| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
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|
| 7 |
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o pkg/autodiff: |
| 8 |
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re-write active I/O high-level (control) S/R: |
| 9 |
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- rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL |
| 10 |
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- add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R. |
| 11 |
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- use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and |
| 12 |
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MDS_READ/WRITE_FIELD); change loops to multi-threads. |
| 13 |
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- update and merge active_file_control_slice.flow into active_file_control.flow |
| 14 |
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- update the calls in lower level S/R (active_file.F, active_file_g.F and |
| 15 |
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active_file_ad.F) keeping the argument list and function unchanged. |
| 16 |
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- also update lower-level "_LOC" version (call same S/R with "useCurrentDir |
| 17 |
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=.TRUE.") and remove high-level (control) _loc version (not called anymore). |
| 18 |
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o autodiff and RS=real*4: |
| 19 |
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- call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf |
| 20 |
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ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ; |
| 21 |
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- change argument type of 3-D mask argument to _RS to match type in the call |
| 22 |
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(in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued. |
| 23 |
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o pkg/thsice: |
| 24 |
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- re-anable balanceEmPmR when useSEAICE=T with useThSIce=T. |
| 25 |
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- option to correct ocean fresh-water flux for imbalance of Atmos+Land |
| 26 |
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fresh-water flux: uniform correction or proportional to local precip. |
| 27 |
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o pkg/ctrl: |
| 28 |
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- new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D |
| 29 |
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- redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to |
| 30 |
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ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC |
| 31 |
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- verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL |
| 32 |
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|
| 33 |
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checkpoint63q (2012/07/30) |
| 34 |
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o pkg/autodiff: |
| 35 |
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note about monitor and snap-shot of ad-variables: |
| 36 |
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a) need to apply ADEXCH before monitor or output of ad-vars to include |
| 37 |
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overlap contributions (was done for adjDump but missing for monitor). |
| 38 |
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b) since ADEXCH implies adding overlap values to interior array, machine |
| 39 |
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truncation error is expected when adding an ADEXCH call in the middle of |
| 40 |
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the time-stepping (although mathematically identical). |
| 41 |
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modifs: |
| 42 |
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- fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars |
| 43 |
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declaration (adEddyPsiX,adEddyPsiY in adcommon.h). |
| 44 |
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- add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to |
| 45 |
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apply ADEXCH before monitor or snap-shot of ad-variables: |
| 46 |
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=0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy. |
| 47 |
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- implement new method (copy+adexch) for snap-shot and monitor of main model |
| 48 |
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ad-vars (initially not used by default -> output unchanged). |
| 49 |
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- change default (set to 2) to use new method and update few output_adm.txt |
| 50 |
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with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo |
| 51 |
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and both tutorial_tracer_adjsens tests). |
| 52 |
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- switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice) |
| 53 |
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and turn off momDissip_In_AB in the 2 other (needed for stable AB-3). |
| 54 |
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o pkg/ctrl: |
| 55 |
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enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of |
| 56 |
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generic control variables via |
| 57 |
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#define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL |
| 58 |
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Only required customization should be S/R ctrl_map_ini_genarr.F |
| 59 |
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(routine in repository contains example) |
| 60 |
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o pkg/exf: |
| 61 |
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- fix and refine checking of surface-relaxation setting when using EXF |
| 62 |
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o verification (adjoint exp): |
| 63 |
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- reduce length of simulation by half for experiment global_ocean.cs32x15 |
| 64 |
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(std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output. |
| 65 |
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o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag) |
| 66 |
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- replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers |
| 67 |
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of KE that can occur with aggressive optimization |
| 68 |
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+ put quadratic bottom drag calculation in separated loops (only done if |
| 69 |
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using bottomDragQuadratic) |
| 70 |
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o model/src: CG2D_NSA |
| 71 |
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- clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF |
| 72 |
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and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE. |
| 73 |
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- in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens), |
| 74 |
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change cg2d residual target to be expressed in Wunits (=> do not normalise |
| 75 |
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RHS ; this fix global_max Pb with TAF); update output. |
| 76 |
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o verification/tutorial_tracer_adjsens: |
| 77 |
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improve parameter consistency (and get rid of warnings): |
| 78 |
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- use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf); |
| 79 |
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- switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical) |
| 80 |
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- use staggerTimeStep (for stability) in som81; use default rotation period. |
| 81 |
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o pkg/exch2: |
| 82 |
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- with empty facet: fix compact-format (W2_mapIO=1) definition (was previously |
| 83 |
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reset to 0 = 1 long line in X) |
| 84 |
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o pkg/mdsio: |
| 85 |
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- fix reading of dimensions from meta file for large-size domain |
| 86 |
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o model/src: |
| 87 |
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- fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long); |
| 88 |
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- to refine CS-grid check, add logical flag "hasWetCSCorners": true if using |
| 89 |
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Cubed-Sphere Exch with CS-corners inside the domain; |
| 90 |
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make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate |
| 91 |
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globalArea and to set hasWetCSCorners. |
| 92 |
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- add warning if usingCurvilinearGrid and momAdvection in flux-form (missing |
| 93 |
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metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form. |
| 94 |
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- re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if |
| 95 |
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useCDscheme and useCubedSphereExchange). |
| 96 |
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o pkg/seaice/seaice_growth.F : |
| 97 |
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- compute the SEAICE_DISABLE_HEATCONSFIX term accordingly |
| 98 |
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for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0) |
| 99 |
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when the previous code was not correct. |
| 100 |
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- in all cases diagnoze the boundary condition mismatch to SIaaflux |
| 101 |
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- in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add |
| 102 |
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that term to QNET (essentially to set the melt/freeze water to 0degC). |
| 103 |
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when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed. |
| 104 |
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o verification/global_ocean.cs32x15/input.seaice : |
| 105 |
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- add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget. |
| 106 |
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- add diagnostics (commented out) for budget test using my matlab codes (gcmfaces). |
| 107 |
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- update results (output.seaice.txt) accordingly. |
| 108 |
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o verification/lab_sea/input/data.seaice : |
| 109 |
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- remove SEAICEheatConsFix, which is now be tested |
| 110 |
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in global_ocean.cs32x15. The presently coded fix |
| 111 |
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is only consistent with real fresh water + nlfs. |
| 112 |
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- update results (output.txt) accordingly. |
| 113 |
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o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd). |
| 114 |
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o AD_CONFIG.h file: |
| 115 |
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- in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h; |
| 116 |
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- remove #include "AD_CONFIG.h" from all included OPTIONS files and |
| 117 |
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add it explicitly in each fortran src file where it is needed. |
| 118 |
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motivation: header file AD_CONFIG.h is generated/modified after "make depend" |
| 119 |
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thus introducing potentially wrong dependency; therefore, better to include |
| 120 |
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it only where it's really needed, and after any other included OPTIONS file |
| 121 |
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(less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN |
| 122 |
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or ALLOW_TANGENTLINEAR_RUN). |
| 123 |
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|
| 124 |
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checkpoint63p (2012/07/06) |
| 125 |
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o pkg/autodiff: |
| 126 |
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- rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ; |
| 127 |
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- create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters |
| 128 |
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which are now read from new parameter file "data.autodiff" (inAdExact |
| 129 |
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previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg) |
| 130 |
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- add file "data.autodiff" in all verification/*/input_ad/ directories. |
| 131 |
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- add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward |
| 132 |
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mode (used in global_ocean.cs32x15.seaice_dynmix test exp.) |
| 133 |
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o verification/tutorial_tracer_adjsens/ |
| 134 |
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- add extra sub-verification which uses "SOM" advection scheme |
| 135 |
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(2nd Order-Moment Advection Scheme, Prather Limiter) with |
| 136 |
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#define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h |
| 137 |
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and in data: |
| 138 |
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multiDimAdvection=.TRUE., |
| 139 |
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tempAdvScheme=81, |
| 140 |
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saltAdvScheme=81, |
| 141 |
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o model/src: |
| 142 |
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- introduce ALLOW_BALANCE_RELAX which allow the removal |
| 143 |
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of the global mean of relaxation terms by setting |
| 144 |
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balanceThetaClimRelax and balanceSaltClimRelax |
| 145 |
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- disable balanceEmPmR and balanceQnet in the case when useSeaice. |
| 146 |
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This case is now treated appropriately in seaice_growth.F |
| 147 |
|
o pkg/seaice: |
| 148 |
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- do balanceEmPmR and balanceQnet based on the net fluxes |
| 149 |
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(SItflux) that enter the ocean+ice system rather than QNET |
| 150 |
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and EMPMR. Works best in real fresh water. |
| 151 |
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- SIatmFW, SIatmQnet, and SItflux computations had to be moved |
| 152 |
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out of the diagnotics bloc, and stored in global arrays. |
| 153 |
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|
| 154 |
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checkpoint63o (2012/06/29) |
| 155 |
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o vertical mixing schemes: |
| 156 |
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- remove unused S/R CALC_BUOYANCY (left from branch-atmos merging) |
| 157 |
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- replace computation of density (in Function STATE1, opps_calc.F) by a call |
| 158 |
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to S/R FIND_RHO_SCALAR |
| 159 |
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- pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC |
| 160 |
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and use it for N^2 calculation in ggl90_calc.F (save 2 density computations); |
| 161 |
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affects output (vermix.ggl90) at truncation level. |
| 162 |
|
o testreport: |
| 163 |
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- change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles |
| 164 |
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(nSx,nSy) for the number of threads (from eedata.mth) |
| 165 |
|
o model/src: |
| 166 |
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- remove 2nd set of calls at the top of initialise_varia.F (Adjoint part) |
| 167 |
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related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary). |
| 168 |
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o verification/tutorial_tracer_adjsens/ |
| 169 |
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- compile with ALLOW_CG2D_NSA |
| 170 |
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- run with nonlinFreeSurf=3 |
| 171 |
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- update reference output_adm.txt |
| 172 |
|
o tools/genmake2: |
| 173 |
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- add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ; |
| 174 |
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refine usePROFILES switching off (only when NetCDF is not available). |
| 175 |
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o verification (atmospheric set-up): |
| 176 |
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- change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration |
| 177 |
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o pkg/profiles : refine profiles and files handling. |
| 178 |
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o model/src and pkg/ecco : introduce run-time switch usePROFILES. |
| 179 |
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o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h : |
| 180 |
|
- changes to use model/src/the_main_loop.F rather than the ecco version |
| 181 |
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in ecco type adjoint runs. |
| 182 |
|
o model/src: |
| 183 |
|
- move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID |
| 184 |
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- move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC |
| 185 |
|
- update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL) |
| 186 |
|
o model/src: |
| 187 |
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- fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before); |
| 188 |
|
update output of test experiment bottom_ctrl_5x5. |
| 189 |
|
o pkg/generic_advdiff: |
| 190 |
|
- implement vertical bi-harmonic diffusion (for now, only for T & S and |
| 191 |
|
only explicitly). |
| 192 |
|
o verification/bottom_ctrl_5x5/ |
| 193 |
|
update reference output (results changed quite some time ago, |
| 194 |
|
not sure when; but new reference results look ok in terms of grdchk) |
| 195 |
|
o verification/1D_ocean_ice_column/ |
| 196 |
|
For verification purposes, the exact adjoint rather than an approx. |
| 197 |
|
should be used (e.g., to comare against F.D. or TLM). |
| 198 |
|
removed autodiff_inadmode*_ad.F routines in code_ad/ |
| 199 |
|
Update results/ accordingly. |
| 200 |
|
o pkg/cal: |
| 201 |
|
- change cal_getdate.F so that output date is function of input time only |
| 202 |
|
(less ambiguous, not mixed up with input iteration number). |
| 203 |
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- fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP). |
| 204 |
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o pkg/diagnostics: |
| 205 |
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- implement calendarDumps also for stats-diags |
| 206 |
|
- implement calendarDumps also for snap-shot output (negative freq) |
| 207 |
|
- for now, ignores calendarDumps if non-zero phase-lag. |
| 208 |
|
|
| 209 |
|
checkpoint63n (2012/06/04) |
| 210 |
|
o model/src: |
| 211 |
|
- recompute rSurfW & S to ensure consistent column thickness (needed for rStar) |
| 212 |
|
between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice; |
| 213 |
|
- use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more |
| 214 |
|
similar to calc_r_star.F); update results of experiment internal_wave and |
| 215 |
|
tutorial_global_oce_in_p (affected @ truncation level). |
| 216 |
|
o pkg/shelfice: |
| 217 |
|
- add parameterisation of advective-diffusive flux into the ice shelf |
| 218 |
|
according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd |
| 219 |
|
- simply eps3/3a computation |
| 220 |
|
o eesupp: |
| 221 |
|
- add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange |
| 222 |
|
between tiles, just fill-in edges assuming locally periodic subdomain) and |
| 223 |
|
add corresponding exchange subroutines (EXCH0); |
| 224 |
|
- new CG-solver version (_EX0) for disconnected-tiles special case. |
| 225 |
|
o model/src (CG-solvers): |
| 226 |
|
- modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached |
| 227 |
|
(similar final residual output and max-Iter number as with standard version); |
| 228 |
|
- allows to store and use lowest-residual solution (standard & _SR versions); |
| 229 |
|
- cleaning up (remove old, commented out code, LETS_MAKE_JAM ...). |
| 230 |
|
- by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h) |
| 231 |
|
o eesup/src: |
| 232 |
|
- global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef |
| 233 |
|
ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012) |
| 234 |
|
o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn |
| 235 |
|
|
| 236 |
|
checkpoint63m (2012/04/27) |
| 237 |
|
o pkg/shelfice: |
| 238 |
|
- account for partical cells in surface level below ice-shelf for hydrostatic |
| 239 |
|
pressure calculion (set uniformFreeSurfLev to F); update isomip experiments. |
| 240 |
|
o ad test experiments: |
| 241 |
|
- update and rename to "ad_optfile.local" local AD-optfile specific to a |
| 242 |
|
particular adjoint verification experiment (in verification/*/code_ad/) |
| 243 |
|
o pkg/seaice & pkg/exf: |
| 244 |
|
- Part two of ECCO-CLIVAR code merges. |
| 245 |
|
Completes merge of seaice area relax. code. |
| 246 |
|
Requires unified CPP option EXF_ALLOW_SEAICE_RELAX |
| 247 |
|
to be set in EXF_OPTIONS.h since this pkg controls its I/O |
| 248 |
|
(and avoids second CPP option in SEAICE_OPTIONS.h) |
| 249 |
|
- change default value of costIceStart & costIceEnd to a valid date. |
| 250 |
|
- add snowPrecip to HSNOW in seaice_growth |
| 251 |
|
o pkg/ptracers: |
| 252 |
|
- move ptracers summary and setup check into separated S/R ; add a check for |
| 253 |
|
valid PTRACERS_Iter0 value (error+stop or just warning). |
| 254 |
|
o pkg/cal (+ pkg/ecco): |
| 255 |
|
- avoid calling a S/R with 2 times the same arg (FWD: unless both are only used |
| 256 |
|
as input; and for AD, unless both are not differentiable (e.g., k index)). |
| 257 |
|
o model/src: |
| 258 |
|
- define internal flag "uniformFreeSurfLev" (=T when free-surface level-index |
| 259 |
|
is everywhere k=1) to speed-up some calculations (by pass kSurf reference); |
| 260 |
|
temporary set to usingZCoords value (to be changed to F when using shelfice). |
| 261 |
|
- hydrostatic pressure: implement partial cell near the surface also for |
| 262 |
|
Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on |
| 263 |
|
usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code). |
| 264 |
|
o pkg/ctrl/ctrl_init.F: |
| 265 |
|
- add a formal parameter to s/r ctrl_init_rec to print |
| 266 |
|
xx_$(ctrl_valiable)_file for easier debugging |
| 267 |
|
- move call of cal_* routines into the if-block where they are really |
| 268 |
|
needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having |
| 269 |
|
to specify a startdate |
| 270 |
|
o pkg/seaice: |
| 271 |
|
- update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and |
| 272 |
|
global_ocean.cs32x15/code versions). |
| 273 |
|
- turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for |
| 274 |
|
verification experiment global_ocean.cs32x15.seaice and update results. |
| 275 |
|
o pkg/exf: |
| 276 |
|
- new S/R EXF_GETFIELD_START to return starting-time of a forcing field |
| 277 |
|
(according to useExfYearlyFields). |
| 278 |
|
o pkg/cal: |
| 279 |
|
- move calendar setting & summary (previously in cal_readparams.F) into new |
| 280 |
|
S/R CAL_INIT_FIXED to be called later in the initialisation process, once |
| 281 |
|
length of the simulation is set (after SET_PARMS call); This is an attempt |
| 282 |
|
to fix Pb when, e.g.: pkg/longstep, modifies the length of the run. |
| 283 |
|
- For safety: keep a record of pkg/cal parameter settings status |
| 284 |
|
to allow to STOP if one pkg/cal S/R is called too early. |
| 285 |
|
- add a stop in all basic pkg/cal subroutines if called before setting is done. |
| 286 |
|
- modify cal_getdate.F: stop when nothing was returned; |
| 287 |
|
if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2); |
| 288 |
|
this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F. |
| 289 |
|
|
| 290 |
|
checkpoint63l (2012/04/04) |
| 291 |
|
o pkg/bbl: |
| 292 |
|
- fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc); |
| 293 |
|
update global_with_exf output.yearly.txt file. |
| 294 |
|
o pkg/cal: |
| 295 |
|
- start to clean-up cal_set.F ; fix for the case where baseTime is non-zero. |
| 296 |
|
- remove 2 unsused and very short (1 line only) functions ; |
| 297 |
|
- remove unsused subroutines from AD-Diff list. |
| 298 |
|
o model/src: |
| 299 |
|
- start to implement clean wait to stop in initialization S/R (config_check.F, |
| 300 |
|
packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage) |
| 301 |
|
o folowing PRINT_MESSAGE changes: |
| 302 |
|
- remove reminder multiple print to the same file (STDOUT) when multi-threads. |
| 303 |
o pkg/bbl: |
o pkg/bbl: |
| 304 |
- modification so it can work with z* |
- modification so it can work with z* |
| 305 |
- replace deltaT with dTtracerLev(k) for asynchronous time stepping |
- replace deltaT with dTtracerLev(k) for asynchronous time stepping |
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