| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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| 7 |
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o eesupp & mdsio (SingleCpuIO): |
| 8 |
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- remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time |
| 9 |
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parameter "W2_useE2ioLayOut" (read from file "data.exch2"). |
| 10 |
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Note: was not effective for globalFile & useSingleCpuIO=F; now fixed. |
| 11 |
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- move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc). |
| 12 |
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- fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same |
| 13 |
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gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array). |
| 14 |
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o pkg/exch2: |
| 15 |
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- new code to set-up W2-Exch2 topology (replace matlab-topology-generator): |
| 16 |
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read parameter file "data.exch2" if it exists; otherwise try default regular |
| 17 |
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cube without blank-tile; new header file "W2_EXCH2_SIZE.h"; |
| 18 |
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- update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible |
| 19 |
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with new code (not to be used, just as a backup solution). |
| 20 |
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- add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2" |
| 21 |
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in utils/exch2/input. |
| 22 |
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|
| 23 |
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checkpoint61n |
| 24 |
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o eesupp & mdsio (SingleCpuIO): |
| 25 |
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- move mapping to global io-buffer inside gather_2d/scater_2d: this save |
| 26 |
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memory (1 less 2D global RL array); skip 1 buffer copy; and only send/ |
| 27 |
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receive real*4 array (instead of real*8) to read/write 32.bit files. |
| 28 |
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(new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S |
| 29 |
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and remove new mapping S/R) |
| 30 |
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o pkg/mdsio: in preparation for topology-generator within pkg/exch2: |
| 31 |
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- Change declaration of SingleCpuIO buffer, reduced to only 1 dim.: |
| 32 |
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xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h |
| 33 |
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when using exch2. Add S/R to map global io-buffer to global model array. |
| 34 |
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- uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt. |
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|
| 36 |
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checkpoint61m |
| 37 |
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o write_utils : change WRITE_1D_R8 to WRITE_1D_RL |
| 38 |
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and add 3 other S/R for other types (R4,R8,RS). |
| 39 |
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Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument. |
| 40 |
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o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros): |
| 41 |
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- ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ; |
| 42 |
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- reduce number of macro definitions (keep only those which are used); |
| 43 |
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can always call directly the corrresponding S/R if needed. |
| 44 |
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- everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix |
| 45 |
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_R4/_R8 to _RS/_RL when applied to _RS/_RL variable. |
| 46 |
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Fixed wrong type of arg in: |
| 47 |
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atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F |
| 48 |
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ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F |
| 49 |
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To fix: global_sum of var in common block is wrong (multi-threaded) in: |
| 50 |
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dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F |
| 51 |
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To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops) |
| 52 |
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o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd |
| 53 |
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"nlfs" mpi test is going to stop when checking for unconnected tile egdes. |
| 54 |
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o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error |
| 55 |
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o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile |
| 56 |
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edges are closed (zero depth); might happen with "blank tiles"; |
| 57 |
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for now, disabled if using OBCS. |
| 58 |
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o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi": |
| 59 |
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link *_mpi files from "MODS" dir) to return to a strait-forward behavior. |
| 60 |
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o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D) |
| 61 |
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to reduce length of 1.D array print in STDOUT. |
| 62 |
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o adjustment.cs-32x32x1: changed to oceanic test with 1 continent |
| 63 |
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+ use 48 tiles (16x8): this will allow to test "blank tiles". |
| 64 |
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o start to test MPI + multi-threaded (change testreport to skip tests |
| 65 |
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where number of tiles do not match). |
| 66 |
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o genmake2: add option "-omp" to turn on Open-MP ; |
| 67 |
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passed to testreport (if using -mth) ; merge few (*+mth) optfiles. |
| 68 |
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o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them) |
| 69 |
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and keep the original tile numbering. Note: compatible with old |
| 70 |
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W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files. |
| 71 |
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|
| 72 |
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checkpoint61l |
| 73 |
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o Overlaps had been forgotten in calculating ijk keys : fixed |
| 74 |
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o fix cyrus makedepend for gcc 4.4 |
| 75 |
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o experiment fizhi-cs-aqualev20: |
| 76 |
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switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE) |
| 77 |
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and generate new output. Note: new output is much closer to the old |
| 78 |
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one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from |
| 79 |
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the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007. |
| 80 |
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o pkg/fizhi: |
| 81 |
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- change to avoid indices going deliberately over array-bounds |
| 82 |
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- remove unnecessary MPI stuff |
| 83 |
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- perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY" |
| 84 |
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- new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE: |
| 85 |
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does not go over array-bounds and therefore returns reliable output. |
| 86 |
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- in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls: |
| 87 |
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this S/R has 4 output arguments, which are used inside "get_alarm"; |
| 88 |
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when it is called with the same variable "ndum" in place of several |
| 89 |
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output arguments, this produces weird side effect inside "get_alarm" |
| 90 |
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(e.g., datein=dates(n) is overwritten by timein=times(n) since both |
| 91 |
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datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum" |
| 92 |
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address) and produces error. |
| 93 |
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o tools/gemake2: (March 27-29 2009) |
| 94 |
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with option "-mpi": link *_mpi files from "MODS" dir (this is what |
| 95 |
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testreport does). |
| 96 |
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o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output |
| 97 |
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o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F: |
| 98 |
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update lab_sea.lsr & lab_sea.salt_plume results |
| 99 |
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o pkg/seaice: |
| 100 |
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Major overhaul of the LSOR solver: change discretization from original |
| 101 |
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finite differences to finite volume. The old routine is still in the |
| 102 |
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file seaice_lsr.F and can be turned on with the CPP-flag |
| 103 |
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SEAICE_OLD_AND_BAD_DISCRETIZATION |
| 104 |
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Along with this change, the discretization of the strain rates is changed. |
| 105 |
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The same flag turns on the old discretization in seaice_calc_strainrates.F |
| 106 |
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All verification experiments with seaice are affected (except for |
| 107 |
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seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old |
| 108 |
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results by setting the above flag. |
| 109 |
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Further changes involve changes in defaults: |
| 110 |
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- ALLOW_FLOODING is defined and turned on by default |
| 111 |
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- SEAICEadvSnow = .true. is now the default |
| 112 |
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- SEAICEadvSalt = .true. is now the default |
| 113 |
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- SEAICEadvAge = .true. is now the default |
| 114 |
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- SEAICE_clipVelocities = .false. is now the default |
| 115 |
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(as per J. Zhang's recommendation) |
| 116 |
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- B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE |
| 117 |
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is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS |
| 118 |
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- seaice_growth: replace computation of UG by a simple copy from wspeed |
| 119 |
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|
| 120 |
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checkpoint61k |
| 121 |
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o pkg/seaice: a few bug fixes mostly concerning the metric terms: |
| 122 |
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seaice_lsr: fixed a few metric terms, |
| 123 |
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affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs |
| 124 |
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add more debugging diagnostics |
| 125 |
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seaice_evp: removed superfluous many metric terms of FV discretization |
| 126 |
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of stress divergence |
| 127 |
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affects lab_sea, lab_sea.hb87 |
| 128 |
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seaice_ocean_stress: removed superfluous many metric terms of FV discretization |
| 129 |
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of stress divergence for non-evp solver |
| 130 |
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(this part is not tested anywhere) |
| 131 |
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seaice_calc_strainrates: fixed a bug in no-slip boundary conditions, |
| 132 |
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they were effectively only half slip |
| 133 |
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affects lab_sea.hb87 |
| 134 |
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updated all relevant verification experiments (except lab_sea//output_adm.txt |
| 135 |
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which was left over, but fails at level 7 & 6) |
| 136 |
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|
| 137 |
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checkpoint61j |
| 138 |
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o pkg/seaice: turn a few hard wired parameters into run time parameters |
| 139 |
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o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model |
| 140 |
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time in seconds as promised by the usints in seaice_monitor and exf_monitor |
| 141 |
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o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids |
| 142 |
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that are not cubed-sphere grids |
| 143 |
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o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR |
| 144 |
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o pkg/ctrl: |
| 145 |
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fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low) |
| 146 |
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o non-hydrostatic (calc_gw.F): |
| 147 |
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fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec |
| 148 |
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update output of exp. global_ocean.cs32x15.viscA4 |
| 149 |
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o remove backward compatibility for thetaMin,phiMin |
| 150 |
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(replaced by xgOrigin,ygOrigin on Jan 27, 2009) |
| 151 |
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o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the |
| 152 |
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interpolated wind field not only for curvilineargrid=.true., but also |
| 153 |
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for a rotated grid (rotateGrid=.true.) |
| 154 |
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o pkg/exf: add capability to bypass interpolation for runoff |
| 155 |
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by setting yet another CPP-flag |
| 156 |
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o eesupp/src, B-grid exchange: |
| 157 |
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add simple (6 tiles, non MPI) CS exch + standard interface S/R. |
| 158 |
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o autodiff |
| 159 |
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new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV |
| 160 |
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allows to switch to single-prec common blocks; |
| 161 |
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corresponding switch occurs in tamc.h, integer isbyte |
| 162 |
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TAF store directivs "byte" and "kind" seem equivalent; |
| 163 |
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Most tamc.h have been updated correspondingly. |
| 164 |
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|
| 165 |
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checkpoint61i |
| 166 |
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o autodiff: |
| 167 |
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fix autodiff_sore/_restore indices for obcs |
| 168 |
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(spotted by I. Hoteit, M. Mazloff) |
| 169 |
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o pkg/autodiff, pkg/ctrl: |
| 170 |
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Add flag to reduce all tapelev I/O to single-prec. |
| 171 |
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In data.ctrl set |
| 172 |
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doSinglePrecTapelev = .TRUE. |
| 173 |
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o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2: |
| 174 |
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check in hack for SX8 compiler (for dxV, dyU); remove it afterwards. |
| 175 |
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o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for |
| 176 |
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real fresh water flux (not yet) |
| 177 |
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o pkg/mdsio & rw: |
| 178 |
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- add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta) |
| 179 |
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- add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX. |
| 180 |
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o pkg/flt: |
| 181 |
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- replace FLT_INIT by 3-steps standard initialization S/R: readparms, |
| 182 |
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init_fixed & ini_varia. |
| 183 |
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- clean-up & simplify linear interpolation S/R: |
| 184 |
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move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid. |
| 185 |
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- fix some indices (mainly vertical index) ; add IMPLICIT NONE. |
| 186 |
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- more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R. |
| 187 |
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- add vert. coordinate & horiz. indices to output files. |
| 188 |
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- change vertical position in initial condition, from index to depth [m]. |
| 189 |
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- store horizontal (decimal) indices i,j in common block (instead of coord. x,y) |
| 190 |
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(easier to get to a curvilinear grid) ; delX,delY no longer used. |
| 191 |
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o pkg/ggl90: a few modifications: |
| 192 |
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- fix bottom boundary condition, and interpolation of KappaE |
| 193 |
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near top and bottom |
| 194 |
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- use same set of viscosity/diffusivity for TKE/momnetum/tracer |
| 195 |
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- add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH) |
| 196 |
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- add a few options for mixing-length upper limit (--> mxlMaxFlag) |
| 197 |
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o rename thetaMin,phiMin -> xgOrigin,ygOrigin |
| 198 |
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(maintain temporary backward compatibility, until next checkpoint) |
| 199 |
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|
| 200 |
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checkpoint61h |
| 201 |
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o pkg/diagnostics with "periodic averaging diagnostics": |
| 202 |
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fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. |
| 203 |
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o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82 |
| 204 |
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o pkg/obcs: fix loop ranges for balancing code |
| 205 |
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o pkg/flt: |
| 206 |
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- improve criteria for finding which tile owns a float. |
| 207 |
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- fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case. |
| 208 |
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o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg |
| 209 |
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aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling |
| 210 |
|
with ocean biogeo) |
| 211 |
|
o pkg/flt: |
| 212 |
|
- do some cleaning and fix the restart ; |
| 213 |
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- add output.txt in flt_example/results to get this pkg tested. |
| 214 |
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o genmake2: add an EXTENDED_SRC option and flag. |
| 215 |
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for now, cannot be turned on on command line (only through genmake_local) |
| 216 |
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o pkg/mdsio: read/write vector: |
| 217 |
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- singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS |
| 218 |
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- singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR |
| 219 |
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& MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. |
| 220 |
|
- affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) |
| 221 |
|
(drop to 4 digits matching for grad). But this test does not look very |
| 222 |
|
reliable (was already failling on eddy, fc5, at 6.digits). Update output. |
| 223 |
|
|
| 224 |
|
checkpoint61g |
| 225 |
|
o pkg/flt: |
| 226 |
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- move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) |
| 227 |
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+ make OPTIONS file more standard. |
| 228 |
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- rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) |
| 229 |
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- fix _BYTESWAPIO CPP-Flag |
| 230 |
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- standard reading of file-parameter "data.flt" |
| 231 |
|
- fix argument list of S/R FLT_RESTART |
| 232 |
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still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F |
| 233 |
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o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell |
| 234 |
|
o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to |
| 235 |
|
a still unfixed compiler/optimization bug |
| 236 |
|
|
| 237 |
|
checkpoint61f |
| 238 |
|
o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; |
| 239 |
|
update results of global_ocean.cs32x15.icedyn test. |
| 240 |
o move getcon.F from model/src to pkg/fizhi. |
o move getcon.F from model/src to pkg/fizhi. |
| 241 |
o pkg/exf: add parameter for extrapolation of temp up to the surface |
o pkg/exf: add parameter for extrapolation of temp up to the surface |
| 242 |
and option to prevent negative evap (in bulk_largeyeager04 only). |
and option to prevent negative evap (in bulk_largeyeager04 only). |
| 2517 |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
| 2518 |
- these scheme operate in a similar manner as KPP (without ghat, of |
- these scheme operate in a similar manner as KPP (without ghat, of |
| 2519 |
course), however there is only one diffusivity that is used for both |
course), however there is only one diffusivity that is used for both |
| 2520 |
temperature and salinity (and passive tracers)ç |
temperature and salinity (and passive tracers) |
| 2521 |
o add offline package |
o add offline package |
| 2522 |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
| 2523 |
provided by Stephanie Dutkiewicz |
provided by Stephanie Dutkiewicz |
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