| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
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| 7 |
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o model/src: |
| 8 |
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a) 1rst version of a new driver S/R to turn-off output freq and flags after the |
| 9 |
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1rst forward sweep, to avoid over-writing output files during recomputations |
| 10 |
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recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?) |
| 11 |
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b) 2nd version: |
| 12 |
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- add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO); |
| 13 |
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- switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast, |
| 14 |
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writePickupAtEnd) + seaice & ptracers output; |
| 15 |
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- do not switch off MNC flags (otherwise, won't get admonitor netcdf file) |
| 16 |
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o model/src: |
| 17 |
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- new S/R rotate_uv2en_rl (..._rs) that rotates vector fields. |
| 18 |
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o pkg/exch2: |
| 19 |
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- remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ; |
| 20 |
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- add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch). |
| 21 |
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o pkg/autodiff & exch2: |
| 22 |
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process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF |
| 23 |
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(for now, only if ALLOW_EXCH2 is defined). |
| 24 |
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o pkg/autodiff: |
| 25 |
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- include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F |
| 26 |
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(not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly. |
| 27 |
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+ clean-up comments (_RS is not always real*4) |
| 28 |
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- fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R) |
| 29 |
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- add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2: |
| 30 |
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was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs. |
| 31 |
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o testreport (AD-tests): |
| 32 |
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no longer link files from dir "../input" (1rst link files from |
| 33 |
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"../input_ad.[xx]" if secondary test "xx" and then from "../input_ad") |
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|
| 35 |
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checkpoint62f (2010/04/29) |
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o model/src/the_main_loop.F: |
| 37 |
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adjust store directives for seaice evp and multicategory according to |
| 38 |
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pkg/ecco/the_main_loop.F |
| 39 |
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o adjoint: |
| 40 |
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global_sum_ad was incomplete (noted many times by many people ;) |
| 41 |
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nice description by Jean U. as follows: |
| 42 |
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* allreduce(var) in global_sum.F can be interpreted as |
| 43 |
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reduce(sum) followed by broadcast of sum. |
| 44 |
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* The adjoint of that is |
| 45 |
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sum(adjoint) followed by broadcast(summed adjoint value) |
| 46 |
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or in other words, allreduce(sum, adjoint vars) |
| 47 |
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We were missing the sum(adjoint)! |
| 48 |
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Benign, except(!) for "global" scalars appearing in tile loops (bi,bj) |
| 49 |
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(noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset). |
| 50 |
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The fix should produce 16-digit accuracy between |
| 51 |
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single-CPU multi-tile (e.g. nSx=2, nPx=1) and |
| 52 |
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multi-CPU single-tile (e.g. nSx=1, nPx-2) |
| 53 |
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We'll probably change this yet again shortly |
| 54 |
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o eesupp/src: |
| 55 |
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- fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?) |
| 56 |
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o pkg/icefront |
| 57 |
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- ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving |
| 58 |
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specification of addmass array based on a 2D field, which is added |
| 59 |
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at bottommost wet level at each horizontal location. |
| 60 |
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o model/src: |
| 61 |
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horizontal grid initialisation (other than curvilinear): add code for Exch2 IO |
| 62 |
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layout; (not always compatible with delX,delY setting; commented out for now). |
| 63 |
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o pkg/exch2: |
| 64 |
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change tile to processor setting (case nSy*nPy > 1): allows default model mapping |
| 65 |
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(myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config. |
| 66 |
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|
| 67 |
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checkpoint62e (2010/04/15) |
| 68 |
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o pkg/obcs: |
| 69 |
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- fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert). |
| 70 |
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o pkg/dic: |
| 71 |
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-fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up; |
| 72 |
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(note: not presently tested in any forward verification exp.) |
| 73 |
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update tutorial_global_oce_biogeo AD output file. |
| 74 |
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o pkg/exf: |
| 75 |
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- account for the variation of albedo as a function of zenith angle |
| 76 |
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by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h |
| 77 |
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o build_options: |
| 78 |
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- rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas" |
| 79 |
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o pkg/dic: |
| 80 |
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change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart: |
| 81 |
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- use binary pickup file for restart; |
| 82 |
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- initialise atmos-CO2 box from dic_pCO2 parameter; |
| 83 |
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- fix multi-threaded. |
| 84 |
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o pkg/rbcs: |
| 85 |
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- clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ; |
| 86 |
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change (+ fix IO calls) type of array RBC_mask from _RL to _RS. |
| 87 |
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- add RBCS to exp4 passive tracer 01 (rbcs was previously untested) |
| 88 |
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and update output.txt |
| 89 |
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o pkg/kpp: |
| 90 |
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- add diagnostics for KPP non-local flux of Temp, Salinity and pTracers; |
| 91 |
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- change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS |
| 92 |
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(= ratio of KPP non-local (salt) flux relative to surface-flux) when |
| 93 |
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using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat '); |
| 94 |
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- change pkg/offline to read-in average KPPghat*KPPdiffKzS from file |
| 95 |
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KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile). |
| 96 |
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o pkg/offline: |
| 97 |
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fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor |
| 98 |
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(bug was added in version 1.10 on 2007-08-23). |
| 99 |
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o pkg/offline: |
| 100 |
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- no need to specify periodicExternalForcing, etc ... to use offline pack |
| 101 |
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- offline input files no longer just single prec --> parameter offlineLoadPrec |
| 102 |
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o verification/lab_sea: |
| 103 |
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change AD test to multi-tile setup and update all 4 AD output. |
| 104 |
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NOTE: while cost function values remain very similar, |
| 105 |
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gradients are very different, although gradient checks are self-consistent |
| 106 |
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Should try to get to the bottom of this (cost function summation order?) |
| 107 |
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o pkg/dic: |
| 108 |
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in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid |
| 109 |
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a weakness of TAF that drops part of double precision in log10 derivative. |
| 110 |
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<= changes removed since problem has been fixed in current TAF version 1.9.71 |
| 111 |
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update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo. |
| 112 |
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o pkg/ecco: |
| 113 |
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add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F |
| 114 |
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update all 4 lab_sea AD output. |
| 115 |
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| 116 |
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checkpoint62d (2010/03/22) |
| 117 |
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o build_options: |
| 118 |
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remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles. |
| 119 |
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o remove unbalanced quote (single or double) in commented line of source code |
| 120 |
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(may cause some warning with some preprocessor/makedepend versions). |
| 121 |
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o pkg/seaice: |
| 122 |
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fix seaice_model.F for adjoint (gael) and update AD results of experiments |
| 123 |
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lab_sea (std + evp + noseaicedyn) and offline_exf_seaice. |
| 124 |
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o testreport: |
| 125 |
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add option '-runonly' (short: '-ro') to just do the run part (without make). |
| 126 |
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o eesupp: remove JAM communication code (obsolete). |
| 127 |
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o add option to genmake2 & testreport to switch "_RS" type to "real*4" |
| 128 |
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(if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return |
| 129 |
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to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1 |
| 130 |
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(update also the output). |
| 131 |
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|
| 132 |
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checkpoint62c (2010/03/02) |
| 133 |
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o tools/build_options : |
| 134 |
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move (some) old optfiles from build_options/ to build_options/unsupported/ |
| 135 |
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o model/src and pkg/exf |
| 136 |
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surface relaxation -- separating data and data.exf options |
| 137 |
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The point is to ensure that we specify the surface relaxation |
| 138 |
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either in data or in data.exf (but not half and half) and to |
| 139 |
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avoid an accidental relaxation to 0 (which happened if a time |
| 140 |
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scale was specified but the file name was left empty) |
| 141 |
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o model/src model/inc and pkg/mom_common |
| 142 |
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ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity |
| 143 |
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=> addition to the viscosity field as computed by others schemes |
| 144 |
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o tools/build_options: |
| 145 |
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- rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile) |
| 146 |
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but keep the former optfile for few weeks for smooth transition |
| 147 |
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o pkg/ecco |
| 148 |
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- allow user defined cost function contributions |
| 149 |
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CPP: ALLOW_USERCOST_CONTRIBUTION |
| 150 |
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USAGE: compute contributions in cost_usercost_all.F |
| 151 |
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- note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. |
| 152 |
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the two options are complementary. |
| 153 |
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o pkg/smooth |
| 154 |
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- migration from contrib to the main repository |
| 155 |
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|
| 156 |
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checkpoint62b (2010/01/26) |
| 157 |
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o pkg/monitor: |
| 158 |
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- change back mon_printstats_rl.F & mon_stats_rl.F and add a stop |
| 159 |
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(in case someone forgot to update customized pieces of code) |
| 160 |
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o nonHydrostatic: |
| 161 |
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- add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested); |
| 162 |
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- add a simple 2-D experiment (short_surf_wave) to test it. |
| 163 |
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o pkg/icefront: |
| 164 |
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adding the shell of, and the hooks to, a new package that |
| 165 |
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will model melting and freezing of vertical glacier ice fronts |
| 166 |
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o momentum: |
| 167 |
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add diagnostics of momentum tendency from Hydrostatic pressure gradient |
| 168 |
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(without surf.pressure term: would need a 2nd filling since implicit term). |
| 169 |
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o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace |
| 170 |
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two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR |
| 171 |
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cannot deal with the former |
| 172 |
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o cleaning: |
| 173 |
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- remove all (except OpenAD) old TLM output from results_ad dirs. |
| 174 |
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- remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R) |
| 175 |
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- comment out maskH definition (replaced by maskInC) |
| 176 |
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o pkg/monitor: |
| 177 |
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- change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl |
| 178 |
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& mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs. |
| 179 |
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|
| 180 |
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checkpoint62a (2010/01/15) |
| 181 |
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o model/src: |
| 182 |
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- bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4) |
| 183 |
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o pkg/diagnostics: |
| 184 |
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- add optional level number diagnostics (i.e., level number to be define |
| 185 |
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explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X". |
| 186 |
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- strictly check for valid parser-code(10) ; |
| 187 |
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- check if adding diag to the list from the right place. |
| 188 |
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o pkg/longstep: |
| 189 |
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- change parameters and fix tracer conservation with rstar/nonlinear free surface |
| 190 |
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o diagnostics: |
| 191 |
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- in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer |
| 192 |
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S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics. |
| 193 |
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o pkg/diagnostics: |
| 194 |
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- Add option for writing vertical integral (sum of selected levels) of an output |
| 195 |
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field instead of writing output field levels. Activate this option on a per |
| 196 |
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output-file basis, by setting the 2nd character of fileflag to 'I'. |
| 197 |
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- Add field-specific information relative to level integral in 3rd postion |
| 198 |
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of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate |
| 199 |
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vertically (x level-thickness x hFac), "r"=same but without hFac. |
| 200 |
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o do_the_model_io: |
| 201 |
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- pass end-of-model-run flag as argument, from forward_step to diagnostics_write: |
| 202 |
|
in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before |
| 203 |
|
writing pickups and stopping. |
| 204 |
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o pkg/diagnostics (for now, only with mdsio): |
| 205 |
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- write time information to meta file (and modify accordingly rdmds.m) : |
| 206 |
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time-averaged diagnostics output: write starting and ending time of the |
| 207 |
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time-averaging interval ; snap-shot diagnostics output remains unchanged; |
| 208 |
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o pkg/timeave: |
| 209 |
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- S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously |
| 210 |
|
always Nr), now assumed to be equal to number of levels of averaged field; |
| 211 |
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only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F |
| 212 |
|
o pkg/sbo: |
| 213 |
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- fix ocean bottom pressure global-average & 2-D time-ave output (was |
| 214 |
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neither initialised nor filled). |
| 215 |
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- add starting iteration in suffix of global-average output file |
| 216 |
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(to avoid over-writing the file after a restart) |
| 217 |
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- use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb). |
| 218 |
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o time-average: |
| 219 |
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- use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj) |
| 220 |
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(pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf, |
| 221 |
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ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice) |
| 222 |
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this fix DIC_COST cumulative-time array (previously: bi,bj,k) |
| 223 |
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- fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice) |
| 224 |
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- fix missing accumulation for pkg/opps. |
| 225 |
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- cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0) |
| 226 |
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(pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81); |
| 227 |
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- fix initialisation of time-ave vars and do only full time-step increment |
| 228 |
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(i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81); |
| 229 |
|
o pkg/layers: |
| 230 |
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- use standard RW pkg S/R to write the output |
| 231 |
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and remove local write_fld version (which had a problem). |
| 232 |
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- use simple cumulative-time array (no level index) to fix time-ave S/R calls. |
| 233 |
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- fix LAYERS_CALC argument list. |
| 234 |
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o pkg/timeave: |
| 235 |
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- store cumulative-time in a simple tiled array (drop the level index) |
| 236 |
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- add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array. |
| 237 |
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o pkg/ocn,aim_compon_interf |
| 238 |
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- changes for multi-threaded coupled run. (tested with ifort-11 on danton) |
| 239 |
|
|
| 240 |
|
checkpoint62 (2009/12/23) |
| 241 |
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o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output. |
| 242 |
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(was not previously tested in any other exp.) |
| 243 |
o pkg/monitor: |
o pkg/monitor: |
| 244 |
- clean-up _RL/_RS version: add specific S/R for statistics with mask & volume: |
- clean-up _RL/_RS version: add specific S/R for statistics with mask & volume: |
| 245 |
mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one |
mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one |
| 246 |
(mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics. |
(mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics. |
| 247 |
- use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F). |
- use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F). |
| 248 |
- change del2 calculation. |
- change del2 calculation. |
| 250 |
- shorter monitor suffix for forcing stats ("forcing" instead of "extforcing"). |
- shorter monitor suffix for forcing stats ("forcing" instead of "extforcing"). |
| 251 |
o mask & obcs: |
o mask & obcs: |
| 252 |
- define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S). |
- define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S). |
| 253 |
- move global area computation from ini_masks_etc.F to ini_linear_phisurf.F |
- move global area computation from ini_masks_etc.F to ini_linear_phisurf.F |
| 254 |
(called after packages_init_fixed) |
(called after packages_init_fixed) |
| 255 |
o pkg/obcs: |
o pkg/obcs: |
| 256 |
- move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once. |
- move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once. |
| 264 |
(in prep. for new NH free surface form). |
(in prep. for new NH free surface form). |
| 265 |
o pkg/obcs: |
o pkg/obcs: |
| 266 |
add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe |
add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe |
| 267 |
o model/src: |
o model/src: |
| 268 |
fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography |
fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography |
| 269 |
|
|
| 270 |
checkpoint61z (2009/12/01) |
checkpoint61z (2009/12/01) |
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