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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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checkpoint65c (2014/08/30) |
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o pkg/dic: |
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- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
| 10 |
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and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
| 11 |
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AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
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o verification: |
| 13 |
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- new experiment testing OBCS and DIC pkgs, using params & output from |
| 14 |
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tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
| 15 |
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passage: take OBCS from the last year of a 2 yrs simulation and initial |
| 16 |
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conditions from t=1.yr while keeping the same forcing. |
| 17 |
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o model/src: |
| 18 |
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- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
| 19 |
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(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
| 20 |
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o pkg/diagnostics (Stats-Diags): |
| 21 |
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- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
| 22 |
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a) refine region where stats are computed, excluding where arrhFac=0 ; |
| 23 |
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b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
| 24 |
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c) extend regional stats over the region edges (for U or V pt location). |
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o pkg/gchem: |
| 26 |
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- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
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pkg/dic is currently changing/updating ptracers values beyond the OB). |
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o verification (hs94): |
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- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
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bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
| 31 |
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hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
| 32 |
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apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
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o pkg/ptracers: |
| 34 |
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- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
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switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
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- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
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with AB-2 code (so that it get tested). |
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o model/src: |
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- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
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with AB-2 code (previously only available with AB-3 code). |
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Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
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to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
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there, by calling CYCLE_AB_TRACER). |
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o pkg/generic_advdiff: |
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- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
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GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
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+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
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S/R temp/salt/ptracers_integrate.F |
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o model/src & pkg/ptracers: |
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- remove common block variables gT,gS (in DYNVARS.h), except when |
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USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
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- remove common block variable gPtr. |
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o model/src & pkgs: |
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- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
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ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
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IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
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GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
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+ change accordingly all calling S/R. |
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- use local temperature/salinity/ptracer tendency array (without bi,bj) |
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in S/R temp/salt/ptracers_integrate.F |
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o pkg/seaice: |
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- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
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to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
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- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
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in seaice_lsr |
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- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
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in s/r seaice_lsr_calc_coeffs |
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o pkg/mdsio: |
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- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
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(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
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too long (e.g., > MAX_LEN_FNAM/2 ) |
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|
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checkpoint65b (2014/08/12) |
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o pkg/matrix: |
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- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
| 76 |
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o model/src: |
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- fix initialisation of geothermalFile; compile geothermal-flux code in |
| 78 |
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natl_box verification experiment. |
| 79 |
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o model/src & pkg/down_slope: |
| 80 |
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- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
| 81 |
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- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
| 82 |
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field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
| 83 |
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results at machine truncation level: update output of experiments |
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global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
| 85 |
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o pkg/diagnostics (Stats-Diags): |
| 86 |
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- do not cumulate the full volume when DIAGNOSTICS_FILL is |
| 87 |
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called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
| 88 |
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This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
| 89 |
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times (but Min,Max and StD are still wrong). |
| 90 |
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o model/src: |
| 91 |
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- add geothermal flux forcing: read in ini_forcing.F as time-constant |
| 92 |
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field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
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o model/src: |
| 94 |
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- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
| 95 |
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_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
| 96 |
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arrays are already updated while adjustments (filters, conv.adjustment) are |
| 97 |
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still applied later, in S/R TRACERS_CORRECTION_STEP. |
| 98 |
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o model/src: |
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- store in common bloc array "rhoInSitu" the virtual potential temperature |
| 100 |
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anomaly that is used to compute geopotential: this make the atmos code |
| 101 |
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more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
| 102 |
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o pkg/seaice/seaice_lsr.F |
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- rename integer variable ilcall to ipass (that's what it is called |
| 104 |
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in the residual diagnostics |
| 105 |
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- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
| 106 |
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default) for improved non-linear convergence of the first few steps |
| 107 |
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- adjust a few comments and add new ones to explain some of the store |
| 108 |
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directives |
| 109 |
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o pkg/generic_advdiff (& ptracers): |
| 110 |
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- re-work the code to check for valid advection scheme and for minimum |
| 111 |
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size of overlap (now stored in local common bloc in gad_advscheme.F) |
| 112 |
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o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
| 113 |
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- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
| 114 |
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- add an auxilliary variable "bet" and fix store directives and keys in |
| 115 |
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seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
| 116 |
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less exact gradients in my tests); but there are still |
| 117 |
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recomputation warning (although gradients are sort of OK), when |
| 118 |
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SEAICE_LSR_VECTORIZE is not defined, so this flag and |
| 119 |
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SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
| 120 |
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- update verification experiments lab_sea. |
| 121 |
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- change some comments in S/R seaice_calc_viscosities |
| 122 |
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o model/src: |
| 123 |
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- if staggerTimeStep=T, always apply exchange to velocity field in |
| 124 |
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do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
| 125 |
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(independent of using multi-dim advection or not); no effect on FWD run |
| 126 |
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but affects AD results (at machine truncation level): update output of |
| 127 |
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experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
| 128 |
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and isomip (oad: 12.d). |
| 129 |
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o pkg/generic_advdiff: |
| 130 |
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- stop if doAB_onGtGs is set to FALSE but ignored |
| 131 |
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- refine warning related to stability of tracer time-stepping |
| 132 |
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regarding internal wave dynamics. |
| 133 |
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- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
| 134 |
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on staggerTimeStep & implicitIntGravWave (will now get a warning |
| 135 |
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if potentially unstable). |
| 136 |
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o pkg/kl10: |
| 137 |
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- add new pkg "kl10" for mixing due to internal wave breaking, from |
| 138 |
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http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
| 139 |
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(contribution from Jody Klymak), tested in verification experiment |
| 140 |
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verification/internal_wave/input.kl10/ |
| 141 |
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o isomip experiment: |
| 142 |
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- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
| 143 |
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(input.htd) and update the output. |
| 144 |
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o cd_code experiments: |
| 145 |
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- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
| 146 |
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#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
| 147 |
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global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
| 148 |
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update the corresponding output. |
| 149 |
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o pkg/seaice: |
| 150 |
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- reduce the number of include files and store directives in |
| 151 |
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S/R seaice_lsr_tridiagu/v |
| 152 |
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- change the order of loops in one case in S/R seaice_lsr_tridiagv |
| 153 |
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(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
| 154 |
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get rid off one store directive (a TAF bug?) |
| 155 |
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- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
| 156 |
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S/R seaice_lsr_tridiagv to change the loop range for consistency |
| 157 |
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- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
| 158 |
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- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
| 159 |
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S/R seaice_lsr_tridiagu/v (requires update of |
| 160 |
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offline_exf_seaice/input.dyn_jfnk) |
| 161 |
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|
| 162 |
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checkpoint65a (2014/07/27) |
| 163 |
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o model/src: |
| 164 |
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- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
| 165 |
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surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
| 166 |
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(topo in p-coords, ice-shelf in z-coords); update output of experiments |
| 167 |
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tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
| 168 |
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o model/src: |
| 169 |
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- collect momentum forcing tendency into local 2-D array (passed as argument |
| 170 |
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to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
| 171 |
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parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
| 172 |
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affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
| 173 |
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- collect T & S forcing tendency into local 2-D array (passed as argument to |
| 174 |
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apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
| 175 |
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affects results at machine truncation level (e.g., ocean: if using |
| 176 |
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SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
| 177 |
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correction due to vertical advection). |
| 178 |
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- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
| 179 |
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global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
| 180 |
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seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
| 181 |
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obcs_ctrl (ad & fwd grd @ 12 & 7). |
| 182 |
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o pkg/ptracers & diagnostics: |
| 183 |
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- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
| 184 |
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title (to avoid some unexpected truncation); sort out ptracers diags units. |
| 185 |
|
- collect ptracer forcing tendency into local 2-D array (passed as argument |
| 186 |
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to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
| 187 |
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|
| 188 |
|
checkpoint65 (2014/07/18) |
| 189 |
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o pkg/fizhi: |
| 190 |
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- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
| 191 |
|
affects results at machine truncation level. Update output of experiments |
| 192 |
|
fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). |
| 193 |
|
o pkg/seaice: more clean up |
| 194 |
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- rename TAF common block tapes to be more consistent and remove |
| 195 |
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unnecessary duplicates |
| 196 |
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- add store directives to remove more recomputations, but use smaller |
| 197 |
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tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. |
| 198 |
|
The idea behind this flag is to reduce the memory footprint when the |
| 199 |
|
adjoint of the LSR is not required. As of now, defining the flag |
| 200 |
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SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by |
| 201 |
|
a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). |
| 202 |
|
For experiment offline_exf_seaice, this means on a linux box with gfortran |
| 203 |
|
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
| 204 |
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this experiment): |
| 205 |
|
> size mitgcmuv_ad |
| 206 |
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text data bss dec hex |
| 207 |
|
5100659 1216 220458952 225560827 d71c8fb |
| 208 |
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5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
| 209 |
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but only a moderate increase of 36% for global_ocean.cs32x15: |
| 210 |
|
text data bss dec hex |
| 211 |
|
6695027 1648 1014578664 1021275339 3cdf6ccb |
| 212 |
|
6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER) |
| 213 |
|
- note: there are still recomputations in global_ocean.cs32x15 and |
| 214 |
|
offline_exf_seaice and the gradient agreement changes (gets a |
| 215 |
|
little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) |
| 216 |
|
- in general, the AD gradients still are wrong |
| 217 |
|
o OpenAD |
| 218 |
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- clean up code_oad/ directories somewhat by moving files |
| 219 |
|
dontCompile, dontTransform, keepOriginal to OAD_support/ |
| 220 |
|
o model/src: |
| 221 |
|
- using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F |
| 222 |
|
(not currently tested): add dissipation terms before NLFS rescaling of |
| 223 |
|
tendencies (previously done after). |
| 224 |
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o pkg/diagnostics: |
| 225 |
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- write stats-diags in ascii file with more digits (same as in monitor). |
| 226 |
|
o pkg/down_slope: |
| 227 |
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- drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with |
| 228 |
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NLFS (not tested), use new recip_hFac value in order to conserve tracer. |
| 229 |
|
o model/src: |
| 230 |
|
- new file "apply_forcing.F" containing all the code previously in |
| 231 |
|
external_forcing.F, but with new argument list: pass, as new argument, |
| 232 |
|
the current level tendency array to update (instead of a direct update |
| 233 |
|
of the common bloc array). Change the corresponding calls. |
| 234 |
|
- add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use |
| 235 |
|
EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility). |
| 236 |
|
o pkg/seaice/seaice_lsr, a little bit of clean up |
| 237 |
|
- rearrange some code blocks, so that now all calculations for |
| 238 |
|
setting up the right-hand-sides done within one single block |
| 239 |
|
(I find that easier to read and understand) |
| 240 |
|
- rearrange freedrift-code to reduce the number of ifdefs |
| 241 |
|
- adjust some indentations and comments |
| 242 |
|
|
| 243 |
|
checkpoint64z (2014/07/10) |
| 244 |
|
o model/src and several pkgs: |
| 245 |
|
- change argument list of all S/R called from external_forcing.F and |
| 246 |
|
called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F) |
| 247 |
|
to pass, as argument, the current level tendency array to update |
| 248 |
|
(instead of a direct update of the common bloc array). |
| 249 |
|
- change also (in the same way) argument list of PTRACERS_APPLY_FORCING; |
| 250 |
|
- rename taueddy_external_forcing.f to taueddy_tendency_apply.F |
| 251 |
|
o pkg/seaice/seaice_lsr.F |
| 252 |
|
- always initialize local arrays in seaice_lsr_tridiagu/v |
| 253 |
|
- add more local tapes to seaice_lsr_tridiagu/v |
| 254 |
|
- move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but |
| 255 |
|
keep it in bi/bj loop; this seems to be essential |
| 256 |
|
- gradients are still wrong but only by 4-7 orders of magnitude |
| 257 |
|
instead of 15 orders of magnitude, lab_sea improves a little |
| 258 |
|
o pkg/seaice |
| 259 |
|
- (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that |
| 260 |
|
generates unnecessary code in seaice_lsr_ad |
| 261 |
|
- add more store directives in seaice_lsr to avoid unnecessary code |
| 262 |
|
in seaice_lsr_ad |
| 263 |
|
- exclude some residual computations in seaice_lsr when |
| 264 |
|
ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code |
| 265 |
|
in seaice_lsr_ad |
| 266 |
|
- add more storing, a new tape (model/src/the_main_loop.F) and |
| 267 |
|
another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey |
| 268 |
|
and klockey should be checked by a specialist) |
| 269 |
|
- modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER ) |
| 270 |
|
and update lab_sea after previous changes in pkg/seaice below |
| 271 |
|
o pkg/autodiff: |
| 272 |
|
- introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and |
| 273 |
|
viscFacInAd : run time parameters allowing for adjoint switches |
| 274 |
|
note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F |
| 275 |
|
o pkg/ecco: |
| 276 |
|
- introduce cost_gencost_boxmean.F that computes a box mean |
| 277 |
|
temperature (for use in adjoint sensitivity studies). |
| 278 |
|
o model/src/set_defaults.F : initialize viscFacAdj to 1. |
| 279 |
|
o pkg/mom_common/mom_calc_visc.F: |
| 280 |
|
- ifdef ALLOW_AUTODIFF then include viscFacAdj factor. |
| 281 |
|
o pkg/seaice/seaice_summary.F: |
| 282 |
|
- statement for SEAICEadjMODE now in autodiff_readparms.F |
| 283 |
|
o pkg/seaice: |
| 284 |
|
- remove some store directives and add new ones in an effort to get |
| 285 |
|
finally rid off the recomputation warnings. This is successful |
| 286 |
|
when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are |
| 287 |
|
defined (i.e. no extensive recomputation warnings left), but there |
| 288 |
|
are still too many recomputations on the solver iteration level |
| 289 |
|
- define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h |
| 290 |
|
- move definition of MPSEUDOTIMESTEPS into TAMC-block in |
| 291 |
|
SEAICE_SIZE.h |
| 292 |
|
- add a store directive in S/R seaice_calc_viscosities |
| 293 |
|
o pkg/seaice (ITD code): |
| 294 |
|
- fix definition of Hlimit for multi-threaded case |
| 295 |
|
- use double precision arithmetic to compute Hlimit: this affects results; |
| 296 |
|
update output of experiment seaice_itd. |
| 297 |
|
o replace content of verification/seaice_itd |
| 298 |
|
- instead of a 1D column use the configuration of offline_exf_seaice |
| 299 |
|
to test the ice thickness distribution code with ridging |
| 300 |
|
- this is a first shot at this experiment |
| 301 |
|
- change of some defaults of ridging parameters SEAICEhStar (from |
| 302 |
|
100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F |
| 303 |
|
and lot of new comments. |
| 304 |
|
|
| 305 |
checkpoint64y (2014/06/20) |
checkpoint64y (2014/06/20) |
| 306 |
o pkg/seaice/seaice_reg_ridge.F: |
o pkg/seaice/seaice_reg_ridge.F: |
| 307 |
- modify the regularization of very small volumes of ice; only check |
- modify the regularization of very small volumes of ice; only check |
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