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$Header$ |
$Header$ |
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$Name$ |
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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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checkpoint58t_post |
| 8 |
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o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) |
| 9 |
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o pkg/mdsio: |
| 10 |
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- clean-up mdsio_readfield.F & mdsio_writefield_new.F and |
| 11 |
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move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & |
| 12 |
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mdsio_write_field.F (S/R MDS_WRITE_FIELD); |
| 13 |
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- fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD |
| 14 |
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- collect old S/R in one file: mdsio_rw_field.F (now just a call to |
| 15 |
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either MDS_READ_FIELD or MDS_WRITE_FIELD ) |
| 16 |
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- new S/R (to replace MDSWRITEMETA), which allows to write more |
| 17 |
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informations (variable names, time ...) to meta files. |
| 18 |
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- modify rdmds.m to give back the meta file content. |
| 19 |
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o pkg/diagnostics: change vertical interpolation to be safer, and more |
| 20 |
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flexible (define p-levels to interpolate to in data.diagnostics); |
| 21 |
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add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right |
| 22 |
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diagnostic pointer. |
| 23 |
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o pkg/seaice: more cleaning up of seaice_growth, added many comments |
| 24 |
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o pkg/exf: put runoff0 and runoff into the appropriate common block |
| 25 |
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o fix multi-category seaice: |
| 26 |
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- change cpp flag SEAICE_MULTILEVEL to more meaningful name: |
| 27 |
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SEAICE_MULTICATEGORY |
| 28 |
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- fix short wave heat flux |
| 29 |
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o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics |
| 30 |
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and allow to use EVP solver. Change forward lab_sea: test both EVP |
| 31 |
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solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) |
| 32 |
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o Initial check-in of lab_sea adjoint |
| 33 |
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(very similar to natl_box_adjoint/code_seaice) |
| 34 |
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* used C-grid and EVP solver |
| 35 |
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* used KPP, GM/Redi |
| 36 |
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* uses inAdExact=.TRUE. |
| 37 |
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* gradient checks fail for both ADM and TLM |
| 38 |
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due to sensitive snow melt code in seaice_grwoth (look for "JZ") |
| 39 |
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f.d. gradients actually seem more problematic than ADM, TLM gradients; |
| 40 |
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issue is related to forward mismatch between g77 an ifort |
| 41 |
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o pkg/seaice: overhaul of thermodynamics |
| 42 |
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- growth.F and groatb.F are replaced by new routine seaice_growth.F |
| 43 |
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- budget.F is replaced by two new routines seaice_budget_ocean/ice.F |
| 44 |
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- move a few global fields out of SEAICE.h into seaice_growth.F and |
| 45 |
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make them 2D (FICE/QNETO/ ...) |
| 46 |
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- remove FO (it is the same as QNETO) |
| 47 |
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- introduce a few local fields to avoid modifying external fields such |
| 48 |
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as atemp, etc. |
| 49 |
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|
| 50 |
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checkpoint58s_post |
| 51 |
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o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F |
| 52 |
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changed exf_set_gen.F so that |
| 53 |
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genperiod=0 means input file is one time-constant field and |
| 54 |
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genperiod=-12 means input file contains 12 monthly means |
| 55 |
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o CG2D: use pre-computed solver main-diagonal (stored in common block); |
| 56 |
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this affects truncation error ; generate new output file for exp. which |
| 57 |
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fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), |
| 58 |
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global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), |
| 59 |
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ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), |
| 60 |
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MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), |
| 61 |
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tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), |
| 62 |
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vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) |
| 63 |
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o start implementation of deep-atmosphere and anelastic formulation |
| 64 |
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o verification: remove 2nd copy of input files and use script "prepare_run" |
| 65 |
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to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) |
| 66 |
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o mom_common/vecinv/fluxform: fix a few initialisation isssues |
| 67 |
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o profiles: fix for multithreaded case |
| 68 |
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|
| 69 |
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o diagnostics: rename few diags: |
| 70 |
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s/'PRESSURE'/'RCENTER '/g |
| 71 |
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s/'TICE '/'oceFreez'/g |
| 72 |
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s/'TAUX '/'oceTAUX '/g |
| 73 |
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s/'TAUY '/'oceTAUY '/g |
| 74 |
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s/'SWFLUX '/'oceQsw '/g |
| 75 |
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s/DIFx/DFxE/g |
| 76 |
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s/DIFy/DFyE/g |
| 77 |
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and add few ocean-forcing diagnostics: |
| 78 |
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atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS |
| 79 |
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o modifications to pkg/seaice/growth.F and budget.F, which change results of |
| 80 |
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lab_sea experiment: HSNOW was sometimes treated as effective and sometimes |
| 81 |
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as actual snow thickness. It now refers everywhere to effective snow |
| 82 |
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thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. |
| 83 |
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|
| 84 |
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checkpoint58r_post |
| 85 |
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o modifications to pkg/seaice/growth.F, which change results of |
| 86 |
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lab_sea experiment: fixes pertain to melting snow over open water, to |
| 87 |
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masking EVAP under sea ice, and to using the correct AREA variable for |
| 88 |
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computations of EVAP, PRECIP, HSNOW, and GHEFF |
| 89 |
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o add ability to read bathy, salt, and theta using MNC (off by def) |
| 90 |
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o add flooding algorithm and advection of HSNOW for pkg/seaice; |
| 91 |
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both are turned off by default and do no change any results |
| 92 |
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o seaice advection with pkg/thsice: a step toward the use of non-linear |
| 93 |
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advection scheme, but #ifdef or commented out for now (requires more EXCH). |
| 94 |
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o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens |
| 95 |
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(identical results) and the standard version of EXTERNAL_FIELDS_LOAD |
| 96 |
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in natl_box (affects results @ truncation level: update output.txt) |
| 97 |
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o multi-threading and IO: |
| 98 |
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- replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. |
| 99 |
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- remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls |
| 100 |
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(needed to work with SingleCpuIO): tested in all verif. exp. |
| 101 |
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o GAD: use simpler DST3 formulation as default (old version left within #ifdef) |
| 102 |
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affects the results (but none of the verification test uses this scheme). |
| 103 |
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o Adding some pkg/diagnostics capability to pkg/seaice |
| 104 |
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(will certainly be subject to changes) |
| 105 |
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o ctrl: adding new control variables: |
| 106 |
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lwflux, lwdown, evap, snowprecip, apressure, runoff |
| 107 |
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|
| 108 |
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checkpoint58q_post |
| 109 |
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o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up |
| 110 |
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1/6-deg Southern Ocean configuration by 8% on IBM Datastar and |
| 111 |
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high_res_cube configuration by 4% on Columbia. |
| 112 |
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o clean-up multi-threaded problems (reported by debugger tcheck on ACES); |
| 113 |
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add (in global_with_exf/code) a version of EXF_INTERP_READ without |
| 114 |
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dynamical allocation (seems to work in multi-threaded). |
| 115 |
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o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using |
| 116 |
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single CPU io) so that TAF does not have to see EESUPPORT.h |
| 117 |
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o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
| 118 |
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|
| 119 |
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checkpoint58p_post |
| 120 |
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o obcs: stop if obcs is used with useCDscheme = .true. |
| 121 |
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o shelfice: |
| 122 |
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- fix a sign error so that no slip at shelfice interface works |
| 123 |
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- remove stop for combination non-hydrostatic code and shelfice. That does |
| 124 |
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not mean, that the results are correct, but at least they are numerically |
| 125 |
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stable |
| 126 |
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o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) |
| 127 |
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o added adjoint exch routined for all exch*3d* routines |
| 128 |
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and updated flow directives |
| 129 |
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|
| 130 |
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checkpoint58o_post |
| 131 |
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o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; |
| 132 |
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remove old subroutines (_XY_ & _XYZ_); update the adjoint version. |
| 133 |
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o change controling S/R for writing pickup file (new S/R do_write_pickup) |
| 134 |
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and clean-up reading/writing of pickup files. |
| 135 |
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o fix local version of read/write pickup (NH part) in rotating_tank/code |
| 136 |
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o simplify EXCH interface: |
| 137 |
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- change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) |
| 138 |
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- not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version |
| 139 |
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o added the regrid package |
| 140 |
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o shelfice: |
| 141 |
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- add a simple boundary layer scheme to reduce noise |
| 142 |
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- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
| 143 |
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|
| 144 |
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checkpoint58n_post |
| 145 |
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o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
| 146 |
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local variable (not in common block). |
| 147 |
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o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
| 148 |
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- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
| 149 |
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- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
| 150 |
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to work with SingleCpuIO. |
| 151 |
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o add "_d 0" to real constant of pkg/cfc subroutines ; |
| 152 |
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update exp. cfc_exemple & tutorial_cfc_offline output files. |
| 153 |
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o multi-threading and IO: |
| 154 |
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- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
| 155 |
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(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
| 156 |
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- barrier before and after reading. |
| 157 |
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- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
| 158 |
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- avoid using MDS_WRITELOCAL for LAND pkg output. |
| 159 |
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- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
| 160 |
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common-block variables ; Allows multi-threading with master-thread IO. |
| 161 |
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o change default MAX_NO_THREADS from 32 to 4 ; |
| 162 |
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and stop cleanly when MAX_NO_THREADS is too small. |
| 163 |
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o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
| 164 |
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|
| 165 |
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checkpoint58m_post |
| 166 |
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o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
| 167 |
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and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
| 168 |
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o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
| 169 |
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keep global_ocean.90x40x15 (for AD testing) with former secondary test |
| 170 |
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(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
| 171 |
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o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
| 172 |
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add MITgcm_tutorials (= code + all the tutorials) |
| 173 |
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o ecco, option to compute cost for total ssh (mean+anom) |
| 174 |
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o consistent with addition of ptracer and ssh in pkg/profiles |
| 175 |
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o profiles: adding ptracer and ssh |
| 176 |
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o testreport: change multi-test output-file name |
| 177 |
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(from output.txt.{name} to output.{name}.txt) |
| 178 |
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o profiles: now ok for mutli-tiles case |
| 179 |
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o seaice: add 4 parameters for different advection schemes for area, |
| 180 |
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(effective) seaice thickness, enthalphy, and snow height. Their default |
| 181 |
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is the standard parameter SEAICEadvScheme |
| 182 |
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o calc_gw: |
| 183 |
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- add cosFacU in zonal viscous flux (harmonic.visc.). |
| 184 |
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- put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. |
| 185 |
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of tutorial_plume_on_slope. |
| 186 |
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o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). |
| 187 |
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o calc_gw: true flux-form, account for horizontal grid spacing. |
| 188 |
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update rotating_tank results, but not plume_on_slope (affected at |
| 189 |
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truncation level, 11 digits). |
| 190 |
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|
| 191 |
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checkpoint58l_post |
| 192 |
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o calc_gw: |
| 193 |
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- take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V |
| 194 |
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- remove side-drag for now (need to fix it); update plume_on_slope results. |
| 195 |
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- fix for partial-cell & non-uniform dz; update plume_on_slope results. |
| 196 |
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o commit code to make SST/SSS weights spatially variable |
| 197 |
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(based on either variable in-situ or variable initial T/S weights) |
| 198 |
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o pkg/ecco: |
| 199 |
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* commit code to relax deviations of xx_theta, xx_salt to 5*sigma, |
| 200 |
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now based on horizontally varying weights wthetaLev, wsaltLev |
| 201 |
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* cost_averagesflags now returns year indices in addition to day, month |
| 202 |
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* sflux balance is performed on annual basis |
| 203 |
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(sflxumm, sfluxmm2, bal_sfluxmm) |
| 204 |
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* for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, |
| 205 |
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including separate counting and multipliers |
| 206 |
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o pkg/rbcs |
| 207 |
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* add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing |
| 208 |
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|
| 209 |
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checkpoint58k_post |
| 210 |
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o testreport: |
| 211 |
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- always build in dir. "build" (if not there, mkdir build instead of building |
| 212 |
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& running in input) |
| 213 |
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- run in dir run (if it exists), in build otherwise. |
| 214 |
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- call prepare_run (if input/prepare_run exists) |
| 215 |
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- run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. |
| 216 |
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o pkg/exf modifications to interpolation and rotation routines for more |
| 217 |
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reasonable treatment of North Pole singularity: for tracers North Pole |
| 218 |
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value is set to northernmost zonal-mean value, for zonal velocity it is |
| 219 |
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set to zero, and for meridional velocity it is set to northernmost value. |
| 220 |
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o pkg/exf/exf_check_range.F |
| 221 |
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- add tile index to diagnostics and move stop statement to the very |
| 222 |
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end of the routine. |
| 223 |
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o pkg/diagnostics: (diagnostics_main_init.F) |
| 224 |
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define title of isomorphic variables according to the current config. |
| 225 |
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o pkg/thsice with pkg/seaice dynamics: |
| 226 |
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- fix domain of computation (interior only, required for exf) and do exchanges |
| 227 |
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- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient |
| 228 |
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o towards a standard way of dealing with multi-threading in MONITOR |
| 229 |
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and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. |
| 230 |
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o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) |
| 231 |
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to W momentum equation in nonhydrostatic and quasihydrostatic runs. |
| 232 |
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o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. |
| 233 |
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o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) |
| 234 |
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o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL |
| 235 |
|
(problems ? with gradient check in bottom_ctrl_5x5 adjoint test) |
| 236 |
|
o tracer advection: |
| 237 |
|
- clean-up and simplify calc_common_factors.F |
| 238 |
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- make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer |
| 239 |
|
advection subroutine (but still not used within DST advection S/R) |
| 240 |
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o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
| 241 |
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|
| 242 |
|
checkpoint58j_post |
| 243 |
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o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
| 244 |
|
from file (collects calls previously in FORWARD_STEP) |
| 245 |
|
o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS |
| 246 |
|
o adjoint store dir. adjusted accordingly |
| 247 |
|
o genmake2 |
| 248 |
|
replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. |
| 249 |
|
|
| 250 |
|
checkpoint58i_post |
| 251 |
|
o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
| 252 |
|
on wind stress (SEAICEstressFactor defaults to 1.) |
| 253 |
|
o Total number of Timers is finite (<=40): comment out 2 non-essential one |
| 254 |
|
in the_main_loop.F to avoid Pb (e.g., when running fizhi test) |
| 255 |
|
o vector_invariant: fix highOrderVorticity(=4.th.Order) advection |
| 256 |
|
on CS-grid: no longer loosing mass. |
| 257 |
|
o exf & curvilinear-grid: no longer modify longitude xC & xG. |
| 258 |
|
o pkg/ggl90: fix sloppy output and fix a bug |
| 259 |
|
o pkg/seaice: added SEAICEuseEVPpickup parameter |
| 260 |
|
- Set to false in order to start EVP solver with |
| 261 |
|
non-EVP pickup files when using SEAICEuseEVP |
| 262 |
|
- fix sign error in diffusion in seaice_calc_rhs |
| 263 |
|
|
| 264 |
|
checkpoint58h_post |
| 265 |
|
* Modifications for bottom topography control |
| 266 |
|
o replace hFacC by _hFacC at various places |
| 267 |
|
o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL |
| 268 |
|
o add non-self-adjoint cg2d_nsa |
| 269 |
|
o update autodiff support routines |
| 270 |
|
o re-initialise hfac after ctrl_depth_ini |
| 271 |
|
o works for 5x5 box, doesnt work for global_ocean.90x40x15 |
| 272 |
|
* Adding verification for 5x5 box (4-layer) bottom topography control |
| 273 |
|
|
| 274 |
|
checkpoint58g_post |
| 275 |
|
o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., |
| 276 |
|
used for mean seasonal cycle, mean diurnal cycle); add an example |
| 277 |
|
in verification/global_ocean.cs32x15/input.thsice/data.diagnostics |
| 278 |
|
o pkg/ggl90: |
| 279 |
|
- add parameter (minimum surface kinetic energy) |
| 280 |
|
- fix bug (avoiding division by zero) |
| 281 |
|
o couple pkg/thsice to pkg/seaice: |
| 282 |
|
- modify advection in seaice to accomodate new scalar fields to be advected |
| 283 |
|
- only muliDimAdection scheme work with seaice/thsice |
| 284 |
|
- mapping of thsice-variables to seaice-variables, back and forth |
| 285 |
|
- does not break the verification experiments, but does not give the |
| 286 |
|
desired results either |
| 287 |
|
o pkg/seaice |
| 288 |
|
- make (default) second order advection a bit less confusing? |
| 289 |
|
|
| 290 |
|
checkpoint58f_post |
| 291 |
|
o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice |
| 292 |
|
to pkg/seaice): |
| 293 |
|
- new routines thsice_map_exf and thsice_get_exf provide the interface |
| 294 |
|
- add an additional formal parameter to thsice_solve4temp |
| 295 |
|
o pkg/exf: |
| 296 |
|
- add new fields wspeed, snowprecip (to be able to couple to thsice) |
| 297 |
|
- correct Stefan-Boltzmann constant |
| 298 |
|
- new parameter for longwave surface emittance |
| 299 |
|
- separate some stuff from exf_bulkformulae into new routines |
| 300 |
|
exf_radiation, exf_wind |
| 301 |
|
- add new parameters and constants: longwave emissivity for ocean, ice |
| 302 |
|
and snow, evaporation parameters over ice |
| 303 |
|
- decouple wind/stress computation from ALLOW_BULKFORMULA: always compute |
| 304 |
|
either wind from stress or stress from wind |
| 305 |
|
o pkg/thSIce: |
| 306 |
|
- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F |
| 307 |
|
- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND |
| 308 |
|
and THSICE_CALC_THICKN |
| 309 |
|
- for now, call to THSICE_GET_BULKF remains inside i,j loops. |
| 310 |
|
- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h |
| 311 |
|
to make debugging easier. |
| 312 |
|
- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output |
| 313 |
|
o pkg/bulk_force: |
| 314 |
|
- clean-up comments and parameters ; |
| 315 |
|
- add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; |
| 316 |
|
o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; |
| 317 |
|
generate new output for test-experiment: aim.5l_cs.thSI |
| 318 |
|
o results_ad : rename "output.txt_adm" to "output_adm.txt" and change |
| 319 |
|
testreport accordingly |
| 320 |
|
|
| 321 |
|
checkpoint58e_post |
| 322 |
|
o SEAICE_CGRID adjoint done |
| 323 |
|
o R_STAR adjoint implemented. |
| 324 |
|
* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
| 325 |
|
* need to sort out init. of h0facc, etc. |
| 326 |
|
o Make pkg/profile fully independent of ecco,cost, etc. stuff |
| 327 |
|
to be able to use it in pure forward. |
| 328 |
|
|
| 329 |
|
checkpoint58d_post |
| 330 |
|
o upgrade simple test-experiment to tutorial example: |
| 331 |
|
step.1: duplicate the experiment and (step.2) will remove the old copy. |
| 332 |
|
tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
| 333 |
|
tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) |
| 334 |
|
tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
| 335 |
|
tutorial_global_oce_biogeo <- copy of dic_example |
| 336 |
|
tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
| 337 |
|
tutorial_plume_on_slope <- copy of plume_on_slope |
| 338 |
|
tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) |
| 339 |
|
tutorial_global_oce_optim <- empty for now (David ?) |
| 340 |
|
tutorial_global_oce_in_p <- copy of global_ocean_pressure |
| 341 |
|
some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
| 342 |
|
o correct a sign problem in cost_scat.F |
| 343 |
|
o obcs and ptracers: fix boundary conditions for advections schemes |
| 344 |
|
with larger stencil |
| 345 |
|
o thsice adjoint: start |
| 346 |
|
o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for |
| 347 |
|
completeness |
| 348 |
|
o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING |
| 349 |
|
and COSINEMETH_III, add comments in default CPP_OPTIONS.h |
| 350 |
|
o ptracers adjoint: |
| 351 |
|
* avoid extensive recomputatations |
| 352 |
|
* fix missing re-init. of gptr (missed by TAF) |
| 353 |
|
o obcs: add a flag (OBCSprintDiags, defaults is true) that allows |
| 354 |
|
me to turn off the excessive output to STDOUT that this package produces |
| 355 |
|
o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common |
| 356 |
|
and add those terms in Vector-Invariant formulation. |
| 357 |
|
o in ctrl pkg, if ALLOW_CAL, use monthly mean controls |
| 358 |
|
if the control period (xx_hfluxperiod etc) is 0 |
| 359 |
|
o in profiles pkg, clean routines and fix details |
| 360 |
|
o in ecco pkg, reading ssh data: |
| 361 |
|
fix problem in case the model does not start at iter0=0 |
| 362 |
|
o fix mnc-pickup/restart for ptracers |
| 363 |
|
o new package prifiles: |
| 364 |
|
code to compute profile-based cost by Gael Forget |
| 365 |
|
(modifs in ecco, ctrl, autodiff) |
| 366 |
|
o Benign bug fix in initialization (spotted by M. Mazloff) of |
| 367 |
|
ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F |
| 368 |
|
|
| 369 |
|
checkpoint58c_post |
| 370 |
|
o adjoint: finish NLFS adjoint and provide reference output in |
| 371 |
|
verification/global_ocean.90x40x15/results_ad_nlfs |
| 372 |
|
o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the |
| 373 |
|
documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in |
| 374 |
|
SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only |
| 375 |
|
with SEAICE_CGRID defined. |
| 376 |
|
o move calendarDumps from "data" to "data.cal" and clean-up the code |
| 377 |
|
with a simple call to pkg/cal S/R: CAL_TIME2WRITE |
| 378 |
|
o add useEXF & useCAL flags (for now, set in hard-coded way) |
| 379 |
|
o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum |
| 380 |
|
(were missing in NH mode, and wrong in quasihydrostatic mode). |
| 381 |
|
waiting for Chris updated version of calc_gw to add those CALLs. |
| 382 |
|
o fix bug in quasihydrostatic S/R ; |
| 383 |
|
add a test for this option: global_ocean.90x40x15.qshyd |
| 384 |
|
o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs. |
| 385 |
|
(called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS) |
| 386 |
|
o add on/off flag useOffLine for package OFFLINE |
| 387 |
|
o seaice: |
| 388 |
|
- modify advection so that it works also on the C-grid |
| 389 |
|
- extend loop ranges in seaice_lsr and seaice_dynsolver; fixes |
| 390 |
|
problem in multi-tile runs with C-grid |
| 391 |
|
- add flags for clipping ice velocities and/or masking solver forcing |
| 392 |
|
- fix drag (ocean on ice) formulation and a bug that caused noise in the |
| 393 |
|
C-grid solver |
| 394 |
|
- added a few comments to seaice_diffusion.F |
| 395 |
|
- separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V |
| 396 |
|
are now exclusive) |
| 397 |
|
- add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which |
| 398 |
|
required re-ordering the code a little: |
| 399 |
|
+ make DAIRN global variable (defined in SEAICE) |
| 400 |
|
+ move computation of the viscosities eta and zeta into a new separate |
| 401 |
|
routine (because I need to recompute them in seaice_ocean_stress.F) |
| 402 |
|
|
| 403 |
|
checkpoint58b_post |
| 404 |
|
o AIM+thSIce: fix sign of Short-Wave through the Ice ; |
| 405 |
|
update output.txt of exp. aim.5l_cs.thSI |
| 406 |
|
o various mnc cleanups and improvements: |
| 407 |
|
+ shrink lookup tables by factor of ~4 |
| 408 |
|
+ better error reporting when running out of lookup space |
| 409 |
|
+ able to handle longer path/file names (up to 500 chars) |
| 410 |
|
o adjoint: |
| 411 |
|
- Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. |
| 412 |
|
- TBD: "hidden" mom_vecinv recomp. in dynamics |
| 413 |
|
o change forcing_In_AB to affects both T,S forcing and Momentum forcing |
| 414 |
|
(allow to differentiate between forcing components using new integer flags: |
| 415 |
|
momForcingOutAB=1/0 & tracForcingOutAB=1/0) |
| 416 |
|
and add new flag to put Dissipation tendency out of Adams-Bashforth. |
| 417 |
|
o ecco |
| 418 |
|
- enable trend removal from SSH anomaly obs. |
| 419 |
|
o adjoint |
| 420 |
|
- a fix for PmEpR when #undef EXACT_CONSERV |
| 421 |
|
- fix of "hidden" recomp. in thermodynamics (no TAF warnings) |
| 422 |
|
- try to fix "hidden" recomp. in forward_step for NLFS |
| 423 |
|
(NLFS seems broken sometimes after I checked it in) |
| 424 |
|
o seaice: |
| 425 |
|
- add c-grid version of the dynamic solver: |
| 426 |
|
+ three new routines that are the c-grid substitute lsr, dynsolver |
| 427 |
|
and ostres |
| 428 |
|
+ put a few fields that were local to dynsolver into global common |
| 429 |
|
blocks, so that I can move the computation of stresses etc into |
| 430 |
|
seaice_lsr (saves coding but may break the adjoint). |
| 431 |
|
- replace more hardwired parameters by runtime parameters |
| 432 |
|
- add ice masks that mask the rhs of the implicit solvers where there |
| 433 |
|
is no ice (commented out in seaice_dynsolver, because i am not sure |
| 434 |
|
if this works properly), eventually this should replace the clipping |
| 435 |
|
of ice velocities in seaice_dynsolver to +/-40cm/s. |
| 436 |
|
o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly |
| 437 |
|
include it only where its needed |
| 438 |
|
o move balancing of fluxes before the call of external_forcing_surf |
| 439 |
|
o seaice: |
| 440 |
|
- correct units of turning angles (now they are really in degrees) |
| 441 |
|
- move computation of GWATX/Y out of main routine into dynsolver |
| 442 |
|
- initialize GWATX/Y in seaice_init |
| 443 |
|
o Apply mask on Fresh-Water flux (needed for SSH forcing). |
| 444 |
|
update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) |
| 445 |
|
o seaice: add runtime flags for turning angles (default to zero) |
| 446 |
|
o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean |
| 447 |
|
and trend from exf forcing and ctrl control adjustments |
| 448 |
|
o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF |
| 449 |
|
(since checkpoint57x_post) |
| 450 |
|
o change the default rotation period to 86164.s = the Earth rotation |
| 451 |
|
o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) |
| 452 |
|
and based on a reference stratification. Tested within hs94.cs-32x32x5. |
| 453 |
|
o seaice advection: add code for choosing between the default (2nd order |
| 454 |
|
central differences) and multiDim advection schemes provided by |
| 455 |
|
pkg/generic_advdiff |
| 456 |
|
o seaice: |
| 457 |
|
- removed all references to SEAICE_GRID.h fields from |
| 458 |
|
dynsolver, advect, diffus, lsr, without changing the results of lab_sea |
| 459 |
|
(cubed-sphere configuration will change a little) |
| 460 |
|
- grid computations in seaice_init are obsolete now. |
| 461 |
|
- cleaned up code a little so that is easier to read (hopefully). |
| 462 |
|
- added new (better?) discretizations of default advection and diffusion |
| 463 |
|
(turn on with SEAICEuseFluxForm) |
| 464 |
|
- replace 1 in 3d global fields by kSurface in growth.F |
| 465 |
|
|
| 466 |
|
checkpoint58a_post |
| 467 |
|
o seaice: |
| 468 |
|
- bug fix in advect.F |
| 469 |
|
o shelfice: |
| 470 |
|
- separate shelfice load anomaly from pload (breaks with time |
| 471 |
|
dependent forcing), => introduce constant field shelficeLoadAnomaly. |
| 472 |
|
Its default is 0., but it may be computed more cleverly from (unknown) |
| 473 |
|
t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be |
| 474 |
|
done offline. A good approximation of the pressure load anomaly is |
| 475 |
|
necessary to avoid large initial adjustment processes underneath |
| 476 |
|
deep-reaching shelfice. |
| 477 |
|
- small fix in ISOMIP shelfice_thermodynamics |
| 478 |
|
- add more sophisticated thermodynamics of Hellmer (1989), this is |
| 479 |
|
now the default |
| 480 |
|
- give a few constants more intuitive names |
| 481 |
|
o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful |
| 482 |
|
if bulk formulae are used in long integration (especially EmPmR). Turn |
| 483 |
|
on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01 |
| 484 |
|
if balancePrintMean, the imbalance that is substracted is printed to |
| 485 |
|
STDOUT. |
| 486 |
|
o fix bug (typo) in obcs_apply_eta.F |
| 487 |
|
o add a new package shelfice which enables us to model the circulation |
| 488 |
|
underneath shelf-ice with draughts of hundreds of meters. |
| 489 |
|
- works |
| 490 |
|
- to do: + include improved thermodynamics |
| 491 |
|
+ check whether kSurfC (from model/inc/SURFACE.h) can be used |
| 492 |
|
instead of new field kTopC |
| 493 |
|
+ can we use topoFile, Ro_surf and existing code in ini_depth.F |
| 494 |
|
instead of new field R_shelfIce and new code in ini_depth.F |
| 495 |
|
and ini_mask_etc.F? |
| 496 |
|
+ adjust vertical mixing schemes? |
| 497 |
|
o seaice pkg: |
| 498 |
|
- add a cpp-flag to include a simple formula for a salinity dependent |
| 499 |
|
freezing point of sea water at the surface |
| 500 |
|
- change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and |
| 501 |
|
meridional stresses are now different (and hopefully correct) |
| 502 |
|
o AIM pkg: change threshold on large-scale condensation to conserve Heat. |
| 503 |
|
update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics |
| 504 |
|
and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG) |
| 505 |
|
o pkg/diagnostics: add options and parameters for regional-statistics |
| 506 |
|
diagnostics ; define regions by reading a region-mask from a file |
| 507 |
|
(might add other options later) |
| 508 |
|
o pkg/bulk_force: |
| 509 |
|
- add option and parameters to use AIM surface-flux formulae. |
| 510 |
|
- Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ; |
| 511 |
|
others forcing fields (defined in PARM05, parameter file "data") are loaded |
| 512 |
|
from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F). |
| 513 |
|
- initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F |
| 514 |
|
- use the right EXCH call for uwind,vwind (to work on CS-grid). |
| 515 |
|
- re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h) |
| 516 |
|
and parameters (note: calcWindStress replaces .NOT.readwindstress). |
| 517 |
|
- cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). |
| 518 |
|
|
| 519 |
|
checkpoint58 |
| 520 |
|
o add "--embed-source" option to genmake2 which, when the supporting |
| 521 |
|
tools can be compiled (as determined by genmake2) will turn on the |
| 522 |
|
embed_files package which then embeds the entire MITgcm source code |
| 523 |
|
(*.[fFhc] + Makefile) used for the build within the executable |
| 524 |
|
- requested by CNH but off by default |
| 525 |
|
- adds a paltry <9MB to the mitgcmuv executable in most cases |
| 526 |
|
- only writes the output when useEMBEDSRC in eedata is true |
| 527 |
|
o clean up 3-dim. relaxation codes: |
| 528 |
|
* Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec |
| 529 |
|
* Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) |
| 530 |
|
* Thanks to Tom Haine for testing! |
| 531 |
|
|
| 532 |
|
checkpoint57z_post |
| 533 |
|
o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): |
| 534 |
|
affects output (@ truncation level) of exp. plume_on_slope ; updated. |
| 535 |
|
o fix the pickup behavior for obcs in combination with ptracers |
| 536 |
|
o fix a bug in ptracers_external_fields_load |
| 537 |
|
o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...) |
| 538 |
|
affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) |
| 539 |
|
o transfered surface NH pressure to eta field (if exactConserv). |
| 540 |
|
o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign) |
| 541 |
|
and update lab_sea output.txt file. |
| 542 |
|
o completing 3-dim. relaxation code: additional term |
| 543 |
|
1/tau*( theta(i,j,k) - thetaStar(i,j,k) ) |
| 544 |
|
in S/R EXTERNAL_FORCING_T (file external_forcing.F) |
| 545 |
|
* At compile time, in "EXF_OPTIONS.h" set |
| 546 |
|
#define ALLOW_CLIMTEMP_RELAXATION |
| 547 |
|
#define ALLOW_CLIMSALT_RELAXATION |
| 548 |
|
* At runtime in "data", under &PARM03 set (e.g., units in seconds) |
| 549 |
|
tauThetaClimRelax3Dim = 15552000.0, |
| 550 |
|
tauSaltClimRelax3Dim = 15552000.0, |
| 551 |
|
* 3 cases: |
| 552 |
|
1) Use a constant-in-time 3-dim. field |
| 553 |
|
2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec. |
| 554 |
|
3) Real-time relax. to time-evolving prescribed field |
| 555 |
|
o Adding Laplacian-type smoothness constraint on |
| 556 |
|
initial and boundary (forcing) controls (ic, bc) |
| 557 |
|
* enable at compile-time via |
| 558 |
|
ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION |
| 559 |
|
* enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1 |
| 560 |
|
* Absolute scale somewhat unclear so far |
| 561 |
|
* no area weighting was included since no other cost term does so far |
| 562 |
|
|
| 563 |
|
checkpoint57y_post |
| 564 |
|
First step for a NLFS adjoint |
| 565 |
|
o initially suppress rStar (new flag DISABLE_RSTAR_CODE) |
| 566 |
|
o new init. routines for calc_r_star, calc_surf_dr |
| 567 |
|
o still need to deal with ini_masks_etc |
| 568 |
|
o testreport seemed happy |
| 569 |
|
checkpoint57y_pre |
| 570 |
|
|
| 571 |
|
o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
| 572 |
|
o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) |
| 573 |
|
o add new offset feature to offline pkg (plus minor cleanup) |
| 574 |
|
o cfc fixes for final year of integration |
| 575 |
|
o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should |
| 576 |
|
be in GCHEM_OPTIONS). |
| 577 |
|
|
| 578 |
|
checkpoint57x_post |
| 579 |
|
o fix testreport Pb in multiple test experiment. |
| 580 |
|
o cleanup our namelist syntax in verification: |
| 581 |
|
- make it more F95 standards compliant (some work still needed) |
| 582 |
|
- allows the vast majority of our tests to work with gfortran |
| 583 |
|
o Non-Hydrostatic: |
| 584 |
|
- put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h |
| 585 |
|
- fix exchange calls for CS-grid using the new EXCH_S3D_RL. |
| 586 |
|
o Allow to apply AB on T,S rather than on AB(gT,gS): |
| 587 |
|
- implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 |
| 588 |
|
- use the same arrays (gtNm,gsNm) to hold tracer field at previous |
| 589 |
|
time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). |
| 590 |
|
- need a "clever" read_pickup to restart from the other AB formulation |
| 591 |
|
o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h |
| 592 |
|
o remove some unused variables (reduces number of compiler warnings) |
| 593 |
|
o adjoint |
| 594 |
|
* Disable useVariableViscosity for adjoint for time being |
| 595 |
|
(there are a number of extensive recomputations) |
| 596 |
|
* Initialize certain variables needed for adjoint |
| 597 |
|
|
| 598 |
|
checkpoint57w_post |
| 599 |
|
o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names |
| 600 |
|
fix the singleCpuIO RS version of MDSWRITEFIELD |
| 601 |
|
and add a WARNING if using globalFiles=T with multi-processors. |
| 602 |
|
o write grid-file(s) in only one format (MDS or MNC): default=MNC (if |
| 603 |
|
using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc |
| 604 |
|
o tracer advection scheme: |
| 605 |
|
add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get |
| 606 |
|
those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, |
| 607 |
|
was not very convenient). |
| 608 |
|
add implicit version for DST-3 & DST3_Flux_Limit vertical advection; |
| 609 |
|
(further tests needed for the implicit DST & Flux-Limiter schemes). |
| 610 |
|
o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef |
| 611 |
|
and sRef for convenience, handy, when you want to initialize |
| 612 |
|
ptracers in a large domain with a constant non-zero value. Also, |
| 613 |
|
untangle ptracers_init.F a little. |
| 614 |
|
|
| 615 |
|
checkpoint57v_post |
| 616 |
|
o change dome exp. to use variable viscosity in side-drag terms. |
| 617 |
|
o remove all the files from the cfc_offline test since they are now |
| 618 |
|
incorporated into tutorial_cfc_offline which has been producing |
| 619 |
|
identical results for a few days of testing |
| 620 |
|
o add new parameter: sideDragFactor to enable half-slip-side BC |
| 621 |
|
and change side-drag S/R to use viscosity from mom_calc_visc |
| 622 |
|
(can switch back by setting sideDragFactor=0.); affects results at |
| 623 |
|
truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), |
| 624 |
|
global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). |
| 625 |
|
o vorticity & strain are now computed without masking, to account for |
| 626 |
|
no-slip-side BC in variable viscosity calculation ; mask is applied |
| 627 |
|
anyway later on, before computing advection/coriolis terms. |
| 628 |
|
o modify exp4 to test new obcs support for reading from external files |
| 629 |
|
and for passive tracers |
| 630 |
|
o fix behavior of ptracers_monitor when monitor output is written to a |
| 631 |
|
netcdf-file; still not independent of monitor.F (writes in the same |
| 632 |
|
file). |
| 633 |
|
o change default value of tRef (put a uniform, meaningful value for ocean |
| 634 |
|
& atmos) and initialize sRef (was missing, as Martin mentioned). |
| 635 |
|
o Redefine viscC?Leith*. Change the coefficients of Leith viscosity |
| 636 |
|
to be proportional to enstrophy dissipation length. Thus, |
| 637 |
|
viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) |
| 638 |
|
This is now consistent with Smagorinsky and with the manual. |
| 639 |
|
|
| 640 |
|
checkpoint57u_post |
| 641 |
|
o OBCS and PTRACERS: add open boundary support for passive tracers |
| 642 |
|
- either use homogenous (pseudo) v.Neumann conditions or prescribe |
| 643 |
|
OB-values from file; this is not different from the way theta and salinity |
| 644 |
|
are treated |
| 645 |
|
- however, Orlanski-radiation conditions are not supported, and the model |
| 646 |
|
will stop if you use pTracers and Orlanski at the same time. |
| 647 |
|
- beefed up the rountine obcs_external_fields_load: now only those open |
| 648 |
|
boundary values are overwritten with values from files for which there |
| 649 |
|
are really files, otherwise the OB-fields remain untouched. This makes |
| 650 |
|
it possible to use different OBs at different ends of the domain (as |
| 651 |
|
with EXF) |
| 652 |
|
o reduce number of exch calls in shap_filt (s2). |
| 653 |
|
o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ |
| 654 |
|
truncation level) 4/5 MLAdjust test results (11&12 digits match). |
| 655 |
|
|
| 656 |
|
checkpoint57t_post |
| 657 |
|
o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
| 658 |
|
o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
| 659 |
|
same truncation, independent of the face number: affects affects several |
| 660 |
|
test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). |
| 661 |
|
o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); |
| 662 |
|
note that biharmonic viscosity + no-slip was not tested in any experiment. |
| 663 |
|
o fix bug in non-linear free-surf side-drag ; generate new output for |
| 664 |
|
global_ocean.cs32x15(+.thsice) & global_ocean_pressure. |
| 665 |
|
o make mnc honor the writeBinaryPrec flag for most kinds of output |
| 666 |
|
o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
| 667 |
|
o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
| 668 |
|
error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
| 669 |
|
o add brackets in multi-terms sum to get same truncation, independent of |
| 670 |
|
the face number (manage to get exactly same value of gU,gV at the cs-edge) |
| 671 |
|
affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
| 672 |
|
o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
| 673 |
|
and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
| 674 |
|
a maximum grid-scale Reynolds number. Also, changes all length calculations |
| 675 |
|
in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
| 676 |
|
Suggested values of viscosity parameters found in mom_calc_visc. |
| 677 |
|
Many new viscosity diagnostics available. |
| 678 |
|
|
| 679 |
|
checkpoint57s_post |
| 680 |
|
o Add clearing-house for viscosity calculations, mom_calc_visc and |
| 681 |
|
correct numerous bugs in LeithD and Smagorinsky discretizations. |
| 682 |
|
mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
| 683 |
|
used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
| 684 |
|
Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
| 685 |
|
and with Strain-Tension viscous term calculation (mom_hdissip.F). |
| 686 |
|
The Strain-Tension form is now called with useStrainTensonVisc=.true. |
| 687 |
|
ViscAhStrain and viscAhTension are now retired. |
| 688 |
|
o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
| 689 |
|
o In response to JMC's bug report, genmake2 now ignores any soft-links |
| 690 |
|
that it finds in the *current* directory when searching for files. |
| 691 |
|
Soft-links found in any other source directories will still work as |
| 692 |
|
they did before. |
| 693 |
|
o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
| 694 |
|
a C routine to unlimit the stack size |
| 695 |
|
o mnc-ify pkg/aim snapshot vars |
| 696 |
|
o mnc-ify pkg/land as requested by Daniel |
| 697 |
|
o various changes to mnc including: |
| 698 |
|
- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
| 699 |
|
- output can now be grouped so that all files within a group |
| 700 |
|
change the ITER portion of their names in lock-step together |
| 701 |
|
- can now read ("global") PER-FACE (in addition to PER-TILE) files |
| 702 |
|
and works with both EXCH1 and EXCH2 (but needs more testing) |
| 703 |
|
- writing works for all verification test cases w/ g77 on Linux |
| 704 |
|
|
| 705 |
|
checkpoint57r_post |
| 706 |
|
o make MNC variable initialization happen earlier |
| 707 |
|
o add diagnostics for (almost) each term of the momentum Eq. |
| 708 |
|
o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
| 709 |
|
o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
| 710 |
|
o remove MINIMAL_TAVE_OUTPUT option ; |
| 711 |
|
add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
| 712 |
|
o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
| 713 |
|
allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
| 714 |
|
o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
| 715 |
|
o add time-dependent SST, SSS control |
| 716 |
|
o cost terms in ecco/ modularized (new cost_generic.F) |
| 717 |
|
o cost_averages routines are modularized (new cost_averagesgeneric.F) |
| 718 |
|
o new infrastructure for seaice model vs. obs misfits in seaice/ |
| 719 |
|
* driver from the_main_loop.F is seaice_cost_driver.F |
| 720 |
|
* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
| 721 |
|
* gradient check in Exp. 6a of natl_box_adjoint/ |
| 722 |
|
o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
| 723 |
|
(see README file) |
| 724 |
|
|
| 725 |
|
checkpoint57q_post |
| 726 |
|
o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
| 727 |
|
o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
| 728 |
|
- bug was reported by Jean-Michel and Ian Fenty |
| 729 |
|
o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
| 730 |
|
update exp. cpl_aim+ocn output. |
| 731 |
|
o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
| 732 |
|
Needed for high-res. runs with large global files |
| 733 |
|
to be able to limit tapelev size |
| 734 |
|
o Changed some tests for adjoint: |
| 735 |
|
* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
| 736 |
|
* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
| 737 |
|
* global_ocean.90x40x15/ back to default 3-level checkpointing |
| 738 |
|
o Modifications to enable scripted COMMON to MODULE conversion |
| 739 |
|
* verification/OpenAD/code/ has necessary scripts and description; |
| 740 |
|
* converts, compiles and runs successfully; |
| 741 |
|
|
| 742 |
|
checkpoint57p_post |
| 743 |
|
o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
| 744 |
|
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
| 745 |
|
(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
| 746 |
|
o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
| 747 |
|
o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
| 748 |
|
(was already the case for dissipation with mom_vecinv, |
| 749 |
|
and also the case for grad.PhiHyd when staggered-timeStep) |
| 750 |
|
This will allow to put dissipation out-off the AB time-stepping. |
| 751 |
|
Unfortunately, affects truncation error. Update output of exp. that "fails" |
| 752 |
|
(cg2d matching number) and leave the others for later: front_relax(10), |
| 753 |
|
global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
| 754 |
|
matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
| 755 |
|
|
| 756 |
|
checkpoint57o_post |
| 757 |
|
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
| 758 |
|
(2) its ready to be documented during the 20050801 DocFest |
| 759 |
|
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
| 760 |
|
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
| 761 |
|
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
| 762 |
|
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
| 763 |
|
(worth another tag) |
| 764 |
|
|
| 765 |
|
checkpoint57n_post |
| 766 |
|
o adding precip control xx_precip 32 |
| 767 |
|
o adding swflux control xx_swflux 33 |
| 768 |
|
o Replacing 10 forcing penalty cost routines by 1 generic. |
| 769 |
|
o Implementing partitioning in time-mean and variable adjustment |
| 770 |
|
for atmos. state. |
| 771 |
|
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
| 772 |
|
o in natl_box_adjoint: |
| 773 |
|
* updated exp 1 to 10 |
| 774 |
|
(but does not have time-mean vs. variable split results yet) |
| 775 |
|
o updated global1x1/*_seaice_adj/ |
| 776 |
|
to incorporate latest changes |
| 777 |
|
o enable useSingleCpuIO for mdsio vector routines |
| 778 |
|
(applies in particular to tapelev I/O) |
| 779 |
|
o removed inefficient K-loop in all active_file*control*.F |
| 780 |
|
|
| 781 |
|
checkpoint57m_post |
| 782 |
|
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
| 783 |
|
and advect_cs (use EXCH-2 and standard cs-32 grid files). |
| 784 |
|
o pkg/exch2: filling of face-corner halo regions is optional |
| 785 |
|
(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
| 786 |
|
|
| 787 |
|
checkpoint57l_post |
| 788 |
|
tag before updating tutorials (pre-release-2) |
| 789 |
|
o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
| 790 |
|
for output and interpolation of input fields onto model grid) |
| 791 |
|
o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
| 792 |
|
Affects results of exp. rotating_tank ; update output.txt. |
| 793 |
|
o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
| 794 |
|
and taking the square quantity and/or using a fraction-weight field. |
| 795 |
|
o fix aim_diagnostics_init.F mate numbers. |
| 796 |
|
o add mnc output capability to diagnostics/diagstat and update |
| 797 |
|
our cvsignore files for the ACSII output generated |
| 798 |
|
|
| 799 |
|
checkpoint57k_post |
| 800 |
|
o lab_sea now uses diagnostics package and provides a suite of |
| 801 |
|
new EXF diagnostics output. |
| 802 |
|
|
| 803 |
|
checkpoint57j_post |
| 804 |
|
o exf |
| 805 |
|
* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
| 806 |
|
Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
| 807 |
|
terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
| 808 |
|
* extended diagnostics output |
| 809 |
|
- now includes all EXF variables |
| 810 |
|
- hs, hl moved to common block |
| 811 |
|
- separate S/R for diagnostics, called after ctrl vector is added |
| 812 |
|
- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
| 813 |
|
- EXFqnet contains true Qnet (i.e. includes qsw) |
| 814 |
|
* updated verif. lab_sea, global_with_exf |
| 815 |
|
* Rearranging hflux (exf_mapfields -> exf_getforcing) |
| 816 |
|
to ensure that diagnostics sees a true EXFqnet |
| 817 |
|
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
| 818 |
|
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
| 819 |
|
several times with different frequencies. |
| 820 |
|
o mnc-ify the thsice package as requested by Daniel Enderton |
| 821 |
|
- the monitor--MNC output needs work |
| 822 |
|
- many attributes need to be added (most are currently blank) |
| 823 |
|
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
| 824 |
|
- many attributes need to be added (most are currently blank) |
| 825 |
|
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
| 826 |
|
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
| 827 |
|
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
| 828 |
|
update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
| 829 |
|
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
| 830 |
|
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
| 831 |
|
(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
| 832 |
|
|
| 833 |
|
checkpoint57i_post |
| 834 |
|
o Diagnostics package was changed: diagnostic allocation is now deactivated |
| 835 |
|
by setting an empty file name in the namelist (used to be by setting 0 frequency) |
| 836 |
|
o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
| 837 |
|
add 1rst Order upwind vertical Shear. |
| 838 |
|
o add a quick fix for A/B checkpointing in OFFLINE mode |
| 839 |
|
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
| 840 |
|
end-run around the C/Fortran linking horror in eesup/src/timers.F |
| 841 |
|
o added pkg/runclock: allows user to terminate run based on wall clock |
| 842 |
|
o added non-hydrostatic scaling parameter: nh_am2 |
| 843 |
|
o pkg/my82: futile attempt to make results compiler-independent by adding |
| 844 |
|
some "_d 0", etc. no effect. |
| 845 |
|
o for mnc output, fill the 'T' coordinate var with myTime and create a |
| 846 |
|
separate 'iter' variable for iteration count |
| 847 |
|
o pkg/diagnostics: |
| 848 |
|
add new capability: output of Global/Regional & per-level statistics ; |
| 849 |
|
tested against monitor output (including land & thSIce) on various exp. |
| 850 |
|
o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
| 851 |
|
|
| 852 |
|
checkpoint57h_done |
| 853 |
|
tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
| 854 |
|
data.diagnostics, data.gchem, data.ptracers) is done. |
| 855 |
|
|
| 856 |
|
o pkg/diagnostics: prepare for Global/Regional statistics. |
| 857 |
|
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
| 858 |
|
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
| 859 |
|
and rename it: DIFFERENT_MULTIPLE |
| 860 |
|
|
| 861 |
|
checkpoint57h_post |
| 862 |
|
o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
| 863 |
|
o pkg/diagnostics: change output frequency, now in seconds (instead |
| 864 |
|
of Nb of iterations). This requires to change data.diagnostics. |
| 865 |
|
checkpoint57h_pre |
| 866 |
|
|
| 867 |
|
o in mnc, let the user create the output dir if both mnc_outdir_date |
| 868 |
|
and mnc_outdir_num are false |
| 869 |
|
o add fflags() to pkg/diagnostics which allows one to specify, on a |
| 870 |
|
per-file basis, the file precision [default behavior is unchanged] |
| 871 |
|
o added diagnostics to pkg/kpp, including computation of mixed layer |
| 872 |
|
depth based on a temperature/density criterion |
| 873 |
|
o updated verification/natl_box to test the new pkg/kpp diagnostics |
| 874 |
|
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
| 875 |
|
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
| 876 |
|
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
| 877 |
|
not mnc -- this mistake was found by JMC and is now corrected |
| 878 |
|
|
| 879 |
|
checkpoint57g_post |
| 880 |
|
o add Adams-Bashforth 3rd Order time stepping: |
| 881 |
|
- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
| 882 |
|
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
| 883 |
|
checkpoint57g_pre |
| 884 |
|
|
| 885 |
|
o make lambda[Theta,Salt]ClimRelax spatially varying |
| 886 |
|
(default remains spatially uniform constant based on tau) |
| 887 |
|
o added new control variables |
| 888 |
|
* init. uVel, vVel, etanN |
| 889 |
|
* lambda[Theta,Salt]ClimRelax |
| 890 |
|
o separate masks used for ctrl_pack/unpack 'from write_grid' output |
| 891 |
|
(suggested by G. Forget) |
| 892 |
|
|
| 893 |
|
checkpoint57f_post |
| 894 |
|
o add parameter "baseTime" = model base time = time at iteration zero |
| 895 |
|
new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
| 896 |
|
account for baseTime shift |
| 897 |
|
o move Coriolis arrays from PARAMS.h to GRID.h |
| 898 |
|
checkpoint57f_pre |
| 899 |
|
|
| 900 |
|
o mnc-ifying the seaice package |
| 901 |
|
o introduced an alternative length scale calculation for use in the limiting |
| 902 |
|
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
| 903 |
|
o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
| 904 |
|
o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
| 905 |
|
as well as grad(vort3). Made it compatible with both approximate form |
| 906 |
|
for the cubed sphere and full form of these gradients. Added flag |
| 907 |
|
useFullLeith to select between approximate and full form. |
| 908 |
|
o add "d0" in getcon.F to reduce differences between compilers/platforms |
| 909 |
|
update output.txt of exp. fizhi-gridalt-hs |
| 910 |
|
o change port_rand funtion to allow to set the seed. |
| 911 |
|
o fix obscure MNC bug involving conversion between reals and integers |
| 912 |
|
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
| 913 |
|
new version is now more standards-compliant |
| 914 |
|
o adjoint-related modifications |
| 915 |
|
* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
| 916 |
|
* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
| 917 |
|
* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
| 918 |
|
|
| 919 |
|
checkpoint57e_post |
| 920 |
|
o Adding eddy stress controls a la Ferreira et al. |
| 921 |
|
checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
| 922 |
|
|
| 923 |
|
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
| 924 |
|
update output.txt of exp. fizhi-gridalt-hs |
| 925 |
|
o add more "Z" dimensions and associated coordinate vars to MNC |
| 926 |
|
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
| 927 |
|
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
| 928 |
|
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
| 929 |
|
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
| 930 |
|
months and years. Requires pkg/cal. |
| 931 |
|
o diagnostics: add pickup functionality |
| 932 |
|
- off by default for backwards compatibility |
| 933 |
|
- current version only uses MDSIO -- MNC will be added |
| 934 |
|
o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
| 935 |
|
o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
| 936 |
|
|
| 937 |
|
checkpoint57d_post |
| 938 |
|
o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
| 939 |
|
o modify verification/ideal_2D_oce so that it tests the creation of mnc |
| 940 |
|
output from the diagnostics package |
| 941 |
|
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
| 942 |
|
o make genmake2 more portable by using ".$FS" instead of ".f" for more |
| 943 |
|
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
| 944 |
|
o add coordinate variables to the MNC output from the diagnostics package |
| 945 |
|
o change MNC-flags default value: true when useMNC=TRUE |
| 946 |
|
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
| 947 |
|
the ability (off by default) to read the grid information using MNC |
| 948 |
|
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
| 949 |
|
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
| 950 |
|
o do snap-shot diagnostics at the middle of the time-interval (instead of |
| 951 |
|
at the end). |
| 952 |
|
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
| 953 |
|
new test for AIM with thSIce + slab-ocean |
| 954 |
|
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
| 955 |
|
o move state variable diagnostics to the beginning of the time step ; |
| 956 |
|
(note: still needs some work specially for snap-shot diagnostics) |
| 957 |
|
duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
| 958 |
|
|
| 959 |
|
checkpoint57c_post |
| 960 |
|
o Change testing option (-ieee) to get closer agreement between g77 & ifort |
| 961 |
|
o generate new output.txt files on faulks with g77 & the new -ieee option |
| 962 |
|
checkpoint57c_pre |
| 963 |
|
|
| 964 |
|
o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
| 965 |
|
update output.txt of exp. global_ocean.90x40x15 |
| 966 |
|
o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
| 967 |
|
results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
| 968 |
|
o add saltFlux(+File) forcing capability with periodicExternalForcing |
| 969 |
|
o allow to use pkg diagnostics for GM-Redi & ThSIce output |
| 970 |
|
o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
| 971 |
|
o improvements for the MNC output from DIAGNOSTICS: |
| 972 |
|
- correct handling of the unlimitied dimension |
| 973 |
|
- all dims now have associated coordinate variables |
| 974 |
|
- variables located at U, V, and Corner ("Z") points are now written |
| 975 |
|
with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
| 976 |
|
*all* data points are output |
| 977 |
|
o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
| 978 |
|
o added pkg/seaice/seaice_monitor.F |
| 979 |
|
o mdsio_readfield.F can now read files visible only to master MPI process. |
| 980 |
|
o pkg/seaice: some test code for ice-modified ocean stress |
| 981 |
|
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
| 982 |
|
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
| 983 |
|
spurious negative numbers for precipitation and humidity. Will cause |
| 984 |
|
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
| 985 |
|
o pkg/ctrl/ |
| 986 |
|
* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
| 987 |
|
May be enabled via doPackDiag |
| 988 |
|
* introduce z-scaling of |
| 989 |
|
+ gradient (doZscalePack) and |
| 990 |
|
+ control (doZscaleUnpack) |
| 991 |
|
o pkg/mdsio/ |
| 992 |
|
* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
| 993 |
|
* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
| 994 |
|
|
| 995 |
|
checkpoint57b_post |
| 996 |
|
o simplify options in diagnostics_fill arguments (remove weird combinations) |
| 997 |
|
o fix MNC coordinate variables so that they now contain per-face index |
| 998 |
|
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
| 999 |
|
general, EXCH2 grids are only aligned to a "local" coordinate system |
| 1000 |
|
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
| 1001 |
|
o Implement instantaneous output within pkg diagnostics: |
| 1002 |
|
setting a negative frequency in data.diagnostics produces |
| 1003 |
|
"snap-shot" output (as opposed to time-average if freq > 0) |
| 1004 |
|
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
| 1005 |
|
NOTE: change ptracer diagnostics name: use 2 characters to work with |
| 1006 |
|
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
| 1007 |
|
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
| 1008 |
|
becomes the coordinate variable for the 'T' dimension |
| 1009 |
|
o add CF-style coordinate variables to MNC |
| 1010 |
|
- just a first cut: numbers are meaningless on the cubesphere and |
| 1011 |
|
missing along the T axis but otherwise it works! |
| 1012 |
|
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
| 1013 |
|
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
| 1014 |
|
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
| 1015 |
|
this is based directly on what the model compute, so that the content of |
| 1016 |
|
each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
| 1017 |
|
o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
| 1018 |
|
o clean up build options files for SunOS, in particular |
| 1019 |
|
- remove -traditional from xmakedepend |
| 1020 |
|
- change -xarch=v9 to -xarch=native for f77 |
| 1021 |
|
- restore use of make (not gmake) |
| 1022 |
|
- add CC=gcc if using g77 |
| 1023 |
|
o changes per discussion of AM, JMC, & EH3 today: |
| 1024 |
|
- move redundant "grid" variables out of "state" -- in preparation of |
| 1025 |
|
creating proper CF-style coordinate variables and in recognition |
| 1026 |
|
that any/all grid variables can be easily copied (eg. w/NCO) from |
| 1027 |
|
the grid files into any of the other NetCDF files |
| 1028 |
|
- *always* output grid variables with MDSIO (this will eventually be |
| 1029 |
|
changed) |
| 1030 |
|
- output MNC grid file if useMNC is true |
| 1031 |
|
o every instance of _END_MASTER() has been found and replaced with |
| 1032 |
|
_END_MASTER( myThid ) in order to satisfy certain picky Sun |
| 1033 |
|
preprocessors |
| 1034 |
|
o re-arrange diagnostics pkg initialisation: |
| 1035 |
|
- allow each package to extend the available diagnostics list |
| 1036 |
|
- add some checking and fix small problems (multi-threaded, ...) |
| 1037 |
|
- new S/R diagnostics_fill (replace fill_diagnostics): |
| 1038 |
|
look through the short list of active diag. (instead of the long list) |
| 1039 |
|
create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
| 1040 |
|
|
| 1041 |
|
checkpoint57a_post |
| 1042 |
|
o this set of changes restores TAMC compatibility |
| 1043 |
|
tested for global_ocean.90x40x15 adjoint on trough |
| 1044 |
|
(what a pain) |
| 1045 |
|
|
| 1046 |
|
checkpoint57a_pre |
| 1047 |
|
o some modifs in tools/build_options for sunos |
| 1048 |
|
o call ctrl_pack for ctrl at end for optimcycle=0 |
| 1049 |
|
|
| 1050 |
|
checkpoint57 |
| 1051 |
|
o add horizontal bi-harmonic viscosity for vertical velocity |
| 1052 |
|
- new parameter viscA4W (defaults to viscA4) |
| 1053 |
|
- affects only non-hydrostatic code |
| 1054 |
|
- to be done: no-slip lateral boundary conditions |
| 1055 |
|
o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
| 1056 |
|
o implement Implicit Vertical advection for pTracers |
| 1057 |
|
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
| 1058 |
|
(implemented also for implicit vertical diffusion & advection) |
| 1059 |
|
o OBCS: extend application of tracer open boundary conditions |
| 1060 |
|
to a strip beyond the boundary of width Olx/Oly |
| 1061 |
|
o add call monitor to TAF set of required calls (flow directives) |
| 1062 |
|
and include in natl_box_adjoint |
| 1063 |
|
o untangle a few ifdefs related to cost, ctrl, autodiff |
| 1064 |
|
untangel a few ALLOW_ECCO_OPTIMIZATION |
| 1065 |
|
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
| 1066 |
|
(theta2, salt2 in ecco_cost_weights) |
| 1067 |
|
|
| 1068 |
|
checkpoint56c_post |
| 1069 |
|
o OBCS as control variables |
| 1070 |
|
- update ctrl_ad_diff.list, obcs_ad_diff.list |
| 1071 |
|
- remove balance of obcs controls from default |
| 1072 |
|
- fix index bug nobcs in ctrl_init |
| 1073 |
|
- fix dummy fields filen in ctrl_pack |
| 1074 |
|
- add dummy weights for obcs |
| 1075 |
|
o lsopt: comment out fort.94 output |
| 1076 |
|
o optim: |
| 1077 |
|
- remove unnecessary header files |
| 1078 |
|
- adjusted namelists |
| 1079 |
|
- add xerbla.F to Makefile |
| 1080 |
|
o exf: |
| 1081 |
|
- multiple modifications of exf_check_range |
| 1082 |
|
- unit change in exf_init_runoff from [m/year] to [m/s] |
| 1083 |
|
o mdsio: |
| 1084 |
|
- i/o-vector change debugLevel from debLevA to debLevB |
| 1085 |
|
|
| 1086 |
|
checkpoint56b_post |
| 1087 |
|
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
| 1088 |
|
is called from DO_THE_MODEL_IO |
| 1089 |
|
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
| 1090 |
|
- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
| 1091 |
|
- clean up PTRACERS_WRITE_TIMEAVE a little |
| 1092 |
|
o add another verification experiment that tests both the cfc-pkg and |
| 1093 |
|
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
| 1094 |
|
reactive tendencies treated inline with regular timestepping |
| 1095 |
|
o testreport previously did a lousy job of comparing small numbers, so |
| 1096 |
|
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
| 1097 |
|
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
| 1098 |
|
testreport. |
| 1099 |
|
o ptracers_monitor: bug fix for MPI |
| 1100 |
|
|
| 1101 |
|
checkpoint56a_post |
| 1102 |
|
o GCHEM: finish reorganizating the package |
| 1103 |
|
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
| 1104 |
|
(introduces another 3D-array for each passive tracer, but only if |
| 1105 |
|
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
| 1106 |
|
gchemTendency is not needed because the timestep is done separately) |
| 1107 |
|
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
| 1108 |
|
- GCHEM is now---more or less cleanly---separate from PTRACERS |
| 1109 |
|
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
| 1110 |
|
so clear to me how that should be done in a general way. |
| 1111 |
|
o CFC: improve formatting of output in CFC_ATMOS |
| 1112 |
|
o PTRACERS: |
| 1113 |
|
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
| 1114 |
|
that ALL experiments with ptracers enable can be checked. This makes |
| 1115 |
|
GCHEM_MONITOR obsolete. |
| 1116 |
|
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
| 1117 |
|
monitorFreq |
| 1118 |
|
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
| 1119 |
|
o add PTRACERS (PTR0[1-5]) to testreport output |
| 1120 |
|
o exf_check_range: |
| 1121 |
|
* default changed to .TRUE. |
| 1122 |
|
* will check values for niter0 if debLevA, every timestep if debLevB |
| 1123 |
|
* STOP in exf_check_range if 'out of range' |
| 1124 |
|
* range chosen generous to allow for potential extema |
| 1125 |
|
TBD: a version with stricter range |
| 1126 |
|
permitted range would be runtime parameters |
| 1127 |
|
o GMredi: |
| 1128 |
|
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
| 1129 |
|
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
| 1130 |
|
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
| 1131 |
|
o GCHEM: |
| 1132 |
|
- move call to GCHEM_FORCING_SEP, so that it is now called before |
| 1133 |
|
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
| 1134 |
|
- introduced a useGCHEM runtime flag and applied it everywhere. |
| 1135 |
|
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
| 1136 |
|
this flag is now only visible within GCHEM-pkg routines. |
| 1137 |
|
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
| 1138 |
|
be replaced by a 3D array that is computed before thermodynamics; for |
| 1139 |
|
this, the tracer ID iTracer had to be included into the parameter list |
| 1140 |
|
of ptracers_forcing |
| 1141 |
|
- set up forward_step to call gchem_forcing, that will replace |
| 1142 |
|
gchem_forcing_int in ptracers_forcing |
| 1143 |
|
- cleaning up |
| 1144 |
|
o small cleaning of exch2: remove files that are also in eesupp/src |
| 1145 |
|
|
| 1146 |
|
checkpoint56 |
| 1147 |
|
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
| 1148 |
|
o mnc: cleanup "full" files--fixes out-of-memory problem |
| 1149 |
|
o ECCO-GODAE |
| 1150 |
|
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
| 1151 |
|
* fully merged and updated from SIO code |
| 1152 |
|
windstress sign change affects |
| 1153 |
|
- exf_inscal_[u/v]stress |
| 1154 |
|
- sign of xx_tau[u/v] adjustments |
| 1155 |
|
- signs in cost_scat |
| 1156 |
|
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
| 1157 |
|
* natl_box_adjoint updated and compressed |
| 1158 |
|
* 2-level checkpoint switch added |
| 1159 |
|
(tested in EXP. 1 of natl_box_adjoint) |
| 1160 |
|
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
| 1161 |
|
o SVD |
| 1162 |
|
* first complete, non-hacked version for SVD calculations |
| 1163 |
|
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
| 1164 |
|
performed via direct access files admtlm_vector.it???? |
| 1165 |
|
(via ctrl_[un]pack) |
| 1166 |
|
* optimcycle is used for ARPACK iteration counter |
| 1167 |
|
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
| 1168 |
|
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
| 1169 |
|
and add linear transforms where necessary |
| 1170 |
|
* controls are initial/final SST, SSS (can be extended; need to check |
| 1171 |
|
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
| 1172 |
|
o mdsio: filename info to both stderr, stdout |
| 1173 |
|
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
| 1174 |
|
from sign change |
| 1175 |
|
|
| 1176 |
|
checkpoint55j_post |
| 1177 |
|
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
| 1178 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 1179 |
|
o add consistent build directories and .cvsignore files to verification |
| 1180 |
|
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
| 1181 |
|
o make all subroutines 30 or less characters in length for certain older |
| 1182 |
|
compilers to work (a thorough search only turns up two routines in |
| 1183 |
|
pkg/ptracers) |
| 1184 |
|
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
| 1185 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 1186 |
|
|
| 1187 |
|
checkpoint55i_post |
| 1188 |
|
o change arrays for total vertical diffusivity (2.D if explicit, |
| 1189 |
|
3.D if implicit) ; each ptracer uses its own background value. |
| 1190 |
|
o added mnc/NetCDF output capability to ocn_compon_interf |
| 1191 |
|
- added bits to verification/cpl_aim+ocn so that it can run on |
| 1192 |
|
ITRDA and other clusters without the mpirun "-wd" option |
| 1193 |
|
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
| 1194 |
|
configuration |
| 1195 |
|
o give MNC the ability to create additional files rather than |
| 1196 |
|
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
| 1197 |
|
- the default is just less than 2GB which is a practical limit |
| 1198 |
|
on many systems |
| 1199 |
|
o Compute the non-local term using either KPP vertical diffusivity (=default) |
| 1200 |
|
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
| 1201 |
|
|
| 1202 |
|
checkpoint55h_post |
| 1203 |
|
o add verification test "vermix" |
| 1204 |
|
o remove all the *_ioinc flags and replace with the single global |
| 1205 |
|
outputTypesInclusive flag |
| 1206 |
|
o allow to set a vertical profile of vertical diffusivity for T & S |
| 1207 |
|
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
| 1208 |
|
o useMNC moved from data.mnc to data.pkg |
| 1209 |
|
|
| 1210 |
|
checkpoint55g_post |
| 1211 |
|
o Renaming carbon AD experiments to comply with testreport conventions |
| 1212 |
|
o Updating adjoint of Held-Suarez hs94.1x64x5 |
| 1213 |
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
| 1214 |
|
have been fixed to avoid recomp. of do_oceanic_phys |
| 1215 |
|
Works well for global_ocean.90x40x15, |
| 1216 |
|
but recomp. issue remains for carbon |
| 1217 |
|
o Updating adjoint output for natl_box_adjoint after |
| 1218 |
|
pkg/ecco has been modified (see taga c55d_post) |
| 1219 |
|
|
| 1220 |
|
checkpoint55f_post |
| 1221 |
|
o rename to timeave_init_fixed |
| 1222 |
|
|
| 1223 |
|
checkpoint55e_post |
| 1224 |
|
o some delicate re-shuffle of store directives to avoid one |
| 1225 |
|
extra call of do_oceanic_physics |
| 1226 |
|
affects ecco_the_main_loop.F, do_oceanic_physics.F |
| 1227 |
|
checkpoint_lev1_directives.h |
| 1228 |
|
o NB: this may break global_ocean adjoint temporarily, |
| 1229 |
|
but it is clear how to fix it. Will do later, need this now. |
| 1230 |
|
|
| 1231 |
|
checkpoint55d_post |
| 1232 |
|
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
| 1233 |
|
o ecco_cost_weights is modified to 1x1 runs |
| 1234 |
|
o modifs to allow observations to be read in as |
| 1235 |
|
single file or yearly files |
| 1236 |
|
o enable to read exf forcing fields as either |
| 1237 |
|
single file or yearly files (flag useExfYearlyFields) |
| 1238 |
|
checkpoint55d_pre |
| 1239 |
|
|
| 1240 |
|
o switch between 2-level and 3-level checkpointing |
| 1241 |
|
o add ability of MNC to write local and "partial" (eg. 2D slices where |
| 1242 |
|
the full 3D field is never actually stored) arrays to NetCDF files |
| 1243 |
|
with the correct (that is, the complete multi-dimensional) set of |
| 1244 |
|
array indicies |
| 1245 |
|
- used in mom_vecinv() to write the diagFreq output |
| 1246 |
|
- tested (demonstrated) in verification/aim.5l_cs |
| 1247 |
|
o further mnc-ification |
| 1248 |
|
- add verification/lab_sea to the list with mnc setups |
| 1249 |
|
- fix undefined mnc v-names in cd_code |
| 1250 |
|
- add kpp to mnc output (both snapshot and timeave) |
| 1251 |
|
o non-hydrostatic code |
| 1252 |
|
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
| 1253 |
|
in calc_gw.F |
| 1254 |
|
- defaults to viscAh |
| 1255 |
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
| 1256 |
|
friction or Leith) in non-hydrostatic mode, as long as there is |
| 1257 |
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
| 1258 |
|
o pkg/cost |
| 1259 |
|
extend simple cost functions to treat time mean quantities |
| 1260 |
|
(T,U,V) via cost_accumulate_state from cost_tile |
| 1261 |
|
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
| 1262 |
|
be 2 times larger than the minimum size the advection scheme requires. |
| 1263 |
|
now get a perfect conservation of salt in advect_cs test-exp (updated) |
| 1264 |
|
o GGL90 (Gaspar's TKE mixed layer) |
| 1265 |
|
- add horizontal diffusion of TKE, requires exchanges in |
| 1266 |
|
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
| 1267 |
|
default. In OPA there is no horizontal diffusion of TKE but the |
| 1268 |
|
mixing coefficients are computed from a horizontal average of TKE of |
| 1269 |
|
6 points or so. I think that diffusion has a little more physical |
| 1270 |
|
justification. |
| 1271 |
|
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
| 1272 |
|
was in vain) |
| 1273 |
|
- mask tke-variable in ggl90_init |
| 1274 |
|
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
| 1275 |
|
o fix biharmonic diffusion on CS-grid. |
| 1276 |
|
o more obcs stuff |
| 1277 |
|
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
| 1278 |
|
for reading boundary values. This routine is called from |
| 1279 |
|
obcs_prescribe_read |
| 1280 |
|
- updated obcs_check |
| 1281 |
|
- changed sponge layer relaxation parameter units for days to seconds |
| 1282 |
|
- turned off sponge layer by default |
| 1283 |
|
- changed argument list of OBCS_CALC to myTime+deltaTclock |
| 1284 |
|
- fixed about 35 bugs in obcs_external_fields_load |
| 1285 |
|
|
| 1286 |
|
checkpoint55c_post |
| 1287 |
|
o obcs stuff |
| 1288 |
|
- new runtime flags useOBCSprescribe, useOBCSbalance |
| 1289 |
|
- re-arranged obcs_calc |
| 1290 |
|
- moved exf_getobcs to obcs_prescibe_read |
| 1291 |
|
obcs_prescibe_read is called after ORLANSKI stuff |
| 1292 |
|
and independent of it (executable can contain all). |
| 1293 |
|
- updated obcs_check |
| 1294 |
|
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
| 1295 |
|
These may be necessary only if tangential velocities are |
| 1296 |
|
prescribed at OB, not sure, needs testing. |
| 1297 |
|
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
| 1298 |
|
which simplifies the calls and passes the ifc check-bounds test |
| 1299 |
|
|
| 1300 |
|
checkpoint55b_post |
| 1301 |
|
o add a 2D scalar, Z location, exchange_2 routine. |
| 1302 |
|
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
| 1303 |
|
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
| 1304 |
|
affects advect_cs results (for the wrong reason): update output.txt |
| 1305 |
|
o use a more standard discretization for biharmonic viscosity ; |
| 1306 |
|
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
| 1307 |
|
affects results of dome set-up: update output.txt |
| 1308 |
|
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
| 1309 |
|
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
| 1310 |
|
|
| 1311 |
|
checkpoint55a_post |
| 1312 |
|
o merged code to |
| 1313 |
|
* prescribe/read time-dependent open boundaries |
| 1314 |
|
(works in conjunction with exf, cal) |
| 1315 |
|
* sponge layer code for open boundaries |
| 1316 |
|
* each boundary N/S/E/W now has its own CPP option |
| 1317 |
|
(healthy for the adjoint) |
| 1318 |
|
|
| 1319 |
|
checkpoint55 |
| 1320 |
|
o up-to-date adjoint of previous breaks |
| 1321 |
|
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
| 1322 |
|
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
| 1323 |
|
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
| 1324 |
|
- carbon: * remove tr1-related adjoint verification |
| 1325 |
|
* add ptracer as control variable |
| 1326 |
|
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
| 1327 |
|
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
| 1328 |
|
|
| 1329 |
|
checkpoint54f_post |
| 1330 |
|
o in verification/carbin/ remove experiment related to |
| 1331 |
|
ALLOW_PASSIVE_TRACER (array tr1 etc) |
| 1332 |
|
code_ad/ input_ad/ results_ad |
| 1333 |
|
|
| 1334 |
|
o add two new packages |
| 1335 |
|
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
| 1336 |
|
+ subject to optimization (memory) |
| 1337 |
|
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
| 1338 |
|
+ subject to reordering (many GOTOs in the original code) |
| 1339 |
|
+ so far opps is called for every (i,j) point, and then operates in |
| 1340 |
|
the vertical; one may want to reorder the scheme in order operate in |
| 1341 |
|
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
| 1342 |
|
fields) |
| 1343 |
|
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
| 1344 |
|
- all verification tests compile and run with linux_ia32_g77 |
| 1345 |
|
- defaults are compatible with current input files--nothing |
| 1346 |
|
should change if you were not previously using MNC |
| 1347 |
|
- MNC output has been added in numerous places (eg. timeave) |
| 1348 |
|
but there are still a few writes not yet do-able with MNC |
| 1349 |
|
(this is in progress) |
| 1350 |
|
- flags now allow for either/or/both use of MDSIO and MNC and |
| 1351 |
|
documentation will soon follow |
| 1352 |
|
- numerous small formatting cleanups for ProTeX |
| 1353 |
|
o add version info (via BUILD_INFO.h) to MNC and stdout |
| 1354 |
|
|
| 1355 |
|
checkpoint54e_post |
| 1356 |
|
o add two new packages |
| 1357 |
|
- pp81 (Packanowski and Philander, 1981), Richardson number and |
| 1358 |
|
stratification dependent mixing |
| 1359 |
|
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
| 1360 |
|
- these scheme operate in a similar manner as KPP (without ghat, of |
| 1361 |
|
course), however there is only one diffusivity that is used for both |
| 1362 |
|
temperature and salinity (and passive tracers)ç |
| 1363 |
|
o add offline package |
| 1364 |
|
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
| 1365 |
|
provided by Stephanie Dutkiewicz |
| 1366 |
|
o genmake2: add ability to search for C compilers and cleanup test output |
| 1367 |
|
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
| 1368 |
|
|
| 1369 |
|
checkpoint54d_post |
| 1370 |
|
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
| 1371 |
|
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
| 1372 |
|
leading to additional shift by 5 days each year of integration |
| 1373 |
|
(i.e. leading to considerable offset over the years) |
| 1374 |
|
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
| 1375 |
|
o start with no AB and no initial filtering (staggerTimeStep): |
| 1376 |
|
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
| 1377 |
|
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
| 1378 |
|
(external loading & cpl import/export stay in forward_step.F) |
| 1379 |
|
o update coupling interface to work with new staggerTimeStep |
| 1380 |
|
o change MDSIO ptracers_pickup. |
| 1381 |
|
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
| 1382 |
|
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
| 1383 |
|
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
| 1384 |
|
|
| 1385 |
|
checkpoint54c_post |
| 1386 |
|
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
| 1387 |
|
this affects (truncation error) output.txt of test-exp: |
| 1388 |
|
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
| 1389 |
|
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
| 1390 |
|
o change Qnet to always be the net heat flux, (+upward). |
| 1391 |
|
affects (truncation error) output of natl_box exp.: updated |
| 1392 |
|
o define the max number of passive tracers in PTRACERS_SIZE.h |
| 1393 |
|
o start to test mnc routinely in exp0 |
| 1394 |
|
o add sea-ice loading (sIceLoad) as a new forcing field. |
| 1395 |
|
|
| 1396 |
|
checkpoint54b_post |
| 1397 |
|
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
| 1398 |
|
impressive on Altix and Opteron systems) |
| 1399 |
|
o diagnostics can now write NetCDF files through the mnc package |
| 1400 |
|
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
| 1401 |
|
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
| 1402 |
|
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
| 1403 |
|
affects (truncation error) output of lab_sea & natl_box exp.: updated |
| 1404 |
|
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
| 1405 |
|
|
| 1406 |
|
checkpoint54a_post |
| 1407 |
|
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
| 1408 |
|
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
| 1409 |
|
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
| 1410 |
|
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
| 1411 |
|
+ internal_wave (shift in writing cg2d_ini_res) |
| 1412 |
|
checkpoint54a_pre |
| 1413 |
|
|
| 1414 |
|
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
| 1415 |
|
- modified verification/lab_sea and natl_box_adjoint accordingly |
| 1416 |
|
|
| 1417 |
|
checkpoint54 |
| 1418 |
|
checkpoint53g_post |
| 1419 |
|
o prepare splitting of thermodynamics: store convect.counter in common block |
| 1420 |
|
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
| 1421 |
|
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
| 1422 |
|
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
| 1423 |
|
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
| 1424 |
|
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
| 1425 |
|
o restore adjointability |
| 1426 |
|
|
| 1427 |
|
checkpoint53f_post |
| 1428 |
|
o modifications that affect AIM experiment results (update output.txt): |
| 1429 |
|
- no advection of S at top interface Nr (pkg/generic_advdiff) |
| 1430 |
|
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
| 1431 |
|
o AIM pkg: |
| 1432 |
|
- include stability function into surf.Flux derivative relative to Tsurf |
| 1433 |
|
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
| 1434 |
|
|
| 1435 |
|
checkpoint53e_post |
| 1436 |
|
o merged cylindrical coord configuration |
| 1437 |
|
o added rotating_tank experiment |
| 1438 |
|
checkpoint53e_pre |
| 1439 |
|
|
| 1440 |
|
checkpoint53d_post |
| 1441 |
|
o faulks upgraded: re-generate output.txt that have changed: |
| 1442 |
|
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
| 1443 |
|
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
| 1444 |
|
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
| 1445 |
|
o added Sadourny discretization of Coriolis |
| 1446 |
|
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
| 1447 |
|
- re-enabled use of omega3 (useAbsVorticity) |
| 1448 |
|
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
| 1449 |
|
vector-invariant equations |
| 1450 |
|
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
| 1451 |
|
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
| 1452 |
|
hopefully without new bugs |
| 1453 |
|
- still to do: biharmonic friction for non-hydrostatic w |
| 1454 |
|
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
| 1455 |
|
o regenerated output for global_ocean_ebm (using -ieee) |
| 1456 |
|
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
| 1457 |
|
of mom_common/ |
| 1458 |
|
- simple re-arrangement of instructions within computing loop |
| 1459 |
|
checkpoint53d_pre |
| 1460 |
|
|
| 1461 |
|
checkpoint53c_post |
| 1462 |
|
o new version of coupler for AIM+thSIce and Ocean models |
| 1463 |
|
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
| 1464 |
|
- land: change Evaporation of snow |
| 1465 |
|
- aim with thSIce: fix bug in snow-precip. |
| 1466 |
|
o changes to calc_gw.F |
| 1467 |
|
- bug fix for w^2 term near the bottom boundary |
| 1468 |
|
- (hopefully) improve the lateral slip boundary condtions for use with |
| 1469 |
|
partial/looped cells |
| 1470 |
|
- because the bug fix changes two verification experiments anyway (exp5 |
| 1471 |
|
and plume on slope), change the lateral boundary condition from half slip |
| 1472 |
|
to the value of no_slip_sides |
| 1473 |
|
o ebm package wasnt quite up to the parallel task. Fixed that. |
| 1474 |
|
o Adjoint of EBM package + verification |
| 1475 |
|
* TLM OK |
| 1476 |
|
* ADM not sufficient accuracy yet (needs further testing) |
| 1477 |
|
|
| 1478 |
|
checkpoint53b_post |
| 1479 |
|
o Commiting new energy balance model to repository |
| 1480 |
|
* package is pkg/ebm |
| 1481 |
|
* verif. is verification/global_ocean_ebm |
| 1482 |
|
* references are in ebm_driver.F |
| 1483 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
| 1484 |
|
C Global thermohaline circulation. Part I: |
| 1485 |
|
C Sensitivity to atmospheric moisture transport. |
| 1486 |
|
C J. Climate 12(1), 71-82 |
| 1487 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
| 1488 |
|
C Global thermohaline circulation. Part II: |
| 1489 |
|
C Sensitivity with interactive transport. |
| 1490 |
|
C J. Climate 12(1), 83-91 |
| 1491 |
|
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
| 1492 |
|
C Destabilization of the thermohaline circulation |
| 1493 |
|
C by atmospheric eddy transports. |
| 1494 |
|
C J. Climate 7(12), 1870-1882 |
| 1495 |
|
o Will need long integration testing. |
| 1496 |
|
checkpoint53b_pre |
| 1497 |
|
|
| 1498 |
|
o created pkg/mom_common in preparation for variable viscosity code |
| 1499 |
|
o renamed and split ini_mnc_io |
| 1500 |
|
o pkg/land: only liquid water can diffuse or run-off |
| 1501 |
|
o AIM using land: soil wetness availability account for snow |
| 1502 |
|
o added printMapIncludesZeros to EEPARMS namelist |
| 1503 |
|
|
| 1504 |
|
checkpoint53a_post |
| 1505 |
|
o restore TAMC compatiility for exf_constants.h |
| 1506 |
|
(no usage of _d in .h) |
| 1507 |
|
o Additional storing in KPP in an attempt to fix |
| 1508 |
|
TAMC problem with adjoint of KPP code. |
| 1509 |
|
(no success...) |
| 1510 |
|
Identical code works fine with TAF. |
| 1511 |
|
o Fixed verification/natl_box_adjoint experiments. |
| 1512 |
|
Initial conditions for Experiments 4 and 5 are now |
| 1513 |
|
set to "SEAICE_initialHEFF=0", which is more reasonable, |
| 1514 |
|
and hence gives results closer to that of Experiment 2. |
| 1515 |
|
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
| 1516 |
|
|
| 1517 |
|
checkpoint53 |
| 1518 |
|
o stable checkpoint with up to date adjoint |
| 1519 |
|
TLM tests only run for 1st grdchk at the moment. Its unclear if |
| 1520 |
|
this is a code problem or a problem with resetting code for g_ |
| 1521 |
|
variables that is being autogenerated wrong. |
| 1522 |
|
Otherwise: |
| 1523 |
|
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
| 1524 |
|
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
| 1525 |
|
are both still in chaos following their security messes. |
| 1526 |
|
|
| 1527 |
|
checkpoint52n_post |
| 1528 |
|
o various build (mostly genmake2) changes including: |
| 1529 |
|
- ability to build/run more easily within Cygwin and MacOS X |
| 1530 |
|
- more complicated Makefiles with a stronger dependence on Gnu Make |
| 1531 |
|
o pkg/seaice modifications |
| 1532 |
|
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
| 1533 |
|
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
| 1534 |
|
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
| 1535 |
|
- changed proxy for geostrophic velocity and updated |
| 1536 |
|
verification/lab_sea/results/* accordingly |
| 1537 |
|
- removed ADI dynamic solver from pkg/seaice |
| 1538 |
|
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
| 1539 |
|
they caused a segmentation fault under certain circumstances |
| 1540 |
|
- removed unused field WATR |
| 1541 |
|
o bug fix in exf-package: |
| 1542 |
|
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
| 1543 |
|
now reflect that. |
| 1544 |
|
o small fixes in the cal-package: |
| 1545 |
|
- set reference date to first of January for the 'model'-calendar |
| 1546 |
|
- failing of cal_CheckDate in cal_FullDate now actually results in a |
| 1547 |
|
warning |
| 1548 |
|
o small modifications in exf-package to increase flexibility: |
| 1549 |
|
- change climtempfreeze from a constant to a runtime parameter that |
| 1550 |
|
is specified in data.exf_clim (default = -1.9) |
| 1551 |
|
- introduce runtime parameter windstressmax (default = 2.0) that is |
| 1552 |
|
specified in data.exf |
| 1553 |
|
o fix in pkg/thsice: |
| 1554 |
|
- update Evap (Tsf changes) to be consistent with Latent heat flux |
| 1555 |
|
- maintain snow precipitation unchanged (even if Tsf >=0). |
| 1556 |
|
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
| 1557 |
|
|
| 1558 |
|
checkpoint52m_post |
| 1559 |
|
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
| 1560 |
|
this does not change any of the results, because myIter=0 in swfrac always |
| 1561 |
|
lead to jwtype=2 (the default anyway), but the call makes little sense |
| 1562 |
|
as a default |
| 1563 |
|
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
| 1564 |
|
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
| 1565 |
|
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
| 1566 |
|
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
| 1567 |
|
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
| 1568 |
|
o extending useSingleCpuIO option to work with new exch2 I/O format |
| 1569 |
|
- old-style, missing-tile I/O is still accessible by defining CPP |
| 1570 |
|
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
| 1571 |
|
o monitor package can write to NetCDF files and/or STDOUT |
| 1572 |
|
o fix re-definition bug in MNC_GRID_INIT_ALL() |
| 1573 |
|
o doc/api_reference added |
| 1574 |
|
- a framework for building an API Reference Manual using all |
| 1575 |
|
the "protex" comments embedded in the code |
| 1576 |
|
- see pkg/generic_advdiff, pkg/mnc for examples |
| 1577 |
|
o MNC: |
| 1578 |
|
- make myThid the last argument for all subroutines |
| 1579 |
|
- new default for the grid files: NO halos |
| 1580 |
|
- add useMNC and other run-time flags |
| 1581 |
|
- separate per-file-group handling of the unlimited dimension |
| 1582 |
|
- early initialization of MNC w/ flags read at the eeboot stage |
| 1583 |
|
and lookup tables set in initialize_fixed |
| 1584 |
|
- write all MNC output to a freshly-created directory |
| 1585 |
|
o thermodynamics sea-ice (thsice) is now tested with testreport. |
| 1586 |
|
o test exp. advect_cs: use the standard cs32 grid ; update output. |
| 1587 |
|
o Added functionality to grdchk: |
| 1588 |
|
pick global i,j,k position (or nearest wet) where to perform check. |
| 1589 |
|
|
| 1590 |
|
checkpoint52l_post |
| 1591 |
|
o new land formulation: |
| 1592 |
|
a) use ground enthalpy as prognostic variable to ensure exact |
| 1593 |
|
energy conservation. |
| 1594 |
|
b) account for water temperature and for latent heat of freezing |
| 1595 |
|
in all processes (rain, run-off, ground storage) |
| 1596 |
|
c) compute surface and ground temperature implicitly. |
| 1597 |
|
o aim_v23 modification for new land model: |
| 1598 |
|
a) Treat separately land / ocean / sea-ice surface fluxes |
| 1599 |
|
to allow implicit computation of land & sea-ice surface temp. |
| 1600 |
|
b) add snow precipitation. |
| 1601 |
|
checkpoint52l_pre |
| 1602 |
|
|
| 1603 |
|
o fix problem (when 1 tile is empty) in min/max monitor. |
| 1604 |
|
o fix bug in timeAve (u,vZetatave in common block) |
| 1605 |
|
o no restoring terms under ice for pkg/seaice |
| 1606 |
|
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
| 1607 |
|
o bug fix for pkg/seaice pickups |
| 1608 |
|
o change MNC call locations and add coordinate attributes |
| 1609 |
|
o mask vorticity at the corner ; affects global_ocean.cs output |
| 1610 |
|
o fix ini_curvilinear_grid ; test CS experiments with mpi |
| 1611 |
|
o aim.5l_cs: modify sea-ice fraction input file ; update output |
| 1612 |
|
o exf: Adding simple range check routine for exf fields after read |
| 1613 |
|
|
| 1614 |
|
checkpoint52k_post |
| 1615 |
|
o removed top-level directory "diags" |
| 1616 |
|
- we migrated these functions to pkg/timeave a long time ago |
| 1617 |
|
o fixed bug introduced in pkg/monitor |
| 1618 |
|
o accuracy ctrlprec = 32 insuffient for gradient checks using |
| 1619 |
|
averaged fields (I/O via cost_averages) |
| 1620 |
|
-> use ctrl.h in active_file*.F to control I/O precision. |
| 1621 |
|
o paramter list of CALL ADTHE_MAIN_LOOP |
| 1622 |
|
o added initial do_the_model_io to ecco |
| 1623 |
|
o set all ...Freq to zero after cost_final |
| 1624 |
|
taveFreq, dumpFreq, pChkptFreq |
| 1625 |
|
o MAIN and ECCO differentiability restored |
| 1626 |
|
|
| 1627 |
|
checkpoint52j_post |
| 1628 |
|
o fix nchklev in tamc.h for global_ocean... |
| 1629 |
|
o Bringing flow and store directives up-to-date |
| 1630 |
|
o Really weird thing! |
| 1631 |
|
call do_the_model_io from the_main_loop with parameters |
| 1632 |
|
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
| 1633 |
|
TAF places a faulty re-call of initialise_varia |
| 1634 |
|
after cost_final call which should not be there! |
| 1635 |
|
checkpoint52j_pre |
| 1636 |
|
|
| 1637 |
|
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
| 1638 |
|
error messages |
| 1639 |
|
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
| 1640 |
|
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
| 1641 |
|
debug output |
| 1642 |
|
o modfied mdsio_writefield.F to handle non-global files under exch2 |
| 1643 |
|
o update AIM Cubed-Sphere exp (aim.5l_cs): |
| 1644 |
|
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
| 1645 |
|
o update AIM Equatorial Channel exp: |
| 1646 |
|
use standard aim_v23 pkg and change the SST fields to be more realistic. |
| 1647 |
|
o globalFile now works with exch2 |
| 1648 |
|
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
| 1649 |
|
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
| 1650 |
|
o limit timeave output for hi-res integrations |
| 1651 |
|
|
| 1652 |
|
checkpoint52i_post |
| 1653 |
|
o removed CPP_EEOPTIONS.h from verification/*/code |
| 1654 |
|
o updated the tiling for global_ocean_pressure |
| 1655 |
|
checkpoint52i_pre |
| 1656 |
|
|
| 1657 |
|
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
| 1658 |
|
the old pkg/aim). |
| 1659 |
|
|
| 1660 |
|
checkpoint52h_pre |
| 1661 |
|
o shortened offending lines in exch2_send_rx?.template |
| 1662 |
|
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
| 1663 |
|
o genmake2: add build & execute test for NetCDF code |
| 1664 |
|
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
| 1665 |
|
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
| 1666 |
|
o added useSingleCPUIO flag to monitor.F and mon_out.F |
| 1667 |
|
o added temporary hack for sea-ice dynamics on the cube: |
| 1668 |
|
metric terms are ignored and it is assumed that |
| 1669 |
|
there is no sea-ice on cube faces 1, 2, 4, and 5. |
| 1670 |
|
|
| 1671 |
|
checkpoint52f_post |
| 1672 |
|
o added exch2 cube routines to pkg/exch2 |
| 1673 |
|
o modified hs94.cs-32x32x5 to use it |
| 1674 |
|
o added new grid files to hs94.cs-32x32x5 |
| 1675 |
|
checkpoint52f_pre |
| 1676 |
|
|
| 1677 |
|
checkpoint52e_post |
| 1678 |
|
o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
| 1679 |
|
for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
| 1680 |
|
o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
| 1681 |
|
to work with implicit vertical advection and AB ; |
| 1682 |
|
o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
| 1683 |
|
o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
| 1684 |
|
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
| 1685 |
|
checkpoint52e_pre |
| 1686 |
|
|
| 1687 |
|
o fix bug in impldiff when Nr=1 or Nr=2. |
| 1688 |
|
o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
| 1689 |
|
o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
| 1690 |
|
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
| 1691 |
|
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
| 1692 |
|
o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
| 1693 |
|
o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
| 1694 |
|
o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
| 1695 |
|
|
| 1696 |
|
checkpoint52d_post |
| 1697 |
|
o re-tiled many expts to allow comparison in multi-processor mode |
| 1698 |
|
- updated output accordingly |
| 1699 |
|
- changed hs94.128x64x5 to use intial T from file rather than use the |
| 1700 |
|
random number generator |
| 1701 |
|
o add infrastructure in model routines for fizhi and gridalt packages |
| 1702 |
|
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
| 1703 |
|
o changes to permit hi-res, cubed-sphere, configuration |
| 1704 |
|
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
| 1705 |
|
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
| 1706 |
|
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
| 1707 |
|
of surface winds for the cube |
| 1708 |
|
(A verification experiment, based on global_ocean.cs32x15, but with |
| 1709 |
|
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
| 1710 |
|
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
| 1711 |
|
complete with example surface forcing files and matlab scripts to look |
| 1712 |
|
at the output and compare it with that of global_ocean.cs32x15.) |
| 1713 |
|
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
| 1714 |
|
but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
| 1715 |
|
to conform to the common rule. |
| 1716 |
|
o check-in the first version of the coupler + interfaces for multi-components |
| 1717 |
|
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
| 1718 |
|
- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
| 1719 |
|
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
| 1720 |
|
- ocean and atmos. share the same horizontal grid (no interpolation). |
| 1721 |
|
- exchanges between component and coupler is done in forward_step |
| 1722 |
|
o new verification experiment, cpl_aim+ocn: |
| 1723 |
|
coupled ocean - AIM atmosphere on cs32 grid. |
| 1724 |
|
|
| 1725 |
|
checkpoint52d_pre |
| 1726 |
|
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
| 1727 |
|
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
| 1728 |
|
|
| 1729 |
|
checkpoint52c_post |
| 1730 |
|
o Fixing OPTIONS files for use of exf: |
| 1731 |
|
- ALLOW_ECCO not needed |
| 1732 |
|
- ECCO_CPPOPTIONS.h should not be included from |
| 1733 |
|
EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
| 1734 |
|
as has been the case in the past |
| 1735 |
|
- All cal/exf related options are currently set in |
| 1736 |
|
single header file. Should remain so until we |
| 1737 |
|
agree on a consistent new policy. |
| 1738 |
|
o Removed all CPP options for cal package. |
| 1739 |
|
cal has no more CPP options. |
| 1740 |
|
o modified STOREs in GAD_ADVECTION |
| 1741 |
|
o corrected key comp. for passkey |
| 1742 |
|
|
| 1743 |
|
checkpoint52b_post |
| 1744 |
|
o new version: "thsice" of thermodynamic sea-ice pkg: |
| 1745 |
|
- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
| 1746 |
|
- modify fluxes but do not change theta directly; |
| 1747 |
|
- light cleaning of bulk_force pkg (still needed with thsice). |
| 1748 |
|
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
| 1749 |
|
+ output_thsice.txt to test thsice & bulk_force pkgs. |
| 1750 |
|
o put back grid & coriolis monitor output. |
| 1751 |
|
checkpoint52b_pre |
| 1752 |
|
|
| 1753 |
|
o call "do_the_model_io" at the beginning (=> dump initial state) |
| 1754 |
|
o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
| 1755 |
|
o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
| 1756 |
|
(need info on NUMBER_OF_PTRACERS) |
| 1757 |
|
o missing PTRACERS headers in some routines |
| 1758 |
|
o default tamc.h in pkg/autodiff supposed to crash |
| 1759 |
|
to ensure proper customization |
| 1760 |
|
|
| 1761 |
|
checkpoint52a_post |
| 1762 |
|
o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
| 1763 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
| 1764 |
|
- subroutine FREEZE_SURFACE now limits only surface temperature |
| 1765 |
|
and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
| 1766 |
|
=> new output.txt for global_ocean.cs32x15 & global_with_exf |
| 1767 |
|
- keep the old version of FREEZE for backward compatibility; |
| 1768 |
|
global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
| 1769 |
|
- corresponding modifs for TAF directives |
| 1770 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
| 1771 |
|
o time-averaged output for pkg/ptracers |
| 1772 |
|
o fix problem with ECCO-related divided adjoint |
| 1773 |
|
snapshot file was missing some ad-variables, |
| 1774 |
|
but no warning issued by TAF |
| 1775 |
|
|
| 1776 |
|
checkpoint52a_pre |
| 1777 |
|
o some bug fixes for #undef REAL4_IS_SLOW |
| 1778 |
|
|
| 1779 |
|
checkpoint52 = ecco_c52_e35 |
| 1780 |
|
o after testing adjoints of checkpoint51u_post |
| 1781 |
|
|
| 1782 |
|
checkpoint51u_post |
| 1783 |
|
o this is the post-merge tag of the ecco-branch |
| 1784 |
|
(needs another clean checkout and re-testing) |
| 1785 |
|
o various natl_box_adjoint configs and results |
| 1786 |
|
but no input fields |
| 1787 |
|
o obcs adjoint not yet merged! |
| 1788 |
|
o adding ECCO global 1x1 and 2x2 degree configs |
| 1789 |
|
o updated/extended some store directives for seaice |
| 1790 |
|
o pkg/ecco now containes ecco-specific part of cost function |
| 1791 |
|
o top level routines the_main_loop, forward_step |
| 1792 |
|
supersede those in model/src/ |
| 1793 |
|
previous input data.cost now in data.ecco |
| 1794 |
|
(new namelist ecco_cost_nml) |
| 1795 |
|
o in ctrl/ cleaned some cross-dependencies and updated CPP options |
| 1796 |
|
|
| 1797 |
|
checkpoint51t_post |
| 1798 |
|
o this is the pre-merge tag of the ecco-branch |
| 1799 |
|
|
| 1800 |
|
checkpoint51s_post |
| 1801 |
|
o cleanup: removed various obsolete #define-s |
| 1802 |
|
o pkg/grdchk |
| 1803 |
|
- renamed 'ph-grd 3' to 'grad-res' |
| 1804 |
|
- merged from ecco-branch |
| 1805 |
|
(remaining bug fixes for obcs gradient checks) |
| 1806 |
|
- additional high-precision output for testreport |
| 1807 |
|
(grep for 'precision_grdchk_result') |
| 1808 |
|
|
| 1809 |
|
checkpoint51r_post |
| 1810 |
|
o cleaned up or removed CPP_OPTIONS.h files |
| 1811 |
|
o updated results for some of the tests to reflect the new |
| 1812 |
|
optfiles (-ieee: -O0 instead of -O3) |
| 1813 |
|
|
| 1814 |
|
checkpoint51q_post |
| 1815 |
|
o cd_code: |
| 1816 |
|
- moved cd_scheme.F -> cd_code_scheme.F |
| 1817 |
|
- separate read_checkpoint from cd_code_ini_vars.F |
| 1818 |
|
- separated cd_code part from write_checkpoint |
| 1819 |
|
- updated AD_SOURCE, generated .flow |
| 1820 |
|
- added CD_CODE_VARS.h to the_main_loop |
| 1821 |
|
- Moving cd_code specific store dir.s to pkg/cd_code |
| 1822 |
|
o ctrl package totally restructured |
| 1823 |
|
- pack/unpack now optional and decoupled from |
| 1824 |
|
xx_/adxx_ I/O |
| 1825 |
|
- ctrl_pack/unpack cleaned |
| 1826 |
|
(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
| 1827 |
|
- confined inclusion of AD_CONFIG.h to where necessary. |
| 1828 |
|
o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
| 1829 |
|
|
| 1830 |
|
checkpoint51p_post |
| 1831 |
|
o create initial cd_code package |
| 1832 |
|
- WARNING: the initialization of fields within packages |
| 1833 |
|
is broken because INI_FIELDS (where READ_CHECKPOINT is |
| 1834 |
|
called) is called *before* PACKAGES_INIT_VARIABLES. |
| 1835 |
|
This seems to be backwards since |
| 1836 |
|
1) its important to initially zero the entire field including |
| 1837 |
|
the "halo" region |
| 1838 |
|
2) zeroing needs to be done *before* reading pickup info |
| 1839 |
|
and the pickup call might or might not happen in any |
| 1840 |
|
particular run |
| 1841 |
|
- this needs an overhaul for R2 |
| 1842 |
|
o cleanup verification/*/code/GMREDI_OPTIONS.h |
| 1843 |
|
o cleanup testreport |
| 1844 |
|
|
| 1845 |
|
checkpoint51o_post |
| 1846 |
|
o bringing AD-related verif's up to date with genmake2 |
| 1847 |
|
- carbon/ |
| 1848 |
|
- global_ocean.90x40x15/ |
| 1849 |
|
- hs.94.1x64x5/ |
| 1850 |
|
- (front_relax/ ) |
| 1851 |
|
o (more) consistent directory structure for AD-related verif.'s |
| 1852 |
|
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
| 1853 |
|
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
| 1854 |
|
o bug fix in find_alpha.F for MDJWF: |
| 1855 |
|
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
| 1856 |
|
change rho -> rho-rhoConst |
| 1857 |
|
- replace call find_rho to find_rhonum |
| 1858 |
|
o initialisation of rFlx extended to full array (required by TAF) |
| 1859 |
|
and shifted to thermodynamics |
| 1860 |
|
o removed PTRACERS.h in ptracers routine |
| 1861 |
|
o added surfacetendencyPtr to S/R parameter list pracers_forcing |
| 1862 |
|
o Correcting initialisations for fVerU, fVerV. |
| 1863 |
|
o helping TAF to recognize dependency on kUp for |
| 1864 |
|
fVerU, fVerV |
| 1865 |
|
o Replacing delZ by delR in pkg/ctrl/ |
| 1866 |
|
checkpoint51o_pre |
| 1867 |
|
|
| 1868 |
|
o undid all of cp51 pending some cleanups and discussion |
| 1869 |
|
o added the [#include "AD_CONFIG.h"] statement to all files that need |
| 1870 |
|
it for adjoint/tl #defines |
| 1871 |
|
o re-worked the build logic in genmake2 to support AD_CONFIG.h |
| 1872 |
|
o removed tools/genmake since it no longer works |
| 1873 |
|
|
| 1874 |
|
checkpoint51n_post |
| 1875 |
|
o modifications to make FREEZE flux visible to pkg/kpp |
| 1876 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
| 1877 |
|
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
| 1878 |
|
- subroutine FREEZE now limits only surface temperature |
| 1879 |
|
(this means new output.txt for global_ocean.90x40x15, |
| 1880 |
|
global_ocean.cs32x15, and global_with_exf) |
| 1881 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
| 1882 |
|
|
| 1883 |
|
checkpoint51n_pre |
| 1884 |
|
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
| 1885 |
|
o added [#include "AD_CONFIG.h"] to all files that use the following |
| 1886 |
|
defines: |
| 1887 |
|
- ALLOW_ADJOINT_RUN |
| 1888 |
|
- ALLOW_TANGENTLINEAR_RUN |
| 1889 |
|
- ALLOW_ECCO_OPTIMIZATION |
| 1890 |
|
|
| 1891 |
|
checkpoint51m_post |
| 1892 |
|
o incorporating changes to get TAMC/TAF working in genmake2 |
| 1893 |
|
- added new TAMC/TAF targets to the Makefile |
| 1894 |
|
- various cleanups related to package handling |
| 1895 |
|
- these changes should have no impact on the forward model |
| 1896 |
|
|
| 1897 |
|
checkpoint51l_post |
| 1898 |
|
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
| 1899 |
|
- faster algorithm for cal_addtime.F |
| 1900 |
|
- higher precision arithmetic, where needed |
| 1901 |
|
- pkg/exf *startdate variables changed from calendar date to |
| 1902 |
|
model integration time |
| 1903 |
|
|
| 1904 |
|
checkpoint51l_pre |
| 1905 |
|
o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
| 1906 |
|
o enable to apply restoring on S & T only in a latitude band. |
| 1907 |
|
o update output (external_forcing_surf modif. change truncation errors) |
| 1908 |
|
global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
| 1909 |
|
|
| 1910 |
|
checkpoint51k_post |
| 1911 |
|
o change default to: useNHMTerms=.FALSE. |
| 1912 |
|
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
| 1913 |
|
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
| 1914 |
|
- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
| 1915 |
|
exp1, ideal_2D_oce |
| 1916 |
|
- change data file of oceanic exp (leave the results unchanged for now) |
| 1917 |
|
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
| 1918 |
|
o set gravitySign automatically according to the vertical coordinate used |
| 1919 |
|
(and change sign: back to "logical" value: +1 when R increases downward) |
| 1920 |
|
o added an include barrier to the default CPP_OPTIONS.h and |
| 1921 |
|
removed the #include "PACKAGES_CONFIG.h" from it |
| 1922 |
|
o fix a bug in mom_fluxform (from chk51j_post) |
| 1923 |
|
|
| 1924 |
|
checkpoint51j_post |
| 1925 |
|
o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
| 1926 |
|
o adjusted some flow directives (dynamics, thermodynamics) |
| 1927 |
|
o added cubed-sphere case to test cost function |
| 1928 |
|
o heckpoint_lev?_directives.h now include |
| 1929 |
|
pkg-specific directives, whenever those are enabled. |
| 1930 |
|
o Moving pkg-specific flow directives to corresponding pkg |
| 1931 |
|
Moving pkg-specific differentiation list to corresponding pkg |
| 1932 |
|
Moving pkg-specific checkpoint-lev storing to corresponding pkg |
| 1933 |
|
---> conventions are |
| 1934 |
|
- pkg_ad.flow |
| 1935 |
|
- pkg_ad_diff.list |
| 1936 |
|
- pkg_ad_check_lev?_dir.h |
| 1937 |
|
|
| 1938 |
|
checkpoint51i_post |
| 1939 |
|
o merge of the branch-genmake2 |
| 1940 |
|
- knowingly breaks the older genmake |
| 1941 |
|
- automatic generation of all ALLOW_${PKG_NAME} defines |
| 1942 |
|
- new testreport supersedes older testscript |
| 1943 |
|
o large number of package inclusion and header cleanups |
| 1944 |
|
checkpoint51i_pre |
| 1945 |
|
|
| 1946 |
|
o new output for adjoin of global ocean vector invariant |
| 1947 |
|
o fix for checkpoint of thermodynamic seaice and bulk_force |
| 1948 |
|
o Steph gchem various cleanups |
| 1949 |
|
|
| 1950 |
|
checkpoint 51h_pre |
| 1951 |
|
o fixed some single quotes |
| 1952 |
|
o modify gchem pkg to be more versatile |
| 1953 |
|
o modifications to clean up dic pkg |
| 1954 |
|
o add pkg/cfc |
| 1955 |
|
|
| 1956 |
|
checkpoint51g_post |
| 1957 |
|
o provide links for ARPACK and ADM*TLM |
| 1958 |
|
o start removing verification/vero/ |
| 1959 |
|
o update AD-related stuff |
| 1960 |
|
(in particular some IF-statements in model/src/ routines) |
| 1961 |
|
o adding to verification/global_ocean.90x40x15/ adjoint of |
| 1962 |
|
vector invariant setup |
| 1963 |
|
|
| 1964 |
|
checkpoint51f_post |
| 1965 |
|
o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
| 1966 |
|
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
| 1967 |
|
of tracer Green's fucntions for ocean inversion project. |
| 1968 |
|
|
| 1969 |
|
checkpoint51f_pre |
| 1970 |
|
o Added on-the-fly spatial interpolation capability |
| 1971 |
|
"USE_EXF_INTERPOLATION" to pkg/exf. |
| 1972 |
|
- This is a temporary Cartesian-grid hack until |
| 1973 |
|
the super-duper ESMF coupler becomes available. |
| 1974 |
|
- See verification/global_with_exf/README for usage example. |
| 1975 |
|
- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
| 1976 |
|
flags and modified pkg/seaice accordingly. |
| 1977 |
|
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
| 1978 |
|
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
| 1979 |
|
non-local transport term. |
| 1980 |
|
|
| 1981 |
|
checkpoint51e_post |
| 1982 |
|
o pkg/mom_vecinv: |
| 1983 |
|
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
| 1984 |
|
- add time-ave diagnostic of vorticity advection. |
| 1985 |
|
o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. |
| 1986 |
|
o atmospheric geopotential: - include water vapor effect; |
| 1987 |
|
- use p^kappa in p* scaling. |
| 1988 |
|
o land pkg: read initial state from files. |
| 1989 |
|
o AIM : add stratospheric drag in the upper level |
| 1990 |
|
|
| 1991 |
|
checkpoint51d_post |
| 1992 |
|
o change function ILNBLNK (=> last non-blank char.) to return zero |
| 1993 |
|
(instead of the string length) when the string. char is empty |
| 1994 |
|
o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) |
| 1995 |
|
o modif's to restore TAMC compatibility |
| 1996 |
|
- avoid "_d" constructs in PARAMETER declarations |
| 1997 |
|
- avoid interrupting lines by comment lines |
| 1998 |
|
o Use cluster local disks for purely local I/O |
| 1999 |
|
vs. globally visible disks needed for ctrl stuff |
| 2000 |
|
(merged from ecco-branch) |
| 2001 |
|
- new active_file_loc... and mdsio_..._loc routines |
| 2002 |
|
- affected packages: autodiff, ctrl, grdchk, mdsio |
| 2003 |
|
|
| 2004 |
|
checkpoint51c_post |
| 2005 |
|
o introducing integer flag debugLevel |
| 2006 |
|
- debLevZero: suppress all output |
| 2007 |
|
- debLevA: standard |
| 2008 |
|
- debLevB: equivalent to current debugMode=.TRUE. |
| 2009 |
|
o introducing pathname variable mdsioLocalDir for mdsio |
| 2010 |
|
that can be specified at runtime |
| 2011 |
|
(relevant for cluster I/O to local disk) |
| 2012 |
|
` |
| 2013 |
|
>>>checkpoint51b_post |
| 2014 |
|
adjoint of ptracers |
| 2015 |
|
o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
| 2016 |
|
o extended state in checkpoint_lev?, etc. |
| 2017 |
|
o alternative ctrl/cost with tr1 or ptracer |
| 2018 |
|
o new comlev1_bibj_ptracers |
| 2019 |
|
o new ptracers.flow |
| 2020 |
|
o made ptracers_forcing same as external_forcing_s |
| 2021 |
|
o added verification for adjoint with ptracers |
| 2022 |
|
- adm. grdchk fail so far |
| 2023 |
|
- tlm. grdchk OK |
| 2024 |
|
- checked tapelev/comlev recomputations: OK |
| 2025 |
|
<<<checkpoint51b_pre |
| 2026 |
|
|
| 2027 |
|
checkpoint51a_post |
| 2028 |
|
o added code for biogeochemistry package |
| 2029 |
|
- new pkgs: dic, gchem |
| 2030 |
|
- new subroutine in ptracers |
| 2031 |
|
o modify code for biogeo packages |
| 2032 |
|
- in model/src and pkg/ptracers |
| 2033 |
|
|
| 2034 |
|
checkpoint51 |
| 2035 |
|
o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN |
| 2036 |
|
- autodiff, ctrl, exf, grdchk, seaice |
| 2037 |
|
kept separate packages |
| 2038 |
|
- cost, ecco, obcs |
| 2039 |
|
o updating verification/internal_wave, verification/lab_sea |
| 2040 |
|
(all verif's pass on faulks.lcs.mit.edu RH7.3, g77) |
| 2041 |
|
|
| 2042 |
|
checkpoint50i_post |
| 2043 |
|
o Preparing next differentiable checkpoint and sync |
| 2044 |
|
of MAIN vs. ecco-branch |
| 2045 |
|
- 1st step: this one is differentiable |
| 2046 |
|
- 2nd step: next(! not this) checkpoint will have updated packages |
| 2047 |
|
from ecco-branch) |
| 2048 |
|
|
| 2049 |
|
checkpoint50h_post |
| 2050 |
|
o new package "land": provide surface BC for AIM. |
| 2051 |
|
o pkg/ptracers: apply exchange to all tracers after reading a pickup. |
| 2052 |
|
o AIM: use true log-P extrapolation for near surface temp (= as in |
| 2053 |
|
F.Molteni paper) ; update aim.5l_cs output. |
| 2054 |
|
o New variable in PARM03 for more flexible pickups |
| 2055 |
|
o somewhat cleaned package initialisation sequence for |
| 2056 |
|
ctrl/ cost/ ecco/ in packages_... routines |
| 2057 |
|
|
| 2058 |
|
checkpoint50g_post |
| 2059 |
|
o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
| 2060 |
|
- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
| 2061 |
|
- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
| 2062 |
|
made the default because of faster convergence than ADI |
| 2063 |
|
|
| 2064 |
|
checkpoint50f_post |
| 2065 |
|
o exf totally restructured |
| 2066 |
|
- replaced all exf_set_ routines by one generic exf_set_gen.F |
| 2067 |
|
and made sure it's still differentiable |
| 2068 |
|
- split exf_getffields.F into new exf_bulkformulae.F |
| 2069 |
|
- exf_inscal_/exf_outscal_ suffixes consistent with field names |
| 2070 |
|
- updated adjoint/makefile and relevant verif. accordingly |
| 2071 |
|
|
| 2072 |
|
checkpoint50f_pre |
| 2073 |
|
o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; |
| 2074 |
|
+ change Evap over land. (update aim.5l_cs output) |
| 2075 |
|
o added missing .cvsignores and made uniform across expts |
| 2076 |
|
o changed configuration of tidal_basin_2d expt |
| 2077 |
|
o added pkg/debug functions for tracing code in fatal crashes |
| 2078 |
|
o tidied pkg/monitor to use MONITOR_OPTIONS.h |
| 2079 |
|
o new fn in pkg/monitor to stop model if solution grows too big |
| 2080 |
|
o removed lots of single quotes from comments |
| 2081 |
|
|
| 2082 |
|
checkpoint50e_post |
| 2083 |
|
o make KPP work with PTRACERS |
| 2084 |
|
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
| 2085 |
|
nearly a copy of kpp_transport_s |
| 2086 |
|
- there is no analogue to SurfaceTendencyS, so I have to use |
| 2087 |
|
gPtr(of the surface layer) instead |
| 2088 |
|
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
| 2089 |
|
checkpoint50e_pre |
| 2090 |
|
|
| 2091 |
|
checkpoint50d_post |
| 2092 |
|
o change kpp output from multiple-record state files to single-record state |
| 2093 |
|
files analogous to write_state.F |
| 2094 |
|
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
| 2095 |
|
analogous to the cg2d-related output. |
| 2096 |
|
o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
| 2097 |
|
so that writing to internal file fn (with length 512) fails. |
| 2098 |
|
checkpoint50d_pre |
| 2099 |
|
|
| 2100 |
|
checkpoint50c_post |
| 2101 |
|
o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) |
| 2102 |
|
o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. |
| 2103 |
|
o add time-average diagnostic of U*V and vertical diffusive flux for theta. |
| 2104 |
|
o bug fixed in convective adjustment diagnostic (multi-tile set-up). |
| 2105 |
|
o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. |
| 2106 |
|
|
| 2107 |
|
checkpoint50c_pre |
| 2108 |
|
Merging from release1_p13: |
| 2109 |
|
o bug fix for pkg/seaice dynamic solver |
| 2110 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
| 2111 |
|
|
| 2112 |
|
checkpoint50b_post |
| 2113 |
|
o store u*,v* in gU,V instead of in guNm1,gvNm1 |
| 2114 |
|
o in order to put the momForcing out of the Adams-Bashforth: |
| 2115 |
|
move forcing & CD-scheme calls from mom_fluxform & mom_vecinv |
| 2116 |
|
to timestep.F |
| 2117 |
|
o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays |
| 2118 |
|
o re-generate output for highly sensitive test-exp: |
| 2119 |
|
global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box |
| 2120 |
|
|
| 2121 |
|
checkpoint50b_pre |
| 2122 |
|
o restore the use of momAdvection & useCoriolis flags (mom_vecinv) |
| 2123 |
|
o corrected CPP option mismatch in exf_Bulk... functions for case |
| 2124 |
|
#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
| 2125 |
|
|
| 2126 |
|
checkpoint50a_post |
| 2127 |
|
o Bug fix for merging between c50 and KPP. |
| 2128 |
|
ikey was passed from thermodynamics to kpp_calc via |
| 2129 |
|
common block rather than being recomputed in kpp_calc, |
| 2130 |
|
in contradiction with new key itdkey. |
| 2131 |
|
New key ikppkey created, and tamc.h headers updated. |
| 2132 |
|
|
| 2133 |
|
checkpoint50 |
| 2134 |
|
- 2nd step of merge with ecco-branch: |
| 2135 |
|
merge changes in ecco-branch back into main trunk |
| 2136 |
|
- bug fix in find_alpha |
| 2137 |
|
- more storing in gmredi_calc_tensor.F, kpp_routines.F |
| 2138 |
|
- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
| 2139 |
|
- merged some sliced AD support routines |
| 2140 |
|
|
| 2141 |
|
checkpoint49 |
| 2142 |
|
merged from ecco-branch: |
| 2143 |
|
o exf: |
| 2144 |
|
- Enable initialisation of forcing fields to constant |
| 2145 |
|
(runtime) values. |
| 2146 |
|
- in exf_getffields.F |
| 2147 |
|
Reduce i-/j-loop to interior domain, discarding overlaps. |
| 2148 |
|
That also fixes wrong TAF-key computations for key_1, key_2 |
| 2149 |
|
with bulf formulae. |
| 2150 |
|
- exf_init.F modify #ifdef for exf_init_evap |
| 2151 |
|
- exf_getffieldrec.F, ctrl_getrec.F |
| 2152 |
|
The following INT-usages are not safe: |
| 2153 |
|
fldsecs = int(fldsecs/fldperiod)*fldperiod |
| 2154 |
|
fldcount = int(fldsecs/fldperiod) + 1 |
| 2155 |
|
and were modified. |
| 2156 |
|
o autodiff: checkpoint_lev... |
| 2157 |
|
- updated storing for bulk formulae (some arrays were missing) |
| 2158 |
|
- added state for seaice package |
| 2159 |
|
- synchronized with main branch |
| 2160 |
|
o DIVA: |
| 2161 |
|
Modif.s in |
| 2162 |
|
- the_main_loop.F |
| 2163 |
|
- the_model_main.F |
| 2164 |
|
and added cost_final_restore.F cost_final_store.F |
| 2165 |
|
o With these changes, it is possible to fully separate |
| 2166 |
|
the first forward run to compute the cost function (mdthe_main_loop) |
| 2167 |
|
and adjoint runs over individual DIVA intervals (adthe_main_loop) |
| 2168 |
|
into separate model executions. |
| 2169 |
|
This enables better tuning of DIVA to given queue sizes. |
| 2170 |
|
o Loss of cost function value in consecutive DIVA runs is |
| 2171 |
|
fixed by storing to 'costfinal' file. |
| 2172 |
|
o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
| 2173 |
|
beginning/end of adjoint integration is accounted for. |
| 2174 |
|
The current changes apply to TAF-1.4.26. |
| 2175 |
|
TAF has one remaining bug, requiring one manual change |
| 2176 |
|
(see MITgcm manual). |
| 2177 |
|
o cal: synchronized between MAIN and ecco-branch |
| 2178 |
|
|
| 2179 |
|
checkpoint48i_post |
| 2180 |
|
o Changes to restore differentiability of code w.r.t. previous tag |
| 2181 |
|
(mostly adding new routines to make list and replacing |
| 2182 |
|
pressure by totPhiHyd). |
| 2183 |
|
o Updated and merged grdchk package |
| 2184 |
|
- has both ADM and TLM checks |
| 2185 |
|
- works for single- and multi-proc. |
| 2186 |
|
- output cleaned |
| 2187 |
|
- worked successfully for parallel DIVA |
| 2188 |
|
o genmake: |
| 2189 |
|
- Adding -platform=SP4 |
| 2190 |
|
- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
| 2191 |
|
o Modif. for DIVA: |
| 2192 |
|
ctrl_unpack should not be called in intermediate DIVA interval. |
| 2193 |
|
(similar thing would apply for active files such as |
| 2194 |
|
tbar, sbar, psbar, which should not be reinitialised; |
| 2195 |
|
only relevant for ecco-branch) |
| 2196 |
|
|
| 2197 |
|
checkpoint48h_post |
| 2198 |
|
o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
| 2199 |
|
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
| 2200 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
| 2201 |
|
o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
| 2202 |
|
|
| 2203 |
|
checkpoint48g_post |
| 2204 |
|
--- EOS: |
| 2205 |
|
o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
| 2206 |
|
store total Potential in totPhyHyd for diagnostics & EOS. |
| 2207 |
|
o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
| 2208 |
|
--- Pressure/geopotential gradient: |
| 2209 |
|
o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
| 2210 |
|
o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
| 2211 |
|
( changes results of global_ocean_pressure ) |
| 2212 |
|
o NLFS + z-coord.: add eta*Rho' contribution. |
| 2213 |
|
o accurate phiHyd when using interface-W at the middle between 2 centers |
| 2214 |
|
( changes results of ideal_2D_oce ) |
| 2215 |
|
o includes r* 2nd term in potential gradient. |
| 2216 |
|
|
| 2217 |
|
checkpoint48f_post |
| 2218 |
|
Merging from release1_p12: |
| 2219 |
|
o Modifications for using pkg/exf with pkg/seaice |
| 2220 |
|
- improved description of the various forcing configurations |
| 2221 |
|
- added basic radiation bulk formulae to pkg/exf |
| 2222 |
|
- units/sign fix for evap computation in exf_getffields.F |
| 2223 |
|
- updated verification/global_with_exf/results/output.txt |
| 2224 |
|
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
| 2225 |
|
(SBO) core products, including oceanic mass, center-of-mass, |
| 2226 |
|
angular, and bottom pressure (see pkg/sbo/README.sbo). |
| 2227 |
|
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
| 2228 |
|
to avoid negative values in shallow regions. |
| 2229 |
|
- updated verification/natl_box/results/output.txt |
| 2230 |
|
- updated verification/lab_sea/results/output.txt |
| 2231 |
|
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
| 2232 |
|
o Added useSingleCpuIO option (see PARAMS.h). |
| 2233 |
|
o Updated useSingleCpuIO option in mdsio_writefield.F to |
| 2234 |
|
work with multi-field files, e.g., for single-file pickup. |
| 2235 |
|
o pkg/seaice: |
| 2236 |
|
- bug fix in growth.F: QNET for no shortwave case |
| 2237 |
|
- added HeffFile for specifying initial sea-ice thickness |
| 2238 |
|
- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
| 2239 |
|
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
| 2240 |
|
kpp_transport_t.F, forward_step.F, and the_main_loop.F |
| 2241 |
|
o pkg/seaice: |
| 2242 |
|
- adjoint-friendly modifications |
| 2243 |
|
- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
| 2244 |
|
|
| 2245 |
|
checkpoint48e_post |
| 2246 |
|
o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) |
| 2247 |
|
o dynamics: change definition of computational domain & adapt mom_fluxform |
| 2248 |
|
accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. |
| 2249 |
|
o following exp works with Olx=Oly=2 (and pass through checkbounds option): |
| 2250 |
|
adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 |
| 2251 |
|
exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 |
| 2252 |
|
global_ocean.90x40x15 global_with_exf global_ocean_pressure |
| 2253 |
|
inverted_barometer solid-body.cs-32x32x1 |
| 2254 |
|
(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) |
| 2255 |
|
|
| 2256 |
|
checkpoint48d_post |
| 2257 |
|
o in preparation for r*: |
| 2258 |
|
a) use pre-computed gradient of hydrostatic potential: |
| 2259 |
|
changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce |
| 2260 |
|
b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: |
| 2261 |
|
=> affects results of glob_oce_pressure (different truncation error) |
| 2262 |
|
update output.txt of ideal_2D_oce & global_ocean_pressure |
| 2263 |
|
|
| 2264 |
|
checkpoint48d_pre |
| 2265 |
|
o in preparation for r*: |
| 2266 |
|
new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
| 2267 |
|
pass the 2 comp. of the grad. as arguments to momentum S/R. |
| 2268 |
|
but for the moment, only used if it does not change the results. |
| 2269 |
|
o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP |
| 2270 |
|
|
| 2271 |
|
checkpoint48c_post |
| 2272 |
|
Modifications in treatment of initial flux forcing controls |
| 2273 |
|
to avoid extra storing of flux fields. |
| 2274 |
|
|
| 2275 |
|
checkpoint48c_pre |
| 2276 |
|
o Added tidal_basin_2d experiment (currently 1D!) |
| 2277 |
|
o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) |
| 2278 |
|
|
| 2279 |
|
checkpoint48b_post |
| 2280 |
|
o r* coordinate added in #ifdef NONLIN_FRSURF block. |
| 2281 |
|
(modification to pressure gradient not yet implemented) |
| 2282 |
|
o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports |
| 2283 |
|
(for U & V) that are used for vertical advection of momentum. |
| 2284 |
|
|
| 2285 |
|
checkpoint48a_post |
| 2286 |
|
o In preparation for r*, use temp. array to compute vertical transport |
| 2287 |
|
in flux-form momentum pkg. => change results of few test-exp. |
| 2288 |
|
Update output of: exp4, exp5, front_relax, global_ocean_pressure, |
| 2289 |
|
lab_sea, natl_box & plume_on_slope |
| 2290 |
|
|
| 2291 |
|
checkpoint48 |
| 2292 |
|
o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') |
| 2293 |
|
|
| 2294 |
|
checkpoint47j_post |
| 2295 |
|
o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. |
| 2296 |
|
o moved adexch from forward_step to addummy_in_stepping |
| 2297 |
|
o added exch in ctrl_map_... |
| 2298 |
|
o aveFreq.=0. at end of cost_final to avoid overwrite in |
| 2299 |
|
reverse checkpointing loop |
| 2300 |
|
o Yet more changes in gmredi: |
| 2301 |
|
* adgmredi_calc_tensor |
| 2302 |
|
avoiding all recomputation of gmredi_slope_limit |
| 2303 |
|
* adgmredi_x/y/rtransport |
| 2304 |
|
added flag for excessive storing to avoid recomp. of |
| 2305 |
|
u/v/rtans, dTdx/y/z |
| 2306 |
|
-> this is not really necessary and very memory-consuming |
| 2307 |
|
* adgmredi_slope_psi: |
| 2308 |
|
consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff |
| 2309 |
|
* gmredi_slope_limit |
| 2310 |
|
re-activated full calculation of taperfct for case 'ac02' |
| 2311 |
|
o updating verification/ adjoints of carbon, global_ocean.90x40x15 |
| 2312 |
|
|
| 2313 |
|
checkpoint47i_post |
| 2314 |
|
o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. |
| 2315 |
|
o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) |
| 2316 |
|
default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) |
| 2317 |
|
o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) |
| 2318 |
|
o gmredi: fix few bugs. |
| 2319 |
|
|
| 2320 |
|
checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) |
| 2321 |
|
This will be a good checkpoint to plug into the ecco-branch. |
| 2322 |
|
o few modif.'s to get latest version adjointed |
| 2323 |
|
(mainly kick out code in ini_linear_phisurf) |
| 2324 |
|
o modif's to run adjoint with exactConserv |
| 2325 |
|
o case GM_BOLUS_ADVEC should be cleaned |
| 2326 |
|
S/R gmredi_slope_psi should be cleaned |
| 2327 |
|
o verification/carbon now has exactConserv=.TRUE. |
| 2328 |
|
|
| 2329 |
|
checkpoint47g_post |
| 2330 |
|
o time-average AIM output: becomes independent from statvars time-average |
| 2331 |
|
(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
| 2332 |
|
o After TAF bug fix: |
| 2333 |
|
Tested adjoint of gmredi package. |
| 2334 |
|
Tests were done with checkpoint47 rather than with latest |
| 2335 |
|
checkpoint47f_post since the latter is broken for the adjoint |
| 2336 |
|
verification/carbon/ contains both ADM and TLM gradient checks. |
| 2337 |
|
Here they are, before they get changed/lost/stolen. |
| 2338 |
|
Mostly modif.'s to fix numerical sensitivities. |
| 2339 |
|
Gradient checks OK for |
| 2340 |
|
- GM_taper_scheme: |
| 2341 |
|
* clipping |
| 2342 |
|
* ac02 |
| 2343 |
|
* linear |
| 2344 |
|
* glw91 |
| 2345 |
|
* dm95 |
| 2346 |
|
* ldd97 |
| 2347 |
|
- GMREDI_OPTIONS: |
| 2348 |
|
* GM_VISBECK_VARIABLE_K |
| 2349 |
|
* GM_NON_UNITY_DIAGONAL |
| 2350 |
|
* GM_EXTRA_DIAGONAL |
| 2351 |
|
* GM_BOLUS_ADVEC |
| 2352 |
|
in conjunction with data.gmredi parameters to be checked in |
| 2353 |
|
in a few minutes under verification/carbon/code/ |
| 2354 |
|
|
| 2355 |
|
checkpoint47f_post |
| 2356 |
|
Merging from release1_p10: |
| 2357 |
|
o modifications for using pkg/exf with pkg/seaice |
| 2358 |
|
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
| 2359 |
|
and SEAICE_EXTERNAL_FLUXES |
| 2360 |
|
- pkg/exf CPP options EXF_READ_EVAP and |
| 2361 |
|
EXF_NO_BULK_COMPUTATIONS |
| 2362 |
|
- usage examples are Experiments 8 and 9 in |
| 2363 |
|
verification/lab_sea/README |
| 2364 |
|
- verification/lab_sea default experiment now uses |
| 2365 |
|
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf |
| 2366 |
|
|
| 2367 |
|
checkpoint47e_post |
| 2368 |
|
o created a tag prior to creating a branch |
| 2369 |
|
|
| 2370 |
|
checkpoint47d_post |
| 2371 |
|
o fixed bug in the oceanic pressure coordinates code: vertical viscosity |
| 2372 |
|
at the bottom boundary had an erroneous half slip boundary condition |
| 2373 |
|
o added bottom drag and no slip boundary condition capabilities to |
| 2374 |
|
oceanic pressure coordinates code |
| 2375 |
|
o added new verification experiment global_ocean_pressure, this experiment is |
| 2376 |
|
also described in the tutorial section of the manual |
| 2377 |
|
checkpoint47d_pre |
| 2378 |
|
|
| 2379 |
|
checkpoint47c_post |
| 2380 |
|
o Added a verification experiment for a global cubed-sphere ocean run |
| 2381 |
|
- verification/global_ocean.cubed32x32x30 |
| 2382 |
|
- uses pkg/therm_seaice and pkg/bulk_forcing |
| 2383 |
|
|
| 2384 |
|
o allow to run AIM physics with SPEEDY input files (from Franco Molteni) |
| 2385 |
|
o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) |
| 2386 |
|
when using P-coordinate; only implemented for atmospheric config. |
| 2387 |
|
o OCEANICP & realFreshWater: include P-E direct effect on wVel ; |
| 2388 |
|
NOTES: requires option NONLIN_FRSURF to be "#define". |
| 2389 |
|
o update advect_xz/results/output.txt (left from checkpoint44g_post) |
| 2390 |
|
|
| 2391 |
|
checkpoint47b_post |
| 2392 |
|
Merging from release1_p9: |
| 2393 |
|
o pkg/seaice |
| 2394 |
|
- removed GOTO's and added taf directives |
| 2395 |
|
- double precision constants to reduce the g77 (Linux) |
| 2396 |
|
to F77 (SGI) differences reported in release1_p8 |
| 2397 |
|
o tools/genmake |
| 2398 |
|
- added SGI options |
| 2399 |
|
o verification/testscript |
| 2400 |
|
- updated to that of checkpoint47a_post |
| 2401 |
|
o verification/global_ocean.90x40x15/input/eedata |
| 2402 |
|
- modified for SGI f77 compatibility |
| 2403 |
|
o verification/lab_sea |
| 2404 |
|
- added description of sea-ice model |
| 2405 |
|
- added missing matlab routines |
| 2406 |
|
- added test of thermodynamics parallelization |
| 2407 |
|
|
| 2408 |
|
checkpoint47a_post |
| 2409 |
|
o new pkg: aim_v23 |
| 2410 |
|
= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
| 2411 |
|
for now, keep the same surface forcing as before. |
| 2412 |
|
- Part-Cell implemented into AIM; check that Heat & Water are conserved |
| 2413 |
|
- aim.5l_cs: use new aim pkg (run 10yr & get better results than before) |
| 2414 |
|
- aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg |
| 2415 |
|
o add diagnostic of surface correction term in monitor output |
| 2416 |
|
|
| 2417 |
|
o bulk_force and therm_seaice |
| 2418 |
|
- Two packages: bulk_force (Bulk forcing) |
| 2419 |
|
and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 |
| 2420 |
|
- Earlier integration from Stephaine Dutkiewicz |
| 2421 |
|
and Patrick Heimbach. |
| 2422 |
|
- Two ifdef statements for compile time, |
| 2423 |
|
ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE |
| 2424 |
|
|
| 2425 |
|
checkpoint47 |
| 2426 |
|
differentiable version of checkpoint46n_post |
| 2427 |
|
o bug fix in quasihydrostaticterms |
| 2428 |
|
o * "clean" adjoint code (in terms of extensive recomputations) |
| 2429 |
|
can now be obtained for all GMREDI options (i.e. for |
| 2430 |
|
- GM_VISBECK_VARIABLE_K |
| 2431 |
|
- GM_NON_UNITY_DIAGONAL |
| 2432 |
|
- GM_EXTRA_DIAGONAL |
| 2433 |
|
- GM_BOLUS_ADVEC ) |
| 2434 |
|
* However, wrong gradient check problem remains unsolved. |
| 2435 |
|
* New CPP options have been introduced for different |
| 2436 |
|
tapering schemes |
| 2437 |
|
o external_fields_load now part of differentiation list |
| 2438 |
|
o pressure needs multiple storing; |
| 2439 |
|
would be nice to have store_pressure at beginning or |
| 2440 |
|
end of forward_step, e.g. by having phiHyd global (5-dim.) |
| 2441 |
|
(NB: pressure is needed for certain cases in find_rho, |
| 2442 |
|
which is also invoked through convective_adjustment). |
| 2443 |
|
o recomputations in find_rho for cases |
| 2444 |
|
'JMD95'/'UNESCO' or 'MDJWF' are OK. |
| 2445 |
|
o #define ATMOSPHERIC_LOADING should be differentiable |
| 2446 |
|
o ini_forcing shifted to begining of initialise_varia |
| 2447 |
|
o Incorporating QNVS line search routines into MITgcm |
| 2448 |
|
(this is separate code, and therefore not under pkg) |
| 2449 |
|
lsopt/, optim/ |
| 2450 |
|
o Updated verification/carbon/ |
| 2451 |
|
- #define GM_VISBECK_VARIABLE_K |
| 2452 |
|
- GM_taper_scheme = 'ldd97' |
| 2453 |
|
|
| 2454 |
|
checkpoint46n_post |
| 2455 |
|
Merging from release1_p8: |
| 2456 |
|
o verification/natl_box: |
| 2457 |
|
updating new external_fields_load routine |
| 2458 |
|
o New package: pkg/seaice |
| 2459 |
|
Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). |
| 2460 |
|
The sea-ice code is based on Hibler (1979-1980). |
| 2461 |
|
Two sea-ice dynamic solvers, ADI and LSR, are included. |
| 2462 |
|
In addition to computing prognostic sea-ice variables and diagnosing |
| 2463 |
|
the forcing/external data fields that drive the ocean model, |
| 2464 |
|
SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
| 2465 |
|
The implied surface heat flux is then stored in variable |
| 2466 |
|
surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and |
| 2467 |
|
kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the |
| 2468 |
|
non-local transport term. Because this call precedes model |
| 2469 |
|
thermodynamics, temperature under sea-ice may not be "exactly" at |
| 2470 |
|
the freezing point by the time theta is dumped or time-averaged. |
| 2471 |
|
N.B.: fairly large differences in accuracy occur across |
| 2472 |
|
different platforms/compilers; comparison between |
| 2473 |
|
g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) |
| 2474 |
|
generated output gives: |
| 2475 |
|
T S U V |
| 2476 |
|
C D M c m s m s m s m s |
| 2477 |
|
n p a R g m m e . m m e . m m e . m m e . |
| 2478 |
|
f n k u 2 i a a d i a a d i a a d i a a d |
| 2479 |
|
g d e n d n x n . n x n . n x n . n x n . |
| 2480 |
|
|
| 2481 |
|
Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea |
| 2482 |
|
o GAD: |
| 2483 |
|
- generated new common blocks to account for call of |
| 2484 |
|
same gad routines with differing traceridentities |
| 2485 |
|
(needed to modify tracerIdentity indices in GAD.h) |
| 2486 |
|
- generated separate common blocks for case useCubedSphereExchange |
| 2487 |
|
(Department of Futurology) |
| 2488 |
|
- parameter lists to gmredi_?transport: added tracerIdentity |
| 2489 |
|
- added new key indices to tamc.h |
| 2490 |
|
o external_fields_load: |
| 2491 |
|
- added this routine to TAF list |
| 2492 |
|
- needed to make some common blocks global and additional storing |
| 2493 |
|
along the same lines as exf package (checkpoint_lev?_directives.h) |
| 2494 |
|
o exf: |
| 2495 |
|
updated external forcing package |
| 2496 |
|
- bug fixes carried over from ecco-branch |
| 2497 |
|
(missing OBCS_OPTIONS.h in two routines) |
| 2498 |
|
- enable easy to use "no forcing". |
| 2499 |
|
- added exf I/O for atmospheric loading |
| 2500 |
|
- added exf I/O for runoff data |
| 2501 |
|
- transfered scaling between exf <-> MITgcm to exf namelist |
| 2502 |
|
o Adding new verification experiment global_with_exf. |
| 2503 |
|
This verification experiment is almost identical to the |
| 2504 |
|
global_ocean.90x40x15 experiment, except that it uses |
| 2505 |
|
the exf (and cal) package instead of the |
| 2506 |
|
external_fields_load routine (cf README file). |
| 2507 |
|
|
| 2508 |
|
checkpoint46m_post |
| 2509 |
|
o modified testscript to return -- when there are no lines of "%MON" output |
| 2510 |
|
o added new flag "quasiHydrostatic" for QH mode |
| 2511 |
|
and new routine quasihydrostaticterms() |
| 2512 |
|
o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
| 2513 |
|
New routine: mom_u_coriolis_nh() |
| 2514 |
|
o fixed sign of non-hydrostatic metric terms in u and v equations. |
| 2515 |
|
Depend on correct sign of gravitySign. |
| 2516 |
|
o added work.pc* to .cvsignore in aim directories using ifc |
| 2517 |
|
o introduced flag for controllin non-hydrostatic metric terms |
| 2518 |
|
o removed gravitySign from PARM04 |
| 2519 |
|
o switched to g77/ifc from pgf77 in aim experiments |
| 2520 |
|
|
| 2521 |
|
checkpoint46l_post |
| 2522 |
|
o made convective adjustment work with pressure coordinates: |
| 2523 |
|
- changed the direction of k-loop in convective_adjustment.F for the |
| 2524 |
|
case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
| 2525 |
|
- adjusted the reference pressure k-index in convective_adjustment.F |
| 2526 |
|
- adjusted the convection condition in convect.F (in analogy to |
| 2527 |
|
calc_ivdc.F) |
| 2528 |
|
- convective_adjustment no longer computes anything on the halos |
| 2529 |
|
- removed the warnings about negative salinity from find_rho.F and |
| 2530 |
|
find_alpha.F; instead the new routine look_for_neg_salinity, called |
| 2531 |
|
at the beginning of find_rho, find_alpha, and find_beta, does a |
| 2532 |
|
check of the entire slice, if CPP-option |
| 2533 |
|
CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined |
| 2534 |
|
checkpoint46l_pre |
| 2535 |
|
|
| 2536 |
|
checkpoint46k_post |
| 2537 |
|
o fixed the verification/global_ocean.90x40x15 experiment: |
| 2538 |
|
- new bathymetry (the world according to A., JMC, and M.) |
| 2539 |
|
- new initial fields and forcing fields (*.bin files) |
| 2540 |
|
- new POLY3.COEFFS (for the next release one should switch to a full |
| 2541 |
|
equation of state: JMD95P or MDJWF) |
| 2542 |
|
- fixed several errors and redundancies in the data file |
| 2543 |
|
- experiment uses looped cells |
| 2544 |
|
- added matlab directory with diagnostic scripts for plotting of output |
| 2545 |
|
|
| 2546 |
|
o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
| 2547 |
|
- read AIM physics parameters from a file (data.aimphys) |
| 2548 |
|
- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
| 2549 |
|
|
| 2550 |
|
checkpoint46j_post |
| 2551 |
|
o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
| 2552 |
|
o move wVel computation at the end of the time step, in S/R integr_continuity |
| 2553 |
|
o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
| 2554 |
|
o update timeave pkg for wVel diagnostic. |
| 2555 |
|
checkpoint46j_pre |
| 2556 |
|
|
| 2557 |
|
checkpoint46i_post |
| 2558 |
|
o Clean up AIM package (and keep the results unchanged): |
| 2559 |
|
include CPP_OPTION and use IMPLICT NONE in all routines ; |
| 2560 |
|
declare all the variables _RL ; use _d 0 for all numerical constants. |
| 2561 |
|
use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
| 2562 |
|
|
| 2563 |
|
checkpoint46h_post |
| 2564 |
|
o cleaned up the use of rhoNil and rhoConst. |
| 2565 |
|
- rhoNil should only appear in the LINEAR equation of state, everywhere |
| 2566 |
|
else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
| 2567 |
|
and the dynamical equations are all divided by rhoConst |
| 2568 |
|
o introduced new parameter rhoConstFresh, a reference density of fresh |
| 2569 |
|
water, to remove the fresh water flux's dependence on rhoNil. The default |
| 2570 |
|
value is 999.8 kg/m^3 |
| 2571 |
|
o cleanup up external_forcing.F and external_forcing_surf.F |
| 2572 |
|
- can now be used by both OCEANIC and OCEANICP |
| 2573 |
|
checkpoint46h_pre |
| 2574 |
|
|
| 2575 |
|
Added code to convert surface volume flux (fresh water) into |
| 2576 |
|
a mass flux when using P coordinates in the ocean (OCEANICP). |
| 2577 |
|
Note: It assumes you have set rho0=rhoConst=density of fresh water. |
| 2578 |
|
|
| 2579 |
|
checkpoint46g_post |
| 2580 |
|
o Include a new diagnostic variable phiHydLow for the ocean model |
| 2581 |
|
- in z-coordinates, it is the bottom pressure anomaly |
| 2582 |
|
- in p-coordinates, it is the sea surface elevation |
| 2583 |
|
- in both cases, these variable have global drift, reflecting the mass |
| 2584 |
|
drift in z-coordinates and the volume drift in p-coordinates |
| 2585 |
|
- included time averaging for phiHydLow, be aware of the drift! |
| 2586 |
|
o depth-dependent computation of Bo_surf for pressure coordinates |
| 2587 |
|
in the ocean (buoyancyRelation='OCEANICP') |
| 2588 |
|
- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
| 2589 |
|
Theta, Salinity, and Pressure in the parameter list. This routine is |
| 2590 |
|
presently contained in find_rho.F. This routine does not give the |
| 2591 |
|
correct density for 'POLY3', which would be a z-dependent reference |
| 2592 |
|
density. |
| 2593 |
|
o cleaned up find_rho |
| 2594 |
|
- removed obsolete 'eqn' from the parameter list. |
| 2595 |
|
o added two new verification experiments: gop and goz |
| 2596 |
|
(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
| 2597 |
|
checkpoint46g_pre |
| 2598 |
|
|
| 2599 |
|
checkpoint46f_post |
| 2600 |
|
o Enable tangent linear (forward mode) gradient checks: |
| 2601 |
|
- extended active file handling to g_... files |
| 2602 |
|
- added TANGENT_SIMULATION to theSimulationMode |
| 2603 |
|
- extended grdchk package accordingly |
| 2604 |
|
o added tangent linear setup in verification/carbon/code_ftl |
| 2605 |
|
o added adjoint setup in verification/front_relax/code_ad |
| 2606 |
|
|
| 2607 |
|
checkpoint46e_post |
| 2608 |
|
o Added new equation of state -> MDJWF |
| 2609 |
|
- EOS of McDougall et al., 2002, JAOT, submitted |
| 2610 |
|
- caveat: the equation of state is only valid for a smaller (more |
| 2611 |
|
realistic?) range of values than JMD95P/Z and UNESCO |
| 2612 |
|
- added masks to the calculation of pressure in store_pressure |
| 2613 |
|
- added more check values for density in check_eos (ini_eos.F), some of |
| 2614 |
|
the old check values are out of the range of the MDJWF-eos, so don't |
| 2615 |
|
expect perfect matches for those |
| 2616 |
|
checkpoint46e_pre |
| 2617 |
|
|
| 2618 |
|
checkpoint46d_post |
| 2619 |
|
o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
| 2620 |
|
'OCEANICP', also initialised field pressure correctly in ini_eos in the |
| 2621 |
|
case of pressure coordinates. eosType='JMD95Z' in |
| 2622 |
|
combination with buoyancyRelation='OCEANICP' now causes an error. |
| 2623 |
|
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
| 2624 |
|
in find_alpha/beta. |
| 2625 |
|
checkpoint46d_pre |
| 2626 |
|
|
| 2627 |
|
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
| 2628 |
|
so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
| 2629 |
|
|
| 2630 |
|
checkpoint46c_post |
| 2631 |
|
o Changes necessary for ocean in p-coordinates |
| 2632 |
|
- Added new buoyancy relation = 'OCEANICP' |
| 2633 |
|
- Added new parameters = gravitySign (this used to be contained inside |
| 2634 |
|
the factor dRdZ which I added when we first switched to R coordinates). |
| 2635 |
|
X GM/Redi is not compatible (yet) |
| 2636 |
|
X bottom drag and no-slip need to be debugged. |
| 2637 |
|
checkpoint46c_pre |
| 2638 |
|
|
| 2639 |
|
checkpoint46b_post |
| 2640 |
|
o Added new equation of state -> JMD95Z and JMD95P |
| 2641 |
|
- EOS of Jackett and McDougall, 1995, JAOT |
| 2642 |
|
- moved all EOS parameters into EOS.h |
| 2643 |
|
- new routines ini_eos.F, store_pressure.F |
| 2644 |
|
o Added UNESCO EOS, but not recommended because it requires |
| 2645 |
|
in-situ temperature (see JMD95) |
| 2646 |
|
o Modified formatting for knudsen2.f in utils/knudsen2 and added |
| 2647 |
|
unesco.f to be used with POLY3 |
| 2648 |
|
checkpoint46b_pre |
| 2649 |
|
|
| 2650 |
|
checkpoint46a_post |
| 2651 |
|
o Added (atmospheric) pressure loading |
| 2652 |
|
- new field in FFIELDS.h, etc... |
| 2653 |
|
- new cpp flag ATMOSPHERIC_LOADING |
| 2654 |
|
o Changed hFacC to _hFacC in calc_phi_hyd.F |
| 2655 |
|
o Added SHORTWAVE_HEATING to some files for consistency |
| 2656 |
|
checkpoint46a_pre |
| 2657 |
|
|
| 2658 |
|
checkpoint46 |
| 2659 |
|
further merges from release1_p5 |
| 2660 |
|
o new ctrl package |
| 2661 |
|
- adopted from ECCO environment to enable optimization |
| 2662 |
|
- added Eliassen Palm fluxes to controls |
| 2663 |
|
o added Eliassen Palm flux controls to gradient check package |
| 2664 |
|
o cost package |
| 2665 |
|
- Compatible with new ctrl package |
| 2666 |
|
- added Eliassen Palm cost hooks |
| 2667 |
|
- modif's of existing cost functions |
| 2668 |
|
o Adjoint-related bug fixes in kpp: |
| 2669 |
|
- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
| 2670 |
|
- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
| 2671 |
|
o autodiff package |
| 2672 |
|
- flow directives: |
| 2673 |
|
+ new for S/R do_the_model_io |
| 2674 |
|
+ enhanced for S/R checkpoint |
| 2675 |
|
+ new gmredi.flow |
| 2676 |
|
- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
| 2677 |
|
disable adcommon.h/g_common.h by default. |
| 2678 |
|
- fixed problem for adjoint of global_max |
| 2679 |
|
o modified verification/carbon/ |
| 2680 |
|
o New setup for adjoint of global_ocean |
| 2681 |
|
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
| 2682 |
|
o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
| 2683 |
|
o incorporated hooks for sponge layer code (external_forcing.F) |
| 2684 |
|
|
| 2685 |
|
checkpoint45d_post |
| 2686 |
|
o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
| 2687 |
|
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
| 2688 |
|
(affects plume_on_slope "cg2d" output) |
| 2689 |
|
o add new parameter deltaTfreesurf for free-surface time stepping |
| 2690 |
|
o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
| 2691 |
|
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
| 2692 |
|
o change phiMin in exp1 (to agree with documentation) |
| 2693 |
|
o add new flags: |
| 2694 |
|
- T,S forcing inside/outside Adams-Bashforth |
| 2695 |
|
- turn off temp,salt advection and/or forcing |
| 2696 |
|
- for each tracer, define internal flag for multiDimAdvection & A-B |
| 2697 |
|
o monitor: change definition of KE to check conservation of Energy |
| 2698 |
|
|
| 2699 |
|
checkpoint45c_post |
| 2700 |
|
o Removed f90 comments ("!") |
| 2701 |
|
o Modified initialisations to enable exf package for MITgcm |
| 2702 |
|
(without invoking ECCO_PACKAGE). |
| 2703 |
|
o modifications to gradient check package (Martin Losch) |
| 2704 |
|
- enable centered differences |
| 2705 |
|
- modified format of standard output |
| 2706 |
|
|
| 2707 |
|
checkpoint45b_post |
| 2708 |
|
o cleaned exchange calls in cg2d |
| 2709 |
|
o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
| 2710 |
|
o included CPP option SINGLE_LAYER_MODE in thermodynamics |
| 2711 |
|
to configure barotropic setup (Martin Losch) |
| 2712 |
|
o moved some initialisations within bi,bj loop in dynamics |
| 2713 |
|
(TAF flow dependency) |
| 2714 |
|
o in initialise_varia, moved call packages_init_variables |
| 2715 |
|
before convective_adjustment_init |
| 2716 |
|
(corresponding adjustment of TAF tape initialisation). |
| 2717 |
|
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
| 2718 |
|
|
| 2719 |
|
checkpoint45a_post |
| 2720 |
|
o compute Rho over the whole domain (extend iMin,jMin indices) |
| 2721 |
|
o specific exchange for X-slice domain (case Ny=1) |
| 2722 |
|
o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
| 2723 |
|
o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
| 2724 |
|
|
| 2725 |
|
checkpoint44h_post = checkpoint45 |
| 2726 |
|
o Fix to restore differentiability: |
| 2727 |
|
place at which packages_init_variables is called in |
| 2728 |
|
initialise_varia is crucial for reverse control flow. |
| 2729 |
|
o modifications in GMRedi to enable stable adjoint |
| 2730 |
|
(corresponding modif's in thermodynamics, dynamics) |
| 2731 |
|
o added missing hook for sponge layer code in external_forcing |
| 2732 |
|
o modified test cost functions |
| 2733 |
|
o storing in gad_advection (plus removal of write(0,*)! |
| 2734 |
|
o missing headers TR1.h added in convective_adjustment routines |
| 2735 |
|
o errorMessageUnit set non-equal zero in eeboot |
| 2736 |
|
(conflict on some platforms, e.g. IBM SP3) |
| 2737 |
|
o modified carbon verif. |
| 2738 |
|
|
| 2739 |
|
checkpoint44h_pre |
| 2740 |
|
o vertical grid option: allow to put the Interface at the middle between |
| 2741 |
|
2 cell-centers ; replace delZ in pkg/kpp by drF. |
| 2742 |
|
o GM Advective form: Tracers are advected using the residual transport (= |
| 2743 |
|
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
| 2744 |
|
|
| 2745 |
|
checkpoint44g_post |
| 2746 |
|
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
| 2747 |
|
results) ; ifdef missing in thermodynamics.F |
| 2748 |
|
|
| 2749 |
|
checkpoint44f_pre,checkpoint44f_post |
| 2750 |
|
o added PTRACERS package |
| 2751 |
|
This allows an arbitrary number of passive tracers to be integrated |
| 2752 |
|
forward simultaneously with the dynamicaly model. |
| 2753 |
|
+ Implemented so far: |
| 2754 |
|
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
| 2755 |
|
- I/O and checkpointing |
| 2756 |
|
- GM/Redi *but* using the GM/Redi coefficient of Salt |
| 2757 |
|
+ Not implemented so far: |
| 2758 |
|
- KPP |
| 2759 |
|
- OBCS |
| 2760 |
|
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
| 2761 |
|
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
| 2762 |
|
line in data.pkg. |
| 2763 |
|
+ This package is disabled by default since it increases storage. |
| 2764 |
|
|
| 2765 |
|
|
| 2766 |
|
o testscript: added -cleanup option |
| 2767 |
|
o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
| 2768 |
|
b) enable to filter 2D fields. |
| 2769 |
|
|
| 2770 |
|
checkpoint44e_pre,post |
| 2771 |
|
o re-wrote convective adjustment to use pre-calculated weights |
| 2772 |
|
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
| 2773 |
|
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
| 2774 |
|
Original calls to convect() still in place. |
| 2775 |
|
|
| 2776 |
|
chkpt44d_pre,post |
| 2777 |
|
o added missing EXCLUDE_MONITOR flags |
| 2778 |
|
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
| 2779 |
|
(incompatible typ in MIN/MAX expressions caused problems |
| 2780 |
|
on IBM SP3) |
| 2781 |
|
o in genmake added variable MAKEDEPEND |
| 2782 |
|
plus resetting for case SunOS |
| 2783 |
|
o added timer_stats.c routine for IBM SP3 |
| 2784 |
|
o removed variables in dynamics |
| 2785 |
|
!!! I forgot to create tag chkpt44d_pre !!! |
| 2786 |
|
!!! But chkpt44d_pre = chkpt44c_post !!! |
| 2787 |
|
|
| 2788 |
|
o real fresh water flux implemented with non-linear free-surface. |
| 2789 |
|
|
| 2790 |
|
chkpt44c_pre,post |
| 2791 |
|
o few fix (mask in shap_s2, EmPmR in external_field_load, |
| 2792 |
|
USE_NATURAL_BCS in solve_for_P); |
| 2793 |
|
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
| 2794 |
|
|
| 2795 |
|
checkpoint44b_pre/_post |
| 2796 |
|
o merge of relevant stuff from the ecco-branch: |
| 2797 |
|
- genmake: removed $S64 overwrite for case SunOS |
| 2798 |
|
- pkg/exf: update and corrections for field swapping and obcs |
| 2799 |
|
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
| 2800 |
|
harmonized between ECCO and MITgcm |
| 2801 |
|
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
| 2802 |
|
updated checkpointing_lev... lists for obcs |
| 2803 |
|
- model/src: minor changes in forward_step, plot_field |
| 2804 |
|
added directive for divided adjoint in the_main_loop |
| 2805 |
|
- pkg/mdsio: added mdsio_gl_slice |
| 2806 |
|
|
| 2807 |
|
o check parameters & config (chkpt44a_pre,post) |
| 2808 |
|
o OBC and NonLin_FrSurf. |
| 2809 |
|
|
| 2810 |
|
checkpoint44 |
| 2811 |
|
o fix bug in mom_vi_del2uv |
| 2812 |
|
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
| 2813 |
|
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
| 2814 |
|
o update AIM experiments (NCEP input files) |
| 2815 |
|
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
| 2816 |
|
o added some stuff for AD |
| 2817 |
|
|
| 2818 |
|
checkpoint43 |
| 2819 |
|
o added two new advection tests |
| 2820 |
|
o added global 4x4 degree ocean test |
| 2821 |
|
o added test of H&S94 with free surface on cube |
| 2822 |
|
o some final mods for gradient check, adjoint,... |
| 2823 |
|
|
| 2824 |
|
checkpoint42 |
| 2825 |
|
Fixed AD-related problems: |
| 2826 |
|
o Store directives up-to-date with re-arranged Adams-Bashforth |
| 2827 |
|
(mainly thermodynamics.F) |
| 2828 |
|
o New store directives for multi-dim. advection schemes |
| 2829 |
|
* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
| 2830 |
|
* new common block and key passkey |
| 2831 |
|
(mainly gad_advection.F) |
| 2832 |
|
o Modified store directives for split of dynamics/thermodynamics |
| 2833 |
|
for the case ALLOW_KPP |
| 2834 |
|
o Cleaned argument list for timestep_tracer.F |
| 2835 |
|
|
| 2836 |
|
checkpoint41 |
| 2837 |
|
o re-formatted/added comments in prologues of key subroutines |
| 2838 |
|
to work with protex |
| 2839 |
|
|
| 2840 |
|
checkpoint40 |
| 2841 |
|
o moved calc_gs, calc_gt and calc_tr1 back to model/src |
| 2842 |
|
o added FLT (floats) package from Arne along with demo. experiment |
| 2843 |
|
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
| 2844 |
|
implementation of forward-in-time forcing terms |
| 2845 |
|
o more mods for non-linear free-surface including new variable |
| 2846 |
|
o modified multi-dim method to work on cube |
| 2847 |
|
o bug fix in KPP (from DM) |
| 2848 |
|
|
| 2849 |
|
checkpoint40pre9 |
| 2850 |
|
o added DST advection schemes |
| 2851 |
|
o fix MPI bug on SGI's |
| 2852 |
|
o modifications for non-linear free-surface |
| 2853 |
|
o fixed conditionals for fixed flow/passive tracer only mode |
| 2854 |
|
o added tension/strain form of stress tensor |
| 2855 |
|
o changes to commenting of arguments for TAF/TAMC |
| 2856 |
|
o added/updated many matlab scripts |
| 2857 |
|
o added multi-dimensional advection method for tracers |
| 2858 |
|
|
| 2859 |
|
checkpoint40pre8 |
| 2860 |
|
o new package rw/ |
| 2861 |
|
Added method for dumping intermediate local arrays: |
| 2862 |
|
mdsio_writetile - same as mdsio_writefield except works from inside |
| 2863 |
|
bi,bj loop |
| 2864 |
|
mdsio_writelocal - same as mdsio_writetile except works for local |
| 2865 |
|
arrays |
| 2866 |
|
write_local_r? - higher-level wrapper for mdsio_writelocal |
| 2867 |
|
Controlled by diagFreq. Defaults to zero (ie. no dumps) |
| 2868 |
|
Example given at end of mom_vecinv.F that dumps some local arrays. |
| 2869 |
|
o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
| 2870 |
|
control flux-form versus vector invariant code. |
| 2871 |
|
Switch is runtime flag vectorInvariantMomentum (defaults to false) |
| 2872 |
|
or genmake -DISABLE ... |
| 2873 |
|
o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
| 2874 |
|
(additional storing is now needed for case vecinv; |
| 2875 |
|
currently nothing implemented to switch this storing off |
| 2876 |
|
in case fluxform is used since no CPP flag available). |
| 2877 |
|
|
| 2878 |
|
checkpoint40pre7 |
| 2879 |
|
o bug fix in dynamics.F |
| 2880 |
|
calc_viscosity called before k=1,Nr loop. |
| 2881 |
|
o added some #ifdef's ALLOW_PASSIVE_TRACER |
| 2882 |
|
o cleaned initialisations in ctrl_map_ini |
| 2883 |
|
related to TAF |
| 2884 |
|
|
| 2885 |
|
checkpoint40pre6 |
| 2886 |
|
o split dynamics into thermodynamics & dynamics |
| 2887 |
|
o corresponding split of calc_diffusivity into |
| 2888 |
|
calc_diffusivity, calc_viscosity |
| 2889 |
|
(kpp_calc_diff, kpp_calc_visc). |
| 2890 |
|
o Added diffkr, kapgm to control variables |
| 2891 |
|
o bug fix in gmredi_slope_limit for ldd97 |
| 2892 |
|
|
| 2893 |
|
checkpoint40pre5 |
| 2894 |
|
o proper initialization of Adams-Bashforth time stepping |
| 2895 |
|
+ uses forward step for very first step of model (iter=0) |
| 2896 |
|
o re-generated *all* output since almost all output is modified by this |
| 2897 |
|
change (sorry but we've been putting this one off for about 2 years) |
| 2898 |
|
+ natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were |
| 2899 |
|
*not* regenerated since they are already out of date and I don't |
| 2900 |
|
want to create the impression that they are suddenly working. |
| 2901 |
|
o removed KAP stuff for DEC's |
| 2902 |
|
o modified/added many .cvsignore files in */code and */input |
| 2903 |
|
o added new expt "solid-body.cs-32x32x1" |
| 2904 |
|
+ this uses an alternative form of ini_curvilinear_grid.F which |
| 2905 |
|
is not necessarily any better than the current one... |
| 2906 |
|
|
| 2907 |
|
checkpoint40pre4 |
| 2908 |
|
o added re-initialisations of utrans,vtrans,rtrans in |
| 2909 |
|
calc_common_factors which are crucial for TAF. |
| 2910 |
|
o extended iMin,jMin range for calc_common_factors, |
| 2911 |
|
calc_diffusivity |
| 2912 |
|
o added option ALLOW_PASSIVE_TRACER |
| 2913 |
|
o a few minor updates and fixes |
| 2914 |
|
|
| 2915 |
|
checkpoint40pre3 |
| 2916 |
|
o created calc_gtr1.F for gad package |
| 2917 |
|
o split the_main_loop and re-introduced forward_step |
| 2918 |
|
o some recomputations of nIter0 for TAMC |
| 2919 |
|
|
| 2920 |
|
checkpoint40pre2 |
| 2921 |
|
o Updated to latest branch of AJA, JMC |
| 2922 |
|
o Added gradient check package |
| 2923 |
|
o Added routines for passive tracer handling |
| 2924 |
|
o Added carbon sequestration sensitivity experiment |
| 2925 |
|
|
| 2926 |
|
checkpoint39 |
| 2927 |
|
o Modifications and fixes to support TAMC |
| 2928 |
|
(mainly missing or wrong directives) |
| 2929 |
|
o Corrected common blocks when fooling TAMC to produce adjoint I/O |
| 2930 |
|
in addummy_in_stepping |
| 2931 |
|
o Updated verification/vero/ (bug fixes in code/, correct pickups in input/) |
| 2932 |
|
o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs. |
| 2933 |
|
o Included following packages: |
| 2934 |
|
cal: calendar |
| 2935 |
|
exf: external forcing |
| 2936 |
|
ecco: essential routines to control use of cal, exf |
| 2937 |
|
(NB: this is not the full ECCO environment) |
| 2938 |
|
o disabled some packages by default in genmake |
| 2939 |
|
|
| 2940 |
|
checkpoint38 |
| 2941 |
|
o see notes_c37_adj.txt |
| 2942 |
|
o corrected wrong layer index in external_forcing_t |
| 2943 |
|
o replaced the_main_loop/forward_step by the_main_loop |
| 2944 |
|
o removed forceoutput from write_state |
| 2945 |
|
(replaced criteria for initial/final state) |
| 2946 |
|
o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
| 2947 |
|
|
| 2948 |
|
checkpoint37 |
| 2949 |
|
o mdsio.F routine split and packaged in pkg/mdsio |
| 2950 |
|
(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
| 2951 |
|
used unless genmake -disable=mdsio) |
| 2952 |
|
o allow a more precise surface-geopotential gradient for the atmosphere |
| 2953 |
|
taking into account the change in space of Alpha (=1/rho) at the surface. |
| 2954 |
|
o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit] |
| 2955 |
|
(ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa]) |
| 2956 |
|
o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and |
| 2957 |
|
Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential |
| 2958 |
|
[m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere). |
| 2959 |
|
o Time-Average diagnostics defined as a pseudo package "timeave". |
| 2960 |
|
o pickup files : old pickup (before c35) did not work with new code (c35 |
| 2961 |
|
and after) unless activating 2 commented lines in initialise-varia. |
| 2962 |
|
o Non-Hydrostatic pickup file Pb fixed. |
| 2963 |
|
o bug with Rigid-lid version (since c35) fixed. |
| 2964 |
|
|
| 2965 |
|
checkpoint36 |
| 2966 |
|
o implement Crank-Nickelson barotropic time-stepping |
| 2967 |
|
o recover Time-Average diagnostics |
| 2968 |
|
o fix Pb in checkpoint (PR#19) |
| 2969 |
|
o AIM become a standard package ; clean unused CPP_kees |
| 2970 |
|
|
| 2971 |
|
checkpoint35 |
| 2972 |
|
o subtantial rewrite of dynamics.f |
| 2973 |
|
o allows staggered time-stepping |
| 2974 |
|
o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
| 2975 |
|
o added bottom drag (linear + quadratic) |
| 2976 |
|
|
| 2977 |
|
checkpoint34 |
| 2978 |
|
o Modified exchange routines for correct reverse simulation. |
| 2979 |
|
o Added verification output to comply with bug fix in impldiff.F |
| 2980 |
|
as of c33 (exp2, natl_box). |
| 2981 |
|
o Corrected store directives in dynamics.F |
| 2982 |
|
o Corrected array boundaries in impldiff.F |
| 2983 |
|
o Corrected array dimensions in gmredi. |
| 2984 |
|
Added temporary scalars to avoid storage by TAMC (gmredi, kpp). |
| 2985 |
|
o Added routine GLOBAL_SUM_INT to global_sum.F |
| 2986 |
|
o Added mdsio_gl.F for ECCO purposes. |
| 2987 |
|
|
| 2988 |
|
checkpoint33 |
| 2989 |
|
o Fixed bug in lower BC in impldiff.F |
| 2990 |
|
o Fixed confusion about units of forcing arrays in FFIELDS.h |
| 2991 |
|
namely Fu,Fv,Qnet,Qsw,EmPmR: |
| 2992 |
|
- Removed verification/natl_box/code/external_fields_scale.F |
| 2993 |
|
(did not differ from that in model/src) |
| 2994 |
|
- Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units |
| 2995 |
|
(see FFIELDS.h for description) |
| 2996 |
|
- Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F, |
| 2997 |
|
kpp_calc.F and kpp_transport_t.F |
| 2998 |
|
- Removed model/src/external_fields_scale.F and calls to it |
| 2999 |
|
- verification/natl_box uses flux data with "atmospheric" sign so |
| 3000 |
|
a special version of external_fields_load.F is used to |
| 3001 |
|
change the data as it's read in. This way, the arrays |
| 3002 |
|
have the right units and signs at all times tha a user could |
| 3003 |
|
possibly use them. |
| 3004 |
|
o Corrected genmake to delete a temporary file during configuration |
| 3005 |
|
|
| 3006 |
|
checkpoint32 |
| 3007 |
|
o Scaling of forcing fields moved from external_forcing.F to |
| 3008 |
|
external_fields_scale.F, called directly after loading fields. |
| 3009 |
|
o Surface relaxation terms added to surface tendency fields in |
| 3010 |
|
extra subroutine. |
| 3011 |
|
o impldiff.F changed to avoid storing by TAMC of huge intermediate |
| 3012 |
|
fields. |
| 3013 |
|
o Changes in GMRedi to comply with packaging structure. |
| 3014 |
|
o Modifications and bug fixes in KPP package. |
| 3015 |
|
o Verification experiment for KPP added (verification/nat_box/) |
| 3016 |
|
|
| 3017 |
|
checkpoint31 |
| 3018 |
|
o Packages interface brought in line with defined standard |
| 3019 |
|
-> new routines packages_...F |
| 3020 |
|
-> changes in initialise_fixed.F, initialise_varia.F |
| 3021 |
|
-> enables initialisation interface for ECCO package |
| 3022 |
|
o Rescaling of external forcing fields immediately after read |
| 3023 |
|
(removed from external_forcing.F) |
| 3024 |
|
-> new: surface_fields_scale.F |
| 3025 |
|
-> affects ini_foorcing.F, external_fields_load.F |
| 3026 |
|
o Computation of surface tendencies before tendency updates. |
| 3027 |
|
-> new: external_forcing_surf.F |
| 3028 |
|
o Change of variable names useGMRedi, useKPP, useECCO |
| 3029 |
|
o Further changes in dynamics.F, impldiff.F for TAMC |
| 3030 |
|
o Tested for experiments 0, 2, 4. |
| 3031 |
|
- not yet tested for GMRedi. |
| 3032 |
|
- not yet tested for KPP. |
| 3033 |
|
|
| 3034 |
|
checkpoint30 |
| 3035 |
|
o Updates for OBCs |
| 3036 |
|
o New experiment for test OBCs (internal_wave) |
| 3037 |
|
o New output.txt in verification/exp4/results/ |
| 3038 |
|
o Updates for KPP: calculation of viscosity corrected, new variables |
| 3039 |
|
kpp_dumpFreq and kpp_taveFreq |
| 3040 |
|
o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) |
| 3041 |
|
and entry for T90 in genmake |
| 3042 |
|
|
| 3043 |
|
checkpoint29 |
| 3044 |
|
o packaged KPP and GM/Redi |
| 3045 |
|
|
| 3046 |
|
checkpoint28 |
| 3047 |
|
o Corrected initialization of hFacMin for difference vertical coordinates |
| 3048 |
|
o Modified calculation of partial cell thickness to more robust algorithm |
| 3049 |
|
o config_summary.F: replaced write_1D_... by write_0D_... |
| 3050 |
|
read_write.F: added subroutines write_0D_... |
| 3051 |
|
o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho: |
| 3052 |
|
included some initialisations required for TAMC. |
| 3053 |
|
o routine calc_isoslopes: modified sqrt computation to make it |
| 3054 |
|
differentiable for zero argument. |
| 3055 |
|
o routines dynamics, impldiff: |
| 3056 |
|
included store directives and tape key computations required for TAMC. |
| 3057 |
|
o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC |
| 3058 |
|
|
| 3059 |
|
checkpoint27 |
| 3060 |
|
o fixed calc_isoslopes() to so that cancellation of terms in tensor |
| 3061 |
|
formulation works properly with variable resolution. |
| 3062 |
|
o restructured the calling tree between the_model_main() and dynamics() |
| 3063 |
|
o split initialise() into initialise_fixed() and initialise_varia() |
| 3064 |
|
o introduced initialization file pSurfInitFile for free surface (cg2d_x) |
| 3065 |
|
in new routine ini_psurf() |
| 3066 |
|
|
| 3067 |
|
checkpoint26 |
| 3068 |
|
o moved some #ifdef in optional routines to encompass everything |
| 3069 |
|
except the argument declarations. This was using up some memory. |
| 3070 |
|
o fixed macros like _ADT to work with both versions of Linux cpp |
| 3071 |
|
o cleaned up some unused and uninitialized variables |
| 3072 |
|
(helps when debugging with strict compile options) |
| 3073 |
|
o split up CPP_EEOPTIONS.h into options and macros |
| 3074 |
|
(macros are now in eesupp/inc/CPP_EEMACROS.h) |
| 3075 |
|
o patch for 2 processor JAM mode |
| 3076 |
|
|
| 3077 |
|
checkpoint25 |
| 3078 |
|
o updates for OBCs and NH |
| 3079 |
|
o dramatically reduced memory usage |
| 3080 |
|
o added "JAM" routines for use on Artic network |
| 3081 |
|
o parameterization of convection by implicit vertical diffusion |
| 3082 |
|
o added a diagnostic of convective index |
| 3083 |
|
o moved call to calc_divg_hat() from dynamics() to solve_for_pressure() |
| 3084 |
|
(this is was partly for OBCs and NH but also in anticipation of |
| 3085 |
|
an explicit free-surface option) |
| 3086 |
|
o initial state input files for U and V |
| 3087 |
|
|
| 3088 |
|
checkpoint24 |
| 3089 |
|
o Removed some spurious "REAL"s |
| 3090 |
|
o Updated KPP to latest version from JPL |
| 3091 |
|
o Added a COS(latitude) in horizontal viscosity |
| 3092 |
|
|
| 3093 |
|
checkpoint23 |
| 3094 |
|
o Added del^4 diffusion for salt and temperature |
| 3095 |
|
o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) |
| 3096 |
|
|
| 3097 |
|
checkpoint22 |
| 3098 |
|
o Made many small changes: implicit none, format(i5), etc... |
| 3099 |
|
o Introduced KPP mixing scheme (compiles and runs but *not* tested) |
| 3100 |
|
|
| 3101 |
|
checkpoint21 |
| 3102 |
|
o Introduced new I/O package that supports direct-access records (mdsio.F) |
| 3103 |
|
o Split-up mid-level I/O routines |
| 3104 |
|
o Updated input data for experiments 0,1,2,4 and 5 |
| 3105 |
|
o Finally removed the genmake.* scripts (everyone seems happy with genmake) |
| 3106 |
|
|
| 3107 |
|
checkpoint20 |
| 3108 |
|
o Tidied up open-boundaries some more |
| 3109 |
|
o Added non-hydrostatic code |
| 3110 |
|
o Fixed some input data |
| 3111 |
|
o Modified MPI start-up to work in "coupled" context. |
| 3112 |
|
|
| 3113 |
|
checkpoint19 |
| 3114 |
|
o Tidied up directory structure for verification experiments. |
| 3115 |
|
o Added new code for open boundaries. |
| 3116 |
|
o Corrected advective terms near boundaries. |
| 3117 |
|
o Added CPP flag for "old UV" geometry and corrected spherical geometry. |
| 3118 |
|
o Implemented free-slip/no-slip BCs and del^4 dissipation. |
| 3119 |
|
o Split default parameters out of ini_parms.F into set_defaults.F. |
| 3120 |
|
|
| 3121 |
|
checkpoint18 |
| 3122 |
|
o Further changes for optional code generation with |
| 3123 |
|
CPP - ugh! |
| 3124 |
|
|
| 3125 |
checkpoint17 |
checkpoint17 |
| 3126 |
o Beginning to incorporating modularity |
o Beginning to incorporating modularity |
| 3127 |
for supporting atmos. and ocean configs. |
for supporting atmos. and ocean configs. |
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