| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
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|
| 7 |
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checkpoint59d |
| 8 |
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o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
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for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
| 10 |
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(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
| 11 |
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o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
| 12 |
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and change default value of parameter "GM_Small_Number"; |
| 13 |
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update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
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global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
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tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
| 16 |
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o pkg/ecco: cost function when applying pkg/smooth to controls |
| 17 |
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o pkg/ctrl: add forcingPrecond run time parameter |
| 18 |
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o pkg/seaice: |
| 19 |
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- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
| 20 |
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- fix bug in metric terms of u-equation in LSR solver (implicit part), |
| 21 |
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changes verification/lab_sea |
| 22 |
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- rearrange implicit part of u-equation in LSR solver to make it easier to |
| 23 |
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read, understand, and debug. This causes changes at the truncation level. |
| 24 |
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- fix (serious) bug in the boundary conditions (sign error in the implicit |
| 25 |
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part) of the LSR solver. Changes all LSR results. |
| 26 |
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- fixed problem with HSNOW initialization to avoid thick snow when AREA |
| 27 |
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is initilized with small values - does not change lab_sea results. |
| 28 |
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- added HsnowFile initialization capability |
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o pkg/smooth: addition to model/src and pkg/ctrl so allow |
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initialization of pkg/smooth and application to control vector |
| 31 |
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o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
| 32 |
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o dependencies: pkg/profiles requires pkg/cal |
| 33 |
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o pkg/profiles: |
| 34 |
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- added option ALLOW_PROFILES_GENERICGRID |
| 35 |
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-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
| 36 |
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that interpolation information (grid points and coefficients) is provided |
| 37 |
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within the netcdf input files. |
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-> sample matlab scripts can be found in MITgcm_contrib/gael |
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that allow you to prepare netcdf input files. |
| 40 |
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- also modified: cleaner include statements, cleaner error print statements, |
| 41 |
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cleaner stops when error, and more tests of the netcdf input files consistency. |
| 42 |
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o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
| 43 |
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o pkg/seaice: |
| 44 |
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- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
| 45 |
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requires a new routine: seaice_diagnostics_fill.F |
| 46 |
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- make sure that seaice does not move if not forced (pressure replacement |
| 47 |
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method, Hibler and Ip, 1995), changes results |
| 48 |
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- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
| 49 |
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- SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). |
| 50 |
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It is turned off by default (=-1.), because it changes the results. |
| 51 |
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- make it possible to read AREA from a file, too. |
| 52 |
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|
| 53 |
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checkpoint59c |
| 54 |
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o add S/R and diagnostics for oceanic mixed-layer depth |
| 55 |
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o move GMRedi call after all vertical mixing schemes (including KPP) |
| 56 |
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o pkg/thsice: |
| 57 |
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- ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs |
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(melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice |
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o pkg/obcs: |
| 60 |
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- bug fix for balance code |
| 61 |
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o pkg/seaice: |
| 62 |
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- allow values of SEAICE_elasticParm > 1 |
| 63 |
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- add new parameter SEAICE_evpTauRelax as an alternative |
| 64 |
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to SEAICE_elasticParm |
| 65 |
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- make lsr boundary conditions free slip (by default), changes result |
| 66 |
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- add code for no slip boundary conditions for lsr |
| 67 |
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- set minimum of zeta to zero (and not 4e8) (changes results) |
| 68 |
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- add a cap on AREA after advecting AREA if seaice_growth is not called |
| 69 |
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o change calculation of Visbeck K: |
| 70 |
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- no longer depend on tapering scheme; instead, compute slope (limited |
| 71 |
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by GM_maxSlope). this is equivalent to what was comuted before with |
| 72 |
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clipping or linear tappering. |
| 73 |
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- fix vertical averaging (wrong by 1/2 level) |
| 74 |
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- leave the old version (but will not be maintained) within |
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#ifdef OLD_VISBECK_CALC / #endif |
| 76 |
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- update output of exp. ideal_2D_oce |
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o change error catch in calc_r_star to improve vectorization |
| 78 |
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o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
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add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
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o adjoint: |
| 81 |
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Re-organized adjoint checkpointing according to Matt Mazloff |
| 82 |
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(but with modifs/completions/cleanups) |
| 83 |
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Storing is now bundled into large arrays to optimized I/O |
| 84 |
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(and second step in cleanup of the_main_loop) |
| 85 |
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|
| 86 |
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checkpoint59b |
| 87 |
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o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
| 88 |
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- export/import (between ocean & coupler) fields needed for ocean DIC. |
| 89 |
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o pkg/seaice: |
| 90 |
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- get rid of three more exchanges seaice_calc_viscosities (required |
| 91 |
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different loop boundaries in seaice_lsr and seaice_ocean_stress) |
| 92 |
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- bug fix in seaice_ocean_stress (update of lab_sea required) |
| 93 |
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- reduce loop boundaries to necessary minimum also in seaice_evp |
| 94 |
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- go back to the old way of computing deltaC/Z as the adjoint likes that |
| 95 |
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better |
| 96 |
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o Refresh of tutorial_global_oce_latlon (includes changing salinity-like |
| 97 |
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passive tracer to an Age Tracer) + update output.txt |
| 98 |
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o pkg/exf: |
| 99 |
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- implement A-grid / C-grid selection for wind-stress input files. |
| 100 |
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- clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) |
| 101 |
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for now, in exf_bulk_largeyeager04.F only : |
| 102 |
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- change implementation for case where windspeed + 2. components wind-stress |
| 103 |
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are read-in. AND use rhoConstFresh to convert evap. |
| 104 |
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o pkg/seaice: |
| 105 |
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- use correct EXCH_UV for wind-forcing (on A-grid). |
| 106 |
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- change SEAICE_OPTIONS.h to limit the number of option combinations (regarding |
| 107 |
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SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops. |
| 108 |
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o pkg/exf: |
| 109 |
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- default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC) |
| 110 |
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EXF_INTERPOLATION: |
| 111 |
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- merge global_with_exf/code version of exf_interp_read.F |
| 112 |
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to the main code ; |
| 113 |
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- Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when |
| 114 |
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reading the file ; Important: This options needs to be defined to recover |
| 115 |
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previous code. |
| 116 |
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otherwise, use fixed size array to read in (size=exf_interp_bufferSize). |
| 117 |
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- no longer loose real*8 precision along the way when using exf_iprec=64. |
| 118 |
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o pkg/seaice: rearrangement of common blocks (really needs more cleaning up) |
| 119 |
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- change discretisation of evp-solver in order to avoid another exchange |
| 120 |
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(changes lab_sea) and clean up a little |
| 121 |
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- replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS) |
| 122 |
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help the adjoint (this also changes the results slightly) |
| 123 |
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- add a few "_d 0" where they had been missing in seaice_evp.F |
| 124 |
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- cleaning up: remove unused seaice_calc_rhs.F |
| 125 |
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o pkg/exf: some cleaning-up: |
| 126 |
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- change various "constants" into runtime parameters |
| 127 |
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- cleaned-up Large&Yeager04 routine which should eventually |
| 128 |
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replace exf_bulkformulae.F (changed names of S/R and CPP) |
| 129 |
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and merged various ALLOW_ATM_WIND options |
| 130 |
|
only used with thsice pkg (in thsice_get_exf.F): |
| 131 |
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- implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04) |
| 132 |
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which are used when useStabilityFct_overIce=TRUE (= the default) |
| 133 |
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- change default values of ice & snow emissivity and scale downward LW |
| 134 |
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by ice & snow emissivity. |
| 135 |
|
o pkg/thsice: |
| 136 |
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fix few little problems, in thsice_calc_thickn.F: |
| 137 |
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- growth vertically (and not laterally) if iceFrac == iceMaskMax |
| 138 |
|
- melt only laterally if hIce < hThinIce (as the comments say) |
| 139 |
|
and in thsice_extend.F: |
| 140 |
|
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
| 141 |
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- start to form ice as soon as the minimum ice-volume is reachable. |
| 142 |
|
update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice), |
| 143 |
|
and cpl_aim+ocn |
| 144 |
|
o pkg/kpp |
| 145 |
|
- move computation of surface related input fields to KPP into a new |
| 146 |
|
subroutine kpp_forcing_surf.F |
| 147 |
|
- remove wrong (within bi,bj loops) EXCH calls. |
| 148 |
|
- little cleaning (add argument myThid in last position, cvs header ...) |
| 149 |
|
- for now, fix conservation problem by exchanging KPPviscAz (may not |
| 150 |
|
be the best fix) |
| 151 |
|
o pkg/seaice |
| 152 |
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- check for inconsistent evp parameter/cpp-flag combination |
| 153 |
|
- remove leftover errIO flat for obsolete name list error handling |
| 154 |
|
o OpenAD |
| 155 |
|
- changed verification/OpenAD to full baroclinic setup (including GM/Redi) |
| 156 |
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|
| 157 |
|
checkpoint59a |
| 158 |
|
o pkg/seaice: some parameter clarifications and a little bit of clean up |
| 159 |
|
o pkg/thsice: rename run-time parameters: |
| 160 |
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himin -> hIceMin |
| 161 |
|
himin0 -> hThinIce |
| 162 |
|
hihig -> hThickIce |
| 163 |
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i0 -> i0swFrac |
| 164 |
|
transCoef -> bMeltCoef |
| 165 |
|
frac_energy -> fracMelting |
| 166 |
|
add new parameters: hNewIceMax, fracFreezing, dhSnowLin |
| 167 |
|
with default values (for now) that do not change the results. |
| 168 |
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remove old version of thsice vars advection in pkg/seaice. |
| 169 |
|
o in FFIELDS.h: |
| 170 |
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- replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD |
| 171 |
|
- make pLoad & sIceLoad always available (but still only used if |
| 172 |
|
ATMOSPHERIC_LOADING is #define). |
| 173 |
|
o pkg/kpp: replaced _KPP_RL with _RL |
| 174 |
|
o bug fixes for vertical diffusivity computations when both KPP and |
| 175 |
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3D diffusivity arrays are used. |
| 176 |
|
o pkg/seaice: fix bug in evp solver, while doing that |
| 177 |
|
- change (improve?) discretization of stress computations for both |
| 178 |
|
cgrid-lsr and evp solver |
| 179 |
|
- add a new routine to compute strain rates |
| 180 |
|
- the above changes lab_sea results |
| 181 |
|
- add no slip conditions for evp solver (off by default), lsr-version |
| 182 |
|
may follow |
| 183 |
|
- fix exchange for shear at Z-points (does not change lab_sea) |
| 184 |
|
- retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp |
| 185 |
|
(to force the user to pick a time step since there is not "safe" way |
| 186 |
|
of choosing it) |
| 187 |
|
- add principal stress diagnostics |
| 188 |
|
- rearrange fields for evp a little to avoid having to call a: too many |
| 189 |
|
exchanges and b: exchanges for stress trensor components which we do |
| 190 |
|
not have. |
| 191 |
|
- modify Hibler+Bryan (1987) stress coupling so that it reuses information |
| 192 |
|
of evp, complete rewrite for lsr case (latter is does not yet work |
| 193 |
|
in all cases) |
| 194 |
|
o pkg/kpp: add code to have mixing in shelf ice caverns |
| 195 |
|
- add myThid to all kpp routines (long overdue) |
| 196 |
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|
| 197 |
|
checkpoint59 |
| 198 |
|
o pkg/exf: |
| 199 |
|
- fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND & |
| 200 |
|
ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid |
| 201 |
|
- move exf header files from lower_case.h to UPPER_CASE.h ; |
| 202 |
|
add missing cvs Header & Name |
| 203 |
|
- add adjoint routines and flow dirs for newly used exch_uv_agrid routines |
| 204 |
|
- add namelist param. selectStressGridPosition, exf_monFreq |
| 205 |
|
- retire many _CLIM routines, and remove data.exf_clim |
| 206 |
|
+ params moved to data.exf |
| 207 |
|
+ climsst, climsss now handled by exf_set_gen, i.e. |
| 208 |
|
climss?period=0 refers to constant field, |
| 209 |
|
climss?period=-12 to monthly forcing |
| 210 |
|
- split up namelists in data.exf |
| 211 |
|
o pkg/seaice: |
| 212 |
|
- remove seaice_exch and seaice_exch_uv |
| 213 |
|
- remove superfluous exchange of theta |
| 214 |
|
- add myThid to seaice_budget_ocean/ice |
| 215 |
|
- add new interface for atmospheric wind forcing (C-grid only) |
| 216 |
|
+ new routine |
| 217 |
|
+ two new field (taux, tauy for stress over ice) |
| 218 |
|
+ removed one global field (DAIRN) for C-grid case only |
| 219 |
|
o pkg/thsise |
| 220 |
|
- 2nd set of modifs for thsice adjoint in conjunction with exf |
| 221 |
|
o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.) |
| 222 |
|
|
| 223 |
|
checkpoint58y_post |
| 224 |
|
o Added capability for latitudinal dependence of Bryan and Lewis, 1979 |
| 225 |
|
vertical diffusivity, similar to that in MOM4; turned on using |
| 226 |
|
#define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using |
| 227 |
|
diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file. |
| 228 |
|
o Added capability for 3D specification of background vertical diffusion |
| 229 |
|
coefficient. This is done by (i) #define ALLOW_3D_DIFFKR |
| 230 |
|
in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime |
| 231 |
|
"data" file that contains the 3D vertical diffusivity coefficients. |
| 232 |
|
o ice dynamics (pkg/seaice) with thsice thermodynamics: |
| 233 |
|
- add code within pkg thsice to advect & diffuse sea-ice fields |
| 234 |
|
similar to (and will replace) what has been added in seaice_advdiff.F, |
| 235 |
|
but: - conserving Mass, Heat & Salt. |
| 236 |
|
- better when using non-linear advection scheme (not yet fully tested) |
| 237 |
|
- can also be used in atmospheric set-up (for now, only the diffusion). |
| 238 |
|
|
| 239 |
|
checkpoint58x_post |
| 240 |
|
o IO option for global-file compact format: |
| 241 |
|
- add options when generating topology (utils/exch2/matlab-topology-generator) |
| 242 |
|
- add I/O capability (pkg/mdsio). |
| 243 |
|
- adapt utils/matlab/rdmds.m to read this format. |
| 244 |
|
for now long-line format not yet supported by pkg/mdsio (& exch2). |
| 245 |
|
o shelfice: add a few diagnostics |
| 246 |
|
|
| 247 |
|
checkpoint58w_post |
| 248 |
|
o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: |
| 249 |
|
rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref |
| 250 |
|
(and replace horiVertRatio in NH code). |
| 251 |
|
Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) |
| 252 |
|
and tutorial_plume_on_slope (sensitive to truncation) |
| 253 |
|
o seaice: if ALLOW_ATM_WIND is undefined use wind stress |
| 254 |
|
directly to drive seaice model (C-grid only) |
| 255 |
|
o exf: when input wind-stress (#undef ALLOW_ATM_WIND): |
| 256 |
|
- reintroduce computation of wind from stress, |
| 257 |
|
- compute tau (in exf_bulkformulae.F) from windstress averaged to |
| 258 |
|
mass points to avoid tau = 0 |
| 259 |
|
- fix serious bug: (1/3) in Fortran is not the same as (1./3.) |
| 260 |
|
o rdmnc.m: make it work with "global" files created with gluemnc |
| 261 |
|
o rdmnc.m : some improvements in dealing with singleton dimension |
| 262 |
|
(tested on all testreport mnc output files). |
| 263 |
|
o genmake2: disable pkg/profiles if netcdf test fails. |
| 264 |
|
o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output. |
| 265 |
|
o move call to cal_readparms up to make calendar parameters/variable available |
| 266 |
|
to all packages |
| 267 |
|
|
| 268 |
|
checkpoint58v_post |
| 269 |
|
o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get |
| 270 |
|
useDynP_inEos_Zc tested. |
| 271 |
|
o pkg/exf: changes to properly interpolate/mask/scale initial fields |
| 272 |
|
o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields |
| 273 |
|
and portions thereof. See read_cs.txt for description and examples. |
| 274 |
|
o utils/matlab/cs_grid/bk_line: to compute transport through passages, |
| 275 |
|
add a script (grt_circ_bkl.m) to generate broken-line between 2 points, |
| 276 |
|
following the great-circle arc between those 2 points. |
| 277 |
|
o trap un-initialized variable with pathscale compiler on weddell.mit.edu |
| 278 |
|
(thanks to Constantinos): fix few problems and get (almost) all exp to pass. |
| 279 |
|
o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in |
| 280 |
|
- enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) |
| 281 |
|
- used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81) |
| 282 |
|
- still needs work (not working with some options ; efficiency to improve) |
| 283 |
|
and serious testing. |
| 284 |
|
- use this scheme for temperature & salinity in 2 advection test exp.: |
| 285 |
|
advect_xy & advect_xz, respectively. |
| 286 |
|
|
| 287 |
|
checkpoint58u_post |
| 288 |
|
o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. |
| 289 |
|
o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. |
| 290 |
|
o testreport: add option "-skipdir" to skip some test. |
| 291 |
|
o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent |
| 292 |
|
momentum calculation. |
| 293 |
|
o gad_advection: fix vertAdvecScheme (if different from advectionScheme) |
| 294 |
|
o some cleaning: usePickupBeforeC35 no longer supported ; remove this option. |
| 295 |
|
remove checkpoint.F and the_correction_step.F (no longer used); |
| 296 |
|
do the k loop inside CYCLE_TRACER (supposed to be more efficient). |
| 297 |
|
o add option (linFSConserveTr) to correct for tracer source/sink due to |
| 298 |
|
Linear Free surface |
| 299 |
|
o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine |
| 300 |
|
o pkg/thsice: fix reading mnc-pickups |
| 301 |
|
|
| 302 |
|
checkpoint58t_post |
| 303 |
|
o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) |
| 304 |
|
o pkg/mdsio: |
| 305 |
|
- clean-up mdsio_readfield.F & mdsio_writefield_new.F and |
| 306 |
|
move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & |
| 307 |
|
mdsio_write_field.F (S/R MDS_WRITE_FIELD); |
| 308 |
|
- fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD |
| 309 |
|
- collect old S/R in one file: mdsio_rw_field.F (now just a call to |
| 310 |
|
either MDS_READ_FIELD or MDS_WRITE_FIELD ) |
| 311 |
|
- new S/R (to replace MDSWRITEMETA), which allows to write more |
| 312 |
|
informations (variable names, time ...) to meta files. |
| 313 |
|
- modify rdmds.m to give back the meta file content. |
| 314 |
|
o pkg/diagnostics: change vertical interpolation to be safer, and more |
| 315 |
|
flexible (define p-levels to interpolate to in data.diagnostics); |
| 316 |
|
add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right |
| 317 |
|
diagnostic pointer. |
| 318 |
|
o pkg/seaice: more cleaning up of seaice_growth, added many comments |
| 319 |
|
o pkg/exf: put runoff0 and runoff1 into the appropriate common block |
| 320 |
|
o fix multi-category seaice: |
| 321 |
|
- change cpp flag SEAICE_MULTILEVEL to more meaningful name: |
| 322 |
|
SEAICE_MULTICATEGORY |
| 323 |
|
- fix short wave heat flux |
| 324 |
|
o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics |
| 325 |
|
and allow to use EVP solver. Change forward lab_sea: test both EVP |
| 326 |
|
solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) |
| 327 |
|
o Initial check-in of lab_sea adjoint |
| 328 |
|
(very similar to natl_box_adjoint/code_seaice) |
| 329 |
|
* used C-grid and EVP solver |
| 330 |
|
* used KPP, GM/Redi |
| 331 |
|
* uses inAdExact=.TRUE. |
| 332 |
|
* gradient checks fail for both ADM and TLM |
| 333 |
|
due to sensitive snow melt code in seaice_grwoth (look for "JZ") |
| 334 |
|
f.d. gradients actually seem more problematic than ADM, TLM gradients; |
| 335 |
|
issue is related to forward mismatch between g77 an ifort |
| 336 |
|
o pkg/seaice: overhaul of thermodynamics |
| 337 |
|
- growth.F and groatb.F are replaced by new routine seaice_growth.F |
| 338 |
|
- budget.F is replaced by two new routines seaice_budget_ocean/ice.F |
| 339 |
|
- move a few global fields out of SEAICE.h into seaice_growth.F and |
| 340 |
|
make them 2D (FICE/QNETO/ ...) |
| 341 |
|
- remove FO (it is the same as QNETO) |
| 342 |
|
- introduce a few local fields to avoid modifying external fields such |
| 343 |
|
as atemp, etc. |
| 344 |
|
|
| 345 |
|
checkpoint58s_post |
| 346 |
|
o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F |
| 347 |
|
changed exf_set_gen.F so that |
| 348 |
|
genperiod=0 means input file is one time-constant field and |
| 349 |
|
genperiod=-12 means input file contains 12 monthly means |
| 350 |
|
o CG2D: use pre-computed solver main-diagonal (stored in common block); |
| 351 |
|
this affects truncation error ; generate new output file for exp. which |
| 352 |
|
fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), |
| 353 |
|
global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), |
| 354 |
|
ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), |
| 355 |
|
MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), |
| 356 |
|
tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), |
| 357 |
|
vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) |
| 358 |
|
o start implementation of deep-atmosphere and anelastic formulation |
| 359 |
|
o verification: remove 2nd copy of input files and use script "prepare_run" |
| 360 |
|
to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) |
| 361 |
|
o mom_common/vecinv/fluxform: fix a few initialisation isssues |
| 362 |
|
o profiles: fix for multithreaded case |
| 363 |
|
|
| 364 |
|
o diagnostics: rename few diags: |
| 365 |
|
s/'PRESSURE'/'RCENTER '/g |
| 366 |
|
s/'TICE '/'oceFreez'/g |
| 367 |
|
s/'TAUX '/'oceTAUX '/g |
| 368 |
|
s/'TAUY '/'oceTAUY '/g |
| 369 |
|
s/'SWFLUX '/'oceQsw '/g |
| 370 |
|
s/DIFx/DFxE/g |
| 371 |
|
s/DIFy/DFyE/g |
| 372 |
|
and add few ocean-forcing diagnostics: |
| 373 |
|
atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS |
| 374 |
|
o modifications to pkg/seaice/growth.F and budget.F, which change results of |
| 375 |
|
lab_sea experiment: HSNOW was sometimes treated as effective and sometimes |
| 376 |
|
as actual snow thickness. It now refers everywhere to effective snow |
| 377 |
|
thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. |
| 378 |
|
|
| 379 |
|
checkpoint58r_post |
| 380 |
|
o modifications to pkg/seaice/growth.F, which change results of |
| 381 |
|
lab_sea experiment: fixes pertain to melting snow over open water, to |
| 382 |
|
masking EVAP under sea ice, and to using the correct AREA variable for |
| 383 |
|
computations of EVAP, PRECIP, HSNOW, and GHEFF |
| 384 |
|
o add ability to read bathy, salt, and theta using MNC (off by def) |
| 385 |
|
o add flooding algorithm and advection of HSNOW for pkg/seaice; |
| 386 |
|
both are turned off by default and do no change any results |
| 387 |
|
o seaice advection with pkg/thsice: a step toward the use of non-linear |
| 388 |
|
advection scheme, but #ifdef or commented out for now (requires more EXCH). |
| 389 |
|
o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens |
| 390 |
|
(identical results) and the standard version of EXTERNAL_FIELDS_LOAD |
| 391 |
|
in natl_box (affects results @ truncation level: update output.txt) |
| 392 |
|
o multi-threading and IO: |
| 393 |
|
- replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. |
| 394 |
|
- remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls |
| 395 |
|
(needed to work with SingleCpuIO): tested in all verif. exp. |
| 396 |
|
o GAD: use simpler DST3 formulation as default (old version left within #ifdef) |
| 397 |
|
affects the results (but none of the verification test uses this scheme). |
| 398 |
|
o Adding some pkg/diagnostics capability to pkg/seaice |
| 399 |
|
(will certainly be subject to changes) |
| 400 |
|
o ctrl: adding new control variables: |
| 401 |
|
lwflux, lwdown, evap, snowprecip, apressure, runoff |
| 402 |
|
|
| 403 |
|
checkpoint58q_post |
| 404 |
|
o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up |
| 405 |
|
1/6-deg Southern Ocean configuration by 8% on IBM Datastar and |
| 406 |
|
high_res_cube configuration by 4% on Columbia. |
| 407 |
|
o clean-up multi-threaded problems (reported by debugger tcheck on ACES); |
| 408 |
|
add (in global_with_exf/code) a version of EXF_INTERP_READ without |
| 409 |
|
dynamical allocation (seems to work in multi-threaded). |
| 410 |
|
o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using |
| 411 |
|
single CPU io) so that TAF does not have to see EESUPPORT.h |
| 412 |
|
o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
| 413 |
|
|
| 414 |
|
checkpoint58p_post |
| 415 |
|
o obcs: stop if obcs is used with useCDscheme = .true. |
| 416 |
|
o shelfice: |
| 417 |
|
- fix a sign error so that no slip at shelfice interface works |
| 418 |
|
- remove stop for combination non-hydrostatic code and shelfice. That does |
| 419 |
|
not mean, that the results are correct, but at least they are numerically |
| 420 |
|
stable |
| 421 |
|
o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) |
| 422 |
|
o added adjoint exch routined for all exch*3d* routines |
| 423 |
|
and updated flow directives |
| 424 |
|
|
| 425 |
|
checkpoint58o_post |
| 426 |
|
o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; |
| 427 |
|
remove old subroutines (_XY_ & _XYZ_); update the adjoint version. |
| 428 |
|
o change controling S/R for writing pickup file (new S/R do_write_pickup) |
| 429 |
|
and clean-up reading/writing of pickup files. |
| 430 |
|
o fix local version of read/write pickup (NH part) in rotating_tank/code |
| 431 |
|
o simplify EXCH interface: |
| 432 |
|
- change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) |
| 433 |
|
- not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version |
| 434 |
|
o added the regrid package |
| 435 |
|
o shelfice: |
| 436 |
|
- add a simple boundary layer scheme to reduce noise |
| 437 |
|
- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
| 438 |
|
|
| 439 |
|
checkpoint58n_post |
| 440 |
|
o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
| 441 |
|
local variable (not in common block). |
| 442 |
|
o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
| 443 |
|
- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
| 444 |
|
- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
| 445 |
|
to work with SingleCpuIO. |
| 446 |
|
o add "_d 0" to real constant of pkg/cfc subroutines ; |
| 447 |
|
update exp. cfc_exemple & tutorial_cfc_offline output files. |
| 448 |
|
o multi-threading and IO: |
| 449 |
|
- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
| 450 |
|
(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
| 451 |
|
- barrier before and after reading. |
| 452 |
|
- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
| 453 |
|
- avoid using MDS_WRITELOCAL for LAND pkg output. |
| 454 |
|
- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
| 455 |
|
common-block variables ; Allows multi-threading with master-thread IO. |
| 456 |
|
o change default MAX_NO_THREADS from 32 to 4 ; |
| 457 |
|
and stop cleanly when MAX_NO_THREADS is too small. |
| 458 |
|
o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
| 459 |
|
|
| 460 |
|
checkpoint58m_post |
| 461 |
|
o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
| 462 |
|
and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
| 463 |
|
o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
| 464 |
|
keep global_ocean.90x40x15 (for AD testing) with former secondary test |
| 465 |
|
(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
| 466 |
|
o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
| 467 |
|
add MITgcm_tutorials (= code + all the tutorials) |
| 468 |
|
o ecco, option to compute cost for total ssh (mean+anom) |
| 469 |
|
o consistent with addition of ptracer and ssh in pkg/profiles |
| 470 |
|
o profiles: adding ptracer and ssh |
| 471 |
|
o testreport: change multi-test output-file name |
| 472 |
|
(from output.txt.{name} to output.{name}.txt) |
| 473 |
|
o profiles: now ok for mutli-tiles case |
| 474 |
|
o seaice: add 4 parameters for different advection schemes for area, |
| 475 |
|
(effective) seaice thickness, enthalphy, and snow height. Their default |
| 476 |
|
is the standard parameter SEAICEadvScheme |
| 477 |
|
o calc_gw: |
| 478 |
|
- add cosFacU in zonal viscous flux (harmonic.visc.). |
| 479 |
|
- put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. |
| 480 |
|
of tutorial_plume_on_slope. |
| 481 |
|
o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). |
| 482 |
|
o calc_gw: true flux-form, account for horizontal grid spacing. |
| 483 |
|
update rotating_tank results, but not plume_on_slope (affected at |
| 484 |
|
truncation level, 11 digits). |
| 485 |
|
|
| 486 |
|
checkpoint58l_post |
| 487 |
|
o calc_gw: |
| 488 |
|
- take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V |
| 489 |
|
- remove side-drag for now (need to fix it); update plume_on_slope results. |
| 490 |
|
- fix for partial-cell & non-uniform dz; update plume_on_slope results. |
| 491 |
|
o commit code to make SST/SSS weights spatially variable |
| 492 |
|
(based on either variable in-situ or variable initial T/S weights) |
| 493 |
|
o pkg/ecco: |
| 494 |
|
* commit code to relax deviations of xx_theta, xx_salt to 5*sigma, |
| 495 |
|
now based on horizontally varying weights wthetaLev, wsaltLev |
| 496 |
|
* cost_averagesflags now returns year indices in addition to day, month |
| 497 |
|
* sflux balance is performed on annual basis |
| 498 |
|
(sflxumm, sfluxmm2, bal_sfluxmm) |
| 499 |
|
* for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, |
| 500 |
|
including separate counting and multipliers |
| 501 |
|
o pkg/rbcs |
| 502 |
|
* add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing |
| 503 |
|
|
| 504 |
|
checkpoint58k_post |
| 505 |
|
o testreport: |
| 506 |
|
- always build in dir. "build" (if not there, mkdir build instead of building |
| 507 |
|
& running in input) |
| 508 |
|
- run in dir run (if it exists), in build otherwise. |
| 509 |
|
- call prepare_run (if input/prepare_run exists) |
| 510 |
|
- run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. |
| 511 |
|
o pkg/exf modifications to interpolation and rotation routines for more |
| 512 |
|
reasonable treatment of North Pole singularity: for tracers North Pole |
| 513 |
|
value is set to northernmost zonal-mean value, for zonal velocity it is |
| 514 |
|
set to zero, and for meridional velocity it is set to northernmost value. |
| 515 |
|
o pkg/exf/exf_check_range.F |
| 516 |
|
- add tile index to diagnostics and move stop statement to the very |
| 517 |
|
end of the routine. |
| 518 |
|
o pkg/diagnostics: (diagnostics_main_init.F) |
| 519 |
|
define title of isomorphic variables according to the current config. |
| 520 |
|
o pkg/thsice with pkg/seaice dynamics: |
| 521 |
|
- fix domain of computation (interior only, required for exf) and do exchanges |
| 522 |
|
- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient |
| 523 |
|
o towards a standard way of dealing with multi-threading in MONITOR |
| 524 |
|
and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. |
| 525 |
|
o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) |
| 526 |
|
to W momentum equation in nonhydrostatic and quasihydrostatic runs. |
| 527 |
|
o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. |
| 528 |
|
o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) |
| 529 |
|
o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL |
| 530 |
|
(problems ? with gradient check in bottom_ctrl_5x5 adjoint test) |
| 531 |
|
o tracer advection: |
| 532 |
|
- clean-up and simplify calc_common_factors.F |
| 533 |
|
- make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer |
| 534 |
|
advection subroutine (but still not used within DST advection S/R) |
| 535 |
|
o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
| 536 |
|
|
| 537 |
|
checkpoint58j_post |
| 538 |
|
o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
| 539 |
|
from file (collects calls previously in FORWARD_STEP) |
| 540 |
|
o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS |
| 541 |
|
o adjoint store dir. adjusted accordingly |
| 542 |
|
o genmake2 |
| 543 |
|
replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. |
| 544 |
|
|
| 545 |
|
checkpoint58i_post |
| 546 |
|
o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
| 547 |
|
on wind stress (SEAICEstressFactor defaults to 1.) |
| 548 |
|
o Total number of Timers is finite (<=40): comment out 2 non-essential one |
| 549 |
|
in the_main_loop.F to avoid Pb (e.g., when running fizhi test) |
| 550 |
|
o vector_invariant: fix highOrderVorticity(=4.th.Order) advection |
| 551 |
|
on CS-grid: no longer loosing mass. |
| 552 |
|
o exf & curvilinear-grid: no longer modify longitude xC & xG. |
| 553 |
|
o pkg/ggl90: fix sloppy output and fix a bug |
| 554 |
|
o pkg/seaice: added SEAICEuseEVPpickup parameter |
| 555 |
|
- Set to false in order to start EVP solver with |
| 556 |
|
non-EVP pickup files when using SEAICEuseEVP |
| 557 |
|
- fix sign error in diffusion in seaice_calc_rhs |
| 558 |
|
|
| 559 |
|
checkpoint58h_post |
| 560 |
|
* Modifications for bottom topography control |
| 561 |
|
o replace hFacC by _hFacC at various places |
| 562 |
|
o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL |
| 563 |
|
o add non-self-adjoint cg2d_nsa |
| 564 |
|
o update autodiff support routines |
| 565 |
|
o re-initialise hfac after ctrl_depth_ini |
| 566 |
|
o works for 5x5 box, doesnt work for global_ocean.90x40x15 |
| 567 |
|
* Adding verification for 5x5 box (4-layer) bottom topography control |
| 568 |
|
|
| 569 |
|
checkpoint58g_post |
| 570 |
|
o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., |
| 571 |
|
used for mean seasonal cycle, mean diurnal cycle); add an example |
| 572 |
|
in verification/global_ocean.cs32x15/input.thsice/data.diagnostics |
| 573 |
|
o pkg/ggl90: |
| 574 |
|
- add parameter (minimum surface kinetic energy) |
| 575 |
|
- fix bug (avoiding division by zero) |
| 576 |
|
o couple pkg/thsice to pkg/seaice: |
| 577 |
|
- modify advection in seaice to accomodate new scalar fields to be advected |
| 578 |
|
- only muliDimAdection scheme work with seaice/thsice |
| 579 |
|
- mapping of thsice-variables to seaice-variables, back and forth |
| 580 |
|
- does not break the verification experiments, but does not give the |
| 581 |
|
desired results either |
| 582 |
|
o pkg/seaice |
| 583 |
|
- make (default) second order advection a bit less confusing? |
| 584 |
|
|
| 585 |
|
checkpoint58f_post |
| 586 |
|
o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice |
| 587 |
|
to pkg/seaice): |
| 588 |
|
- new routines thsice_map_exf and thsice_get_exf provide the interface |
| 589 |
|
- add an additional formal parameter to thsice_solve4temp |
| 590 |
|
o pkg/exf: |
| 591 |
|
- add new fields wspeed, snowprecip (to be able to couple to thsice) |
| 592 |
|
- correct Stefan-Boltzmann constant |
| 593 |
|
- new parameter for longwave surface emittance |
| 594 |
|
- separate some stuff from exf_bulkformulae into new routines |
| 595 |
|
exf_radiation, exf_wind |
| 596 |
|
- add new parameters and constants: longwave emissivity for ocean, ice |
| 597 |
|
and snow, evaporation parameters over ice |
| 598 |
|
- decouple wind/stress computation from ALLOW_BULKFORMULA: always compute |
| 599 |
|
either wind from stress or stress from wind |
| 600 |
|
o pkg/thSIce: |
| 601 |
|
- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F |
| 602 |
|
- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND |
| 603 |
|
and THSICE_CALC_THICKN |
| 604 |
|
- for now, call to THSICE_GET_BULKF remains inside i,j loops. |
| 605 |
|
- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h |
| 606 |
|
to make debugging easier. |
| 607 |
|
- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output |
| 608 |
|
o pkg/bulk_force: |
| 609 |
|
- clean-up comments and parameters ; |
| 610 |
|
- add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; |
| 611 |
|
o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; |
| 612 |
|
generate new output for test-experiment: aim.5l_cs.thSI |
| 613 |
|
o results_ad : rename "output.txt_adm" to "output_adm.txt" and change |
| 614 |
|
testreport accordingly |
| 615 |
|
|
| 616 |
|
checkpoint58e_post |
| 617 |
|
o SEAICE_CGRID adjoint done |
| 618 |
|
o R_STAR adjoint implemented. |
| 619 |
|
* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
| 620 |
|
* need to sort out init. of h0facc, etc. |
| 621 |
|
o Make pkg/profile fully independent of ecco,cost, etc. stuff |
| 622 |
|
to be able to use it in pure forward. |
| 623 |
|
|
| 624 |
|
checkpoint58d_post |
| 625 |
|
o upgrade simple test-experiment to tutorial example: |
| 626 |
|
step.1: duplicate the experiment and (step.2) will remove the old copy. |
| 627 |
|
tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
| 628 |
|
tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) |
| 629 |
|
tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
| 630 |
|
tutorial_global_oce_biogeo <- copy of dic_example |
| 631 |
|
tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
| 632 |
|
tutorial_plume_on_slope <- copy of plume_on_slope |
| 633 |
|
tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) |
| 634 |
|
tutorial_global_oce_optim <- empty for now (David ?) |
| 635 |
|
tutorial_global_oce_in_p <- copy of global_ocean_pressure |
| 636 |
|
some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
| 637 |
o correct a sign problem in cost_scat.F |
o correct a sign problem in cost_scat.F |
| 638 |
o obcs and ptracers: fix boundary conditions for advections schemes |
o obcs and ptracers: fix boundary conditions for advections schemes |
| 639 |
with larger stencil |
with larger stencil |
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