| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
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| 7 |
o add adTapeDir to specify a special directory where adjoint tapes are |
o adding allowInteriorFreezing option to check for water below freezing point |
| 8 |
written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05 |
at depth and bring the negative heat anomaly to the surface level |
| 9 |
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o external_fields_load: |
| 10 |
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new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear |
| 11 |
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interpolation weights) to use in a periodic time-series ; do not divide by |
| 12 |
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time-step to convert to integer: |
| 13 |
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- this fixes case where externForcingPeriod is not multiple of time-step |
| 14 |
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(Thanks to Christopher L. Wolfe) |
| 15 |
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- this fixes case where externForcingPeriod is an odd multiple of time-step |
| 16 |
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(was wrong by half of time-step); update results of tutorial_global_oce_in_p. |
| 17 |
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store index of time-record which is currently loaded: |
| 18 |
|
- works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ; |
| 19 |
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- needed for the adjoint but not yet used because of extensive recomputations; |
| 20 |
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(to be fixed soon) |
| 21 |
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|
| 22 |
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checkpoint62v (2011/04/02) |
| 23 |
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o verification/1D_ocean_ice_column added to test Ian Fenty's |
| 24 |
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pkg/seaice_growth.F modifications for improving sea ice code differentiability |
| 25 |
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o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope |
| 26 |
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(new velocity statistics after changing maskInW & maskInS definition) |
| 27 |
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o pkg/generic_advdiff with OBCS: |
| 28 |
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use maksInW & maskInS in advective flux and in biharmonic diffusion calculation: |
| 29 |
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equivalent to assumption of no tracer gradient outside the OB region. |
| 30 |
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This will affect the results if using obcs+biharmonic diffusion. |
| 31 |
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update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc) |
| 32 |
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o pkg/obcs: |
| 33 |
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change definition of maskInW & maskInS: leave OB edges inside (maskIn=1) |
| 34 |
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(e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still |
| 35 |
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in Interior region. No impact on solution but affects Velocity monitor stats. |
| 36 |
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o pkg/ptracers (adjoint) |
| 37 |
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New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate |
| 38 |
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tape file for each tracer |
| 39 |
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o model/inc/src and pkg/autodiff: add parameters that allow to turn |
| 40 |
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of parts of the adjoint code at run time. For now, there are only |
| 41 |
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useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These |
| 42 |
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parameters are set in data.pkg. |
| 43 |
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This is the lazy coward's version of doing this, but still useful for |
| 44 |
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debugging. In order to do it right, everything needs to be moved to |
| 45 |
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pkg/autodiff. |
| 46 |
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o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at |
| 47 |
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the end; this fixes the adjoint balancing code for open boundaries. |
| 48 |
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o pkg/ctrl: |
| 49 |
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- change behavior of xx_${varname}period to be analogous to exf-conventions: |
| 50 |
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xx_${varname}period = 0., means time-independent control part |
| 51 |
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xx_${varname}period = -12., means one-year-periodic monthly control part |
| 52 |
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- introduce helper routine ctrl_init_rec (part of ctrl_init.F) to |
| 53 |
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clean up ctrl_init a little, remove unused variables |
| 54 |
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- ctrl_init: fixed the handling of the start/endrec for obcs-variables |
| 55 |
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- move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec |
| 56 |
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|
| 57 |
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checkpoint62u (2011/03/15) |
| 58 |
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o model/src: |
| 59 |
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- for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in |
| 60 |
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h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ; |
| 61 |
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- in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to |
| 62 |
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INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF. |
| 63 |
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o pkg/ctrl/obcs/ecco: |
| 64 |
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- remove obsolete, unused, and partially broken code: |
| 65 |
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ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within |
| 66 |
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ALLOW_CTRL_OBCS_BALANCE |
| 67 |
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- put a stop statement into ecco/cost_obcsvol.F, but also add |
| 68 |
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cost_obcsvol to ecco_ad_diff.list |
| 69 |
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o pkg/ecco: fix counting cost function contributions for obcs (code |
| 70 |
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by Matt M.) and diffkr for diagnostics |
| 71 |
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o pkg/ecco, pkg/ctrl, pkg/grdchk: |
| 72 |
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add cost penalty terms for initial uvel, vvel, eta controls |
| 73 |
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and I/O for prior error files |
| 74 |
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o pkg/mdsio: |
| 75 |
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move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option |
| 76 |
|
(new argument) to check for tiled file in mdsioLocalDir : this fix the |
| 77 |
|
restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir. |
| 78 |
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o pkg/ctrl: |
| 79 |
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- ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by |
| 80 |
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ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove |
| 81 |
|
unused and superfluous variables |
| 82 |
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- ctrl_get_gen_rec.F: catch the case of xx_genperiod=0. |
| 83 |
|
o pkg/ecco |
| 84 |
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- enable adjoint of Stevens OB |
| 85 |
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o pkg/ctrl/ecco/grdchk: |
| 86 |
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- remove global declaration of tmpfldx/yz and tmpfldx/yz2. |
| 87 |
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Fortunately, we do not have any tests for the numerous cpp-flagged |
| 88 |
|
option of "obcs as control parameters" so we will never know |
| 89 |
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if this is an improvement (but at least now things compile). |
| 90 |
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- remove an obsolete initialization from ecco_cost_init_barfiles.F |
| 91 |
|
- fix some problems within never used ifdefs to make the code compile |
| 92 |
|
o pkg/obcs: |
| 93 |
|
- Refine Interior mask definition to work with more complex OB (e.g. |
| 94 |
|
if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to |
| 95 |
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read in Interior mask from file. Check if Interior mask is consistent |
| 96 |
|
with OB list of indices. |
| 97 |
|
o pkg/seaice |
| 98 |
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- beginning code for a seaice tracer package, |
| 99 |
|
but currently only used for seaice age: SEAICE_AGE |
| 100 |
|
SEAICE_num = 4 |
| 101 |
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iTracer = 1: area-weighted ice age |
| 102 |
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= 2: volume-weighted ice age |
| 103 |
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= 3, 4: template for one-year vs. multi-year ice |
| 104 |
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data.seaice has new namelist SEAICE_PARM03 for arrays related to |
| 105 |
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SEAICE_num |
| 106 |
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|
| 107 |
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checkpoint62t (2011/03/05) |
| 108 |
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o pkg/obcs: |
| 109 |
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- obcs_apply_uv.F: change to a 2 steps method, first tangential component; |
| 110 |
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then normal component. This ensures that the normal component is set |
| 111 |
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correctly even when it conficts with tangential setting from an other OB. |
| 112 |
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Affects results of test-experiment seaice_obcs: update the output.txt |
| 113 |
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o pkg/obcs: |
| 114 |
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- add code to monitor statistics of dynamical fields at OB. |
| 115 |
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- take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW : |
| 116 |
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- fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection). |
| 117 |
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- change default: balance the Net inflow through all OB (instead of balancing |
| 118 |
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each OB separately); keep the old method if setting OBC_balanceFacX < 0. |
| 119 |
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- switch on useOBCSbalance in dome experiment: only correct Western OB outflow |
| 120 |
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to match Nortern OB inflow (OBCS_balanceFacN=0). |
| 121 |
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o pkg/seaice: |
| 122 |
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- redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL |
| 123 |
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o pkg/seaice (seaice_growth v 1.113): |
| 124 |
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- reverting seaice_growth to v 1.111 in order to have code with exact bit |
| 125 |
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compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge |
| 126 |
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CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced |
| 127 |
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runtime flag SEAICEareaFormula is kept but is inactive |
| 128 |
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o model/src: |
| 129 |
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- add new param to scale curvilinear grid distance and area when using |
| 130 |
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a different sphere radius from the grid-files. |
| 131 |
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- test/check multi-threads EXCH applied to local variable (cg2d_x) |
| 132 |
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o adjoint: |
| 133 |
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- enable adjoint of Stevens OB |
| 134 |
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- add dummy_in_dynamics to enable extraction of ADJrhoinsitu |
| 135 |
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(a bit delicate because of potentially modified adj. common block structure; |
| 136 |
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current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later) |
| 137 |
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|
| 138 |
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checkpoint62s (2011/02/15) |
| 139 |
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o pkg/seaice (seaice_growth v 1.112): |
| 140 |
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- introduce SEAICEareaFormula run time parameter, which selects the recipe for |
| 141 |
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computing the ice cover tendency from effective thickness tendencies. Include |
| 142 |
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Ian Fenty's formula. |
| 143 |
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- remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using |
| 144 |
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SEAICEareaFormula. |
| 145 |
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- simplify notations for the various d_HEFF/d_AREA terms. |
| 146 |
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o pkg/gmredi: |
| 147 |
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- add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code |
| 148 |
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from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative; |
| 149 |
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add a verification test-run (front_relax.bvp) to test GM_useBVP. |
| 150 |
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o pkg/seaice (seaice_growth v 1.111): |
| 151 |
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- for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's. |
| 152 |
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- the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to |
| 153 |
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also melt ice. |
| 154 |
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o pkg/seaice: |
| 155 |
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- McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty). |
| 156 |
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- can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h |
| 157 |
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o pkg/cheapaml: |
| 158 |
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- from Nico Wienders: New version of this package. |
| 159 |
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o pkg/flt: |
| 160 |
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- add CPP options to prevent floats to re-enter the opposite side of |
| 161 |
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a periodic domain (default: keep periodicity) |
| 162 |
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o pkg/gmredi: |
| 163 |
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- apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners |
| 164 |
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(needed for multi-dim advection). |
| 165 |
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- switch on GM Advective form in global_ocean.cs32x15 and update output.txt |
| 166 |
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o model/src: |
| 167 |
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- fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run. |
| 168 |
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o tutorial_tracer_adjsens |
| 169 |
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- extend to NLFS and replace maskC by hFacC |
| 170 |
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(change reference output accordingly) |
| 171 |
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|
| 172 |
|
checkpoint62r (2011/01/24) |
| 173 |
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o testreport: |
| 174 |
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- add option -deloutp (-do) to remove output file after successful run |
| 175 |
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- add option -mfile (-mf) for MPI machile-file and for each test-exp, |
| 176 |
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extract exact list of procs from this file ; adjust COMMAND by |
| 177 |
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replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs. |
| 178 |
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o pkg/ecco: replace old ineffective way of penalizing deviations from |
| 179 |
|
first guess (of obcs) with code by Matt Mazloff |
| 180 |
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o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without |
| 181 |
|
exf/cal |
| 182 |
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- ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl |
| 183 |
|
and handle case of obcs?period == 0 |
| 184 |
|
Not affected by these changes: There is still an inconsistency in |
| 185 |
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the computation of start/endrec for the obcs variables for ALLOW_CAL |
| 186 |
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defined (see comment by Menemenlis, 7-Mar-2003) |
| 187 |
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- make S/R ctrl_get_gen_rec return something meaningful even if |
| 188 |
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ALLOW_CAL is not defined |
| 189 |
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- ctrl_getobcs?: simplify code so that it does not need to use |
| 190 |
|
S/R exf_swapfields |
| 191 |
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o testreport: |
| 192 |
|
allow to test MPI with different number of processors for each experiment: |
| 193 |
|
create file "SIZE.h.mpi" in each build dir. |
| 194 |
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Note: update of "-command" argument not yet implemented. |
| 195 |
|
o model/src, pkg/autodiff, pkg/ecco, pkg/seaice: |
| 196 |
|
alleviate the need for additional 3D tapes when using |
| 197 |
|
the non-inear free surface in the adjoint. This is done |
| 198 |
|
by adding an 'update' of hfacc etc. to their current |
| 199 |
|
value at the beginning of forward_step.F. |
| 200 |
|
o pkg/seaice |
| 201 |
|
seaice_lsr: move stress-divergence computations out of outer pseudo- |
| 202 |
|
timestepping loop |
| 203 |
|
o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD' |
| 204 |
|
up, so that the calls of the ctrl_* subroutines are really at the end |
| 205 |
|
of the routine. |
| 206 |
|
o pkg/gmredi: |
| 207 |
|
allow to specify a 2-D horizontal map and a 1-D vertical profil |
| 208 |
|
as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity. |
| 209 |
|
o pkg/seaice: |
| 210 |
|
move lsr iterations from seaice_dynsolver to seaice_lsr. |
| 211 |
|
o pkg/seaice: |
| 212 |
|
reduce memory footprint of seaice mutldim advection tapes, |
| 213 |
|
by using a 2D tape independent of the generic_advdiff ones, |
| 214 |
|
and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc. |
| 215 |
|
|
| 216 |
|
checkpoint62q (2010/12/29) |
| 217 |
|
o model/src: |
| 218 |
|
- check horizontal grid-spacing for unset or zero/negative values. |
| 219 |
|
- change AD test hs94.1x64x5 to be truly a 2-D set-up. |
| 220 |
|
o pkg/flt: |
| 221 |
|
- use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR |
| 222 |
|
- precision of input and output files set according to readBinaryPrec |
| 223 |
|
and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits. |
| 224 |
|
- initial float position from tiled file was not converted to index space |
| 225 |
|
(looks like a bug): fixed to make it similar to initial pos. global file. |
| 226 |
|
o global_ocean.cs32x15: |
| 227 |
|
change SIZE.h of AD set-up to get same tiling as with MPI. |
| 228 |
|
Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11) |
| 229 |
|
o model/src: |
| 230 |
|
add flag to control printing of domain fields (bathymetry, hFac ...) in |
| 231 |
|
ini_mask_etc (call to plot_fieds_xy*). |
| 232 |
|
o pkg/thsice: |
| 233 |
|
if useEXF, some forcing fields are not valid in overlap: fixed by computing |
| 234 |
|
over the interior only + apply EXCH at the end (like with SEAICE advection). |
| 235 |
|
o pkg/mdsio: |
| 236 |
|
- add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer |
| 237 |
|
to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS. |
| 238 |
|
- change barrier call for safe multi-threads access to 3-D shared buffer. |
| 239 |
|
- MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones) |
| 240 |
|
- replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and |
| 241 |
|
remove the 4 S/R MDS_PASS_WH_R4/8toRL/S. |
| 242 |
|
o pkg/flt: |
| 243 |
|
- add fourth-order Runge-Kutta integration |
| 244 |
|
- add basic exch2 support (only 1 facet supported so far!) |
| 245 |
|
o pkg/mdsio+rw: |
| 246 |
|
new S/R to read local (or tile independent) vector (read counterpart of |
| 247 |
|
mds_writevec_loc, and front-end write_glvec_rl/rs). |
| 248 |
|
o global_ocean.cs32x15: additional input_ad.seaice experiment |
| 249 |
|
that uses pkg/seaice rather than pkg/thsice. |
| 250 |
|
(using multidim advection for seaice) |
| 251 |
|
o towards more F95 syntax for array specification in namelist: |
| 252 |
|
- change "data.diagnostics" (data.ptracers was changed before checkpoint62p) |
| 253 |
|
of all verification experiments. |
| 254 |
|
e.g.: line: fields(1,3)='ETAN ','ETANSQ ', |
| 255 |
|
was changed to: fields(1:2,3)='ETAN ','ETANSQ ', |
| 256 |
|
- finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles |
| 257 |
|
o global_ocean.cs32x15: additional input.seaice experiment |
| 258 |
|
that uses pkg/seaice rather than pkg/thsice. |
| 259 |
|
|
| 260 |
|
checkpoint62p (2010/12/17) |
| 261 |
|
o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it |
| 262 |
|
to THSICE_SIZE.h to avoid conflict with pkg/seaice. |
| 263 |
|
o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint. |
| 264 |
|
allow for use of multim. advection in seaice adjoint. |
| 265 |
|
o pkg/seaice: add diagnostics for snow precipitation and sublimation flux |
| 266 |
|
- first attempt to close budgets by taking into account the freshwater |
| 267 |
|
flux implied by the sublimation of snow and ice. So far only the |
| 268 |
|
volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag |
| 269 |
|
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET |
| 270 |
|
o eesupp/src: |
| 271 |
|
new S/R with new option (NML_EXTENDED_F77) to change array specification |
| 272 |
|
from F95 standard to commonly accepted extended F77 form. |
| 273 |
|
This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5) |
| 274 |
|
and to revert back to the original syntax (with -DNML_EXTENDED_F77) |
| 275 |
|
for less tolerant f77 compiler (e.g., pgf77, g77). |
| 276 |
|
o globalFiles: |
| 277 |
|
commented out in parameter file "data" since it's not safe with MPI |
| 278 |
|
(e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much |
| 279 |
|
in this case); no longer commented out in restart test (tst_2+2). |
| 280 |
|
o add adTapeDir to specify a special directory where adjoint tapes are |
| 281 |
|
written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05 |
| 282 |
and cannot be used together with mdsioLocalDir. |
and cannot be used together with mdsioLocalDir. |
| 283 |
o nesting pkgs: |
o nesting pkgs: |
| 284 |
- packages_init_variables : put call to OBCS_INIT_VARIABLES in last position |
- packages_init_variables : put call to OBCS_INIT_VARIABLES in last position |
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