| 1046 |
|
that it finds in the *current* directory when searching for files. |
| 1047 |
|
Soft-links found in any other source directories will still work as |
| 1048 |
|
they did before. |
| 1049 |
|
o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
| 1050 |
|
a C routine to unlimit the stack size |
| 1051 |
|
o mnc-ify pkg/aim snapshot vars |
| 1052 |
|
o mnc-ify pkg/land as requested by Daniel |
| 1053 |
|
o various changes to mnc including: |
| 1054 |
|
- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
| 1055 |
|
- output can now be grouped so that all files within a group |
| 1056 |
|
change the ITER portion of their names in lock-step together |
| 1057 |
|
- can now read ("global") PER-FACE (in addition to PER-TILE) files |
| 1058 |
|
and works with both EXCH1 and EXCH2 (but needs more testing) |
| 1059 |
|
- writing works for all verification test cases w/ g77 on Linux |
| 1060 |
|
|
| 1061 |
|
checkpoint57r_post |
| 1062 |
|
o make MNC variable initialization happen earlier |
| 1063 |
|
o add diagnostics for (almost) each term of the momentum Eq. |
| 1064 |
|
o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
| 1065 |
|
o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
| 1066 |
|
o remove MINIMAL_TAVE_OUTPUT option ; |
| 1067 |
|
add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
| 1068 |
|
o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
| 1069 |
|
allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
| 1070 |
|
o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
| 1071 |
|
o add time-dependent SST, SSS control |
| 1072 |
|
o cost terms in ecco/ modularized (new cost_generic.F) |
| 1073 |
|
o cost_averages routines are modularized (new cost_averagesgeneric.F) |
| 1074 |
|
o new infrastructure for seaice model vs. obs misfits in seaice/ |
| 1075 |
|
* driver from the_main_loop.F is seaice_cost_driver.F |
| 1076 |
|
* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
| 1077 |
|
* gradient check in Exp. 6a of natl_box_adjoint/ |
| 1078 |
|
o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
| 1079 |
|
(see README file) |
| 1080 |
|
|
| 1081 |
|
checkpoint57q_post |
| 1082 |
|
o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
| 1083 |
|
o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
| 1084 |
|
- bug was reported by Jean-Michel and Ian Fenty |
| 1085 |
|
o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
| 1086 |
|
update exp. cpl_aim+ocn output. |
| 1087 |
|
o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
| 1088 |
|
Needed for high-res. runs with large global files |
| 1089 |
|
to be able to limit tapelev size |
| 1090 |
|
o Changed some tests for adjoint: |
| 1091 |
|
* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
| 1092 |
|
* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
| 1093 |
|
* global_ocean.90x40x15/ back to default 3-level checkpointing |
| 1094 |
|
o Modifications to enable scripted COMMON to MODULE conversion |
| 1095 |
|
* verification/OpenAD/code/ has necessary scripts and description; |
| 1096 |
|
* converts, compiles and runs successfully; |
| 1097 |
|
|
| 1098 |
|
checkpoint57p_post |
| 1099 |
|
o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
| 1100 |
|
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
| 1101 |
|
(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
| 1102 |
|
o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
| 1103 |
|
o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
| 1104 |
|
(was already the case for dissipation with mom_vecinv, |
| 1105 |
|
and also the case for grad.PhiHyd when staggered-timeStep) |
| 1106 |
|
This will allow to put dissipation out-off the AB time-stepping. |
| 1107 |
|
Unfortunately, affects truncation error. Update output of exp. that "fails" |
| 1108 |
|
(cg2d matching number) and leave the others for later: front_relax(10), |
| 1109 |
|
global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
| 1110 |
|
matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
| 1111 |
|
|
| 1112 |
|
checkpoint57o_post |
| 1113 |
|
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
| 1114 |
|
(2) its ready to be documented during the 20050801 DocFest |
| 1115 |
|
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
| 1116 |
|
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
| 1117 |
|
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
| 1118 |
|
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
| 1119 |
|
(worth another tag) |
| 1120 |
|
|
| 1121 |
|
checkpoint57n_post |
| 1122 |
|
o adding precip control xx_precip 32 |
| 1123 |
|
o adding swflux control xx_swflux 33 |
| 1124 |
|
o Replacing 10 forcing penalty cost routines by 1 generic. |
| 1125 |
|
o Implementing partitioning in time-mean and variable adjustment |
| 1126 |
|
for atmos. state. |
| 1127 |
|
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
| 1128 |
|
o in natl_box_adjoint: |
| 1129 |
|
* updated exp 1 to 10 |
| 1130 |
|
(but does not have time-mean vs. variable split results yet) |
| 1131 |
|
o updated global1x1/*_seaice_adj/ |
| 1132 |
|
to incorporate latest changes |
| 1133 |
|
o enable useSingleCpuIO for mdsio vector routines |
| 1134 |
|
(applies in particular to tapelev I/O) |
| 1135 |
|
o removed inefficient K-loop in all active_file*control*.F |
| 1136 |
|
|
| 1137 |
|
checkpoint57m_post |
| 1138 |
|
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
| 1139 |
|
and advect_cs (use EXCH-2 and standard cs-32 grid files). |
| 1140 |
|
o pkg/exch2: filling of face-corner halo regions is optional |
| 1141 |
|
(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
| 1142 |
|
|
| 1143 |
|
checkpoint57l_post |
| 1144 |
|
tag before updating tutorials (pre-release-2) |
| 1145 |
|
o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
| 1146 |
|
for output and interpolation of input fields onto model grid) |
| 1147 |
|
o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
| 1148 |
|
Affects results of exp. rotating_tank ; update output.txt. |
| 1149 |
|
o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
| 1150 |
|
and taking the square quantity and/or using a fraction-weight field. |
| 1151 |
|
o fix aim_diagnostics_init.F mate numbers. |
| 1152 |
|
o add mnc output capability to diagnostics/diagstat and update |
| 1153 |
|
our cvsignore files for the ACSII output generated |
| 1154 |
|
|
| 1155 |
|
checkpoint57k_post |
| 1156 |
|
o lab_sea now uses diagnostics package and provides a suite of |
| 1157 |
|
new EXF diagnostics output. |
| 1158 |
|
|
| 1159 |
|
checkpoint57j_post |
| 1160 |
|
o exf |
| 1161 |
|
* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
| 1162 |
|
Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
| 1163 |
|
terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
| 1164 |
|
* extended diagnostics output |
| 1165 |
|
- now includes all EXF variables |
| 1166 |
|
- hs, hl moved to common block |
| 1167 |
|
- separate S/R for diagnostics, called after ctrl vector is added |
| 1168 |
|
- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
| 1169 |
|
- EXFqnet contains true Qnet (i.e. includes qsw) |
| 1170 |
|
* updated verif. lab_sea, global_with_exf |
| 1171 |
|
* Rearranging hflux (exf_mapfields -> exf_getforcing) |
| 1172 |
|
to ensure that diagnostics sees a true EXFqnet |
| 1173 |
|
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
| 1174 |
|
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
| 1175 |
|
several times with different frequencies. |
| 1176 |
|
o mnc-ify the thsice package as requested by Daniel Enderton |
| 1177 |
|
- the monitor--MNC output needs work |
| 1178 |
|
- many attributes need to be added (most are currently blank) |
| 1179 |
|
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
| 1180 |
|
- many attributes need to be added (most are currently blank) |
| 1181 |
|
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
| 1182 |
|
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
| 1183 |
|
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
| 1184 |
|
update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
| 1185 |
|
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
| 1186 |
|
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
| 1187 |
|
(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
| 1188 |
|
|
| 1189 |
|
checkpoint57i_post |
| 1190 |
|
o Diagnostics package was changed: diagnostic allocation is now deactivated |
| 1191 |
|
by setting an empty file name in the namelist (used to be by setting 0 frequency) |
| 1192 |
|
o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
| 1193 |
|
add 1rst Order upwind vertical Shear. |
| 1194 |
|
o add a quick fix for A/B checkpointing in OFFLINE mode |
| 1195 |
|
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
| 1196 |
|
end-run around the C/Fortran linking horror in eesup/src/timers.F |
| 1197 |
|
o added pkg/runclock: allows user to terminate run based on wall clock |
| 1198 |
|
o added non-hydrostatic scaling parameter: nh_am2 |
| 1199 |
|
o pkg/my82: futile attempt to make results compiler-independent by adding |
| 1200 |
|
some "_d 0", etc. no effect. |
| 1201 |
|
o for mnc output, fill the 'T' coordinate var with myTime and create a |
| 1202 |
|
separate 'iter' variable for iteration count |
| 1203 |
|
o pkg/diagnostics: |
| 1204 |
|
add new capability: output of Global/Regional & per-level statistics ; |
| 1205 |
|
tested against monitor output (including land & thSIce) on various exp. |
| 1206 |
|
o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
| 1207 |
|
|
| 1208 |
|
checkpoint57h_done |
| 1209 |
|
tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
| 1210 |
|
data.diagnostics, data.gchem, data.ptracers) is done. |
| 1211 |
|
|
| 1212 |
|
o pkg/diagnostics: prepare for Global/Regional statistics. |
| 1213 |
|
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
| 1214 |
|
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
| 1215 |
|
and rename it: DIFFERENT_MULTIPLE |
| 1216 |
|
|
| 1217 |
|
checkpoint57h_post |
| 1218 |
|
o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
| 1219 |
|
o pkg/diagnostics: change output frequency, now in seconds (instead |
| 1220 |
|
of Nb of iterations). This requires to change data.diagnostics. |
| 1221 |
|
checkpoint57h_pre |
| 1222 |
|
|
| 1223 |
|
o in mnc, let the user create the output dir if both mnc_outdir_date |
| 1224 |
|
and mnc_outdir_num are false |
| 1225 |
|
o add fflags() to pkg/diagnostics which allows one to specify, on a |
| 1226 |
|
per-file basis, the file precision [default behavior is unchanged] |
| 1227 |
|
o added diagnostics to pkg/kpp, including computation of mixed layer |
| 1228 |
|
depth based on a temperature/density criterion |
| 1229 |
|
o updated verification/natl_box to test the new pkg/kpp diagnostics |
| 1230 |
|
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
| 1231 |
|
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
| 1232 |
|
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
| 1233 |
|
not mnc -- this mistake was found by JMC and is now corrected |
| 1234 |
|
|
| 1235 |
|
checkpoint57g_post |
| 1236 |
|
o add Adams-Bashforth 3rd Order time stepping: |
| 1237 |
|
- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
| 1238 |
|
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
| 1239 |
|
checkpoint57g_pre |
| 1240 |
|
|
| 1241 |
|
o make lambda[Theta,Salt]ClimRelax spatially varying |
| 1242 |
|
(default remains spatially uniform constant based on tau) |
| 1243 |
|
o added new control variables |
| 1244 |
|
* init. uVel, vVel, etanN |
| 1245 |
|
* lambda[Theta,Salt]ClimRelax |
| 1246 |
|
o separate masks used for ctrl_pack/unpack 'from write_grid' output |
| 1247 |
|
(suggested by G. Forget) |
| 1248 |
|
|
| 1249 |
|
checkpoint57f_post |
| 1250 |
|
o add parameter "baseTime" = model base time = time at iteration zero |
| 1251 |
|
new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
| 1252 |
|
account for baseTime shift |
| 1253 |
|
o move Coriolis arrays from PARAMS.h to GRID.h |
| 1254 |
|
checkpoint57f_pre |
| 1255 |
|
|
| 1256 |
|
o mnc-ifying the seaice package |
| 1257 |
|
o introduced an alternative length scale calculation for use in the limiting |
| 1258 |
|
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
| 1259 |
|
o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
| 1260 |
|
o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
| 1261 |
|
as well as grad(vort3). Made it compatible with both approximate form |
| 1262 |
|
for the cubed sphere and full form of these gradients. Added flag |
| 1263 |
|
useFullLeith to select between approximate and full form. |
| 1264 |
|
o add "d0" in getcon.F to reduce differences between compilers/platforms |
| 1265 |
|
update output.txt of exp. fizhi-gridalt-hs |
| 1266 |
|
o change port_rand funtion to allow to set the seed. |
| 1267 |
|
o fix obscure MNC bug involving conversion between reals and integers |
| 1268 |
|
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
| 1269 |
|
new version is now more standards-compliant |
| 1270 |
|
o adjoint-related modifications |
| 1271 |
|
* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
| 1272 |
|
* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
| 1273 |
|
* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
| 1274 |
|
|
| 1275 |
|
checkpoint57e_post |
| 1276 |
|
o Adding eddy stress controls a la Ferreira et al. |
| 1277 |
|
checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
| 1278 |
|
|
| 1279 |
|
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
| 1280 |
|
update output.txt of exp. fizhi-gridalt-hs |
| 1281 |
|
o add more "Z" dimensions and associated coordinate vars to MNC |
| 1282 |
|
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
| 1283 |
|
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
| 1284 |
|
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
| 1285 |
|
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
| 1286 |
|
months and years. Requires pkg/cal. |
| 1287 |
|
o diagnostics: add pickup functionality |
| 1288 |
|
- off by default for backwards compatibility |
| 1289 |
|
- current version only uses MDSIO -- MNC will be added |
| 1290 |
|
o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
| 1291 |
|
o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
| 1292 |
|
|
| 1293 |
|
checkpoint57d_post |
| 1294 |
|
o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
| 1295 |
|
o modify verification/ideal_2D_oce so that it tests the creation of mnc |
| 1296 |
|
output from the diagnostics package |
| 1297 |
|
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
| 1298 |
|
o make genmake2 more portable by using ".$FS" instead of ".f" for more |
| 1299 |
|
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
| 1300 |
|
o add coordinate variables to the MNC output from the diagnostics package |
| 1301 |
|
o change MNC-flags default value: true when useMNC=TRUE |
| 1302 |
|
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
| 1303 |
|
the ability (off by default) to read the grid information using MNC |
| 1304 |
|
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
| 1305 |
|
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
| 1306 |
|
o do snap-shot diagnostics at the middle of the time-interval (instead of |
| 1307 |
|
at the end). |
| 1308 |
|
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
| 1309 |
|
new test for AIM with thSIce + slab-ocean |
| 1310 |
|
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
| 1311 |
|
o move state variable diagnostics to the beginning of the time step ; |
| 1312 |
|
(note: still needs some work specially for snap-shot diagnostics) |
| 1313 |
|
duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
| 1314 |
|
|
| 1315 |
|
checkpoint57c_post |
| 1316 |
|
o Change testing option (-ieee) to get closer agreement between g77 & ifort |
| 1317 |
|
o generate new output.txt files on faulks with g77 & the new -ieee option |
| 1318 |
|
checkpoint57c_pre |
| 1319 |
|
|
| 1320 |
|
o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
| 1321 |
|
update output.txt of exp. global_ocean.90x40x15 |
| 1322 |
|
o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
| 1323 |
|
results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
| 1324 |
|
o add saltFlux(+File) forcing capability with periodicExternalForcing |
| 1325 |
|
o allow to use pkg diagnostics for GM-Redi & ThSIce output |
| 1326 |
|
o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
| 1327 |
|
o improvements for the MNC output from DIAGNOSTICS: |
| 1328 |
|
- correct handling of the unlimitied dimension |
| 1329 |
|
- all dims now have associated coordinate variables |
| 1330 |
|
- variables located at U, V, and Corner ("Z") points are now written |
| 1331 |
|
with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
| 1332 |
|
*all* data points are output |
| 1333 |
|
o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
| 1334 |
|
o added pkg/seaice/seaice_monitor.F |
| 1335 |
|
o mdsio_readfield.F can now read files visible only to master MPI process. |
| 1336 |
|
o pkg/seaice: some test code for ice-modified ocean stress |
| 1337 |
|
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
| 1338 |
|
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
| 1339 |
|
spurious negative numbers for precipitation and humidity. Will cause |
| 1340 |
|
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
| 1341 |
|
o pkg/ctrl/ |
| 1342 |
|
* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
| 1343 |
|
May be enabled via doPackDiag |
| 1344 |
|
* introduce z-scaling of |
| 1345 |
|
+ gradient (doZscalePack) and |
| 1346 |
|
+ control (doZscaleUnpack) |
| 1347 |
|
o pkg/mdsio/ |
| 1348 |
|
* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
| 1349 |
|
* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
| 1350 |
|
|
| 1351 |
|
checkpoint57b_post |
| 1352 |
|
o simplify options in diagnostics_fill arguments (remove weird combinations) |
| 1353 |
|
o fix MNC coordinate variables so that they now contain per-face index |
| 1354 |
|
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
| 1355 |
|
general, EXCH2 grids are only aligned to a "local" coordinate system |
| 1356 |
|
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
| 1357 |
|
o Implement instantaneous output within pkg diagnostics: |
| 1358 |
|
setting a negative frequency in data.diagnostics produces |
| 1359 |
|
"snap-shot" output (as opposed to time-average if freq > 0) |
| 1360 |
|
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
| 1361 |
|
NOTE: change ptracer diagnostics name: use 2 characters to work with |
| 1362 |
|
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
| 1363 |
|
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
| 1364 |
|
becomes the coordinate variable for the 'T' dimension |
| 1365 |
|
o add CF-style coordinate variables to MNC |
| 1366 |
|
- just a first cut: numbers are meaningless on the cubesphere and |
| 1367 |
|
missing along the T axis but otherwise it works! |
| 1368 |
|
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
| 1369 |
|
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
| 1370 |
|
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
| 1371 |
|
this is based directly on what the model compute, so that the content of |
| 1372 |
|
each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
| 1373 |
|
o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
| 1374 |
|
o clean up build options files for SunOS, in particular |
| 1375 |
|
- remove -traditional from xmakedepend |
| 1376 |
|
- change -xarch=v9 to -xarch=native for f77 |
| 1377 |
|
- restore use of make (not gmake) |
| 1378 |
|
- add CC=gcc if using g77 |
| 1379 |
|
o changes per discussion of AM, JMC, & EH3 today: |
| 1380 |
|
- move redundant "grid" variables out of "state" -- in preparation of |
| 1381 |
|
creating proper CF-style coordinate variables and in recognition |
| 1382 |
|
that any/all grid variables can be easily copied (eg. w/NCO) from |
| 1383 |
|
the grid files into any of the other NetCDF files |
| 1384 |
|
- *always* output grid variables with MDSIO (this will eventually be |
| 1385 |
|
changed) |
| 1386 |
|
- output MNC grid file if useMNC is true |
| 1387 |
|
o every instance of _END_MASTER() has been found and replaced with |
| 1388 |
|
_END_MASTER( myThid ) in order to satisfy certain picky Sun |
| 1389 |
|
preprocessors |
| 1390 |
|
o re-arrange diagnostics pkg initialisation: |
| 1391 |
|
- allow each package to extend the available diagnostics list |
| 1392 |
|
- add some checking and fix small problems (multi-threaded, ...) |
| 1393 |
|
- new S/R diagnostics_fill (replace fill_diagnostics): |
| 1394 |
|
look through the short list of active diag. (instead of the long list) |
| 1395 |
|
create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
| 1396 |
|
|
| 1397 |
|
checkpoint57a_post |
| 1398 |
|
o this set of changes restores TAMC compatibility |
| 1399 |
|
tested for global_ocean.90x40x15 adjoint on trough |
| 1400 |
|
(what a pain) |
| 1401 |
|
|
| 1402 |
|
checkpoint57a_pre |
| 1403 |
|
o some modifs in tools/build_options for sunos |
| 1404 |
|
o call ctrl_pack for ctrl at end for optimcycle=0 |
| 1405 |
|
|
| 1406 |
|
checkpoint57 |
| 1407 |
|
o add horizontal bi-harmonic viscosity for vertical velocity |
| 1408 |
|
- new parameter viscA4W (defaults to viscA4) |
| 1409 |
|
- affects only non-hydrostatic code |
| 1410 |
|
- to be done: no-slip lateral boundary conditions |
| 1411 |
|
o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
| 1412 |
|
o implement Implicit Vertical advection for pTracers |
| 1413 |
|
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
| 1414 |
|
(implemented also for implicit vertical diffusion & advection) |
| 1415 |
|
o OBCS: extend application of tracer open boundary conditions |
| 1416 |
|
to a strip beyond the boundary of width Olx/Oly |
| 1417 |
|
o add call monitor to TAF set of required calls (flow directives) |
| 1418 |
|
and include in natl_box_adjoint |
| 1419 |
|
o untangle a few ifdefs related to cost, ctrl, autodiff |
| 1420 |
|
untangel a few ALLOW_ECCO_OPTIMIZATION |
| 1421 |
|
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
| 1422 |
|
(theta2, salt2 in ecco_cost_weights) |
| 1423 |
|
|
| 1424 |
|
checkpoint56c_post |
| 1425 |
|
o OBCS as control variables |
| 1426 |
|
- update ctrl_ad_diff.list, obcs_ad_diff.list |
| 1427 |
|
- remove balance of obcs controls from default |
| 1428 |
|
- fix index bug nobcs in ctrl_init |
| 1429 |
|
- fix dummy fields filen in ctrl_pack |
| 1430 |
|
- add dummy weights for obcs |
| 1431 |
|
o lsopt: comment out fort.94 output |
| 1432 |
|
o optim: |
| 1433 |
|
- remove unnecessary header files |
| 1434 |
|
- adjusted namelists |
| 1435 |
|
- add xerbla.F to Makefile |
| 1436 |
|
o exf: |
| 1437 |
|
- multiple modifications of exf_check_range |
| 1438 |
|
- unit change in exf_init_runoff from [m/year] to [m/s] |
| 1439 |
|
o mdsio: |
| 1440 |
|
- i/o-vector change debugLevel from debLevA to debLevB |
| 1441 |
|
|
| 1442 |
|
checkpoint56b_post |
| 1443 |
|
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
| 1444 |
|
is called from DO_THE_MODEL_IO |
| 1445 |
|
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
| 1446 |
|
- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
| 1447 |
|
- clean up PTRACERS_WRITE_TIMEAVE a little |
| 1448 |
|
o add another verification experiment that tests both the cfc-pkg and |
| 1449 |
|
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
| 1450 |
|
reactive tendencies treated inline with regular timestepping |
| 1451 |
|
o testreport previously did a lousy job of comparing small numbers, so |
| 1452 |
|
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
| 1453 |
|
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
| 1454 |
|
testreport. |
| 1455 |
|
o ptracers_monitor: bug fix for MPI |
| 1456 |
|
|
| 1457 |
|
checkpoint56a_post |
| 1458 |
|
o GCHEM: finish reorganizating the package |
| 1459 |
|
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
| 1460 |
|
(introduces another 3D-array for each passive tracer, but only if |
| 1461 |
|
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
| 1462 |
|
gchemTendency is not needed because the timestep is done separately) |
| 1463 |
|
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
| 1464 |
|
- GCHEM is now---more or less cleanly---separate from PTRACERS |
| 1465 |
|
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
| 1466 |
|
so clear to me how that should be done in a general way. |
| 1467 |
|
o CFC: improve formatting of output in CFC_ATMOS |
| 1468 |
|
o PTRACERS: |
| 1469 |
|
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
| 1470 |
|
that ALL experiments with ptracers enable can be checked. This makes |
| 1471 |
|
GCHEM_MONITOR obsolete. |
| 1472 |
|
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
| 1473 |
|
monitorFreq |
| 1474 |
|
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
| 1475 |
|
o add PTRACERS (PTR0[1-5]) to testreport output |
| 1476 |
|
o exf_check_range: |
| 1477 |
|
* default changed to .TRUE. |
| 1478 |
|
* will check values for niter0 if debLevA, every timestep if debLevB |
| 1479 |
|
* STOP in exf_check_range if 'out of range' |
| 1480 |
|
* range chosen generous to allow for potential extema |
| 1481 |
|
TBD: a version with stricter range |
| 1482 |
|
permitted range would be runtime parameters |
| 1483 |
|
o GMredi: |
| 1484 |
|
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
| 1485 |
|
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
| 1486 |
|
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
| 1487 |
|
o GCHEM: |
| 1488 |
|
- move call to GCHEM_FORCING_SEP, so that it is now called before |
| 1489 |
|
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
| 1490 |
|
- introduced a useGCHEM runtime flag and applied it everywhere. |
| 1491 |
|
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
| 1492 |
|
this flag is now only visible within GCHEM-pkg routines. |
| 1493 |
|
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
| 1494 |
|
be replaced by a 3D array that is computed before thermodynamics; for |
| 1495 |
|
this, the tracer ID iTracer had to be included into the parameter list |
| 1496 |
|
of ptracers_forcing |
| 1497 |
|
- set up forward_step to call gchem_forcing, that will replace |
| 1498 |
|
gchem_forcing_int in ptracers_forcing |
| 1499 |
|
- cleaning up |
| 1500 |
|
o small cleaning of exch2: remove files that are also in eesupp/src |
| 1501 |
|
|
| 1502 |
|
checkpoint56 |
| 1503 |
|
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
| 1504 |
|
o mnc: cleanup "full" files--fixes out-of-memory problem |
| 1505 |
|
o ECCO-GODAE |
| 1506 |
|
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
| 1507 |
|
* fully merged and updated from SIO code |
| 1508 |
|
windstress sign change affects |
| 1509 |
|
- exf_inscal_[u/v]stress |
| 1510 |
|
- sign of xx_tau[u/v] adjustments |
| 1511 |
|
- signs in cost_scat |
| 1512 |
|
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
| 1513 |
|
* natl_box_adjoint updated and compressed |
| 1514 |
|
* 2-level checkpoint switch added |
| 1515 |
|
(tested in EXP. 1 of natl_box_adjoint) |
| 1516 |
|
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
| 1517 |
|
o SVD |
| 1518 |
|
* first complete, non-hacked version for SVD calculations |
| 1519 |
|
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
| 1520 |
|
performed via direct access files admtlm_vector.it???? |
| 1521 |
|
(via ctrl_[un]pack) |
| 1522 |
|
* optimcycle is used for ARPACK iteration counter |
| 1523 |
|
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
| 1524 |
|
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
| 1525 |
|
and add linear transforms where necessary |
| 1526 |
|
* controls are initial/final SST, SSS (can be extended; need to check |
| 1527 |
|
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
| 1528 |
|
o mdsio: filename info to both stderr, stdout |
| 1529 |
|
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
| 1530 |
|
from sign change |
| 1531 |
|
|
| 1532 |
|
checkpoint55j_post |
| 1533 |
|
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
| 1534 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 1535 |
|
o add consistent build directories and .cvsignore files to verification |
| 1536 |
|
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
| 1537 |
|
o make all subroutines 30 or less characters in length for certain older |
| 1538 |
|
compilers to work (a thorough search only turns up two routines in |
| 1539 |
|
pkg/ptracers) |
| 1540 |
|
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
| 1541 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 1542 |
|
|
| 1543 |
|
checkpoint55i_post |
| 1544 |
|
o change arrays for total vertical diffusivity (2.D if explicit, |
| 1545 |
|
3.D if implicit) ; each ptracer uses its own background value. |
| 1546 |
|
o added mnc/NetCDF output capability to ocn_compon_interf |
| 1547 |
|
- added bits to verification/cpl_aim+ocn so that it can run on |
| 1548 |
|
ITRDA and other clusters without the mpirun "-wd" option |
| 1549 |
|
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
| 1550 |
|
configuration |
| 1551 |
|
o give MNC the ability to create additional files rather than |
| 1552 |
|
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
| 1553 |
|
- the default is just less than 2GB which is a practical limit |
| 1554 |
|
on many systems |
| 1555 |
|
o Compute the non-local term using either KPP vertical diffusivity (=default) |
| 1556 |
|
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
| 1557 |
|
|
| 1558 |
|
checkpoint55h_post |
| 1559 |
|
o add verification test "vermix" |
| 1560 |
|
o remove all the *_ioinc flags and replace with the single global |
| 1561 |
|
outputTypesInclusive flag |
| 1562 |
|
o allow to set a vertical profile of vertical diffusivity for T & S |
| 1563 |
|
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
| 1564 |
|
o useMNC moved from data.mnc to data.pkg |
| 1565 |
|
|
| 1566 |
|
checkpoint55g_post |
| 1567 |
|
o Renaming carbon AD experiments to comply with testreport conventions |
| 1568 |
|
o Updating adjoint of Held-Suarez hs94.1x64x5 |
| 1569 |
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
| 1570 |
|
have been fixed to avoid recomp. of do_oceanic_phys |
| 1571 |
|
Works well for global_ocean.90x40x15, |
| 1572 |
|
but recomp. issue remains for carbon |
| 1573 |
|
o Updating adjoint output for natl_box_adjoint after |
| 1574 |
|
pkg/ecco has been modified (see taga c55d_post) |
| 1575 |
|
|
| 1576 |
|
checkpoint55f_post |
| 1577 |
|
o rename to timeave_init_fixed |
| 1578 |
|
|
| 1579 |
|
checkpoint55e_post |
| 1580 |
|
o some delicate re-shuffle of store directives to avoid one |
| 1581 |
|
extra call of do_oceanic_physics |
| 1582 |
|
affects ecco_the_main_loop.F, do_oceanic_physics.F |
| 1583 |
|
checkpoint_lev1_directives.h |
| 1584 |
|
o NB: this may break global_ocean adjoint temporarily, |
| 1585 |
|
but it is clear how to fix it. Will do later, need this now. |
| 1586 |
|
|
| 1587 |
|
checkpoint55d_post |
| 1588 |
|
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
| 1589 |
|
o ecco_cost_weights is modified to 1x1 runs |
| 1590 |
|
o modifs to allow observations to be read in as |
| 1591 |
|
single file or yearly files |
| 1592 |
|
o enable to read exf forcing fields as either |
| 1593 |
|
single file or yearly files (flag useExfYearlyFields) |
| 1594 |
|
checkpoint55d_pre |
| 1595 |
|
|
| 1596 |
|
o switch between 2-level and 3-level checkpointing |
| 1597 |
|
o add ability of MNC to write local and "partial" (eg. 2D slices where |
| 1598 |
|
the full 3D field is never actually stored) arrays to NetCDF files |
| 1599 |
|
with the correct (that is, the complete multi-dimensional) set of |
| 1600 |
|
array indicies |
| 1601 |
|
- used in mom_vecinv() to write the diagFreq output |
| 1602 |
|
- tested (demonstrated) in verification/aim.5l_cs |
| 1603 |
|
o further mnc-ification |
| 1604 |
|
- add verification/lab_sea to the list with mnc setups |
| 1605 |
|
- fix undefined mnc v-names in cd_code |
| 1606 |
|
- add kpp to mnc output (both snapshot and timeave) |
| 1607 |
|
o non-hydrostatic code |
| 1608 |
|
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
| 1609 |
|
in calc_gw.F |
| 1610 |
|
- defaults to viscAh |
| 1611 |
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
| 1612 |
|
friction or Leith) in non-hydrostatic mode, as long as there is |
| 1613 |
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
| 1614 |
|
o pkg/cost |
| 1615 |
|
extend simple cost functions to treat time mean quantities |
| 1616 |
|
(T,U,V) via cost_accumulate_state from cost_tile |
| 1617 |
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
| 1618 |
be 2 times larger than the minimum size the advection scheme requires. |
be 2 times larger than the minimum size the advection scheme requires. |
| 1619 |
now get a perfect conservation of salt in advect_cs test-exp (updated) |
now get a perfect conservation of salt in advect_cs test-exp (updated) |
| 1637 |
- changed sponge layer relaxation parameter units for days to seconds |
- changed sponge layer relaxation parameter units for days to seconds |
| 1638 |
- turned off sponge layer by default |
- turned off sponge layer by default |
| 1639 |
- changed argument list of OBCS_CALC to myTime+deltaTclock |
- changed argument list of OBCS_CALC to myTime+deltaTclock |
| 1640 |
|
- fixed about 35 bugs in obcs_external_fields_load |
| 1641 |
|
|
| 1642 |
checkpoint55c_post |
checkpoint55c_post |
| 1643 |
o obcs stuff |
o obcs stuff |
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