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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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checkpoint44g_post |
o eesupp: |
| 8 |
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- shift standardMessageUnit in eeboot.F and I/O units in mdsfindunit.F |
| 9 |
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for coupling to GEOS AGCM: HACK_FOR_GMAO_CPL option in CPP_EEOPTIONS.h |
| 10 |
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|
| 11 |
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checkpoint66k (2017/09/20) |
| 12 |
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o model/src: |
| 13 |
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- add missing CPP brackets (ALLOW_COST, ALLOW_CTRL in load_fields_driver.F |
| 14 |
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and the_model_main.F) |
| 15 |
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o ctrl: |
| 16 |
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- use zeroRL in place of fc when ALLOW_COST is not compiled (in ctrl_pack.F) |
| 17 |
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- call MDS_READ_FIELD / MDS_WRITE_FIELD instead of deprecated |
| 18 |
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mdsreadfield / mdswritefield (in ctrl_get_gen.F, ctrl_map_ini_gen.F, |
| 19 |
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ctrl_map_ini_genarr.F, and ctrl_map_ini_gentim2d.F ) |
| 20 |
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o eesupp: |
| 21 |
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- add CPP option to activate some pieces of code for coupling to GEOS AGCM; |
| 22 |
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- shift commonly used IO unit (in eeboot.F) for coupling to GEOS AGCM. |
| 23 |
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o pkg/bling: |
| 24 |
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- bling_production: Fix typo in calcium carbonate uptake. Also rearranging |
| 25 |
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and cleaning |
| 26 |
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o model/src: |
| 27 |
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- move k loop inside correction_step.F (+ update calling S/R) |
| 28 |
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- collect implicit pressure gradient tendencies in local 2-D array; |
| 29 |
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affect results (at machine truncation level) when using 3-D solver; update |
| 30 |
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output of exp.: exp4 (x1), global_ocean.cs32x15 (x2),hs94.cs-32x32x5.impIGW, |
| 31 |
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rotating_tank, short_surf_wave,tutorial_deep_convection (x2) |
| 32 |
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& tutorial_plume_on_slope. |
| 33 |
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|
| 34 |
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checkpoint66j (2017/08/15) |
| 35 |
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o pkg/ptracers: |
| 36 |
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- fix surface forcing under ice-shelf (useShelfIce=T). |
| 37 |
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o pkg/atm_phys: |
| 38 |
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- use hFac weighted average when applying A-grid atm-phys momentum tendency |
| 39 |
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to C-grid dynamics; this ensures wind-stress match mom tendency. |
| 40 |
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o eesupp/src: |
| 41 |
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- change default for opening scratch files to avoid STATUS='SCRATCH' |
| 42 |
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- close scratch files with STATUS='DELETE' |
| 43 |
|
- changes affect eeset_parms.F and open_copy_data_file.F and many routines |
| 44 |
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that read namelists (because they close the scratch files) |
| 45 |
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- you can revert to old default by setting USE_FORTRAN_SCRATCH_FILES |
| 46 |
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in CPP_EEOPTIONS.h (tested in ideal_2D_oce/code & lab_sea/code_ad) |
| 47 |
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o pkg/atm_phys: |
| 48 |
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- fix unset arguments in (unused) S/R surface_flux_0d. |
| 49 |
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o eesupp/src: |
| 50 |
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- add argument "procId" to S/R EESET_PARMS to fix scratchFile1 & 2 setting |
| 51 |
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(case TARGET_BGL or TARGET_CRAYXT) for early call (from eeboot_minimal.F): |
| 52 |
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called with myProcId in eeboot.F and with mpiMyWId in eeboot_minimal.F |
| 53 |
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o pkg/streamice: |
| 54 |
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- remove blank between _EXCH_XY_RL and "()", which my Apple Xcode |
| 55 |
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preprocessor /usr/bin/cpp cannot interpret; 3 instances in total in |
| 56 |
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streamice_driving_stress_fd.F and streamice_advect_2dtracer.F |
| 57 |
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o pkg/diagnostics: |
| 58 |
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- new option to allow to cumulate thickness-factor (hFac) weighted field |
| 59 |
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(if field permitted); implemented by changing sign of "jdiag" pointer |
| 60 |
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(> 0: cumlulate field, < 0: cumulate hFac weighted field). |
| 61 |
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a) restricted to 3-d (Nr levels), level centered diagnostics at U,V or Cell |
| 62 |
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center position (gcode(2)='U','V','M' & gcode(3,5,9:10)='R',' ','MR') |
| 63 |
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b) for now, activated by setting fileFlags 3rd character to 'h'. |
| 64 |
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|
| 65 |
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checkpoint66i (2017/07/18) |
| 66 |
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o pkg/cheapaml: |
| 67 |
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- add parameter "useRelativeWind", default set to False; this change the |
| 68 |
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previous setting which was always using relative wind. |
| 69 |
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o add hooks for the Parallel Data Assimilation Framework PDAF |
| 70 |
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(http://pdaf.awi.de/) in eeboot_minimal.F and the_main_loop.F; |
| 71 |
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to use set CPP-flag USE_PDAF in CPP_EEOPTIONS.h |
| 72 |
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o pkg/exf: |
| 73 |
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- interpolation of vector fields (exf_interp_uv.F): fix bug in calculation |
| 74 |
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of South-Pole mean value. |
| 75 |
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- interpolation near the poles, case where second additional row is at the |
| 76 |
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pole (or beyond the pole and moved to the pole): change first addition row |
| 77 |
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value to a linear interpolation between pole and 1rst (S.pole)/last (N.pole) |
| 78 |
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row (instead of just a copy of it). |
| 79 |
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o pkg/seaice: |
| 80 |
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- prevent JFNK and KRYLOV solvers from trying to reduce a residual of 0 |
| 81 |
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- add the option to compute no-slip du/dy, dv/dx (i.e. |
| 82 |
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the offdiagonal strain rate e12) by a second order approximation |
| 83 |
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on the boundary; works only with JFNK, KRYLOV, or EVP solvers, because |
| 84 |
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it is too messy to implement for the implicit LSR matrix. |
| 85 |
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SEAICE_2ndOrderBC = .FALSE. by default |
| 86 |
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|
| 87 |
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checkpoint66h (2017/06/02) |
| 88 |
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o pkg/seaice: |
| 89 |
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- add new routines to compute stress tensor components and stress tensor |
| 90 |
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divergence to be reused in s/r seaice_lsr and s/r seaice_calc_lhs |
| 91 |
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- change names of diagnostics SIsigI/II (commonly used for invariants) |
| 92 |
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to SIsig1/sig2 (more common for principal components) to avoid confusion |
| 93 |
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o pkf/exf: |
| 94 |
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- add a stop if useRelativeWind with un-updated uwind/vwind (e.g., constant); |
| 95 |
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similarly, stop if rotateStressOnAgrid with constant wind-stress. |
| 96 |
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o pkg/seaice: |
| 97 |
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- remove (comment out) diagnostics SIuwind,SIvwind,SIfu,SIfv (duplicate of |
| 98 |
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EXFuwind,EXFvwind,oceTAUX,oceTAUY) and point them to their equivalent. |
| 99 |
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- add diagnostics of wind-stress over seaice (SItaux,SItauy) and seaice |
| 100 |
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fraction weighted wind stress over ocean+seaice (SIatmTx,SIatmTy). |
| 101 |
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o pkg/diagnostics: |
| 102 |
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- small piece of code to rename (old) diagnostics, when namelist is processed. |
| 103 |
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o model/src: |
| 104 |
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- new run-time param (useMin4hFacEdges) to select method for setting hFacW,S: |
| 105 |
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originally, set as minimum of adjacent hFacC factor ; now (new default) |
| 106 |
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computed from rSurfW,S and rLowW,S by applying same rules as for hFacC. |
| 107 |
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Only matters when useShelfIce=T with particular ice-shelf cavity geometry. |
| 108 |
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o pkg/seaice: |
| 109 |
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- add momemtum advection, off by default, still in test phase |
| 110 |
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most of the momentum advection code is adapted and reused from mom_vecinv |
| 111 |
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o pkg/mom_vecinv: |
| 112 |
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- pass these runtime flags: |
| 113 |
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selectVortScheme, highOrderVorticity, upwindVorticity, useJamartMomAdv |
| 114 |
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as formal parameters to s/r mom_vi_u/v_coriolis, mom_vi_u/v_coriolis_c4, |
| 115 |
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so that these routines can also be used in pkg/seaice. |
| 116 |
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|
| 117 |
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checkpoint66g (2017/04/24) |
| 118 |
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o model/src: |
| 119 |
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- more robust ordering of column thickness integral (=Sum_k(drF*hFac) ) |
| 120 |
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to get same expression (regarding machine truncation) in different places |
| 121 |
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in ini_masks_etc.F (e.g., rSurfC,W,S is now exactly zero when it should). |
| 122 |
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Update forward output of experiments: global_ocean.cs32x15 (all 5 except |
| 123 |
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viscA4), isomip (x3), tutorial_global_oce_in_p & tutorial_plume_on_slope. |
| 124 |
|
o pkg/shelfice: |
| 125 |
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- ALLOW_SHIFWFLX_CONTROL: move setting of maskSHI from shelfice_update_masks.F |
| 126 |
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to shelfice_init_fixed.F |
| 127 |
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- change S/R SHELFICE_UPDATE_MASKS to SHELFICE_INIT_DEPTHS (still called from |
| 128 |
|
ini_masks_etc.F for now) to update ocean upper boundary position according |
| 129 |
|
to ice-shelf topography (instead of directly updating hFacC). |
| 130 |
|
o model/src: |
| 131 |
|
- move call to CTRL_INIT & CTRL_ADMTLM from the middle to the bottom of |
| 132 |
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packages_init_fixed.F to allow other pkgs to set mask and weight fields. |
| 133 |
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|
| 134 |
|
checkpoint66f (2017/04/06) |
| 135 |
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o model/src: |
| 136 |
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- add specific run-time param to select level of printed plot-field-maps, |
| 137 |
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set by default to debugLevel. Remove internal param "printDomain". |
| 138 |
|
o pkg/seaice: |
| 139 |
|
- add flag to add snow mass to seaiceMassC/U/V, the default is |
| 140 |
|
SEAICEaddSnowMass=.FALSE., not to change previous results |
| 141 |
|
o pkg/bling |
| 142 |
|
- Bug fix in bling_production regarding unit conversion for diagnostics |
| 143 |
|
being put in the wrong place |
| 144 |
|
o model/src: |
| 145 |
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- add back recomputation of rSurfW & S to ensure consistent column thickness |
| 146 |
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(needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only |
| 147 |
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when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F |
| 148 |
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revision 1.51) but was removed accidentally on 2014/02/08 (v1.53). |
| 149 |
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o pkg/autodiff: |
| 150 |
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- clean-up "checkpoint.flow" |
| 151 |
|
o pkg/rw (Contribution from Jody Klymak): |
| 152 |
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option to set mds file suffix as function of time in simulation: |
| 153 |
|
*) new input parameter "rwSuffixType" (read from PARM03 namelist) |
| 154 |
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to select file suffix format; by default (=0), use iteration number; |
| 155 |
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*) add simple routine to return file suffix according to rwSuffixType; |
| 156 |
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*) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice), |
| 157 |
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use new S/R to get file suffix, except for debug output file (diagFreq) |
| 158 |
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and pkgs offline & rbcs input files. |
| 159 |
|
o pkg/rw: |
| 160 |
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- uniform processing of "I10" suffix across writing fld routines; used to |
| 161 |
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simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F |
| 162 |
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(similar to cg3d.F, cg3d_ex0.F) |
| 163 |
|
o pkg/mom_vecinv: |
| 164 |
|
- highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted |
| 165 |
|
vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp). |
| 166 |
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o pkg/bling: |
| 167 |
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- Many small changes intended to clean the code. |
| 168 |
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Unnecessary ADJOINT_SAFEs removed ; |
| 169 |
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removed BLING_COST.h BLING_CTRL.h bling_cost.F ; |
| 170 |
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diagnostics added. |
| 171 |
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|
| 172 |
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checkpoint66e (2017/03/14) |
| 173 |
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o pkg/exf: |
| 174 |
|
- interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size |
| 175 |
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definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h; |
| 176 |
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use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to |
| 177 |
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avoid any dynamic allocation ; |
| 178 |
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- S/R EXF_CHECK: add new check & stop when file-name is defined but not |
| 179 |
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read-in ; add warning when file is read-in but not used within pkg/exf ; |
| 180 |
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+ check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC). |
| 181 |
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- update exf_summary.F (print {FLD}RepCycle). |
| 182 |
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o verification/global_with_exf: |
| 183 |
|
- switch on exf interpolation in AD test (just like the forward test) |
| 184 |
|
o pkg/mom_vecinv: |
| 185 |
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- add storage directives to avoid recomputations within mom_vecinv.F |
| 186 |
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which were generating seg. fault with gfortran -devel |
| 187 |
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o pkg/ctrl, pkg/smooth: |
| 188 |
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- initialize array halos which were generating seg. fault with |
| 189 |
|
gfortran -devel in adjoint mode |
| 190 |
|
o pkg/exf: |
| 191 |
|
- for each input field, enable to specify a field specific repeat-cycle |
| 192 |
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({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod". |
| 193 |
|
o verification/lab_sea: |
| 194 |
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- update AD results of primary test and noseaicedyn test after switching |
| 195 |
|
to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient |
| 196 |
|
check stays about the same. |
| 197 |
|
o pkg/exf: |
| 198 |
|
- fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T. |
| 199 |
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- exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat |
| 200 |
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o pkg/bling, USE_EXFCO2 code: |
| 201 |
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- add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default); |
| 202 |
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- update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD). |
| 203 |
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o pkg/exf: |
| 204 |
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- rename S/R EXF_INIT to EXF_INIT_VARIA ; |
| 205 |
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- add arguments: fldName (for debug msg) and fldRepeatCycle (set to |
| 206 |
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repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD) |
| 207 |
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and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ; |
| 208 |
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- add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed |
| 209 |
|
EXF_INIT_FLD) and update calls in exf_init_varia.F |
| 210 |
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- For now, for backward compatibility, keep a simplified version of S/Rs |
| 211 |
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EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F |
| 212 |
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- add and pass new arguments: fldName (for debug msg) and fldRepeatCycle |
| 213 |
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to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F |
| 214 |
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o tools/genmake2: |
| 215 |
|
- replace "bc -l" (only used once) by "expr" (already used). |
| 216 |
|
o verification/global_ocean.cs32x15: |
| 217 |
|
- turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn". |
| 218 |
|
Note: exf setting (data.exf) can be compared to other exf secondary exp |
| 219 |
|
"seaice" (kept with useCAL=T) which has same time dependent forcing. |
| 220 |
|
|
| 221 |
|
checkpoint66d (2017/02/13) |
| 222 |
|
o pkg/exf: |
| 223 |
|
- remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning |
| 224 |
|
early on (in packages_boot.F) to stress this change in pkg setting. |
| 225 |
|
- In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg |
| 226 |
|
o model/src: |
| 227 |
|
- move call to ecco_phys to end of time step; this may induce minor |
| 228 |
|
cost function changes by shifting time averages by one time step |
| 229 |
|
for some variables; this revision resulted in changed adjoint results |
| 230 |
|
in MITgcm_contrib/verification_other/global_oce_cs32 |
| 231 |
|
o pkg/exf: |
| 232 |
|
- Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ; |
| 233 |
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this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields, |
| 234 |
|
e.g. precip, are not available. |
| 235 |
|
o pkg/flt: |
| 236 |
|
- flt_init_varia.F: use pickupSuff if specified |
| 237 |
|
- add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first, |
| 238 |
|
intermediate, step towards completing pkg/exch2 support within pkg/flt; |
| 239 |
|
ifdef DEVEL_FLT_EXCH2 then: |
| 240 |
|
- flt_init_fixed.F: comment out stop |
| 241 |
|
- flt_exch2.F: conserve ipart, jpart (grid coordinates) |
| 242 |
|
- exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates) |
| 243 |
|
- flt_mapping.F: attempt to fix longitude diagnostic near date-line |
| 244 |
|
- flt_init_varia.F: hack initialization (for testing purposes w. LLC90) |
| 245 |
|
o tools/genmake2 & pkg/pkg_depend: |
| 246 |
|
- define new type of pkg dependency rule ("=pkg_x"), less strict than |
| 247 |
|
the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled |
| 248 |
|
(-pkg_x in packages.conf). |
| 249 |
|
- change pkg/exf dependency rule from "exf +cal" to "exf =cal"; |
| 250 |
|
- add "+cal" to dependency list of pkg/ecco (needed to compile). |
| 251 |
|
- simplify FWD experiment "offline_exf_seaice" by removing pkg/cal. |
| 252 |
|
o utils/matlab: |
| 253 |
|
- adding ocean_basin routines for defining basin masks. |
| 254 |
|
o pkg/exf: |
| 255 |
|
- new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more |
| 256 |
|
arguments, allowing to check (and stop) if parameter setting of |
| 257 |
|
{FLD}startdate1 & date2 and of {FLD}StartTime are consistent with |
| 258 |
|
useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START |
| 259 |
|
for backward compatibility. |
| 260 |
|
- change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in |
| 261 |
|
exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field). |
| 262 |
|
o pkg/bling (USE_EXFCO2 code): |
| 263 |
|
- fix missing setting of apco2StartTime according to apco2startdate1 & date2 |
| 264 |
|
by adding a call to S/R EXF_GETFFIELD_START. |
| 265 |
|
o pkg/exf: |
| 266 |
|
- allows to compile without pkg/cal (but disabled by current dependency |
| 267 |
|
rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to |
| 268 |
|
run with useCAL=F ; this involves setting directly {FLD}StartTime instead |
| 269 |
|
of {FLD}startdate1 & date2 ; consistency check not yet coded. |
| 270 |
|
o verification/global_ocean.cs32x15: |
| 271 |
|
- fix all data.exf for a shift of 1 day in all field startdate1 so that it now |
| 272 |
|
corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm). |
| 273 |
|
o pkg/exf: |
| 274 |
|
- allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some |
| 275 |
|
calculations); change FWD experiment global_ocean.cs32x15 |
| 276 |
|
(#define ALLOW_ZENITHANGLE) to test/check that this code compiles. |
| 277 |
|
o pkg/exf: |
| 278 |
|
- In preparation for addition to NAMELIST, rename internal (_RL) parameter |
| 279 |
|
{FIELD}startdate to {FIELD}StartTime |
| 280 |
|
Note: new name also fit better the content, i.e, a start time in second. |
| 281 |
|
o eesupp/src: |
| 282 |
|
- add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF |
| 283 |
|
o pkg/exf: |
| 284 |
|
- add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters) |
| 285 |
|
to allow to read-in Sensible & Latent Heat flux ; |
| 286 |
|
- simplify pkg/exf main options: |
| 287 |
|
1) move small piece of code (case ALLOW_ATM_TEMP undef) out of |
| 288 |
|
exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is |
| 289 |
|
compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined; |
| 290 |
|
2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option |
| 291 |
|
ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ; |
| 292 |
|
3) improve options documentation in EXF_OPTIONS.h. |
| 293 |
|
o pkg/ecco: |
| 294 |
|
- cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and |
| 295 |
|
ecco_summary.F: add passive tracer cost functions to gencost; |
| 296 |
|
m_ptracer and m_boxmean_ptracer |
| 297 |
|
o pkg/ctrl: |
| 298 |
|
- ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input |
| 299 |
|
parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list |
| 300 |
|
of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw, |
| 301 |
|
xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn |
| 302 |
|
o model/src: |
| 303 |
|
- forward_step.F: pass myIter and myTime to ctrl_map_forcing as input |
| 304 |
|
parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing |
| 305 |
|
o pkg/exf: |
| 306 |
|
- exf_getffields.F: add to list of implemented gentim2d contol parameters: |
| 307 |
|
xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask |
| 308 |
|
|
| 309 |
|
checkpoint66c (2017/01/19) |
| 310 |
|
o verification: |
| 311 |
|
- add new option "-src" to testreport to only produce source code (*.f), |
| 312 |
|
including taf output src code (if using '-adm'/'-tlm' option). |
| 313 |
|
o pkg/exf: |
| 314 |
|
- add saltflx :: Net upward salt flux in psu.kg/m^2/s |
| 315 |
|
o pkg/diagnostics: |
| 316 |
|
- add run-time variable diagMdsDir to specify a subdirectory for |
| 317 |
|
diagnostic output when mds is being used and mdsioLocalDir is not. |
| 318 |
|
o pkg/mnc: |
| 319 |
|
- mnc_utils.F: edit stop message |
| 320 |
|
o pkg/autodiff: |
| 321 |
|
- autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER, |
| 322 |
|
add HAVE_SYSTEM bracket around system call to mkdir |
| 323 |
|
o pkg/profiles: |
| 324 |
|
- profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F, |
| 325 |
|
profiles_readparms.F: call ALL_PROC_DIE before 'stop' |
| 326 |
|
- profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER, |
| 327 |
|
add HAVE_SYSTEM bracket around system call to mkdir |
| 328 |
|
o pkg/smooth: |
| 329 |
|
- smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop' |
| 330 |
|
- smooth_init2d.F, smooth_init3d.F: move print statements to readparms |
| 331 |
|
- smooth_readparms.F: add cleaner print statements from smooth_init?d.F |
| 332 |
|
o pkg/exf: |
| 333 |
|
- check: count errors and stop cleanly at the end (call to ALL_PROC_DIE); |
| 334 |
|
issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500 |
| 335 |
|
generalize tests on interpMethod, nlat, and lon_inc to all exf variables. |
| 336 |
|
- summary: skip detailed field report if not used (empty file-name). |
| 337 |
|
o tools/xmakedepend: |
| 338 |
|
- In case line editor "ed" is missing, switch to "sed" command to clean-up |
| 339 |
|
Makefile from previous dependencies (anything after "# DO NOT DELETE" line). |
| 340 |
|
o pkg/exf: |
| 341 |
|
- change definition of "hflux" input file to always include Short-Wave; |
| 342 |
|
this is now consistent with hflux computation (if using bulk-formulae) |
| 343 |
|
and hflux diagnostic & documentation (in EXF_FIELDS.h). |
| 344 |
|
|
| 345 |
|
checkpoint66b (2016/12/01) |
| 346 |
|
o model & momentum pkgs: |
| 347 |
|
- implement fully implicit bottom friction combined with implicit surf. |
| 348 |
|
pressure, for now, only in hydrostic formulation: |
| 349 |
|
+ to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h |
| 350 |
|
and run with selectImplicitDrag=2 ; |
| 351 |
|
+ currently missing diagnostics of bottom drag and vert. viscosity tendency; |
| 352 |
|
- partial implicit time-stepping (bot. friction + vert. visc first, then |
| 353 |
|
surf. press) corresponding to selectImplicitDrag=1 should be applicable |
| 354 |
|
to NH formulation but not available until we solve for surf. pressure |
| 355 |
|
increment (instead of full etaN). |
| 356 |
|
- change exp. global_ocean.cs32x15.thsice to test implicit bottom drag |
| 357 |
|
with implicit vertical viscosity. |
| 358 |
|
o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model |
| 359 |
|
- this is a first version that includes many regularisations that may |
| 360 |
|
not all be necessary, to be sorted out, |
| 361 |
|
- turned on by runtime parameter SEAICEuseLinRemapITD (true by default) |
| 362 |
|
- change one verification experiment in seaice_itd to use and test new code |
| 363 |
|
- seaice_growth: catch a case where the argument of log can be zero |
| 364 |
|
or smaller (important for code stability) |
| 365 |
|
o model/src: |
| 366 |
|
- modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F |
| 367 |
|
& solve_pentadiagonal.F to enable to re-used inverse matrix for solving |
| 368 |
|
similar A.X'=Y' system (with same matrix A) in subsequent calls; |
| 369 |
|
switch based on errCode (In/Out) argument value; in calling routines, |
| 370 |
|
initialise errCode before first call. |
| 371 |
|
|
| 372 |
|
checkpoint66a (2016/10/18) |
| 373 |
|
o pkg/bling: |
| 374 |
|
- BLING package now loads in atmospheric pCO2 file using exf package routines |
| 375 |
|
Enable with #define USE_EXFCO2 in BLING_OPTIONS.h |
| 376 |
|
o model/src & pkg/ptracers: |
| 377 |
|
- with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R & |
| 378 |
|
GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and |
| 379 |
|
implicitDiffusion (respectively) are used (even without momImplVertAdv |
| 380 |
|
or temp,salt,PTRACERS_ImplVertAdv). |
| 381 |
|
o model/src & generic_advdiff: |
| 382 |
|
- add parenthesis in main diagonal calculation of implicit vertical |
| 383 |
|
diffusion matrix (impldiff.F & gad_implicit_r.F). |
| 384 |
|
This affects results at machine truncation level; update output of many |
| 385 |
|
verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad). |
| 386 |
|
o pkg/mom_commom & generic_advdiff: |
| 387 |
|
- add deep atmosphere and anelastic scaling factor in implicit vertical |
| 388 |
|
advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F). |
| 389 |
|
o model/src: |
| 390 |
|
- remove few unnecessary temp array copies in solve_tridiagonal.F |
| 391 |
|
& solve_pentadiagonal.F |
| 392 |
|
|
| 393 |
|
checkpoint65z (2016/09/28) |
| 394 |
|
o pkg/seaice: fix multithreading for seaice_fgmres.F |
| 395 |
|
- remove unecessary variables from common blocks |
| 396 |
|
- use extra dimension MAX_NO_THREADS for all variables of the Krylov space |
| 397 |
|
basis, that are stored in commom blocks (including integer variable i1) |
| 398 |
|
- clean up code a little by removing commented lines that refer to |
| 399 |
|
original code |
| 400 |
|
- turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk. |
| 401 |
|
o MITgcm manual: |
| 402 |
|
- add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex), |
| 403 |
|
preliminary documentation for generic controls (8.3; ctrl.tex), |
| 404 |
|
a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated |
| 405 |
|
ecco_costfunction.tex |
| 406 |
|
o pkg/ecco: |
| 407 |
|
- update and cleanup list of CCP options |
| 408 |
|
- re-assign gencost_mask to specify masks rather than gencost_errfile; 'c' |
| 409 |
|
is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM |
| 410 |
|
- add checks that retired run-time options are not used, and in relation |
| 411 |
|
to gencost_mask and gencost_errfile |
| 412 |
|
- finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and |
| 413 |
|
gencost_nrecperiod |
| 414 |
|
- fix m_eta computation for virtual salt flux case |
| 415 |
|
- add m_horflux_vol case (selected via gencost_barfile) that computes |
| 416 |
|
transports via cost_gencost_boxmean (gencost_flag=-3) |
| 417 |
|
- use gencost_flag more systematically (i.e., avoid using gencost_name) |
| 418 |
|
for code switches (aside from physical variable selection) |
| 419 |
|
o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first |
| 420 |
|
attempt appears to be a bit of a hack and my need some repair down the road |
| 421 |
|
o pkg/exf: |
| 422 |
|
- interpolation near South Pole: fix criteria on input field latitude. |
| 423 |
|
o pkg/icefront & pkg/exf: |
| 424 |
|
- move setting of icefront Sub-Glacial RunOff forcing (currently unused) |
| 425 |
|
from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront) |
| 426 |
|
o pkg/exf: |
| 427 |
|
- replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter |
| 428 |
|
"exf_output_interp" (in namelist: EXF_NML_04); change output file name |
| 429 |
|
(add suffix "_out" instead of a prefix); keep same record number as in |
| 430 |
|
input file but always write record 1 first (to avoid a STOP in I/O S/R). |
| 431 |
|
Change output file content by writing interpolated field before applying |
| 432 |
|
land-sea mask (helpful for debug). |
| 433 |
|
- 2 compon. vector interpolation with rotation: apply scaling factor on |
| 434 |
|
each compon. (Eastward and Northward) just before rotation. |
| 435 |
|
o pkg/bling: |
| 436 |
|
- Cleaned package. Removed not needed code and comments. |
| 437 |
|
- adjoint example now works |
| 438 |
|
(MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad) |
| 439 |
|
o pkg/ptracers: |
| 440 |
|
- add Bruno Deremble's code to complete the linear surface correction |
| 441 |
|
for tracer conservation; |
| 442 |
|
- enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE. |
| 443 |
|
|
| 444 |
|
checkpoint65y (2016/07/29) |
| 445 |
|
o pkg/debug (stats): |
| 446 |
|
- change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to |
| 447 |
|
proc/thread mapping); |
| 448 |
|
- fix Min & Max for case where 1 thread has only empty tiles; |
| 449 |
|
- use RL variable to count number of wet grid points (with big domain, |
| 450 |
|
can be too large to fit into integer*4). |
| 451 |
|
o pkg/monitor: |
| 452 |
|
- use RL variable to count number of wet grid points (but used only for del2) |
| 453 |
|
- add new routine to compute Advective CFL within tracer time-stepping with |
| 454 |
|
writing delayed until next monitor output. |
| 455 |
|
o pkg/obcs: |
| 456 |
|
- fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW) |
| 457 |
|
o pkg/cal: |
| 458 |
|
- calandar-dump: treat case myTime < timePhase in the same way as in |
| 459 |
|
eesupp/src/diff_phase_multiple.F (when not using calandar-dump). |
| 460 |
|
o pkg/dic & seaice: |
| 461 |
|
- fix compilation of ocean component for coupled atm+ocn model with |
| 462 |
|
seaice dynamics & dic. |
| 463 |
|
|
| 464 |
|
checkpoint65x (2016/06/11) |
| 465 |
|
o add a license text file in main MITgcm tree. |
| 466 |
|
o added pkg/bling: |
| 467 |
|
- intermediate complexity biogeochemical model |
| 468 |
|
- see bling_description.txt for details |
| 469 |
|
- verification experiment is global_oce_biogeo_bling (for now, in |
| 470 |
|
Contrib/verification_other/); tested daily on baudelaire with gfortran. |
| 471 |
|
- add entry point in pkg/gchem for new pkg "bling". |
| 472 |
|
o pkg/seaice: fix tensile stength computation |
| 473 |
|
- replace global field tensileStrength by tensileStrFac |
| 474 |
|
- tensileStrFac can be computed once in S/R seaice_init_varia |
| 475 |
|
- fortunately that does not affect any verification results |
| 476 |
|
|
| 477 |
|
checkpoint65w (2016/05/12) |
| 478 |
|
o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles |
| 479 |
|
with ECCO_CTRL_DEPRECATED defined |
| 480 |
|
o verification/global_ocean.cs32x15: |
| 481 |
|
- change secondary test "viscA4" to also test "selectP_inEOS_Zc=3" |
| 482 |
|
with "selectNHfreeSurf=1". |
| 483 |
|
o model/src (non-hydrostatic free-surface): |
| 484 |
|
- More "natural" expression of NH free-surface term (case selectNHfreeSurf=1): |
| 485 |
|
was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf. |
| 486 |
|
- Calculate surface vertical velocity after 2-D solver adjustment (accounts |
| 487 |
|
for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv |
| 488 |
|
and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1. |
| 489 |
|
This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux. |
| 490 |
|
- Update output (changes at machine truncation level) of verification exp: |
| 491 |
|
exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d), |
| 492 |
|
short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d). |
| 493 |
|
o pkg/seaice: ITD code |
| 494 |
|
- fix picking up from a single category model by initialising |
| 495 |
|
heff/area/hsnowITD = 0. in seaice_itd_pickup.F |
| 496 |
|
- split a long warning message in seaice_check_pickup.F into two lines, |
| 497 |
|
because NEC SX-ACE cannot deal with the long line. |
| 498 |
|
o model/src: |
| 499 |
|
- fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3) |
| 500 |
|
o pkg/seaice: |
| 501 |
|
- add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG |
| 502 |
|
o pkg/seaice: |
| 503 |
|
- add basal stress as parameterisation for grounding ice |
| 504 |
|
following Lemieux et al. (2015) |
| 505 |
|
- turn on by setting new parameter SEAICEbasalDragK2 to a value |
| 506 |
|
larger than 0. Lemieux et al. (2015) recommend 15. |
| 507 |
|
- The adjoint complains with extra recomputations so there is also a |
| 508 |
|
new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in |
| 509 |
|
order to postpone the problem |
| 510 |
|
- compile the new code in lab_sea |
| 511 |
|
o verification/halfpipe_streamice: |
| 512 |
|
- update both TAF and OpenAD adm output (machine truncation differences) |
| 513 |
|
|
| 514 |
|
checkpoint65v (2016/04/08) |
| 515 |
|
o verification/advect_xz: |
| 516 |
|
- increase overlap size from 3 to 4 and add new secondary test for PQM |
| 517 |
|
advection scheme (with mono & wino limiter). |
| 518 |
|
- change main exp. to test PPM (with weno limiter) adv.scheme on Temp. |
| 519 |
|
o model/src: |
| 520 |
|
- new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently |
| 521 |
|
added phi0Ref) to set vertical axis origin and phiRef origin; |
| 522 |
|
keep Ro_SeaLevel for backward compatibility (with a warning). |
| 523 |
|
According to coordinate and fluid type: |
| 524 |
|
OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top) |
| 525 |
|
ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom) |
| 526 |
|
OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top) |
| 527 |
|
ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom) |
| 528 |
|
- remove Ro_SeaLevel from ATM experiment parameter files; |
| 529 |
|
- in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the |
| 530 |
|
complement; update output.txt (changes at machine truncation level). |
| 531 |
|
o pkg/seaice/seaice_evp.F |
| 532 |
|
- simplify computation of deltaZ and zetaZ to simple averaging following |
| 533 |
|
Bouillon et al. (2013). This removes a lot of code, but also changes |
| 534 |
|
verification experiment lab_sea.hb87 -> updated |
| 535 |
|
|
| 536 |
|
checkpoint65u (2016/03/14) |
| 537 |
|
o pkg/generic_advdiff: |
| 538 |
|
- from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52) |
| 539 |
|
with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP); |
| 540 |
|
Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for |
| 541 |
|
testing and not for actual use. |
| 542 |
|
o model/src: |
| 543 |
|
- add parameter "phi0Ref" to specify reference [pressure/geo] potential at |
| 544 |
|
origin r = rF(1); |
| 545 |
|
- add options (parameter selectP_inEOS_Zc) to select which pressure to use |
| 546 |
|
in EOS for height coordinate: enable to include NH Pressure or to use |
| 547 |
|
more accurate pressure vertical profile; options not linked to EOS type |
| 548 |
|
(as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type; |
| 549 |
|
- start to implement variable gravity (along vertical): for now, only with |
| 550 |
|
z-coords (not even z*). |
| 551 |
|
- add Ideal Gas equation of state for height coordinate. |
| 552 |
|
- update OpenAD output (affected at machine truncation level) of exp: |
| 553 |
|
global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo. |
| 554 |
|
o pkg/exf: |
| 555 |
|
- add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result |
| 556 |
|
of exf interpolation (before any rescaling, rotation or interpolation |
| 557 |
|
to velocity point) for each field that gets loaded from file. This option |
| 558 |
|
identically mimics the input file organization (e.g. record numbers in year |
| 559 |
|
by year input files) besides the change in horizontal grid. |
| 560 |
|
- add rotateStressOnAgrid run-time switch so that wind stress fields |
| 561 |
|
can be provided on the A-grid in zonal/meridional direction and |
| 562 |
|
rotated on the fly. This only applies to the case when the exf |
| 563 |
|
interpolation is off and rotateStressOnAgrid is false by default. |
| 564 |
|
o model/src: |
| 565 |
|
- rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since |
| 566 |
|
it's also used with pkg/atm_phys) and add few more parameters (but still |
| 567 |
|
inactive, src code yet to come) |
| 568 |
|
|
| 569 |
|
checkpoint65t (2016/02/10) |
| 570 |
|
o pkg/atm_phys: |
| 571 |
|
- from Ruth Geen: add optical depth dependence on CO2 concentration. |
| 572 |
|
o model/src: |
| 573 |
|
- fix vertical inter/extra-polation of density factor rhoFacF (for anelastic) |
| 574 |
|
for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F. |
| 575 |
|
Update output of exp. deep_anelastic (changes at truncation level). |
| 576 |
|
o tools: |
| 577 |
|
- add a hack in "remove_comments_sed" (used only with TAF) for recent |
| 578 |
|
version of OpenMPI (shipped with FC.23): comment out the new header |
| 579 |
|
file "mpif-sizeof.h" which causes problems to TAF. |
| 580 |
|
o pkg/seaice: |
| 581 |
|
- change the termination criterion so that maxits (SEAICElinearIterMax) |
| 582 |
|
has an effect |
| 583 |
|
- unify iteration parameters for implicit solvers (JFNK and Picard) |
| 584 |
|
SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS |
| 585 |
|
SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER |
| 586 |
|
SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner |
| 587 |
|
SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner |
| 588 |
|
SEAICEnonLinTol replaces JFNKgamma_nonlin |
| 589 |
|
- remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN |
| 590 |
|
- add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and |
| 591 |
|
use with SEAICEuseKrylov |
| 592 |
|
o pkg/seaice/seaice_lsr.F |
| 593 |
|
fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only |
| 594 |
|
relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have |
| 595 |
|
an effect. |
| 596 |
|
o pkg/seaice: add two new parameters |
| 597 |
|
- SEAICEuseLSR to simplify the logic in seaice_dynsolver (this |
| 598 |
|
parameter is not in any namelist) |
| 599 |
|
- SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as |
| 600 |
|
a preconditioner for the non-linear Newton iteration of the JFNK |
| 601 |
|
solver |
| 602 |
|
o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT, |
| 603 |
|
affects some experiments at truncation level: |
| 604 |
|
- global_ocean.cs32x15.icedyn (11 digits), |
| 605 |
|
- global_ocean.cs32x15.seaice (11 digits), |
| 606 |
|
- seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update |
| 607 |
|
- also update global_ocean.cs32x15 adjoint and tangent-linear results |
| 608 |
|
o pkg/salt_plume & pkg/thsice: |
| 609 |
|
- for coupled set-up with pkg/thsice in ATM and pkg/salt_plume in OCN, |
| 610 |
|
connect salt_plume flux to ATM-OCN coupling pkgs interface: |
| 611 |
|
a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for |
| 612 |
|
export to coupler interface) even without compiling pkg/salt_plume ; |
| 613 |
|
b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field |
| 614 |
|
(saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH. |
| 615 |
|
o pkg/dic: |
| 616 |
|
- use the updated seaice fraction (from seaice pkgs) for DIC forcing |
| 617 |
|
instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE |
| 618 |
|
called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD); |
| 619 |
|
- move also update with values from ATM-OCN Coupler in the same new S/R |
| 620 |
|
(previously done in ocn_apply_import.F). |
| 621 |
|
o tools/adjoint_options: |
| 622 |
|
- specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default) |
| 623 |
|
has been changed on Jan 14, 2016. |
| 624 |
|
o pkg/ggl90: |
| 625 |
|
- add alternative discretisation of vertical shear (off by default), to |
| 626 |
|
compute the mean (@ grid-cell center) of vertical shear compon instead of |
| 627 |
|
vertical shear of mean flow (@ grid-cell center). |
| 628 |
|
- add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated |
| 629 |
|
results on adjacent faces of cubed-sphere grids; this fix the restart. |
| 630 |
|
o pkg/atm_compon_interf: |
| 631 |
|
- skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just |
| 632 |
|
pass last value, stored directly before export to CPL ; |
| 633 |
|
Note: this affects results of Coupled set-up where OCN uses useImportSLP=T |
| 634 |
|
- remove atmSLPr from pickup files (no longer needed for restart) |
| 635 |
|
|
| 636 |
|
checkpoint65s (2016/01/13) |
| 637 |
|
o eesupp & genmake2: |
| 638 |
|
- first check for Function ETIME and, if it fails, then check for subroutine |
| 639 |
|
ETIME and consistent output; use the appropriate version in timers.F |
| 640 |
|
o model/src: |
| 641 |
|
- to check restart test, add option to apply EXCH to U,V earlier, just before |
| 642 |
|
integr_continuity; turned off by default. |
| 643 |
|
o pkg/dic: |
| 644 |
|
- remove CPP option USE_ATMOSCO2 (not needed) |
| 645 |
|
o tools/tst_2+2: |
| 646 |
|
- try to ignore difference between +0 and -0 in binary file, causing test |
| 647 |
|
to fail for no good reason. |
| 648 |
|
o eesupp & genmake2: |
| 649 |
|
- put back modif from Jinxuan Zhu - change etime fct call to S/R call - |
| 650 |
|
but also check (in genmake2) that test runs and returns meaningful results. |
| 651 |
|
o coupler pkgs: |
| 652 |
|
Finish implementation of optionally-exchanged variable switches (started on |
| 653 |
|
Nov 12) with addition of few more exchanged fields, including 2-way exchange |
| 654 |
|
of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice |
| 655 |
|
advection in OCN component; this requires sequential coupling. |
| 656 |
|
coupler (pkg/atm_ocn_coupler): |
| 657 |
|
- add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS |
| 658 |
|
routines (useful for debug). |
| 659 |
|
- only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume |
| 660 |
|
flux, DIC fields) if corresponding switch is ON. |
| 661 |
|
- add option to export RunOff to OCN (to use for DIC river input) |
| 662 |
|
- add 2-way thSIce vars exchange; check for consistent cpl_sequential setting. |
| 663 |
|
components (pkg/atm_ & ocn_compon_interf): |
| 664 |
|
- to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around |
| 665 |
|
optionally exchanged fields; add a check & stop in cpl_readparms.F. |
| 666 |
|
ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2; |
| 667 |
|
OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice. |
| 668 |
|
- rename: fracIce -> sIceFrac_cpl (<- match coupler var name) |
| 669 |
|
+ in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime. |
| 670 |
|
- add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN. |
| 671 |
|
- hold in common block coupler optionally-exchanged variable switch |
| 672 |
|
and set default "useImportXXX" accordingly; + check & stop if inconsistent. |
| 673 |
|
- add diagnostics for all imported fields from coupler (in both OCN & ATM); |
| 674 |
|
this is intended to replace the OCN cplFldtave.* output files (not updated |
| 675 |
|
to contain new additional exchanged fields). |
| 676 |
|
o pkg/dic: |
| 677 |
|
- fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code. |
| 678 |
|
o pkg/thsice: |
| 679 |
|
- when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading |
| 680 |
|
and writing of thsice pickup files. |
| 681 |
|
o pkg/atm_compon_interf: |
| 682 |
|
- move all field individual export-call out of cpl_export_import_data.F |
| 683 |
|
into new S/R ATM_EXPORT_FIELDS |
| 684 |
|
o pkg/atm_compon_interf: |
| 685 |
|
- store state variables (for now, only thSIce fields) just before beeing |
| 686 |
|
exported (in cpl_export_import_data.F, like on ocean side) instead of from |
| 687 |
|
atm_store_my_data.F like all exported fluxes. |
| 688 |
|
- new version of pickup_cpl: write field names into meta file and read meta |
| 689 |
|
file to find field postion in pickup. Also only write/read fields meeded for |
| 690 |
|
restart (same logic as main pickup file ; also using pickupStrictlyMatch) |
| 691 |
|
o pkg/dic: |
| 692 |
|
- fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3. |
| 693 |
|
o pkg/seaice: add new parameter SEAICEpressReplFac to choose between |
| 694 |
|
pressure replacement method (=1., default) or original Hibler (1979) (=0.) |
| 695 |
|
value can be from domain [0,1] to average between the two methods |
| 696 |
|
o pkg/atm_phys: |
| 697 |
|
- allow to provide 2-d map of albedo and mixed-layer depth from files (but |
| 698 |
|
hold fixed in time). |
| 699 |
|
|
| 700 |
|
checkpoint65r (2015/12/21) |
| 701 |
|
o pkg/seaice: |
| 702 |
|
fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK |
| 703 |
|
solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated |
| 704 |
|
o pkg/seaice: |
| 705 |
|
- fix a bug in computing areaS in (J-J -> J-1) that affects runs |
| 706 |
|
when SEAICEscaleSurfStress=.TRUE., |
| 707 |
|
- apply areaW and areaS in S/R seaice_calc_lhs |
| 708 |
|
o pkg/atm_phys: |
| 709 |
|
- add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes |
| 710 |
|
(shortwave & longwave, net & downward) and diagnostics of temp. tendency |
| 711 |
|
for individual contribution (convection, LSC cond, radiation) |
| 712 |
|
- add Ruth Geen etal, GRL 2016, radiation options (see paper supp. |
| 713 |
|
information); activated with: solar_exponent=0. and wv_exponent=-1. |
| 714 |
|
o pkg/ggl90: |
| 715 |
|
- within IDEMIX add upper limit for horizontal group velocity to |
| 716 |
|
avoid instability problems in the explicit horizontal diffusion term for |
| 717 |
|
long time steps or high resolution |
| 718 |
|
o pkg/diagnostics: |
| 719 |
|
- simplify setting of local-array size in diagstats_output.F: uses "numLevels" |
| 720 |
|
(from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels. |
| 721 |
|
o testreport: |
| 722 |
|
- remove "-v" (verbose option) in default mpirun command. |
| 723 |
|
o pkg/seaice/seaice_growth: |
| 724 |
|
- catch potential division by zero in ITD code, does not change |
| 725 |
|
verification results |
| 726 |
|
o pkg/ecco: |
| 727 |
|
- retire old codes to the Attic. The calls to retired functions are |
| 728 |
|
left in a commented form in case they ever need to be re-activated. |
| 729 |
|
- ecco_check.F: issue warning if any old CPP option is |
| 730 |
|
defined that corresponds to retired codes -- then stop. |
| 731 |
|
o pkg/atm_compon_interf: |
| 732 |
|
- change seaice fraction (use for OCN dic surf.flux) stored and sent to |
| 733 |
|
coupler: use last time-step value instead of average over cplSendFrq_iter |
| 734 |
|
time-step, similar to what is done for seaIceMass. |
| 735 |
|
This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up. |
| 736 |
|
o eesupp & genmake2: |
| 737 |
|
- from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME); |
| 738 |
|
<= remove until a fix is found for some ifort version on ia32 machine. |
| 739 |
|
o pkg/seaice/seaice_evp: |
| 740 |
|
- refine residual computation |
| 741 |
|
|
| 742 |
|
checkpoint65q (2015/11/18) |
| 743 |
|
o pkg/seaice/seaice_evp: |
| 744 |
|
- fix residual computations so that they no longer affect the actual |
| 745 |
|
simulation code |
| 746 |
|
- fix seaice_readparams to be able to actually set new parameters |
| 747 |
|
SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little |
| 748 |
|
o model/src: |
| 749 |
|
- fix wrong truncation (single prec) from "FLOAT" function in expressions |
| 750 |
|
like: deltaT*FLOAT(myIter) when myIter is large: |
| 751 |
|
a) replaced by DFLOAT (if not seen by TAF); |
| 752 |
|
b) remove "FLOAT" and use implicit type conversion (if seen by TAF). |
| 753 |
|
o pkg/aim_v23: |
| 754 |
|
- write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading |
| 755 |
|
when pickupSuff is set ; do write rolling pickups + at the end of the run. |
| 756 |
|
o pkg/atm_ocn_coupler + ocn_compon_interf: |
| 757 |
|
- in prep for using pkg/seaice Dyn in coupled set-up, implement sequential |
| 758 |
|
coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ; |
| 759 |
|
add corresponding call in DO_OCEANIC_PHYS. |
| 760 |
|
o coupler pkgs: |
| 761 |
|
Start a new way to set-up optionally-exchanged variables (previously, only |
| 762 |
|
there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler |
| 763 |
|
data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ; |
| 764 |
|
send switch to ATM & OCN compon before reading their own "data.cpl" (so that |
| 765 |
|
compononent param default can be set accordingly). |
| 766 |
|
Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch |
| 767 |
|
but rather applies to a group a fields (going both ways like for DIC) |
| 768 |
|
and corresponds to an option of coupling config. |
| 769 |
|
coupler (pkg/atm_ocn_coupler): |
| 770 |
|
- change parameter file from "data" to "data.cpl" (in cpl_read_params.F), |
| 771 |
|
and read namelist directly (without eessup S/R calls) instead of |
| 772 |
|
in the very un-flexible old way, 1 param per line, in fixed order; |
| 773 |
|
- add error-counter to track errors (e.g., missing "data.cpl") and to stop |
| 774 |
|
cleanly in CPL_CHECK_CPLCONFIG |
| 775 |
|
- add new coupling-exchange selectors (some not yet active) including |
| 776 |
|
cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h |
| 777 |
|
and ocnCpl_exchange_DIC=T in OCNIDS.h); |
| 778 |
|
- add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each |
| 779 |
|
component ; called directly from coupler.F, after comp. registrations; |
| 780 |
|
- rename few variable-ID names (in ATMIDS.h & OCNIDS.h): |
| 781 |
|
atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name -> |
| 782 |
|
-> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName |
| 783 |
|
components (pkg/atm_ & ocn_compon_interf): |
| 784 |
|
- add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding |
| 785 |
|
CPP header file in all pkg source files. |
| 786 |
|
- move checking of comp. configs out of cpl_exch_configs.F into new S/R |
| 787 |
|
ATM/OCN_CHECK_CPLCONFIG; |
| 788 |
|
- add error-counter to track errors (e.g., in "data.cpl") and to stop |
| 789 |
|
cleanly in ATM/OCN_CHECK_CPLCONFIG; |
| 790 |
|
- add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors |
| 791 |
|
from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and |
| 792 |
|
before PACKAGES_READPARMS; |
| 793 |
|
verification/cpl_aim+ocn/: |
| 794 |
|
- update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file |
| 795 |
|
"data.cpl" for coupler (in input_cpl). |
| 796 |
|
o eesupp/inc: |
| 797 |
|
- change the MPI-global-sum default (in CPP_EEOPTIONS.h) to: |
| 798 |
|
#define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F) |
| 799 |
|
to always cumulate tile local-sum in the same order (still uses |
| 800 |
|
MPI_Allreduce like standard code). |
| 801 |
|
- in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files |
| 802 |
|
that are now identical to standard version (in eesupp/inc). |
| 803 |
|
o pkg/shelfice: |
| 804 |
|
- add SHELFICETransCoeffTFile for initializing spatially varying |
| 805 |
|
heat and salt transfer coefficients |
| 806 |
|
o pkg/atm_compon_interf & ocn_compon_interf: |
| 807 |
|
- combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous |
| 808 |
|
S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA |
| 809 |
|
- move bi,bj loops inside S/R OCN_STORE_MY_DATA |
| 810 |
|
o pkg/atm_ocn_coupler: |
| 811 |
|
- initialise to zero ATMVARS.h & OCNVARS.h arrays. |
| 812 |
|
o pkg/rbcs: |
| 813 |
|
- select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows |
| 814 |
|
to compile with maskLEN=1 when all tracers use the same RBCS-mask. |
| 815 |
|
- add a short report (to STDOUT) about RBCS-mask settings. |
| 816 |
|
|
| 817 |
|
checkpoint65p (2015/10/23) |
| 818 |
|
o pkg/seaice/seaice_evp.F: fix store directives and key computations, since |
| 819 |
|
there is no adjoint test for EVP, we don't know what it does to the adjoint |
| 820 |
|
solution, but at least there are no more recomputation warnings left |
| 821 |
|
o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands |
| 822 |
|
a chance of giving the same results as a fully converged VP (JFNK) solver |
| 823 |
|
o tools/adjoint_options/adjoint_diva: |
| 824 |
|
- fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA |
| 825 |
|
o pkg/streamice: |
| 826 |
|
- spotted bug in streamice_driving_stress using dyG where should have been dxG |
| 827 |
|
o pkg/exf: |
| 828 |
|
- remove STOP statement that prevented to use wind or (wind-)stress |
| 829 |
|
interpolation for constant-in-time forcing fields (wind/stress period = 0). |
| 830 |
|
o pkg/seaice: |
| 831 |
|
- replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires |
| 832 |
|
5 additionals 2D fields and 6 new store directives |
| 833 |
|
- change logic in seaice_readparms.F: EVP code can now be turned on in |
| 834 |
|
various ways, setting SEAICE_deltaTev is no longer required, |
| 835 |
|
alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev, |
| 836 |
|
or SEAICEaEVPcoeff |
| 837 |
|
o pkg/shelfice/shelfice_thermodynamics.F |
| 838 |
|
- redefining uLoc/vLoc to u/v, instead of 2u/v |
| 839 |
|
o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz |
| 840 |
|
- this is an intermediate state of a truely converging EVP that has |
| 841 |
|
the potential of outperforming implicit VP methods, I do not recommend |
| 842 |
|
using it yet. |
| 843 |
|
- for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION |
| 844 |
|
and all parameters are hardwired |
| 845 |
|
- for convergence it still requires very smooth regularisations, that means, |
| 846 |
|
if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is |
| 847 |
|
different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also |
| 848 |
|
specific averaging appears to be required, still subject to tuning |
| 849 |
|
- still needs cleaning and I need to turn parameter into runtime parameters |
| 850 |
|
- add code to compute and print residuals of iteration, compile with |
| 851 |
|
defining ALLOW_SEAICE_EVP_RESIDUAL to enable it |
| 852 |
|
o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq) |
| 853 |
|
that entered with r1.54 on Sep04, 2015, -> update results |
| 854 |
|
|
| 855 |
|
checkpoint65o (2015/09/14) |
| 856 |
|
o pkg/mom_vecinv & mom_common: |
| 857 |
|
- add deep-atmosphere geometry factor in mom_calc_visc.F + in routines |
| 858 |
|
called from there. |
| 859 |
|
- add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this |
| 860 |
|
allows to use Vector-Invariant form in deep atmos and anelastic formulation |
| 861 |
|
o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015) |
| 862 |
|
and Koenig-Beatty+Holland (2012) |
| 863 |
|
- two new parameters SEAICE_tensilFac and SEAICE_tensilDepth |
| 864 |
|
- global 2D field tensileStrength, computed in seaice_calc_ice_strength |
| 865 |
|
- requires an extra input argument for S/R seaice_calc_viscosities |
| 866 |
|
- tensileStrength's depth dependence is different from Itkin et al. (2015) |
| 867 |
|
(to be changed and played with, for now exponential) |
| 868 |
|
o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.) |
| 869 |
|
- if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice |
| 870 |
|
by AREA according to Connelly et al. (2004), JPO. |
| 871 |
|
- For EVP and the LSR solver, the implicit part of the drag term is |
| 872 |
|
the only non-zero term in the denominator when there is no ice (which |
| 873 |
|
prevented running the model with zero ice-ocean drag). If |
| 874 |
|
SEAICEscaleSurfStress = .TRUE., this results in a division by zero |
| 875 |
|
(or zero main diagonals BU/BV) which need to be caught. A practical |
| 876 |
|
consequence is that for open water, the momentum equation reduce |
| 877 |
|
to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if |
| 878 |
|
they happen to be zero, often leading to a non-zero solution over |
| 879 |
|
open water. |
| 880 |
|
o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more |
| 881 |
|
efficient EVP method. |
| 882 |
|
- introduce area-weighted averages for e12 (analogously to |
| 883 |
|
seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits |
| 884 |
|
remain, but also changing the order of terms in the previous average |
| 885 |
|
changed the results as much) -> update experiment |
| 886 |
|
- add SEAICE_DELTA_SMOOTHREG code |
| 887 |
|
- disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for |
| 888 |
|
TEM-code |
| 889 |
|
- adjust loop bounds so that only required fields are computed |
| 890 |
|
- add new averaging code for zetaZ/deltaZ (again similar to |
| 891 |
|
seaice_calc_viscosities.F), inactive by default for now (will change |
| 892 |
|
results again), but will replace old code eventually |
| 893 |
|
o eesupp/src: |
| 894 |
|
- add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F) |
| 895 |
|
to always cumulate tile local-sum in the same order |
| 896 |
|
(option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h). |
| 897 |
|
Still uses MPI_Allreduce (like standard code) but on array of tiles |
| 898 |
|
and should be faster than GLOBAL_SUM_SEND_RECV code. |
| 899 |
|
- switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV |
| 900 |
|
(defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead. |
| 901 |
|
- add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.: |
| 902 |
|
aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40, |
| 903 |
|
fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example, |
| 904 |
|
natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre, |
| 905 |
|
tutorial_baroclinic_gyre and tutorial_held_suarez_cs. |
| 906 |
|
|
| 907 |
|
checkpoint65n (2015/07/29) |
| 908 |
|
o pkg/thsice: |
| 909 |
|
- add a warning when used with pkg/aim but without updating SST |
| 910 |
|
(stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ). |
| 911 |
|
o pkg/offline: |
| 912 |
|
- change where Offline-Fields are loaded, from load_fields_driver.F to |
| 913 |
|
directly within FORWARD_STEP, just after updating iter number and time; |
| 914 |
|
- move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new |
| 915 |
|
S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS; |
| 916 |
|
These changes allow: |
| 917 |
|
a) to recover exactly on-line results using deltaToffline=deltaTClock, |
| 918 |
|
tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2) |
| 919 |
|
both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous |
| 920 |
|
time-step, both with GM & KPP files and with recomputing these fields; |
| 921 |
|
b) no needs to switch on staggerTimeStep anymore; |
| 922 |
|
c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf. |
| 923 |
|
- update output of experiment tutorial_dic_adjoffline (only 3 digits left). |
| 924 |
|
o pkg/offline: |
| 925 |
|
- change (rarely used) offset-iteration parameter to an offset time (in s): |
| 926 |
|
can easily recover previous offset-iter effect by setting offset-time |
| 927 |
|
(offlineTimeOffset) to offset-iter x deltaToffline; |
| 928 |
|
- do not turn-off Temp & Salinity surface relaxation when using KPP (used |
| 929 |
|
in KPP as part of surface buoyancy forcing) in offline run. |
| 930 |
|
- fix ptracers KPP non-local term in the case where KPP is re-computed. |
| 931 |
|
o OpenAD |
| 932 |
|
- Adding preliminary ggl90 test to OpenAD verification. |
| 933 |
|
Config. with ggl90 currently diverges after 64 time steps |
| 934 |
|
so will need more work to become more stable |
| 935 |
|
- Adding preliminary kpp test to OpenAD verification. |
| 936 |
|
required small tweakes in kpp_routines.F |
| 937 |
|
- Merge and update from Krishna Narayanan's contrib area: |
| 938 |
|
* Add one variable for preliminary OpenAD DIVA |
| 939 |
|
* Add replacement time-stepping for OpenAD DIVA |
| 940 |
|
* genmake2 flag -diva (but only for OpenAD; preliminary) |
| 941 |
|
* required modifs for OAD_support |
| 942 |
|
successful preliminary test for tutorial_global_oce_biogeo/ |
| 943 |
|
o pkg/seaice: |
| 944 |
|
- initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr |
| 945 |
|
- add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising |
| 946 |
|
delta with a smooth function in s/r seaice_calc_viscosity |
| 947 |
|
(no effect on EVP) |
| 948 |
|
- rename local suffix "sqr" into "sq" for more consistent variable names |
| 949 |
|
o pkg/seaice: |
| 950 |
|
add new parameter SEAICE_deltaMin that is used ***only*** |
| 951 |
|
for regularizing Delta (and nothing else, like the parameter |
| 952 |
|
which is also used for all sorts of things SEAICE_EPS). |
| 953 |
|
Defaults to SEAICE_EPS for backward compatibility only. |
| 954 |
|
o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with |
| 955 |
|
the wrong key by inialising it before use -> fixes a recomputation |
| 956 |
|
problem but does not fix the gradient |
| 957 |
|
o pkg/layers: |
| 958 |
|
- move resetting of flux arrays to outside the iLa loop |
| 959 |
|
(this caused layers_diapycnal to not work with more than one layer coord.) |
| 960 |
|
- fix bug in calculation of layers_recip_delta in layers_init_fixed.F |
| 961 |
|
o pkg/layers: |
| 962 |
|
- remove from common block 3D layers fields (used to diagnose transport |
| 963 |
|
in tracer coords) and declare them as local arrays in layers_calc.F |
| 964 |
|
o pkg/seaice: |
| 965 |
|
- Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it |
| 966 |
|
in lab_sea forward experiment (changes results -> updated) |
| 967 |
|
- update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v |
| 968 |
|
o pkg/seaice: modify seaice_lsr.F in order to improve the gradient |
| 969 |
|
computations; for SEAICE_VECTORIZE_LSR |
| 970 |
|
- move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v) |
| 971 |
|
sweep to the outside, |
| 972 |
|
- remove store directives and add "CADJ loop sequential" directives |
| 973 |
|
in analogy to model/src/solve_tridiagonal.F |
| 974 |
|
- replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop |
| 975 |
|
boundaries to yield more readable code. This has also the charming side |
| 976 |
|
effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without |
| 977 |
|
SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in |
| 978 |
|
seaice_lsr_tridiagu/v now requires either of these flags, vectorization |
| 979 |
|
still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as |
| 980 |
|
an additional option) |
| 981 |
|
The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F |
| 982 |
|
but the adjoint gradients (which are affected by this change) still explode. |
| 983 |
|
o coupler (atm & ocn _compon_interf): |
| 984 |
|
- avoid using Exch2 IO mapping if not suitable. |
| 985 |
|
|
| 986 |
|
checkpoint65m (2015/06/15) |
| 987 |
|
o pkg/layers: |
| 988 |
|
- clean-up old parameters setting (from Sep 2012): |
| 989 |
|
+ remove old parameters setting from common block (declared locally); |
| 990 |
|
+ stop if any old parameter is mixed with new parameters; |
| 991 |
|
+ check for valid or consistent parameter setting (e.g., layers_name) |
| 992 |
|
- check that layers_bounds for Pot.Density are in the right range; |
| 993 |
|
this is supposed to catch un-updated setting after recently shifting |
| 994 |
|
potential density field "prho" by -1000 (now in "sigma" scale). |
| 995 |
|
o pkg/layers: |
| 996 |
|
- Added missing call to layers_fill for keeping track of tottend in |
| 997 |
|
pkg/diagnostics/diagnostics_fill_state.F |
| 998 |
|
o pkg/layers: |
| 999 |
|
- added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning |
| 1000 |
|
of diapycnal fluxes |
| 1001 |
|
o pkg/layers: |
| 1002 |
|
- reverted changes to interpolation to previous treatment; there |
| 1003 |
|
was never actually a problem |
| 1004 |
|
o pkg/layers: |
| 1005 |
|
- fix interpolation of layers tracers in the presence of partial cells |
| 1006 |
|
- add lots of new functionality to compute water mass transformation |
| 1007 |
|
(enabled by CPP flag LAYERS_THERMODYNAMICS) |
| 1008 |
|
- add new calls from main code (diags_oceanic_surf_flux.F, |
| 1009 |
|
thermodynamics.F, impldiff.F) and gad to save the necessary fields |
| 1010 |
|
for layers_thermodynamics calculations |
| 1011 |
|
o pkg/ptracers: |
| 1012 |
|
- add capability of stepping a passive tracer forward without advection |
| 1013 |
|
by setting PTRACERS_advScheme to 0. |
| 1014 |
|
o pkg/diagnostics: |
| 1015 |
|
- add few (threads) _BARRIER around any update of "diag_pkgStatus". |
| 1016 |
|
o pkg/layers: |
| 1017 |
|
- shift potential density field "prho" by -1000 for density layer averaging so |
| 1018 |
|
that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000); |
| 1019 |
|
Note that density bin boundaries (layers_bounds in data.layers) have |
| 1020 |
|
to be set accordingly (i.e., shifted, in sigma scale). |
| 1021 |
|
o pkg/layers: |
| 1022 |
|
- fix snap-shot output of layer thickness @ V.pt and output of pot.density |
| 1023 |
|
- fix calculation of layer non-weighted velocity and layer probability |
| 1024 |
|
- add diagnostics for pot.density used for layer averaging |
| 1025 |
|
o pkg/seaice: |
| 1026 |
|
- seaice_calc_viscosity.F: change computation of deltaC**2 to ensure |
| 1027 |
|
positiveness, modify a few comments and improve variable names, |
| 1028 |
|
- the changed computation of deltaC affects most seaice-related |
| 1029 |
|
experiments at the truncation level. |
| 1030 |
|
seaice_itd.thermo is affected by far the most, with |
| 1031 |
|
only 7 digits of agreement remaining; update experiments. |
| 1032 |
|
|
| 1033 |
|
checkpoint65l (2015/05/04) |
| 1034 |
|
o pkg/shelfice: |
| 1035 |
|
- in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set |
| 1036 |
|
factor drKp1 to zero where it is negative (ie. do not use |
| 1037 |
|
SHELFICEBoundaryLayer if hFacC>1) |
| 1038 |
|
- the same for factor drLoc in shelfice_forcing.F |
| 1039 |
|
o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem |
| 1040 |
|
with modules in ptracers, when using testreport option "-small_f" |
| 1041 |
|
o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD) |
| 1042 |
|
- replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1)) |
| 1043 |
|
o verification/testreport |
| 1044 |
|
- add new option -small_f |
| 1045 |
|
with this option testreport first makes the target small_f (*.f files) |
| 1046 |
|
before running make (all). This is useful for explicit inlining when |
| 1047 |
|
all sources need to be full available. |
| 1048 |
|
o pkg/exf/exf_interp.F: |
| 1049 |
|
remove previous changes related to reverse (decreasing) input grids latitude |
| 1050 |
|
|
| 1051 |
|
checkpoint65k (2015/04/01) |
| 1052 |
|
o pkg/ecco: |
| 1053 |
|
fix missing cosphi initialization; use eccoiter in place of optimcycle; |
| 1054 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
| 1055 |
|
instead of active read/write |
| 1056 |
|
o pkg/ctrl: |
| 1057 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
| 1058 |
|
instead of active read/write. |
| 1059 |
|
o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F |
| 1060 |
|
return if .NOT.useAUTODIFF |
| 1061 |
|
o pkg/seaice: add CPP brackets (cost function related). |
| 1062 |
|
o model/src: |
| 1063 |
|
add useAUTODIFF run time switch. |
| 1064 |
|
o pkg/exf/exf_interp.F: |
| 1065 |
|
add code to allow input grids with latitude starting in the north (i.e. when |
| 1066 |
|
j=1 corresponds to northern edge of field); modify global_with_exf to test |
| 1067 |
|
this feature. |
| 1068 |
|
o verification/testreport: |
| 1069 |
|
- replace "grep -A3" with POSIX conformal sed command, because there are |
| 1070 |
|
implementations of grep that cannot do contextual searches |
| 1071 |
|
- replace "cat -n" by "nl" (two occurrences), because not all implementations |
| 1072 |
|
of "cat" have the option "-n" |
| 1073 |
|
o model/src: |
| 1074 |
|
add new file gsw_teos10.F that contains 3 functions, more or less a copy |
| 1075 |
|
of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to |
| 1076 |
|
convert from conservative to potential temperature. For now they are not |
| 1077 |
|
called anywhere. |
| 1078 |
|
o pkg/ggl90: make "useIDEMIX" useful |
| 1079 |
|
- re-organize code in s/r ggl90_calc a little to move computations that |
| 1080 |
|
are different for idemix into separate loops (changes verification |
| 1081 |
|
experiment idemix at truncation level, 12 digits remain -> updated) |
| 1082 |
|
- requires 2 new 2D fields KappaM, verticalShear |
| 1083 |
|
- make hFacI and recip_hFacI local 3D variables that are passed to |
| 1084 |
|
s/r ggl90_idemix |
| 1085 |
|
- fix and improve some comments |
| 1086 |
|
|
| 1087 |
|
checkpoint65j (2015/02/25) |
| 1088 |
|
o pkg/openad |
| 1089 |
|
- synchronize seawater.F with version in model/src: replace routine |
| 1090 |
|
body of sw_temp by calling sw_ptmp and fix/add a few comments. |
| 1091 |
|
o pkg/mnc: |
| 1092 |
|
- change default value of pickup_read/write_mnc params to FALSE |
| 1093 |
|
(since few features are missing in reading MNC pickup files). |
| 1094 |
|
o model/src: |
| 1095 |
|
- change default (background) vertical diffusivity for salt to be the |
| 1096 |
|
temperature (background) vertical diffusivity. |
| 1097 |
|
- change background vertical diffusivity in vertical mixing pkgs ggl90, |
| 1098 |
|
kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity. |
| 1099 |
|
This makes ptracers default diffusivity (that uses salt diffKr) more |
| 1100 |
|
consistent with vertical mixing schemes. |
| 1101 |
|
o verification/testreport: |
| 1102 |
|
- fix typo in "-pcls" option ; |
| 1103 |
|
- put temp files in /tmp (instead of in local dir) |
| 1104 |
|
- add option "-ncad" to use genmake2 new option "-nocat4ad" |
| 1105 |
|
- allow to use "-j" option (for multi-procs make) for AD, OAD and TLM. |
| 1106 |
|
o pkg/ggl90 (idemix code): |
| 1107 |
|
- apply few fixes ; add some missing "_d 0" ; update output of exp. |
| 1108 |
|
global_ocean.90x40x15.idemix |
| 1109 |
|
o OpenAD |
| 1110 |
|
- enable active file I/O and begin removal of work-around code |
| 1111 |
|
for OpenAD for handling control variables (memory vs. active files) |
| 1112 |
|
- new CPP options file OPENAD_OPTIONS.h |
| 1113 |
|
- revert to genarr2d gradient check for hs94.1x64x5 |
| 1114 |
|
- (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens) |
| 1115 |
|
- gentim2d works for halfpipe_streamice but not yet hs94.1x64x5 |
| 1116 |
|
o tools/genmake2: |
| 1117 |
|
- add option for an alternative Makefile (from Martin) where multiple |
| 1118 |
|
source files are sent to TAF (instead of all in one file). |
| 1119 |
|
o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013) |
| 1120 |
|
- code provided by Carsten Eden as an extension of ggl90 |
| 1121 |
|
- so far the code is turned on within ggl90 by setting a CPP-flag at |
| 1122 |
|
compile time; a runtime flag implementation is not yet complete |
| 1123 |
|
- tested in new verification experiment global_ocean.90x40x15.idemix |
| 1124 |
|
o verification: |
| 1125 |
|
- reduce length of the AD test run by half for experiments |
| 1126 |
|
global_ocean.cs32x15 (std + thsice) and isomip |
| 1127 |
|
- enable active file I/O for OpenAD, adjust verifications accordingly |
| 1128 |
|
- halfpipe_streamice: change gradient check from genarr2d to gentim2d |
| 1129 |
|
o verification/testreport: |
| 1130 |
|
- fix two non-POSIX sed statements so that there are no error messages |
| 1131 |
|
on Mac OS X |
| 1132 |
|
- replace hostname -s with hostname | sed 's/\..*$//' |
| 1133 |
|
o model/src/seawater.F: |
| 1134 |
|
- simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged |
| 1135 |
|
(following the matlab code), which would have avoided the bug caught |
| 1136 |
|
by Matt (see below) in the first place |
| 1137 |
|
o pkg/shelfice: |
| 1138 |
|
- implement alternative discretisation of quadratic drag (selectBotDragQuadr) |
| 1139 |
|
and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag. |
| 1140 |
|
- fix sign of friction tendency (no-slip BC) and fix u,v drag for thin |
| 1141 |
|
ice-shelf case (i.e., within surface level). |
| 1142 |
|
- add config summary in shelfice_check.F |
| 1143 |
|
- remove global variable recip_SHELFICElatentHeat and replace by a local |
| 1144 |
|
variable recip_latentHeat |
| 1145 |
|
- introduce diagnostics for friction velocity uStar (in case of |
| 1146 |
|
SHELFICEuseGammaFrict) |
| 1147 |
|
- change verification experiment isomip.htd: |
| 1148 |
|
+ start from pickup (as input_ad at nIter0=8640) |
| 1149 |
|
+ start from SHELFICEmassFile instead of SHELFICEloadAnomaly file |
| 1150 |
|
+ test SHELFICEuseGammaFrict = .TRUE. |
| 1151 |
|
+ test SHELFICEadvDiffHeatFlux = .TRUE. |
| 1152 |
|
o model/src: |
| 1153 |
|
- fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to |
| 1154 |
|
in-situ Temp) and in routine SW_TEMP (in pkg/openad); |
| 1155 |
|
update output of experiments global_with_exf.yearly and isomip (all 6). |
| 1156 |
|
o pkg/shelfice: |
| 1157 |
|
- change setting of kTopC to also be zero where there is no ice-shelf. |
| 1158 |
|
- zero out surface forcing arrays (for now, for T & S + EmPmR) where |
| 1159 |
|
ice-shelf is. |
| 1160 |
|
- first attempt to get RealFreshWaterFlux effects: for now, only without |
| 1161 |
|
SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping. |
| 1162 |
|
o pkg/seaice: add the option to prescribe a fixed thickness PDF |
| 1163 |
|
for thermodynamic calculations |
| 1164 |
|
- because of divisions of the type 7/7 not exactly equal to 1, this change |
| 1165 |
|
affects results of some verification experiments by up to 4 digits: |
| 1166 |
|
global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume, |
| 1167 |
|
seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides |
| 1168 |
|
adjoint: lab_sea, lab_sea.noseaicedyn |
| 1169 |
|
-> updated |
| 1170 |
|
|
| 1171 |
|
checkpoint65i (2015/01/23) |
| 1172 |
|
o model/src: |
| 1173 |
|
- change units of frictionHeating field from W to W/m^2 |
| 1174 |
|
- fix bug in frictional heating from stratospheric drag in |
| 1175 |
|
S/R ATM_PHYS_TENDENCY_APPLY_V |
| 1176 |
|
- with synchronous time-stepping: move resetting to zero of frictionHeating |
| 1177 |
|
field from load_fields_driver.F to thermodynamics.F ; |
| 1178 |
|
- add diagnostics for frictional heating. |
| 1179 |
|
o model/src & gmredi K3D: |
| 1180 |
|
- add frictionHeating field to pickup-files (for synchronous time-stepping) |
| 1181 |
|
- move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h |
| 1182 |
|
- rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name |
| 1183 |
|
and name in pickup file). |
| 1184 |
|
- fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F |
| 1185 |
|
o model/src: |
| 1186 |
|
- move (from ini_forcing.F) initialisation of all arrays in header file |
| 1187 |
|
FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart |
| 1188 |
|
(since Nov 2012) with option selectAddFluid=1. |
| 1189 |
|
o pkg/shelfice: |
| 1190 |
|
- change units (+ document) of newly added field "shelfIceMassDynTendency" |
| 1191 |
|
- upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays. |
| 1192 |
|
o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers |
| 1193 |
|
o pkg/seaice: two new runtime parameters: |
| 1194 |
|
- SEAICE_cStar replaces the hard wired "20" in the strength formulation, |
| 1195 |
|
long overdue |
| 1196 |
|
- SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012) |
| 1197 |
|
parameterization of tensil stress for fast ice (does not do anything yet) |
| 1198 |
|
o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method |
| 1199 |
|
for LSR: move checking overlaps out of JFNK-if-block |
| 1200 |
|
o pkg/atm_phys: |
| 1201 |
|
- move copy of grid and dynamical fields out of atm_phys_driver.F into |
| 1202 |
|
new S/R ATM_PHYS_DYN2PHYS. |
| 1203 |
|
- fix level height for Linear Free-Surf case (to be consistent with |
| 1204 |
|
fixed-in-time pressure levels). |
| 1205 |
|
o pkg/mom_common (bottomdrag): |
| 1206 |
|
- average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center |
| 1207 |
|
to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG; |
| 1208 |
|
update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag. |
| 1209 |
|
o pkg/shelfice (u/v_drag): |
| 1210 |
|
- add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG; |
| 1211 |
|
- use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F |
| 1212 |
|
(now similar to shelfice_u_drag.F) |
| 1213 |
|
- remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG |
| 1214 |
|
from mom_vecinv.F (similar to mom_fluxform calls). |
| 1215 |
|
o pkg/mom_common (bottomdrag): |
| 1216 |
|
- add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG; |
| 1217 |
|
- add options for alternative discretisation of velocity norm in quadratic |
| 1218 |
|
bottom drag: averaging of grid-cell-center KE to U.point and V.point |
| 1219 |
|
(selectBotDragQuadr=0, original code) can produce noisy patterns; this |
| 1220 |
|
improves when averaging only the other component (e.g. vVel for U bottom |
| 1221 |
|
drag) using wet-point method (selectBotDragQuadr=2) or not (=1). |
| 1222 |
|
- add options (bottomVisc_pCell) to account for partial-cell in bottom |
| 1223 |
|
friction (no-slip BC) thus getting the true distance from the bottom; |
| 1224 |
|
off by default since this also reduces model stability (explicit bottom |
| 1225 |
|
friction). Changes produce different machine truncation with linear-drag |
| 1226 |
|
+ no-slip BC: update output of experiments exp4.stevens (10 digits) and |
| 1227 |
|
front_relax (bvp & mxl, 10 & 11 digits). |
| 1228 |
|
o model/src & mom pkgs: |
| 1229 |
|
- add one more level to vertical viscosity local arrays (Nr+1, previously Nr) |
| 1230 |
|
since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k |
| 1231 |
|
- for now and until vertical mixing scheme are updated to fill up level Nr+1, |
| 1232 |
|
just copy level Nr value to level Nr+1. |
| 1233 |
|
o doc: |
| 1234 |
|
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
| 1235 |
|
o pkg/shelfice: |
| 1236 |
|
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
| 1237 |
|
SHELFICE.h: move array shelficemass to init_varia, initialise |
| 1238 |
|
from array shelficemassinit, which is set in init_fixed and |
| 1239 |
|
has option to be set from file; introduce array |
| 1240 |
|
shelficeMassDynTend array, set thru file in init_fixed |
| 1241 |
|
- NEW FILE: shelfice_step_icemass.F: update shelficemass from either |
| 1242 |
|
shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in |
| 1243 |
|
pkg/streamice |
| 1244 |
|
- shelfice_thermodynamics.F: call shelfice_step_icemass if |
| 1245 |
|
SHELFICEMassStepping = .true. |
| 1246 |
|
- shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f |
| 1247 |
|
|
| 1248 |
|
checkpoint65h (2014/12/17) |
| 1249 |
|
o verification/global_ocean.90x40x15, global_ocean_ebm: |
| 1250 |
|
- update to generic controls. |
| 1251 |
|
o pkg/ctrl: |
| 1252 |
|
- ctrl_map_ini_genarr.F: test for igen>0 |
| 1253 |
|
- ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. |
| 1254 |
|
- move gentim2d part of ctrl_map_ini_genarr.F to |
| 1255 |
|
new separate routine : ctrl_map_ini_gentim2d.F |
| 1256 |
|
- ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: |
| 1257 |
|
add time variable weights and cyclic controls (time mean, |
| 1258 |
|
seasonal cycle, etc) capabilities to gentim2d |
| 1259 |
|
o pkg/ecco: |
| 1260 |
|
- move reading of error, conversion to weights from |
| 1261 |
|
ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei) |
| 1262 |
|
o global_oce_llc90, cs32: |
| 1263 |
|
- activte sbo. |
| 1264 |
|
- CTRL_SIZE.h : add maxCtrlProc. |
| 1265 |
|
- activate the new genctrl capabilities. |
| 1266 |
|
- update following reorganization of global_oce_input_fields.tar.gz |
| 1267 |
|
o pkg/ctrl/ctrl_ad_diff.list: |
| 1268 |
|
- add missing ctrl_init_rec.f |
| 1269 |
|
o tools/OAD_support/keepOriginal: |
| 1270 |
|
- add ctrl_init_rec.F |
| 1271 |
|
o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F: |
| 1272 |
|
- avoid recomputations of xx_gentim2d_dummy. |
| 1273 |
|
o momentum diagnostics: |
| 1274 |
|
- move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and |
| 1275 |
|
mom_vecinv.F to timestep.F (to include Smag-3D contribution). |
| 1276 |
|
o pkg/seaice/seaice_lsr.F: |
| 1277 |
|
- fix computation of BU/BV, make sure they are non-zero, only necessary |
| 1278 |
|
for cubed sphere exchanges and SEAICE_OLx/y>0. |
| 1279 |
|
This makes calling s/r fill_cs_corner_rl obsolete (removed). |
| 1280 |
|
o verification/global_ocean.cs32x15/input.seaice |
| 1281 |
|
- add test for strong implicit coupling and restricted addtive Schwarz |
| 1282 |
|
methods for LSR |
| 1283 |
|
- update results/output.seaice.txt |
| 1284 |
|
o verification/tutorial_global_oce_biogeo: |
| 1285 |
|
- AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up) |
| 1286 |
|
and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK); |
| 1287 |
|
update output_adm,_oadm,_tlm.txt |
| 1288 |
|
o pkg/dic: |
| 1289 |
|
- change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h |
| 1290 |
|
- add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn |
| 1291 |
|
for tracer 1 & 2 is set (to avoid double counting of dilution effect). |
| 1292 |
|
o verification/tutorial_global_oce_biogeo: |
| 1293 |
|
- AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since |
| 1294 |
|
dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ; |
| 1295 |
|
update output_adm,_oadm,_tlm.txt |
| 1296 |
|
o eesupp/src: |
| 1297 |
|
- add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F) |
| 1298 |
|
and call it in seaice_lsr when using nonzero SEAICE_OLx/y |
| 1299 |
|
o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing |
| 1300 |
|
LSR (following Hutchings et al. 2004) |
| 1301 |
|
- introduce zetaZ as a global variable (requires adjustments in |
| 1302 |
|
seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ |
| 1303 |
|
in seaice_calc_viscosities.F |
| 1304 |
|
- new flag SEAICEuseStrImpCpl (default off) |
| 1305 |
|
- add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the |
| 1306 |
|
momentum equations |
| 1307 |
|
- JFNK-solver (preconditioner) adjusted to allow using this method |
| 1308 |
|
(where it does not have any positive effect) |
| 1309 |
|
o pkg/seaice |
| 1310 |
|
- add overlap for restrictive additive Schwartz method also to LSR, but |
| 1311 |
|
turn it off by default (because it only seems to work for non-cubed |
| 1312 |
|
sphere/llc topologies) |
| 1313 |
|
o pkg/autodiff |
| 1314 |
|
- add extra exchanges in addummy_in_steppging also for mnc output |
| 1315 |
|
o pkg/seaice: |
| 1316 |
|
- add extra exchanges before dumping adjoint fields in seaice_ad_dump.F |
| 1317 |
|
to avoid stripes in the adjoint output (similar to addummy_in_stepping.F) |
| 1318 |
|
o pkg/obcs: |
| 1319 |
|
- add option to specify domain-connected piece Id along OB though files |
| 1320 |
|
(for now, only used to diagnose PhiVel; default =1 -> global correction) |
| 1321 |
|
- modify obcs_diag_balance.F to process each connected-part separately; |
| 1322 |
|
exclude OB where Id = 0 but keep the full divergence there (-> constant |
| 1323 |
|
Psi along this portion of OB and all inflow derived from grad(Phi)) |
| 1324 |
|
- add example of OB-conect files in verification/so_box_biogeo/input. |
| 1325 |
|
o pkg/diagnostics: |
| 1326 |
|
- improve treatment of Open-Boundaries in Velocity-Potential calculation: |
| 1327 |
|
a) use non zero matrix element across OB and solve for Phi 1 grid point |
| 1328 |
|
outside OB (i.e, where tracer OBCS are applied). |
| 1329 |
|
b) global imbalance of inFlow/outFlow across OB: instead of modifying |
| 1330 |
|
velocity across OB, spread it uniformly along the OB in the RHS. |
| 1331 |
|
|
| 1332 |
|
checkpoint65g (2014/11/19) |
| 1333 |
|
o pkg/diagnostcis: |
| 1334 |
|
- add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param |
| 1335 |
|
o pkg/my82,pp81,kl10: |
| 1336 |
|
- fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D |
| 1337 |
|
field diffKr as background diffusivity to set minimum diffusivity value. |
| 1338 |
|
o pkg/seaice: |
| 1339 |
|
- add new parameter SEAICEuseEVPrev (for revisited EVP by |
| 1340 |
|
Bouillon et al 2013) |
| 1341 |
|
- add SEAICE_evpAlpha/Beta to namelist |
| 1342 |
|
- modify seaice_evp code to able to use SEAICEuseEVPrev. These changes |
| 1343 |
|
involve trivial re-ordering of divisions/multiplications that should not |
| 1344 |
|
have any effects, but ... they do change the results of lab_sea.hb87 so |
| 1345 |
|
that only 2 digits of agreement remain, in line with the general |
| 1346 |
|
instability/fragility of the evp-code. For now, I do not care and just |
| 1347 |
|
update the verification experiment |
| 1348 |
|
o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc) |
| 1349 |
|
- remove xx_genarr2d_numsmooth etc |
| 1350 |
|
- use xx_genarr2d_preproc etc instead |
| 1351 |
|
- carry out smooth_correl2D at initialization stage rather than during |
| 1352 |
|
time stepping. |
| 1353 |
|
- get smoothOpNb from xx_gentim2d_preproc |
| 1354 |
|
o global_oce_cs32 : |
| 1355 |
|
- add test of generic ecco capabilities. |
| 1356 |
|
o pkg/exf/exf_getsurfacefluxes.F : |
| 1357 |
|
- add to tmpUE/tmpVN rather than re-initializing them (conventional behavior). |
| 1358 |
|
o pkg/ctrl,ecco : |
| 1359 |
|
- omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED |
| 1360 |
|
is defined. |
| 1361 |
|
o pkg/seaice: add diagnostics for Delta (deformation parameter) |
| 1362 |
|
o model/src: |
| 1363 |
|
- when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical |
| 1364 |
|
diffusivity (background) is specified but ignored. |
| 1365 |
|
o verification: |
| 1366 |
|
- in testreport, convert hostname to lower case for default output dir name |
| 1367 |
|
o model, pkg : add useCTRL, useECCO parameters (on/off run time switch). |
| 1368 |
|
o pkg/dic: add modifications from Hajoon: |
| 1369 |
|
- add iron sedimentation flux function of the flux of PO4 out of bottom layer |
| 1370 |
|
- light attenuation: add self-shading effect by climatological Chlorophyll |
| 1371 |
|
(read from file). |
| 1372 |
|
o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also |
| 1373 |
|
compiles when SEAICE_ALLOW_DYNAMICS is undefined |
| 1374 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
| 1375 |
|
AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
| 1376 |
|
ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
| 1377 |
|
approach where CPP_OPTIONS.h includes an omnipotent |
| 1378 |
|
ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
| 1379 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
| 1380 |
|
ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
| 1381 |
|
o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
| 1382 |
|
to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
| 1383 |
|
(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
| 1384 |
|
o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
| 1385 |
|
add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
| 1386 |
|
- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
| 1387 |
|
- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
| 1388 |
|
- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
| 1389 |
|
o pkg/ctrl,ecco,exf : |
| 1390 |
|
- remove variables associated with NON-generic costs, |
| 1391 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
| 1392 |
|
- remove NON-generic NON-obcs controls, |
| 1393 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
| 1394 |
|
o pkg/ctrl : added ctrl_local_params.h |
| 1395 |
|
o pkg/ecco : added ecco_local_params.h |
| 1396 |
|
o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
| 1397 |
|
experiments, which will progressively be removed once the |
| 1398 |
|
experiments are revised to use only generic controls/costs. |
| 1399 |
|
|
| 1400 |
|
checkpoint65f (2014/10/13) |
| 1401 |
|
o pkg/ctrl, ecco, seaice : minor changes in headers |
| 1402 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
| 1403 |
|
cost function and control capabilities added since checkpoint65c. |
| 1404 |
|
o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
| 1405 |
|
o pkg/ecco: increase modularity and improve logic |
| 1406 |
|
- ecco_toolbox.F (new) : basic operations that are often used, |
| 1407 |
|
including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk, |
| 1408 |
|
ecco_addcost, ecco_add, ecco_div, ecco_readbar. |
| 1409 |
|
- cost_gencal.F (new) : determine filnames and records. |
| 1410 |
|
- cost_genread.F, cost_generic.F : condense code using ecco_toolbox. |
| 1411 |
|
- cost_generic.F : use spzeroloc rather than hard-coded -9999, |
| 1412 |
|
and exploit the above functions leading to more compact code. |
| 1413 |
|
- cost_genread.F : rm un-necessary arguments, re-arrange args order. |
| 1414 |
|
- ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj, |
| 1415 |
|
using_ers, using_gfo, using_mdt is now only defined within gencost) |
| 1416 |
|
o pkg/ecco: extend generic cost capabilities |
| 1417 |
|
- pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost |
| 1418 |
|
capabilities via gencost_preproc (+ _c,_i,_r related params), |
| 1419 |
|
gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod, |
| 1420 |
|
gencost_outputlevel arguments to cost_generic |
| 1421 |
|
- pkg/ecco/cost_genread.F (new) : interface between cost_generic |
| 1422 |
|
and active_read, making room for gencost_preproc to take effect. |
| 1423 |
|
Added preproc code ('climmon') to replace GENERIC_BAR_MONTH. |
| 1424 |
|
- pkg/ecco/cost_generic.F : |
| 1425 |
|
compute and store misfit maks*(model-data) in localdif that is |
| 1426 |
|
then used in cost and for output, output misfit if outlev.GT.0 |
| 1427 |
|
- pkg/ecco/cost_averagesfields.F : depend on gencost_barskip |
| 1428 |
|
rather gencost_barfile for deciding whether to write barfile |
| 1429 |
|
- pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd |
| 1430 |
|
- pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from |
| 1431 |
|
ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip |
| 1432 |
|
- pkg/ecco/ecco_summary.F : report gencost variables |
| 1433 |
|
- pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs |
| 1434 |
|
o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA |
| 1435 |
|
o pkg/ecco: internal re-organization |
| 1436 |
|
- resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl |
| 1437 |
|
(rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter, |
| 1438 |
|
mv relevant variables definition from ecco_cost.h to ecco.h, |
| 1439 |
|
make sure gencost routines only include ecco.h) |
| 1440 |
|
- throughout : add missing CCP switches, rm unused variables, |
| 1441 |
|
and rm un-necessary CPP switches |
| 1442 |
|
- throughout gencost routines : replace modelstartdate with |
| 1443 |
|
gencost_startdate when needed |
| 1444 |
|
- cost_bp_read.F : use arguments, instead of common blocs |
| 1445 |
|
so that it can be used also by (new) cost_gencost_bpv4.F |
| 1446 |
|
- ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0 |
| 1447 |
|
- ecco_phys.F : compute etanFull |
| 1448 |
|
- ecco_readparms.F : rename using_topex as using_tpj, add |
| 1449 |
|
bpv4-grace to gencost list, initialize added parameters |
| 1450 |
|
- ecco_summary.F : include SIZE.h needed for augmented ecco.h |
| 1451 |
|
|
| 1452 |
|
checkpoint65e (2014/09/28) |
| 1453 |
|
o pkg/obcs: |
| 1454 |
|
- replaced the just-added CPP options with run-time variables |
| 1455 |
|
(see pkg/obcs/OBCS_PARAMS.h for details) |
| 1456 |
|
o pkg/obcs: |
| 1457 |
|
- add additional CPP options for sponge boundary layers |
| 1458 |
|
(see pkg/obcs/OBCS_OPTIONS.h for details) |
| 1459 |
|
o pkg/atm_phys: |
| 1460 |
|
- implement simple (obliquity only, assuming circular planet orbit) |
| 1461 |
|
seasonal cycle for incoming insolation ; used when run-time parameter |
| 1462 |
|
"select_incSW" is set to 1 ; by default (=0), uses old unchanged formula. |
| 1463 |
|
o pkg/exf, pkg/ecco, pkg/ctrl: |
| 1464 |
|
- add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets |
| 1465 |
|
- activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip |
| 1466 |
|
- implement gentim2d for xx_tauu, xx_tauv |
| 1467 |
|
o pkg/ctrl, pkg/ecco : |
| 1468 |
|
- fix and complement the generic controls implementation |
| 1469 |
|
o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F, |
| 1470 |
|
pkg/shelfice/shelfice_thermodynamics.F, |
| 1471 |
|
verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F, |
| 1472 |
|
verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F : |
| 1473 |
|
- add weight in CTRL_GET_GEN calls |
| 1474 |
|
o pkg/ctrl : |
| 1475 |
|
- ctrl_get_gen.F : add weight as input parameter, and apply |
| 1476 |
|
it directly rather than using smooth_correl2Dw (to be retired). |
| 1477 |
|
- ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call |
| 1478 |
|
o pkg/ctrl : |
| 1479 |
|
- introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, |
| 1480 |
|
ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) |
| 1481 |
|
- re-activate ctrl_summary (call in ctrl_init.F) |
| 1482 |
|
o pkg/ctrl/ctrl_cost_gen.F : |
| 1483 |
|
- fix CCP brackets, remove un-necessary myiter, mytime |
| 1484 |
|
o pkg/ecco, pkg/ctrl : |
| 1485 |
|
- remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) |
| 1486 |
|
- remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) |
| 1487 |
|
- add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) |
| 1488 |
|
- add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) |
| 1489 |
|
|
| 1490 |
|
checkpoint65d (2014/09/15) |
| 1491 |
|
o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : |
| 1492 |
|
- add xx_genarr2d_bounds,xx_genarr3d_bounds, |
| 1493 |
|
xx_genarr2d_numsmooth, xx_genarr3d_numsmooth |
| 1494 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : |
| 1495 |
|
- remove compilation failure |
| 1496 |
|
- replace hard coded example |
| 1497 |
|
- use ctrl_map_ini_gen2D, 3D |
| 1498 |
|
o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : |
| 1499 |
|
- on/off switch based upon xx_genarr2d_weight,3d |
| 1500 |
|
o src/packages_init_variables.F : |
| 1501 |
|
- regroup pkg/estimation calls |
| 1502 |
|
- remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
| 1503 |
|
(moved to ctrl_init_variables) |
| 1504 |
|
o cost/cost_init_varia.F : |
| 1505 |
|
- remove ecco_cost_init_varia |
| 1506 |
|
(moved to ecco_init_varia) |
| 1507 |
|
o ctrl/ctrl_init_variables.F : |
| 1508 |
|
- add CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
| 1509 |
|
- add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI |
| 1510 |
|
o ctrl/ctrl_map_ini.F : |
| 1511 |
|
- remove ctrl_map_ini_genarr, seaice_ctrl_map_ini |
| 1512 |
|
(moved to ctrl_init_variables) |
| 1513 |
|
o ctrl/ctrl_map_ini_ecco.F : |
| 1514 |
|
- remove ECCO_PHYS (mv to ecco_init_varia) |
| 1515 |
|
- remove seaice_ctrl_map_ini (mv to ctrl_init_variables) |
| 1516 |
|
o ecco/ecco_ad_diff.list : |
| 1517 |
|
- add ecco_init_varia.f |
| 1518 |
|
o ecco/ecco_init_varia.F |
| 1519 |
|
- new routine |
| 1520 |
|
o pkg/streamice: |
| 1521 |
|
- move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F |
| 1522 |
|
to streamice_init_fixed.F ; fix setting of STREAMICEisOn. |
| 1523 |
|
- from model/src, only call pkg/streamice routines if useStreamIce is TRUE. |
| 1524 |
|
o pkg/generic_advdiff: |
| 1525 |
|
- fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. |
| 1526 |
|
o pkg/exf: |
| 1527 |
|
- exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, |
| 1528 |
|
xxg_precip capability |
| 1529 |
|
- exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch |
| 1530 |
|
o pkg/ctrl: |
| 1531 |
|
- ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d |
| 1532 |
|
o model/src/load_fields_driver.F : |
| 1533 |
|
- move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING |
| 1534 |
|
so xx_gentim2d can be applied to e.g. exf fields in a timely manner. |
| 1535 |
|
o OpenAD verification experiments: |
| 1536 |
|
- Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h |
| 1537 |
|
in src files (to enable to skip the ECCO_CPPOPTIONS.h); |
| 1538 |
|
for now, only in pkgs used in OpenAD verification experiments. |
| 1539 |
|
- Change all except one (halfpipe_streamice) OpenAD experiments to use pkg |
| 1540 |
|
specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) |
| 1541 |
|
instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). |
| 1542 |
|
This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. |
| 1543 |
|
o OpenAD verification tests: |
| 1544 |
|
- finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); |
| 1545 |
|
- finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for |
| 1546 |
|
tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. |
| 1547 |
|
- leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) |
| 1548 |
|
and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). |
| 1549 |
|
o model/src & generic_advdiff: |
| 1550 |
|
- change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S |
| 1551 |
|
forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model |
| 1552 |
|
dynamics requires valid tracer forcing only over tile interior but, for |
| 1553 |
|
some diagnostics, may need to extend it over 1 point in tile halo region. |
| 1554 |
|
- in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid |
| 1555 |
|
tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max |
| 1556 |
|
setting in temp/salt/ptracer_integrate.F |
| 1557 |
|
o pkg/dic: |
| 1558 |
|
- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
| 1559 |
|
gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
| 1560 |
|
in gchem_forcing_sep.F |
| 1561 |
|
o pkg/autodiff & obcs: |
| 1562 |
|
- add storage of current OB values for U & V (was already done for T & S). |
| 1563 |
|
|
| 1564 |
|
checkpoint65c (2014/08/30) |
| 1565 |
|
o pkg/dic: |
| 1566 |
|
- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
| 1567 |
|
and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
| 1568 |
|
AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
| 1569 |
|
o verification: |
| 1570 |
|
- new experiment testing OBCS and DIC pkgs, using params & output from |
| 1571 |
|
tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
| 1572 |
|
passage: take OBCS from the last year of a 2 yrs simulation and initial |
| 1573 |
|
conditions from t=1.yr while keeping the same forcing. |
| 1574 |
|
o model/src: |
| 1575 |
|
- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
| 1576 |
|
(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
| 1577 |
|
o pkg/diagnostics (Stats-Diags): |
| 1578 |
|
- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
| 1579 |
|
a) refine region where stats are computed, excluding where arrhFac=0 ; |
| 1580 |
|
b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
| 1581 |
|
c) extend regional stats over the region edges (for U or V pt location). |
| 1582 |
|
o pkg/gchem: |
| 1583 |
|
- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
| 1584 |
|
pkg/dic is currently changing/updating ptracers values beyond the OB). |
| 1585 |
|
o verification (hs94): |
| 1586 |
|
- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
| 1587 |
|
bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
| 1588 |
|
hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
| 1589 |
|
apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
| 1590 |
|
o pkg/ptracers: |
| 1591 |
|
- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
| 1592 |
|
switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
| 1593 |
|
- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
| 1594 |
|
with AB-2 code (so that it get tested). |
| 1595 |
|
o model/src: |
| 1596 |
|
- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
| 1597 |
|
with AB-2 code (previously only available with AB-3 code). |
| 1598 |
|
Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
| 1599 |
|
to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
| 1600 |
|
there, by calling CYCLE_AB_TRACER). |
| 1601 |
|
o pkg/generic_advdiff: |
| 1602 |
|
- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
| 1603 |
|
GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
| 1604 |
|
+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
| 1605 |
|
S/R temp/salt/ptracers_integrate.F |
| 1606 |
|
o model/src & pkg/ptracers: |
| 1607 |
|
- remove common block variables gT,gS (in DYNVARS.h), except when |
| 1608 |
|
USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
| 1609 |
|
- remove common block variable gPtr. |
| 1610 |
|
o model/src & pkgs: |
| 1611 |
|
- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
| 1612 |
|
ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
| 1613 |
|
IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
| 1614 |
|
GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
| 1615 |
|
+ change accordingly all calling S/R. |
| 1616 |
|
- use local temperature/salinity/ptracer tendency array (without bi,bj) |
| 1617 |
|
in S/R temp/salt/ptracers_integrate.F |
| 1618 |
|
o pkg/seaice: |
| 1619 |
|
- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
| 1620 |
|
to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
| 1621 |
|
- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
| 1622 |
|
in seaice_lsr |
| 1623 |
|
- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
| 1624 |
|
in s/r seaice_lsr_calc_coeffs |
| 1625 |
|
o pkg/mdsio: |
| 1626 |
|
- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
| 1627 |
|
(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
| 1628 |
|
too long (e.g., > MAX_LEN_FNAM/2 ) |
| 1629 |
|
|
| 1630 |
|
checkpoint65b (2014/08/12) |
| 1631 |
|
o pkg/matrix: |
| 1632 |
|
- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
| 1633 |
|
o model/src: |
| 1634 |
|
- fix initialisation of geothermalFile; compile geothermal-flux code in |
| 1635 |
|
natl_box verification experiment. |
| 1636 |
|
o model/src & pkg/down_slope: |
| 1637 |
|
- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
| 1638 |
|
- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
| 1639 |
|
field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
| 1640 |
|
results at machine truncation level: update output of experiments |
| 1641 |
|
global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
| 1642 |
|
o pkg/diagnostics (Stats-Diags): |
| 1643 |
|
- do not cumulate the full volume when DIAGNOSTICS_FILL is |
| 1644 |
|
called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
| 1645 |
|
This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
| 1646 |
|
times (but Min,Max and StD are still wrong). |
| 1647 |
|
o model/src: |
| 1648 |
|
- add geothermal flux forcing: read in ini_forcing.F as time-constant |
| 1649 |
|
field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
| 1650 |
|
o model/src: |
| 1651 |
|
- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
| 1652 |
|
_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
| 1653 |
|
arrays are already updated while adjustments (filters, conv.adjustment) are |
| 1654 |
|
still applied later, in S/R TRACERS_CORRECTION_STEP. |
| 1655 |
|
o model/src: |
| 1656 |
|
- store in common bloc array "rhoInSitu" the virtual potential temperature |
| 1657 |
|
anomaly that is used to compute geopotential: this make the atmos code |
| 1658 |
|
more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
| 1659 |
|
o pkg/seaice/seaice_lsr.F |
| 1660 |
|
- rename integer variable ilcall to ipass (that's what it is called |
| 1661 |
|
in the residual diagnostics |
| 1662 |
|
- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
| 1663 |
|
default) for improved non-linear convergence of the first few steps |
| 1664 |
|
- adjust a few comments and add new ones to explain some of the store |
| 1665 |
|
directives |
| 1666 |
|
o pkg/generic_advdiff (& ptracers): |
| 1667 |
|
- re-work the code to check for valid advection scheme and for minimum |
| 1668 |
|
size of overlap (now stored in local common bloc in gad_advscheme.F) |
| 1669 |
|
o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
| 1670 |
|
- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
| 1671 |
|
- add an auxilliary variable "bet" and fix store directives and keys in |
| 1672 |
|
seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
| 1673 |
|
less exact gradients in my tests); but there are still |
| 1674 |
|
recomputation warning (although gradients are sort of OK), when |
| 1675 |
|
SEAICE_LSR_VECTORIZE is not defined, so this flag and |
| 1676 |
|
SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
| 1677 |
|
- update verification experiments lab_sea. |
| 1678 |
|
- change some comments in S/R seaice_calc_viscosities |
| 1679 |
|
o model/src: |
| 1680 |
|
- if staggerTimeStep=T, always apply exchange to velocity field in |
| 1681 |
|
do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
| 1682 |
|
(independent of using multi-dim advection or not); no effect on FWD run |
| 1683 |
|
but affects AD results (at machine truncation level): update output of |
| 1684 |
|
experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
| 1685 |
|
and isomip (oad: 12.d). |
| 1686 |
|
o pkg/generic_advdiff: |
| 1687 |
|
- stop if doAB_onGtGs is set to FALSE but ignored |
| 1688 |
|
- refine warning related to stability of tracer time-stepping |
| 1689 |
|
regarding internal wave dynamics. |
| 1690 |
|
- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
| 1691 |
|
on staggerTimeStep & implicitIntGravWave (will now get a warning |
| 1692 |
|
if potentially unstable). |
| 1693 |
|
o pkg/kl10: |
| 1694 |
|
- add new pkg "kl10" for mixing due to internal wave breaking, from |
| 1695 |
|
http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
| 1696 |
|
(contribution from Jody Klymak), tested in verification experiment |
| 1697 |
|
verification/internal_wave/input.kl10/ |
| 1698 |
|
o isomip experiment: |
| 1699 |
|
- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
| 1700 |
|
(input.htd) and update the output. |
| 1701 |
|
o cd_code experiments: |
| 1702 |
|
- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
| 1703 |
|
#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
| 1704 |
|
global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
| 1705 |
|
update the corresponding output. |
| 1706 |
|
o pkg/seaice: |
| 1707 |
|
- reduce the number of include files and store directives in |
| 1708 |
|
S/R seaice_lsr_tridiagu/v |
| 1709 |
|
- change the order of loops in one case in S/R seaice_lsr_tridiagv |
| 1710 |
|
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
| 1711 |
|
get rid off one store directive (a TAF bug?) |
| 1712 |
|
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
| 1713 |
|
S/R seaice_lsr_tridiagv to change the loop range for consistency |
| 1714 |
|
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
| 1715 |
|
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
| 1716 |
|
S/R seaice_lsr_tridiagu/v (requires update of |
| 1717 |
|
offline_exf_seaice/input.dyn_jfnk) |
| 1718 |
|
|
| 1719 |
|
checkpoint65a (2014/07/27) |
| 1720 |
|
o model/src: |
| 1721 |
|
- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
| 1722 |
|
surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
| 1723 |
|
(topo in p-coords, ice-shelf in z-coords); update output of experiments |
| 1724 |
|
tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
| 1725 |
|
o model/src: |
| 1726 |
|
- collect momentum forcing tendency into local 2-D array (passed as argument |
| 1727 |
|
to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
| 1728 |
|
parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
| 1729 |
|
affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
| 1730 |
|
- collect T & S forcing tendency into local 2-D array (passed as argument to |
| 1731 |
|
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
| 1732 |
|
affects results at machine truncation level (e.g., ocean: if using |
| 1733 |
|
SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
| 1734 |
|
correction due to vertical advection). |
| 1735 |
|
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
| 1736 |
|
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
| 1737 |
|
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
| 1738 |
|
obcs_ctrl (ad & fwd grd @ 12 & 7). |
| 1739 |
|
o pkg/ptracers & diagnostics: |
| 1740 |
|
- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
| 1741 |
|
title (to avoid some unexpected truncation); sort out ptracers diags units. |
| 1742 |
|
- collect ptracer forcing tendency into local 2-D array (passed as argument |
| 1743 |
|
to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
| 1744 |
|
|
| 1745 |
|
checkpoint65 (2014/07/18) |
| 1746 |
|
o pkg/fizhi: |
| 1747 |
|
- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
| 1748 |
|
affects results at machine truncation level. Update output of experiments |
| 1749 |
|
fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). |
| 1750 |
|
o pkg/seaice: more clean up |
| 1751 |
|
- rename TAF common block tapes to be more consistent and remove |
| 1752 |
|
unnecessary duplicates |
| 1753 |
|
- add store directives to remove more recomputations, but use smaller |
| 1754 |
|
tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. |
| 1755 |
|
The idea behind this flag is to reduce the memory footprint when the |
| 1756 |
|
adjoint of the LSR is not required. As of now, defining the flag |
| 1757 |
|
SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by |
| 1758 |
|
a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). |
| 1759 |
|
For experiment offline_exf_seaice, this means on a linux box with gfortran |
| 1760 |
|
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
| 1761 |
|
this experiment): |
| 1762 |
|
> size mitgcmuv_ad |
| 1763 |
|
text data bss dec hex |
| 1764 |
|
5100659 1216 220458952 225560827 d71c8fb |
| 1765 |
|
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
| 1766 |
|
but only a moderate increase of 36% for global_ocean.cs32x15: |
| 1767 |
|
text data bss dec hex |
| 1768 |
|
6695027 1648 1014578664 1021275339 3cdf6ccb |
| 1769 |
|
6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER) |
| 1770 |
|
- note: there are still recomputations in global_ocean.cs32x15 and |
| 1771 |
|
offline_exf_seaice and the gradient agreement changes (gets a |
| 1772 |
|
little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) |
| 1773 |
|
- in general, the AD gradients still are wrong |
| 1774 |
|
o OpenAD |
| 1775 |
|
- clean up code_oad/ directories somewhat by moving files |
| 1776 |
|
dontCompile, dontTransform, keepOriginal to OAD_support/ |
| 1777 |
|
o model/src: |
| 1778 |
|
- using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F |
| 1779 |
|
(not currently tested): add dissipation terms before NLFS rescaling of |
| 1780 |
|
tendencies (previously done after). |
| 1781 |
|
o pkg/diagnostics: |
| 1782 |
|
- write stats-diags in ascii file with more digits (same as in monitor). |
| 1783 |
|
o pkg/down_slope: |
| 1784 |
|
- drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with |
| 1785 |
|
NLFS (not tested), use new recip_hFac value in order to conserve tracer. |
| 1786 |
|
o model/src: |
| 1787 |
|
- new file "apply_forcing.F" containing all the code previously in |
| 1788 |
|
external_forcing.F, but with new argument list: pass, as new argument, |
| 1789 |
|
the current level tendency array to update (instead of a direct update |
| 1790 |
|
of the common bloc array). Change the corresponding calls. |
| 1791 |
|
- add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use |
| 1792 |
|
EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility). |
| 1793 |
|
o pkg/seaice/seaice_lsr, a little bit of clean up |
| 1794 |
|
- rearrange some code blocks, so that now all calculations for |
| 1795 |
|
setting up the right-hand-sides done within one single block |
| 1796 |
|
(I find that easier to read and understand) |
| 1797 |
|
- rearrange freedrift-code to reduce the number of ifdefs |
| 1798 |
|
- adjust some indentations and comments |
| 1799 |
|
|
| 1800 |
|
checkpoint64z (2014/07/10) |
| 1801 |
|
o model/src and several pkgs: |
| 1802 |
|
- change argument list of all S/R called from external_forcing.F and |
| 1803 |
|
called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F) |
| 1804 |
|
to pass, as argument, the current level tendency array to update |
| 1805 |
|
(instead of a direct update of the common bloc array). |
| 1806 |
|
- change also (in the same way) argument list of PTRACERS_APPLY_FORCING; |
| 1807 |
|
- rename taueddy_external_forcing.f to taueddy_tendency_apply.F |
| 1808 |
|
o pkg/seaice/seaice_lsr.F |
| 1809 |
|
- always initialize local arrays in seaice_lsr_tridiagu/v |
| 1810 |
|
- add more local tapes to seaice_lsr_tridiagu/v |
| 1811 |
|
- move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but |
| 1812 |
|
keep it in bi/bj loop; this seems to be essential |
| 1813 |
|
- gradients are still wrong but only by 4-7 orders of magnitude |
| 1814 |
|
instead of 15 orders of magnitude, lab_sea improves a little |
| 1815 |
|
o pkg/seaice |
| 1816 |
|
- (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that |
| 1817 |
|
generates unnecessary code in seaice_lsr_ad |
| 1818 |
|
- add more store directives in seaice_lsr to avoid unnecessary code |
| 1819 |
|
in seaice_lsr_ad |
| 1820 |
|
- exclude some residual computations in seaice_lsr when |
| 1821 |
|
ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code |
| 1822 |
|
in seaice_lsr_ad |
| 1823 |
|
- add more storing, a new tape (model/src/the_main_loop.F) and |
| 1824 |
|
another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey |
| 1825 |
|
and klockey should be checked by a specialist) |
| 1826 |
|
- modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER ) |
| 1827 |
|
and update lab_sea after previous changes in pkg/seaice below |
| 1828 |
|
o pkg/autodiff: |
| 1829 |
|
- introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and |
| 1830 |
|
viscFacInAd : run time parameters allowing for adjoint switches |
| 1831 |
|
note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F |
| 1832 |
|
o pkg/ecco: |
| 1833 |
|
- introduce cost_gencost_boxmean.F that computes a box mean |
| 1834 |
|
temperature (for use in adjoint sensitivity studies). |
| 1835 |
|
o model/src/set_defaults.F : initialize viscFacAdj to 1. |
| 1836 |
|
o pkg/mom_common/mom_calc_visc.F: |
| 1837 |
|
- ifdef ALLOW_AUTODIFF then include viscFacAdj factor. |
| 1838 |
|
o pkg/seaice/seaice_summary.F: |
| 1839 |
|
- statement for SEAICEadjMODE now in autodiff_readparms.F |
| 1840 |
|
o pkg/seaice: |
| 1841 |
|
- remove some store directives and add new ones in an effort to get |
| 1842 |
|
finally rid off the recomputation warnings. This is successful |
| 1843 |
|
when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are |
| 1844 |
|
defined (i.e. no extensive recomputation warnings left), but there |
| 1845 |
|
are still too many recomputations on the solver iteration level |
| 1846 |
|
- define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h |
| 1847 |
|
- move definition of MPSEUDOTIMESTEPS into TAMC-block in |
| 1848 |
|
SEAICE_SIZE.h |
| 1849 |
|
- add a store directive in S/R seaice_calc_viscosities |
| 1850 |
|
o pkg/seaice (ITD code): |
| 1851 |
|
- fix definition of Hlimit for multi-threaded case |
| 1852 |
|
- use double precision arithmetic to compute Hlimit: this affects results; |
| 1853 |
|
update output of experiment seaice_itd. |
| 1854 |
|
o replace content of verification/seaice_itd |
| 1855 |
|
- instead of a 1D column use the configuration of offline_exf_seaice |
| 1856 |
|
to test the ice thickness distribution code with ridging |
| 1857 |
|
- this is a first shot at this experiment |
| 1858 |
|
- change of some defaults of ridging parameters SEAICEhStar (from |
| 1859 |
|
100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F |
| 1860 |
|
and lot of new comments. |
| 1861 |
|
|
| 1862 |
|
checkpoint64y (2014/06/20) |
| 1863 |
|
o pkg/seaice/seaice_reg_ridge.F: |
| 1864 |
|
- modify the regularization of very small volumes of ice; only check |
| 1865 |
|
total volume HEFF, and do not apply correction to individual ice |
| 1866 |
|
classes because that leads to funny patterns in the heat and fw-fluxes |
| 1867 |
|
into the ocean. Adjust seaice_itd/results/output.txt |
| 1868 |
|
- replace nITD by SEAICE_multDim in loop-ranges |
| 1869 |
|
o pkg/exf: |
| 1870 |
|
- add code to process the case field period = -12. with UV interpolation. |
| 1871 |
|
- move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec |
| 1872 |
|
into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F) |
| 1873 |
|
o verification/global_with_exf: |
| 1874 |
|
- switch all fields period to -12. (was previously untested) in input/data.exf |
| 1875 |
|
(but keep secondary test ".yearly" unchanged); update the reference output. |
| 1876 |
|
o pkg/cal: |
| 1877 |
|
- new calendar type "noLeapYear" for 365 days calendar without any leap year. |
| 1878 |
|
o pkg/exf: |
| 1879 |
|
- new integer parameter "exf_debugLev" (default set to main model debugLevel) |
| 1880 |
|
to replace logical switch "exf_verbose" |
| 1881 |
|
- report in STDOUT when loading a new record (if exf_debugLev >= 3) |
| 1882 |
|
o pkg/sbo: |
| 1883 |
|
- update from Katherine Quinn: evaluate mass directly from density and SSH |
| 1884 |
|
(budget using Finite Volume method) instead of from bottom pressure. |
| 1885 |
|
- allow testreport to collect few selected SBO output ; tested in exp. |
| 1886 |
|
global_ocean.90x40x15 (after updating the results, to include SBO output). |
| 1887 |
|
- fix some multi-threading issues (in output part). |
| 1888 |
|
o model/src & most packages: |
| 1889 |
|
- always call {PKG}_READPARMS even if corresponding use{PKG}=F; |
| 1890 |
|
- in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R |
| 1891 |
|
PACKAGES_UNUSED_MSG to print a weak warning when parameter file |
| 1892 |
|
"data.{pkg}" exist ; and leave the S/R (return) just after. |
| 1893 |
|
- more standard LAND pkg interface (land_init_fixed.F, land_check.F). |
| 1894 |
|
+ call LAND_READPARMS from packages_readparms.F |
| 1895 |
|
o pkg/seaice: |
| 1896 |
|
- remove code that resets useThSice in S/R seaice_readparms and |
| 1897 |
|
replace it by a warning in S/R seaice_check |
| 1898 |
|
- remove parameter MULTDIM, replace with nITD and runtime |
| 1899 |
|
parameter SEAICE_multDim (still hard-wired to nITD if |
| 1900 |
|
SEAICE_ITD is defined) |
| 1901 |
|
|
| 1902 |
|
checkpoint64x (2014/05/24) |
| 1903 |
|
o verification/lab_sea: |
| 1904 |
|
- update adjoint and TLM output following changes to pkg/salt_plume |
| 1905 |
|
- un-do the update after putting back local recip_Cp in few places. |
| 1906 |
|
o pkg/salt_plume: modifications by An Nguyen: |
| 1907 |
|
- add capability to do brine rejection (salt-plume) as function of |
| 1908 |
|
volume+tracers (instead of only salinity tracer). |
| 1909 |
|
- conserve volume by exchanging volume from each kLev to above to |
| 1910 |
|
accommodate in-coming brine volume |
| 1911 |
|
- store surface and klev exchanged fraction + volume in 4 new 3-d arrays |
| 1912 |
|
- switch KPP surf buoyancy due to brine forcing to 3-d |
| 1913 |
|
(3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume) |
| 1914 |
|
- add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t |
| 1915 |
|
- unrelatedly, also add ad-hoc capability to vary salt_plume scheme |
| 1916 |
|
in East/West Arctic. |
| 1917 |
|
o pkg/sbo: |
| 1918 |
|
- incorporate modifications from Katherine Quinn to enable the use of sbo |
| 1919 |
|
pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like |
| 1920 |
|
output for future testreport verification (unfinished). |
| 1921 |
|
o pkg/atm_phys: |
| 1922 |
|
- change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R: |
| 1923 |
|
skip the reseting of t_ref & q_ref to initial t & q ; this preserve the |
| 1924 |
|
output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics. |
| 1925 |
|
o pkg/seaice |
| 1926 |
|
seaice_calc_ice_strength.F: modify expression to avoid divisions |
| 1927 |
|
(affects truncation) |
| 1928 |
|
seaice_do_ridging.F: clean up the insectarium |
| 1929 |
|
- fix a bug that was compensated by areaScaling (-> remove areaScaling code) |
| 1930 |
|
- added SEAICEsnowFracRidge to redistributed snow (2nd bug) |
| 1931 |
|
- set closing/openingRate to zero where no extra iteration is need (3rd bug) |
| 1932 |
|
- add some debugging information and error messages (warnings) |
| 1933 |
|
o model/src: modifications relatd to atmosphere p*: |
| 1934 |
|
- Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F) |
| 1935 |
|
- With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead |
| 1936 |
|
of vertical profile tRef in geopotential background and anomaly. |
| 1937 |
|
- Acount for true p* correction in theta <-> T conversion in pkg/aim_v23 |
| 1938 |
|
and pkg/atm_phys. |
| 1939 |
|
- Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40, |
| 1940 |
|
fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn. |
| 1941 |
|
o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt |
| 1942 |
|
o pkg/ptracers: compute ptracer source/sink due to linear free surface. |
| 1943 |
|
not used right now, but can be used in BGC packages to fix conservation. |
| 1944 |
|
o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by |
| 1945 |
|
other packages too. |
| 1946 |
|
o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by |
| 1947 |
|
SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix) |
| 1948 |
|
o model/src: |
| 1949 |
|
- since we have several heat capacity (even in model/src), define "recip_Cp" |
| 1950 |
|
as local variable (no longer in common block) to avoid any confusion. |
| 1951 |
|
- add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords). |
| 1952 |
|
o pkg/exf: |
| 1953 |
|
- from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local |
| 1954 |
|
air density as function of air Temp, Humidity and atm pressure. |
| 1955 |
|
|
| 1956 |
|
checkpoint64w (2014/05/02) |
| 1957 |
|
o verification: |
| 1958 |
|
- update output_adm.txt files for experiment global_ocean.cs32x15 (seaice & |
| 1959 |
|
seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing |
| 1960 |
|
code from seaice_growth.F & seaice_advdiff.F to new ridging routines |
| 1961 |
|
seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient |
| 1962 |
|
(down to 8-7 matching digits for global_ocean and 5-6 for lab_sea). |
| 1963 |
|
o model/src: for atmosphere in p* coords: |
| 1964 |
|
- store factor rStarFacC**atm_kappa (= pStarFacK) in common block |
| 1965 |
|
- implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F), |
| 1966 |
|
but not yet activated. |
| 1967 |
|
o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation: |
| 1968 |
|
- move computation of opnWtrFrac = 1-AREA to before computing ice strength |
| 1969 |
|
- this changes the results (but not for any verification experiment, because |
| 1970 |
|
none tests this), but avoids having an extra field in the restart files |
| 1971 |
|
o pkg/seaice: remove global variable TICE (not needed) |
| 1972 |
|
- replace by TICES or local variable where necessary (cost_seaice_test, |
| 1973 |
|
seaice_diagnostics_state) |
| 1974 |
|
- move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup |
| 1975 |
|
- use specific read/write routines for reading and writing individual leves |
| 1976 |
|
of a multilevel field |
| 1977 |
|
o pkg/ctrl & model/inc: |
| 1978 |
|
- move additional anomaly fields of control vars (related to options: |
| 1979 |
|
ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL) |
| 1980 |
|
from DYNVARS.h into new header file: CTRL_FIELDS.h |
| 1981 |
|
o pkg/seaice: some small modifications to the ridging code |
| 1982 |
|
- make fw2ObyRidge a global variable and add the freshwater flux to |
| 1983 |
|
seaice_growth |
| 1984 |
|
- pass actual thickness from seaice_prepare_ridging, so that it is |
| 1985 |
|
computed only in one place and compute it in the same way as in |
| 1986 |
|
seaice_growth |
| 1987 |
|
- initialise more fields in seaice_do_ridging that where cause floating |
| 1988 |
|
point exceptions over land |
| 1989 |
|
o pkg/seaice: preparations for ridging code and first real ridging code |
| 1990 |
|
- move most of "PART 1" of S/R seaice_growth into a new and separate |
| 1991 |
|
S/R seaice_reg_ridge that will both regularize the state variable after |
| 1992 |
|
advection call the actual ridging routine; |
| 1993 |
|
- requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG, |
| 1994 |
|
d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust; |
| 1995 |
|
- remove ridging code from seaice_advdiff |
| 1996 |
|
- clean up remaining part 1 of seaice_growth in an attempt to make it |
| 1997 |
|
more readable (this is probably subjective) |
| 1998 |
|
- call seaice_itd_redist once in the initialisation phase to have the initial |
| 1999 |
|
conditions in the correct category |
| 2000 |
|
- finally: add new ridging routine for ITD code |
| 2001 |
|
|
| 2002 |
|
checkpoint64v (2014/04/11) |
| 2003 |
|
o pkg/ecco: |
| 2004 |
|
- add runtime parameters mdt[start,end]date[1,2] |
| 2005 |
|
- rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile" |
| 2006 |
|
o pkg/seaice: |
| 2007 |
|
- make deltaC a global variable, so that it can be used in ridging code |
| 2008 |
|
- first step towards ridging: introduce new routines that compute |
| 2009 |
|
ice strength based on ridging parameters |
| 2010 |
|
- add diagnostic for HSNOWITD |
| 2011 |
|
- add opnWtrFrac as a global variable (required for ridging scheme) |
| 2012 |
|
o pkg/salt_plume + pkg/seaice/seaice_growth.F |
| 2013 |
|
- add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice |
| 2014 |
|
AREA exceeds a threshold (code contributed by I.Fenty in 2011) |
| 2015 |
|
o verification/hs94.1x64x5: |
| 2016 |
|
- leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h |
| 2017 |
|
- do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests. |
| 2018 |
|
o autodiff: |
| 2019 |
|
- Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, |
| 2020 |
|
and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h) |
| 2021 |
|
For now, only in pkgs used in verification/hs94.1x64x5. |
| 2022 |
|
- Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage |
| 2023 |
|
which are specific to TAF/TAMC). |
| 2024 |
|
- Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD: |
| 2025 |
|
since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad |
| 2026 |
|
is compiled), this simplifies/reduces which *_OPTIONS.h file to include. |
| 2027 |
|
- OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when |
| 2028 |
|
building mitgcmuv_ad (make adAll). |
| 2029 |
|
o pkg/ecco: |
| 2030 |
|
- cost_gencost_seaicev4.F: |
| 2031 |
|
reformulate proxy cost as function of sst and local param SEAICE_freeze |
| 2032 |
|
change cost names from siv4-[sst,vol] to siv4-[deconc,exconc] |
| 2033 |
|
- add stop statement if old names siv4-[sst,vol] are used |
| 2034 |
|
- add snapshots + cost reports for atmospheric longwave |
| 2035 |
|
- remove factor 0.1 in front of wtau[u,v] |
| 2036 |
|
- replace never used flag ALLOW_TMI_COST_CONTRIBUTION with |
| 2037 |
|
ALLOW_TMI_SST_COST_CONTRIBUTION |
| 2038 |
|
o pkg/atm_phys: |
| 2039 |
|
- add some diagnostics for Short-wave and for convection S/R. |
| 2040 |
|
o pkg/seaice/seaice_growth: |
| 2041 |
|
- fix a bug in the lateral melt parameterization for SEAICE_ITD |
| 2042 |
|
in seaice_growth; tempFrz needs to be computed inside the i/j-loop |
| 2043 |
|
- rearrange loop order for better vector code in the same code block |
| 2044 |
|
- rewrite the floeDiameter formula to have fewer divisions |
| 2045 |
|
- (miraculously) none of this changes the results of seaice_itd |
| 2046 |
|
o pkg/smooth: |
| 2047 |
|
- move param smooth2Ddiffnbt to pkg/ecco |
| 2048 |
|
o pkg/salt_plume: |
| 2049 |
|
- salt_plume_frac.F: |
| 2050 |
|
clean up local param names |
| 2051 |
|
reformulate (1-frac) to frac; original 1-frac was based on swfrac code |
| 2052 |
|
o pkg/rw: |
| 2053 |
|
- add RS version of S/R READ_MFLDS_LEV. |
| 2054 |
|
o pkg/streamice: |
| 2055 |
|
- fix the restart test by writing/reading pickup_streamice files. |
| 2056 |
|
o pkg/seaice: |
| 2057 |
|
- refine checks for jfnk-related parameters |
| 2058 |
|
- comment out if statement with SEAICEuseIMEX parameter as long as there |
| 2059 |
|
is no IMEX code to avoid confusion and surprises |
| 2060 |
|
|
| 2061 |
|
checkpoint64u (2014/03/07) |
| 2062 |
|
o verification/MLAdjust: |
| 2063 |
|
- rename secondary test suffix: |
| 2064 |
|
1.leith -> A4FlxF + switch to flux-form & add side-drag |
| 2065 |
|
0.leithD -> AhFlxF + switch to flux-form |
| 2066 |
|
0.smag -> AhVrDv (use Vorticity-Div. visc form) + add side-drag |
| 2067 |
|
0.leith -> AhStTn (use Strain-Tension visc form) + add side-drag |
| 2068 |
|
o pkg/mom_vecinv: |
| 2069 |
|
- remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used |
| 2070 |
|
to be before mom_calc_visc.F) |
| 2071 |
|
- skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed. |
| 2072 |
|
- add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip): |
| 2073 |
|
this is simpler for the adjoint and for diagnostics. |
| 2074 |
|
o model/src + pkg/momentum: |
| 2075 |
|
- add input files for 2-D additional Western and Southern cell-edge wall |
| 2076 |
|
(e.g., to add "thin-wall" where it is =1). |
| 2077 |
|
- fix sideDrag option for thin-walls with Non-Lin Free-Surf |
| 2078 |
|
using 2nd hFacZ that is computed from initial (fix domain) hFac |
| 2079 |
|
- known limitations of thin wall implementation: not yet coded for sigma |
| 2080 |
|
coords; not working with CD-scheme neither. |
| 2081 |
|
o pkg/seaice: |
| 2082 |
|
- rename recently introduced parameters from (wrong name) AB to |
| 2083 |
|
BDF (backward difference time discretisation) |
| 2084 |
|
- retire runtime parameters SEAICEuseAB2, SEAICE_abEps |
| 2085 |
|
o tools/adjoint_options: |
| 2086 |
|
- remove setting of "OPENAD=true" (now set by command line "genmake2 -oad") |
| 2087 |
|
|
| 2088 |
|
checkpoint64t (2014/02/01) |
| 2089 |
|
o pkg/ecco |
| 2090 |
|
- add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and |
| 2091 |
|
runtime logical flag gencost_timevaryweight to read daily sea-ice sigma |
| 2092 |
|
- replace hard-coded record number and period which only work for monthly |
| 2093 |
|
with read-in runtime param that works for other periods (month,day,year) |
| 2094 |
|
o pkg/thsice |
| 2095 |
|
- corrected store directive fixes thsice adjoint gradient checks |
| 2096 |
|
o genmake2 & testreport: |
| 2097 |
|
- add genmake2 option "-oad" to generate a Makefile for OpenAD built and |
| 2098 |
|
in this case, use tools/adjoint_options/adjoint_oad as default AD optfile. |
| 2099 |
|
Update testreport accordingly. No need to set "export OPENAD=true" |
| 2100 |
|
in adjoint_options/adjoint_oad anymore (will be removed later). |
| 2101 |
|
o pkg/shelfice: |
| 2102 |
|
- put T & S shelfice forcing into model surfaceForcing_T,_S (for now, |
| 2103 |
|
only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F |
| 2104 |
|
so that surface forcing applies to k=kSurf if using pkg/shelfice. |
| 2105 |
|
o pkg/ctrl, pkg/grdchk, pkg/ecco: |
| 2106 |
|
- Changes to make GENARR more modular (i.e. invisible if not used) |
| 2107 |
|
o model/src/temp_integrate.F and salt_integrate.F |
| 2108 |
|
- re-include store directives that were removed on Dec 27th. |
| 2109 |
|
o model/src/external_forcing_surf.F |
| 2110 |
|
- add storage directives for EmPmR and PmEpR to avoid recomputation of |
| 2111 |
|
seaice_model in the adjoint that is problematic when seaice_model is |
| 2112 |
|
turned off in the adjoint. The resolved issue dated back to July when |
| 2113 |
|
EXTERNAL_FORCING_SURF call was moved. |
| 2114 |
|
Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly. |
| 2115 |
|
o pkg/exf/exf_check.F |
| 2116 |
|
- fix a small bug again (originally found by Wentao Liu, now found again) |
| 2117 |
|
- streamline error output |
| 2118 |
|
o pkg/streamice and aim_v23: |
| 2119 |
|
- replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that |
| 2120 |
|
Apple's /usr/bin/cpp knows what to do: |
| 2121 |
|
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) |
| 2122 |
|
Target: x86_64-apple-darwin13.0.0 |
| 2123 |
|
|
| 2124 |
|
checkpoint64s (2014/01/05) |
| 2125 |
|
o tools/adjoint_options: |
| 2126 |
|
- switch to fastopt.net TAF server (instead of default fastopt.de) for |
| 2127 |
|
AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default). |
| 2128 |
|
o model/src: |
| 2129 |
|
- remove some unnecessary TAF storage directives in forward_step.F and |
| 2130 |
|
in dynamics.F (note: not always removed by TAF, e.g., double storage |
| 2131 |
|
of kappaRU,kappaRV in former version of dynamics.F). |
| 2132 |
|
o model/src & pkg/ptracers: |
| 2133 |
|
- call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F |
| 2134 |
|
salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F) |
| 2135 |
|
and remove ptracers_dwnslp_apply.F & ptracers_implicit.F |
| 2136 |
|
- call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F) |
| 2137 |
|
- add fZon & fMer as output argument of S/R GAD_CALC_RHS. |
| 2138 |
|
- update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad). |
| 2139 |
|
o useSingleCpuInput separates single-CPU input from single-CPU output; |
| 2140 |
|
for now only implemented for in exf_interp_read.F |
| 2141 |
|
o verification/advect_xy: |
| 2142 |
|
- fix missing EXCH call in local version of ini_salt.F and update output. |
| 2143 |
|
o momentum diagnostics: |
| 2144 |
|
- fix which deltaT is used in Total-Tendency diagnostics. |
| 2145 |
|
- fix typo in diagnostics for momentum tendency from AB. |
| 2146 |
|
o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the |
| 2147 |
|
SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8 |
| 2148 |
|
|
| 2149 |
|
checkpoint64r (2013/12/08) |
| 2150 |
|
o verification/*/results: |
| 2151 |
|
- Update reference output of experiments that were passing with just 13 digits |
| 2152 |
|
(make it easier to detect future changes in results) |
| 2153 |
|
o model/src & pkg/ptracers: |
| 2154 |
|
- move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to |
| 2155 |
|
inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F |
| 2156 |
|
to inside ptracers_integrate.F ; remove ptracers_advection.F |
| 2157 |
|
o coupling interface pkgs: |
| 2158 |
|
[atm_compon_interf, ocn_compon_interf & atm_ocn_coupler] |
| 2159 |
|
- change the config check to test the agreement of Ocean Depth |
| 2160 |
|
with ATM land/sea mask (instead of ATM orography); |
| 2161 |
|
- send to coupler the number of coupler time-steps to do for this run: |
| 2162 |
|
this allows to check for consistency and don't need anymore to be |
| 2163 |
|
specified in parameter file "data"; |
| 2164 |
|
in coupler: |
| 2165 |
|
- check consistency of RunOff map versus Ocean Depth and ATM land/sea mask. |
| 2166 |
|
- improve report to log-file of config setting (pass log-file unit to few S/R) |
| 2167 |
|
o pkg/compon_communic: |
| 2168 |
|
- add coupling send/receive for non-tiled integer vector; |
| 2169 |
|
- add S/R to check and stop if any proc has an error (similar to |
| 2170 |
|
eesupp/src/stop_if_error.F but single thread and across Comm_World). |
| 2171 |
|
o pkg/exch2: |
| 2172 |
|
- in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search |
| 2173 |
|
through list of all tiles my proc owns. |
| 2174 |
|
o model/src: |
| 2175 |
|
- AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying |
| 2176 |
|
from rTrans) to simplify dependencies (no need to store rTrans anymore in |
| 2177 |
|
calling S/R); this affects AD results at machine truncation level: |
| 2178 |
|
update AD-output (TAF) of experiments: 1D_ocean_ice_column, |
| 2179 |
|
bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad). |
| 2180 |
|
o tools/build_options: |
| 2181 |
|
- simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran |
| 2182 |
|
o coupling interface pkgs: |
| 2183 |
|
[compon_communic, atm_compon_interf & ocn_compon_interf] |
| 2184 |
|
- move declaration of local array "ibuf" out of header file "CPLR_SIG.h" |
| 2185 |
|
to each S/R that needs it; remove un-used variables. |
| 2186 |
|
- change component tile registration (cpl_register.F in both compon_interf |
| 2187 |
|
and mitcomponent_tile_register.F) to pass the full list of tiles |
| 2188 |
|
information (including bi,bj) in 1 vector (instead of in a bi,bj matrix). |
| 2189 |
|
- with pkg/exch2: adopt the same convention used for I/O to define mapping |
| 2190 |
|
towards coupler global array (unless W2_useE2ioLayOut=F): |
| 2191 |
|
a) can now use different tiling between atm & ocn comp. |
| 2192 |
|
b) no needs to modify the run-Off map when changing tiling (was needed |
| 2193 |
|
even if using the same tiling between atm & ocn). |
| 2194 |
|
c) will allow to run with blank-tiles in 1 component (e.g., for ocean |
| 2195 |
|
full land tiles); not yet tested. |
| 2196 |
|
- check for valid mapping from comp. tile to coupler global array |
| 2197 |
|
- improve report of tile registration results to log file. |
| 2198 |
|
o pkg/exch2: |
| 2199 |
|
- in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler |
| 2200 |
|
tile-registration (CPL_REGISTER); |
| 2201 |
|
- activate (un-comment) definition and setting of "W2_tileIndex" list to |
| 2202 |
|
store the local bi,bj indices of each tile; |
| 2203 |
|
- also print bi,bj in local report to log file; |
| 2204 |
|
- fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from |
| 2205 |
|
Jun 2009 modif of pkg/exch2). |
| 2206 |
|
o testing on baudelaire: |
| 2207 |
|
- run 2 tests at a time: no significant slow down (since enough cpu) and |
| 2208 |
|
get the full set of test done earlier |
| 2209 |
|
- switch the ifort test to "-devel" ; run the OpenAD test everyday. |
| 2210 |
|
o model/src/thermodynamics.F and routines called from it: |
| 2211 |
|
- pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F & |
| 2212 |
|
gmredi_calc_wflow.F) to update eulerian velocity (input) into residual |
| 2213 |
|
velocity (outp) by adding bolus velocity. |
| 2214 |
|
- model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute |
| 2215 |
|
mass transport from velocity + lateral grid cell area |
| 2216 |
|
- rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER) |
| 2217 |
|
- rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER) |
| 2218 |
|
in thermodynamics.F |
| 2219 |
|
- remove k from thermodynamics.F and move it to temp_integrate.F |
| 2220 |
|
salt_integrate.F and ptracers_integrate.F (now done inside the tracer |
| 2221 |
|
loop). |
| 2222 |
|
- compute locally (in thermodynamics.F) 3-D velocity field that is used to |
| 2223 |
|
advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT, |
| 2224 |
|
PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE, |
| 2225 |
|
GAD_IMPLICIT_R and PTRACERS_IMPLICIT |
| 2226 |
|
- update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column, |
| 2227 |
|
global_ocean.90x40x15, tutorial_global_oce_biogeo and |
| 2228 |
|
tutorial_tracer_adjsens (+ TLM output). |
| 2229 |
|
o tools/OAD_support and (verification/*/) code_oad: |
| 2230 |
|
- OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to |
| 2231 |
|
module conversion ; remove unneeded CPP_EEOPTIONS.h. |
| 2232 |
|
- code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard |
| 2233 |
|
version (closer to model/inc/CPP_OPTIONS.h). |
| 2234 |
|
o model/src: |
| 2235 |
|
- remove parameter "useOldFreezing" from PARAMS.h and push it to the |
| 2236 |
|
retired list of parameters (routine FREEZE has been replace by surface |
| 2237 |
|
freezing (10.yrs ago) and by pkg/frazil (interior freezing). |
| 2238 |
|
o pkg/gmredi: |
| 2239 |
|
- add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from |
| 2240 |
|
velocity (same scheme but affects machine truncation) for GM_AdvForm. |
| 2241 |
|
- update output of FWD experiments: front_relax.bvp, |
| 2242 |
|
global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce. |
| 2243 |
|
|
| 2244 |
|
checkpoint64q (2013/11/17) |
| 2245 |
|
o verification: |
| 2246 |
|
- generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments |
| 2247 |
|
tutorial_global_oce_biogeo and global_ocean.90x40x15. |
| 2248 |
|
- generate new output (growth & melt) for seaice_itd experiment after |
| 2249 |
|
updating the input pickup_seaice files (previously wrong). |
| 2250 |
|
o pkg/cost: |
| 2251 |
|
- define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL |
| 2252 |
|
(instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads: |
| 2253 |
|
o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL |
| 2254 |
|
cannot be applied to var in common block). |
| 2255 |
|
o allows to get results independent of tile-per-proc setting (if using |
| 2256 |
|
slower GLOBAL_SUM_SEND_RECV option). |
| 2257 |
|
- update accordingly: seaice_cost_final.F, shelfice_cost_final.F, |
| 2258 |
|
thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea |
| 2259 |
|
forward gradients: update output). |
| 2260 |
|
- update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL |
| 2261 |
|
S/R and, for most exp., also comment out GLOBAL_SUM_R8. |
| 2262 |
|
o pkg/mom_common: |
| 2263 |
|
- move to pkg/mom_common and model/src (previously in tutorial_deep_convection |
| 2264 |
|
code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and |
| 2265 |
|
viscosity are locally declared in dynmics.F and pass as argument to CALC_GW; |
| 2266 |
|
ensure that all field value that are used are set. |
| 2267 |
|
o tutorial_deep_convection (smag3d): |
| 2268 |
|
- add missing scaling in mom_calc_smag_3d.F; |
| 2269 |
|
- set smag3D_coeff in input.smag3d such that results do not change. |
| 2270 |
|
o pkg/dic: |
| 2271 |
|
- change dic_cost.F to compute cost on each tile first and then apply |
| 2272 |
|
GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments |
| 2273 |
|
tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output. |
| 2274 |
|
- remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea. |
| 2275 |
|
o eesupp/src & pkg/mdsio: |
| 2276 |
|
- remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F |
| 2277 |
|
(from pkg/mdsio) since they are no longer used for tape IO. |
| 2278 |
|
- move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src |
| 2279 |
|
(+ keep a copy in pkg/atm_ocn_coupler). |
| 2280 |
|
o verification/isomip: |
| 2281 |
|
- split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests. |
| 2282 |
|
o tools/build_options: |
| 2283 |
|
- optfile linux_amd64_ifort11, fast (no ieee) case: |
| 2284 |
|
to get a working restart for all experiments, add "-fp-model source" |
| 2285 |
|
to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default). |
| 2286 |
|
|
| 2287 |
|
checkpoint64p (2013/10/20) |
| 2288 |
|
o pkg/autodiff: |
| 2289 |
|
- adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO |
| 2290 |
|
criteria, return to simple (default) tape IO format. |
| 2291 |
|
o pkg/mdsio (+ eesupp/src): |
| 2292 |
|
- rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace |
| 2293 |
|
previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8); |
| 2294 |
|
- fix globalFile and singleCpuIO options using simpler global mapping. |
| 2295 |
|
- new pairs of scatter/gather vector S/R (one for each type, generated from |
| 2296 |
|
template) corresponding to simpler global mapping. |
| 2297 |
|
- adread_write.F: switch to new S/R (but leave old calls commented) and write |
| 2298 |
|
to globalFile when parameter globalFiles is set to True. |
| 2299 |
|
- switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip. |
| 2300 |
|
o pkg/autodiff: |
| 2301 |
|
- adread_adwrite.F: add a hack for RS arrays (when RS=real*4); |
| 2302 |
|
with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is |
| 2303 |
|
missing, just add a STOP if array type do not match. |
| 2304 |
|
o pkg/exf: |
| 2305 |
|
- to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice: |
| 2306 |
|
rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION |
| 2307 |
|
and rename array obsSIce to exf_iceFraction. |
| 2308 |
|
o tutorial_deep_convection: |
| 2309 |
|
- add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe), |
| 2310 |
|
for now all in this exp. code dir. |
| 2311 |
|
- add secondary test using Smag-3D viscosity (keep very low backgroud visc for |
| 2312 |
|
testing) and flux-limter advection scheme for Temp. (no explicit diffusion). |
| 2313 |
|
o eesupp/src: |
| 2314 |
|
- added SINGLE_DISK_IO option because reading of parameter files on |
| 2315 |
|
very large number of processors did not work with existing set-up |
| 2316 |
|
|
| 2317 |
|
checkpoint64o (2013/09/25) |
| 2318 |
|
o pkg/atm_phys & atm_compon_interf: |
| 2319 |
|
- allows for coupling of gray-atmosphere (atm_phys) with ocean. |
| 2320 |
|
o tools/build_options: |
| 2321 |
|
- switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran |
| 2322 |
|
& linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also |
| 2323 |
|
remove CPP setting (was identical to genmake2 default). |
| 2324 |
|
o pkg/gmredi & model/src: Some updating and work done on the residual model. |
| 2325 |
|
- created new file model/src/calc_eddy_stress.F to calculate the eddy stress. |
| 2326 |
|
- fixed up the calculation of the eddy stress and how it is added to the |
| 2327 |
|
external forcing via taueddy_external_forcing.F |
| 2328 |
|
- at the moment, it is very experimental and only works with the variable eddy |
| 2329 |
|
diffusivity calculated in gmredi_k3d.F |
| 2330 |
|
o pkg/seaice/seaice_check.F: add a check to catch the case of specifying |
| 2331 |
|
lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice |
| 2332 |
|
o testreport (& tools/do_tst_2+2): |
| 2333 |
|
- for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}' |
| 2334 |
|
o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11: |
| 2335 |
|
- remove CPP='cpp -traditional -P' (this is genmake2 default) |
| 2336 |
|
- add switch (for big setups) to use 'medium' memory-model (but leave it |
| 2337 |
|
commented out for now). Note: needed with FC 19 to compile big setups. |
| 2338 |
|
o pkg/atm_compon_interf: |
| 2339 |
|
- regroup per field origin (model & pkgs) the coupling storage routines |
| 2340 |
|
(which accumalate in time each coupling field) |
| 2341 |
|
- move bi,bj loops inside atm_store_my_data.F and store also wind-stress; |
| 2342 |
|
update accordingly + simplify aim_do_physics.F |
| 2343 |
|
|
| 2344 |
|
checkpoint64n (2013/08/26) |
| 2345 |
|
o pkg/bbl: |
| 2346 |
|
- update formulation to reduce dispersion of tracer properties in bbl |
| 2347 |
|
- replaced horizontal and vertical transport parameters with velocities |
| 2348 |
|
- changes results for verification/global_with_exf.yearly |
| 2349 |
|
o verification/halfpipe_streamice: |
| 2350 |
|
- change to matrix construction; update both Fwd & AD output. |
| 2351 |
|
o verification/tutorial_tracer_adjsens: |
| 2352 |
|
- OpenAD test: switch to vector-invariant momentum since fluxform with |
| 2353 |
|
rStar causes problems with OpenAD; update output. |
| 2354 |
|
o tools: |
| 2355 |
|
- genmake2: define a common prefix for all temp-file names ; move them |
| 2356 |
|
to local /tmp disk (but would be easy to move them back); |
| 2357 |
|
- xmakedepend: apply the same switch for temp-files. |
| 2358 |
|
o pkg/offline: |
| 2359 |
|
- changes for use with rStar (NLFS): assume that we continue to provide |
| 2360 |
|
UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid |
| 2361 |
|
output files) and apply r* scaling at each time-step (function of the time |
| 2362 |
|
varying Eta field); use normal pickup files (needed for restart with NLFS). |
| 2363 |
|
o adjoint with OpenAD: |
| 2364 |
|
- move OpenAD-specific files from verification/OpenAD/code_oad_all to a new |
| 2365 |
|
package openad. This package has to be compiled for all runs with OpenAD |
| 2366 |
|
instead of specifying code_oad_all as a modification directory. |
| 2367 |
|
- link the fortran templates from tools/OAD_support to the build directory |
| 2368 |
|
for preprocessing to avoid conflicts between different setups compiled |
| 2369 |
|
simultaneously and simplify cleanup. |
| 2370 |
|
o pkg/exf: |
| 2371 |
|
- in exf_getforcing.F: comment out most of the EXCH calls (fields used by |
| 2372 |
|
main model or other pkgs are exchanged in EXF_MAPFIELDS). |
| 2373 |
|
o model/src: |
| 2374 |
|
- do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline |
| 2375 |
|
(similar to do_fields_blocking_exchanges.F). |
| 2376 |
|
o tools/genmake2: |
| 2377 |
|
- remove TAF output src code just before calling staf (when not doing a fresh |
| 2378 |
|
built, will stop if things go wrong with staf). |
| 2379 |
|
- fix target "adobj" (left from TAF version-2 transition) |
| 2380 |
|
o pkg/diagnostics: |
| 2381 |
|
- add a parameter to track the status of pkg/diagnostics activation; |
| 2382 |
|
this replace/extend the use of logical param "settingDiags" (to check |
| 2383 |
|
when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call. |
| 2384 |
|
New S/R to print error message and stop when pkgStatus is not right. |
| 2385 |
|
- to try: add a warning when "data.diagnostics" exist but useDiagnostics=F. |
| 2386 |
|
|
| 2387 |
|
checkpoint64m (2013/08/13) |
| 2388 |
|
o model/inc: |
| 2389 |
|
- move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from |
| 2390 |
|
8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) |
| 2391 |
|
o pkg/kpp & aim_v23: |
| 2392 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
| 2393 |
|
o pkg/seaice: |
| 2394 |
|
- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
| 2395 |
|
undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
| 2396 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
| 2397 |
|
o eesupp/src: |
| 2398 |
|
- fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) |
| 2399 |
|
in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). |
| 2400 |
|
o switch to TAF version-2: |
| 2401 |
|
- add flow directives to "freeze" naming convention for ad-routines that |
| 2402 |
|
are used in I/O routines of adjoint state and associated common blocks |
| 2403 |
|
that are used in adcommon.h (backward compatible with version-1) |
| 2404 |
|
- update all ad-optfiles (in tools/adjoint_options + few local to some |
| 2405 |
|
verification exp) to switch to latest TAF version (currently 2.5.5); |
| 2406 |
|
merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented |
| 2407 |
|
out except for diva). |
| 2408 |
|
- the major change with TAF version-2 is that both the differentiated |
| 2409 |
|
routines and the forward routines (new) are returned as part of the TAF |
| 2410 |
|
output source code. Update genmake2 accordingly. |
| 2411 |
|
- new output for AD experiment tutorial_global_oce_biogeo (better AD gradient |
| 2412 |
|
with version-2 when compared to TLM or FWD gradient); other experiments |
| 2413 |
|
output show minor changes (machine truncation level); update the few AD & |
| 2414 |
|
TLM output with 12 matching digits only (some prior to version-2 switch). |
| 2415 |
|
|
| 2416 |
|
checkpoint64l (2013/08/05) |
| 2417 |
|
o model/src: |
| 2418 |
|
- in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F |
| 2419 |
|
- main_do_loop.F: no longer includes additional (AUTODIFF) header files |
| 2420 |
|
when using TAF but only if using OpenAD. |
| 2421 |
|
o pkg/mom_common+fluxform+vecinv: |
| 2422 |
|
- always set horiz. viscosity arrays to background value before calling |
| 2423 |
|
MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC |
| 2424 |
|
only when using variable horiz. viscosity (useVariableVisc=T); |
| 2425 |
|
- simplify mom_vecinv.F (only 1 block for momViscosity). |
| 2426 |
|
o pkg/mom_common: variable horiz. viscosity in NH code |
| 2427 |
|
- move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F) |
| 2428 |
|
from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h |
| 2429 |
|
- store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, |
| 2430 |
|
useBiharmonicVisc & useVariableVisc. |
| 2431 |
|
- fix old bug (already in 1rst implementation of variable horizontal viscosity |
| 2432 |
|
in calc_gw.F, version 1.27, 2006/06/20): |
| 2433 |
|
horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 |
| 2434 |
|
even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. |
| 2435 |
|
- change background horiz viscosity in vertical momentum (gW) to always be |
| 2436 |
|
viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using |
| 2437 |
|
any type of variable viscosity, e.g., viscAh/4Grid) |
| 2438 |
|
- change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of |
| 2439 |
|
viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing |
| 2440 |
|
horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since |
| 2441 |
|
default viscAh,viscA4 is zero). |
| 2442 |
|
o model/src: |
| 2443 |
|
- extend length of drC & recip_drC from Nr to Nr+1. |
| 2444 |
|
o Divided Adjoint (DIVA) with MPI: |
| 2445 |
|
- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
| 2446 |
|
- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
| 2447 |
|
and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h. |
| 2448 |
|
|
| 2449 |
|
checkpoint64k (2013/07/23) |
| 2450 |
|
o tools/OAD_support: |
| 2451 |
|
- avoid the need for file "oadtempflile" in insertTemplateDir.bash |
| 2452 |
|
and remove it from genmake2. |
| 2453 |
|
o tools/build_options: |
| 2454 |
|
- remove MPI_HEADER_FILES_INC setting (no longer used) and comment out |
| 2455 |
|
MPI_HEADER_FILES list (let genmake2 find the missing headers) |
| 2456 |
|
o verification/halfpipe_streamice: |
| 2457 |
|
- change to driving stress formulation; update both Fwd & AD output. |
| 2458 |
|
o tools/genmake2 and Divided Adjoint with MPI: |
| 2459 |
|
- remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken); |
| 2460 |
|
- only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set; |
| 2461 |
|
- add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in |
| 2462 |
|
Makefile, which is set by genmake2, and check which mpi-headers are needed. |
| 2463 |
|
Note: need to update adjoint_options/adjoint_diva_mpi accordingly. |
| 2464 |
|
- update target "CLEAN" (to also remove ./mpi_headers/ dir). |
| 2465 |
|
o testreport: |
| 2466 |
|
- changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, |
| 2467 |
|
perform additional runs (number of additional runs is "add_DIVA_runs" taken |
| 2468 |
|
from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h"). |
| 2469 |
|
o verification/lab_sea (AD test): |
| 2470 |
|
- change to test Divided Adjoint Run in this set-up (both standard AD test |
| 2471 |
|
and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test. |
| 2472 |
|
o pkg atm_ & ocn_compon_interf: |
| 2473 |
|
- remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old |
| 2474 |
|
staggerTimeStep implementation) and disable (retired) corresponding |
| 2475 |
|
parameter. |
| 2476 |
|
o pkg/offline: |
| 2477 |
|
- comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01]; |
| 2478 |
|
- add S/R OFFLINE_CHECK to print offline parameter summary |
| 2479 |
|
and stop if loading a file that is not used; |
| 2480 |
|
- enable to calculate GMRedi tensor, KPP mixing and convective index |
| 2481 |
|
when the corresponding file(s) is/are not specified (but pkg is used). |
| 2482 |
|
- comment out resetting of monitorFreq (to endTime) since it still useful |
| 2483 |
|
for monitoring CFL numbers and checking offline fields. |
| 2484 |
|
o OpenAD: |
| 2485 |
|
- do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get |
| 2486 |
|
smaller standard output) and generate new (smaller) output (on baudelaire |
| 2487 |
|
using gfortran with -ieee) for exp. tutorial_tracer_adjsens |
| 2488 |
|
o model/src: |
| 2489 |
|
- call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F), |
| 2490 |
|
(where external_forcing_adjust was called) and change list of arguments; |
| 2491 |
|
- merge external_forcing_adjust.F into external_forcing_surf.F |
| 2492 |
|
- put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F) |
| 2493 |
|
which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX, |
| 2494 |
|
previously in file "balance_relax.F", now removed); remove corresponding |
| 2495 |
|
arrays in FFIELDS.h. |
| 2496 |
|
- EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement |
| 2497 |
|
a hack for getting back surfaceForcingS (loaded from file) when using |
| 2498 |
|
ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up. |
| 2499 |
|
- update output of AD test experiment global_ocean.cs32x15.seaice_dynmix |
| 2500 |
|
(was getting only 11 digits for AD-grad, due to different truncation |
| 2501 |
|
error in AD code). |
| 2502 |
|
|
| 2503 |
|
checkpoint64j (2013/07/04) |
| 2504 |
|
o pkg/offline: |
| 2505 |
|
- to enable the use of other features with pkg offline (e.g., obcs), |
| 2506 |
|
also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come. |
| 2507 |
|
- comment out "allowFreezing" (now active) in 2 offline testing exp. |
| 2508 |
|
o pkg/exf ALLOW_RUNOFTEMP |
| 2509 |
|
- fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL |
| 2510 |
|
- ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice |
| 2511 |
|
- changes verification/global_ocean.cs32x15/results/output.seaice.txt |
| 2512 |
|
o pkg/atm_phys: |
| 2513 |
|
- allows to add some damping on uVel,vVel (strength only function of k). |
| 2514 |
|
o verification, ad-tests: |
| 2515 |
|
- reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, |
| 2516 |
|
global_ocean_ebm and offline_exf_seaice.thsice. |
| 2517 |
|
o verification/halfpipe_streamice: |
| 2518 |
|
- found a bug in s/r pkg/streamice/streamice_advect_thickness which caused |
| 2519 |
|
flux input boundary conditions to be ignored; a fix for this bug changed |
| 2520 |
|
verification results for forward test. |
| 2521 |
|
- add adjoint test. |
| 2522 |
|
o pkg/ptracers: |
| 2523 |
|
- allow to restart without SOM pickup (resetting SOM to zero). |
| 2524 |
|
o pkg/gmredi: |
| 2525 |
|
- New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added. |
| 2526 |
|
- It uses mixing length theory and suppression by steering level effects to |
| 2527 |
|
calculate a diffusivity used in the Redi tensor (see Bates et al., submitted |
| 2528 |
|
to JPO, for more details). |
| 2529 |
|
- It also uses the diffusivity to calculate an eddy induced streamfunction |
| 2530 |
|
based on a PV closure (rather than a buoyancy closure as in GM). |
| 2531 |
|
- New files added to pkg/gmredi: |
| 2532 |
|
gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy |
| 2533 |
|
induced overturning streamfunction (called from gmredi_calc_tensor) |
| 2534 |
|
gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required |
| 2535 |
|
for use in gmredi_k3d |
| 2536 |
|
gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate |
| 2537 |
|
the eddy diffusivity |
| 2538 |
|
|
| 2539 |
|
checkpoint64i (2013/06/18) |
| 2540 |
|
o pkg/cheapaml: |
| 2541 |
|
- take src files from MITgcm_contrib/verification_other/offline_cheapaml/code |
| 2542 |
|
that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics) |
| 2543 |
|
with pkg/cheapaml. |
| 2544 |
|
o utils/python: add subpackage for cubed sphere function, first example is |
| 2545 |
|
simple cs.pcol to plot 2D fields on a map |
| 2546 |
|
o pkg/streamice: |
| 2547 |
|
- This is a new package in MITgcm, which solves dynamic equations for ice |
| 2548 |
|
sheets and ice streams |
| 2549 |
|
- At the moment it is independent of atmosphere/ocean dynamics, or any |
| 2550 |
|
other physical packages in MITgcm, even ShelfIce (although it is anticipat- |
| 2551 |
|
ed that this will change) |
| 2552 |
|
- There is a new verification exercise that tests it, halfpipe_streamice, |
| 2553 |
|
evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a |
| 2554 |
|
rectangular embayment |
| 2555 |
|
- halfpipe_streamice is forward-only for now, will have TAF test soon |
| 2556 |
|
- for questions, email dgoldber@mit.edu |
| 2557 |
|
o pkg/thsice: |
| 2558 |
|
- fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing |
| 2559 |
|
of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40); |
| 2560 |
|
- remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new |
| 2561 |
|
call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect ); |
| 2562 |
|
- allow precip from pkg/cheapaml to make snow over seaice. |
| 2563 |
|
o pkg/cfc: |
| 2564 |
|
- move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC |
| 2565 |
|
- remove atmos CFC 2-D arrays from common bloc (now local variables) |
| 2566 |
|
- change some hard-coded constant to run time parameter for reading and |
| 2567 |
|
and interpolating atmospheric CFC ; keep same default as previously. |
| 2568 |
|
- more flexible reading of Atmos CFC (number of records no longer hard-coded) |
| 2569 |
|
- put arguments in standard order: myTime, myIter, myThid |
| 2570 |
|
- use standard S/R GET_PERIODIC_INTERVAL for time interpolation of |
| 2571 |
|
atmospheric CFC ; fix for the case myIter < PTRACERS_iter0. |
| 2572 |
|
- fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf |
| 2573 |
|
- new routine to print summary of CFC params and check for consistency. |
| 2574 |
|
o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff, |
| 2575 |
|
similar to thsice_advdiff. |
| 2576 |
|
Note that for the B-grid case the routine parameters uc/vc are overwritten. |
| 2577 |
|
o pkg/cfc: |
| 2578 |
|
- change time interpolation for atmospheric CFC-11 (now same as for CFC-12); |
| 2579 |
|
update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline. |
| 2580 |
|
- fix interpolation of atmphspheric CFC between Sorthern and Northern |
| 2581 |
|
hemisphere value. |
| 2582 |
|
o pkg/seaice: |
| 2583 |
|
- allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml) |
| 2584 |
|
o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics; |
| 2585 |
|
so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE. |
| 2586 |
|
- requires an additional time level that is stored in the pickup |
| 2587 |
|
- you can start with AB2 from a pickup without this time level with |
| 2588 |
|
pickupStrictlyMatch = .false. |
| 2589 |
|
|
| 2590 |
|
checkpoint64h (2013/05/26) |
| 2591 |
|
o pkg/cheapaml: |
| 2592 |
|
- replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux); |
| 2593 |
|
affect machine truncation (but exp cheapAML_box still pass with 13 digits). |
| 2594 |
|
- consistent treatment of uWind,vWind location: assume everywhere in |
| 2595 |
|
pkg/cheapaml that they are on C-grid (@ uVel,vVel location) |
| 2596 |
|
(Note: was already the case for Tair,Qair advection); |
| 2597 |
|
add option (INCONSISTENT_WIND_LOCATION) to recover old results. |
| 2598 |
|
- compute diabatic forcing only in the interior (excluding overlap regions) |
| 2599 |
|
- fill in array "Qsw" (for short-wave heating); |
| 2600 |
|
- add diagnostic for precip ; fill-in diagnostics for cheapAML state vars |
| 2601 |
|
before any update (consistent with MITgcm state var diagnostics); |
| 2602 |
|
- cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if |
| 2603 |
|
non periodic ; + adjusted for uWind,vWind (C-grid). |
| 2604 |
|
o pkg/seaice: |
| 2605 |
|
- remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and |
| 2606 |
|
add explicitly pkg/exf in experiments that currently use pkg/seaice. |
| 2607 |
|
- allows to compile pkg/seaice without pkg/exf. |
| 2608 |
|
o tools/OAD_support: |
| 2609 |
|
- use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds |
| 2610 |
|
of array "ourStepOf" in function rvNextAction (revolve.F90). |
| 2611 |
|
o pkg/aim_compon_interf renamed to pkg/atm_compon_interf |
| 2612 |
|
- change pkg name (to be used with other atmospheric physics pkg) |
| 2613 |
|
but by-pass CVS when making the new pkg so that we keep the CVS history. |
| 2614 |
|
o pkg/offline: |
| 2615 |
|
- call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F |
| 2616 |
|
(previously called from pkg/dic_surfforcing_init.F) |
| 2617 |
|
o model/src: |
| 2618 |
|
- re-order sequence of calls within packages_init_variables.F, using |
| 2619 |
|
standard order, except for: |
| 2620 |
|
DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top), |
| 2621 |
|
CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom) |
| 2622 |
|
o new pkg: atm_phys |
| 2623 |
|
- add entry point and source code (previously in contrib |
| 2624 |
|
verification_other/atm_gray/code_gray/) for new pkg "atm_phys" |
| 2625 |
|
(atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008). |
| 2626 |
|
- re-order sequence of calls within packages_readparms.F, |
| 2627 |
|
packages_init_fixed.F and packages_write_pickup.F |
| 2628 |
|
(but skip packages_init_variables.F because of TAF issues). |
| 2629 |
|
- update contrib/*/atm_gray/ experiment. |
| 2630 |
|
o pkg/seaice (ITD code): |
| 2631 |
|
- simplify and fix the writing of pickup-files for ITD case |
| 2632 |
|
o pkg/seaice (ITD code): |
| 2633 |
|
- introduce floe size dependent lateral melt for ITD case; |
| 2634 |
|
- cleaning (avoid division by zero, change to f77 syntax, remove tabs) |
| 2635 |
|
- update seaice_itd experiment main output. |
| 2636 |
|
o pkg/thsice: |
| 2637 |
|
- remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and |
| 2638 |
|
declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F; |
| 2639 |
|
changed accordingly pkg/atm2d. |
| 2640 |
|
|
| 2641 |
|
checkpoint64g (2013/05/01) |
| 2642 |
|
o pkg/exf ALLOW_RUNOFTEMP |
| 2643 |
|
- if defined, river and glacier runoff temperature can be read-in from |
| 2644 |
|
runoftempfile; runoftempfile needs to have same format as runofffile |
| 2645 |
|
o pkg/thsice (& pkg/bulk_force): |
| 2646 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
| 2647 |
|
for energy content of Precip + RunOff & Evap (like with pkg/exf). |
| 2648 |
|
- change computation domain to always be the interior (without overlap). |
| 2649 |
|
- fix bug (wrong overlap) when using EXF and stressReduction > 0. |
| 2650 |
|
o verification/tutorial_global_oce_biogeo: |
| 2651 |
|
- add preliminary OpenAD setup (still has problems) |
| 2652 |
|
o pkg/seaice: |
| 2653 |
|
- turn some parameters for choosing the convergence criterion of |
| 2654 |
|
the inexact Newton method (JFNK) into runtime parameters for convenience |
| 2655 |
|
- clean up seaice_calc_viscosities.F: remove/retire two options for |
| 2656 |
|
SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes |
| 2657 |
|
the results of lab_sea/input because a division has been replaced by |
| 2658 |
|
a multiplication with the reciprocal (sumNorm) |
| 2659 |
|
- modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve |
| 2660 |
|
convergence of solver (changes results, of course), and to test some |
| 2661 |
|
new features |
| 2662 |
|
o model/src: |
| 2663 |
|
- remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call. |
| 2664 |
|
- remove unused forcing field "dQdT" and associated parameter "dQdTFile". |
| 2665 |
|
- move forcing adjustment (balancing surface forcing) in specific S/R |
| 2666 |
|
where might also be applied exchanges (if needed) to forcing arrays. |
| 2667 |
|
o pkg/shelfice: |
| 2668 |
|
- allow to specify the Ice-Shelf mass per unit area (instead of |
| 2669 |
|
shelficeLoadAnomaly) and do the conversion from one to the other |
| 2670 |
|
- move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA |
| 2671 |
|
to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and |
| 2672 |
|
(b) will be loaded in time (before calling INI_PRESSURE) in case it is |
| 2673 |
|
needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc |
| 2674 |
|
- update isomip experiment forward output (get machine truncation error |
| 2675 |
|
from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly) |
| 2676 |
|
o verification/offline_exf_seaice: |
| 2677 |
|
revise data.seaice in input.thermo and input_ad and update results accordingly |
| 2678 |
|
HO = 0.2, SEAICE_areaLossFormula = 2, |
| 2679 |
|
SEAICE_growMeltByConv = .TRUE., |
| 2680 |
|
SEAICE_doOpenWaterMelt = .TRUE., |
| 2681 |
|
Improve consistency with input.thsice and fix the spurious 500m ice corners |
| 2682 |
|
o verification/global_ocean.cs32x15: |
| 2683 |
|
- set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0., |
| 2684 |
|
in icedyn (thsice+seaice-dyn) test and update output. |
| 2685 |
|
o verification/offline_exf_seaice: |
| 2686 |
|
- adjust list of tested variables (with testreport) and update |
| 2687 |
|
standard test output with better slection of monitored fields. |
| 2688 |
|
o pkg/cd_code: |
| 2689 |
|
- swtich off Adams-Bashforth on the 1rst iteration. Update output of |
| 2690 |
|
experiment lab_sea.hb87 |
| 2691 |
|
o tools/genmake2: |
| 2692 |
|
- change default makedepend from the system default to tools/xmakedepend: |
| 2693 |
|
When no makedepend is specified, select tools/xmakedepend it the test pass, |
| 2694 |
|
otherwise select the system default (if exist and pass the test) or |
| 2695 |
|
try to build cyrus-makedepend ; stop if none of the 3 works. |
| 2696 |
|
o pkg/exf & pkg/thsice: |
| 2697 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
| 2698 |
|
for energy content of Precip + RunOff & Evap. Assumes: |
| 2699 |
|
1) Rain has same temp as Air. |
| 2700 |
|
2) Snow has no heat capacity (consistent with seaice & thsice pkgs) |
| 2701 |
|
3) Run-Off comes at the temp of surface water (with same Cp) |
| 2702 |
|
4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be |
| 2703 |
|
put directly into Latent Heat flux & should use water-vapor heat capacity. |
| 2704 |
|
5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent |
| 2705 |
|
with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL). |
| 2706 |
|
o pkg/seaice: simplify the use of CPP flags in JFNK-related files |
| 2707 |
|
(compile when SEAICE_ALLOW_JFNK is defined) |
| 2708 |
|
o pkg/thsice: |
| 2709 |
|
- fix oceanic flux diagnostics & timeave (left from new sequence of calls |
| 2710 |
|
implementation): move THSICE_AVE call after the advection (called directly |
| 2711 |
|
from thsice_do_advect.F). |
| 2712 |
|
o verification/global_ocean.90x40x15 and OpenAD: |
| 2713 |
|
New experiment for OpenAD is identical to the one in input_ad except that |
| 2714 |
|
multiDimAdvection=.FALSE., |
| 2715 |
|
There is still an issue with this. |
| 2716 |
|
o pkg/thsice: |
| 2717 |
|
- account for ice velocity (ocean relative velocity) in turbulent heat flux |
| 2718 |
|
at the base of the ice; update output of global_ocean.cs32x15 (icedyn) |
| 2719 |
|
and offline_exf_seaice (main test). |
| 2720 |
|
|
| 2721 |
|
checkpoint64f (2013/03/31) |
| 2722 |
|
o verification/OpenAD: |
| 2723 |
|
- new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran. |
| 2724 |
|
o verification/isomip, pkg/shelfice and OpenAD: |
| 2725 |
|
- add OpenAD setup to this exp and make shelfice package work with OpenAD |
| 2726 |
|
o verification/tutorial_global_oce_biogeo: |
| 2727 |
|
- update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h) |
| 2728 |
|
o verification/offline_exf_seaice: |
| 2729 |
|
- replace adjoint experiment (now similar to fwd input.thermo/ setup). |
| 2730 |
|
o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD: |
| 2731 |
|
- add OpenAD setup to this exp and make ptracers package work with OpenAD |
| 2732 |
|
o pkg/seaice/seaice_evp.F: |
| 2733 |
|
mask the asymmetric contribution of the ice-ocean stress (when |
| 2734 |
|
the turningAngle is non-zero) over open water to avoid stripes |
| 2735 |
|
in the EVP-solutions after many EVP-substeps. This does not change |
| 2736 |
|
the verification experiment (because turningAngle=0 in that experiment), |
| 2737 |
|
but will affect other EVP solutions with turningAngle.ne.0 |
| 2738 |
|
o verification, AD & TLM output: |
| 2739 |
|
- new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple |
| 2740 |
|
additions and multiplications which affect results at machine truncation |
| 2741 |
|
level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5, |
| 2742 |
|
lab_sea.noseaicedyn & offline_exf_seaice) and TLM output |
| 2743 |
|
(1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12 |
| 2744 |
|
digits of matching. |
| 2745 |
|
o pkg/seaice: |
| 2746 |
|
modify lsr-algorithm so that it vectorizes AND converges by using a |
| 2747 |
|
"zebra" method: split vector loop into two with step size 2; this |
| 2748 |
|
solves a general convergence problem for the JFNK solver on a vector |
| 2749 |
|
computer. It has the potential to even improve convergence for |
| 2750 |
|
non-vector machines, but it does change the results so it is turned |
| 2751 |
|
off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and |
| 2752 |
|
SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h |
| 2753 |
|
|
| 2754 |
|
checkpoint64e (2013/03/05) |
| 2755 |
|
o pkg/ecco and several verification experiments: |
| 2756 |
|
Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F |
| 2757 |
|
from ecco package, and revert to unified routine in model/src/ |
| 2758 |
|
Adjust verification experiments accordingly, especially gloal_oce_llc90 |
| 2759 |
|
Should conclude long-standing work by Gael to reconsile the_main_loop with |
| 2760 |
|
ECCO and will enable OpenAD's revolve loop in ECCO setup. |
| 2761 |
|
o pkg/generic_advdiff: |
| 2762 |
|
- implement compressible flow method for multi-dim advection (similar to |
| 2763 |
|
gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since |
| 2764 |
|
TAF generates many recomputations) to use it; no yet coded with implicit |
| 2765 |
|
vertical advection. |
| 2766 |
|
- change experiment advect_cs (new output) and advect_xy (same output) |
| 2767 |
|
to test compressible flow multi-dim advection. |
| 2768 |
|
o pkg/generic_advdiff: |
| 2769 |
|
- fix SOM advection for unusual cases (linear Free-Surf in r*, other |
| 2770 |
|
cases where linear Free-Surf is not @ k=1, e.g., useShelfIce) |
| 2771 |
|
o pkg/seaice: |
| 2772 |
|
- fix bug in the no-slip implementation in seaice_calc_strainrates.F, this |
| 2773 |
|
bug affects two verification experiments (lab_sea and lab_sea.hb87), |
| 2774 |
|
recover old (wrong) results by setting noSlipFac = 2. in |
| 2775 |
|
seaice_calc_strainrates.F; |
| 2776 |
|
- add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0 |
| 2777 |
|
- add runtime parameter SEAICE_JFNKepsilon for that finite difference |
| 2778 |
|
gradient in the Jacobian times vector operation (s/r seaice_jacvec) |
| 2779 |
|
- fix line search in seaice_jfnk.F (s/r seaice_jfnk_update) |
| 2780 |
|
o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code: |
| 2781 |
|
- new subroutines seaice_lsr_tridiagu/v |
| 2782 |
|
- introduce loop bounds i/jmin/max to be able to use a restricted |
| 2783 |
|
additive Schwarz method, but not used for now. |
| 2784 |
|
- rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS |
| 2785 |
|
- use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner |
| 2786 |
|
o OpenAD support |
| 2787 |
|
Reorganize S/R call for overall time-stepping loop to facilitate |
| 2788 |
|
OpenAD revolve loop replacement |
| 2789 |
|
(new S/R main_do_loop.F) |
| 2790 |
|
o model/src: |
| 2791 |
|
- add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3; |
| 2792 |
|
- pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R |
| 2793 |
|
ADAMS_BASHFORTH2. |
| 2794 |
|
o pkg/cheapaml: |
| 2795 |
|
- add new parameter (default=F, same as before) to disable full domain |
| 2796 |
|
(including land) periodicity in X & Y dir. |
| 2797 |
|
- new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of |
| 2798 |
|
prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer |
| 2799 |
|
into single S/R CHEAPAML_TIMESTEP. |
| 2800 |
|
|
| 2801 |
|
checkpoint64d (2013/02/17) |
| 2802 |
|
o pkg/monitor (angular momentum): |
| 2803 |
|
- do not add Eta contribution to the total AM if using rigid-lid; |
| 2804 |
|
- correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta). |
| 2805 |
|
- horizontal discretisation: compute Zonal wind contribution separately for |
| 2806 |
|
each component (instead of from cell centered averaged) and use the 4 |
| 2807 |
|
grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part. |
| 2808 |
|
- Check that AM is conserved with linear dynamics (momAdvection=F and linear |
| 2809 |
|
FreeSurf) if using vectorInvariant momentum. |
| 2810 |
|
o model/src (horizontal grid): |
| 2811 |
|
- move initialisation of all horizontal grid arrays to null value |
| 2812 |
|
from specific horizontal grid S/R to main S/R INI_GRID; |
| 2813 |
|
- add 2 new arrays to project model C-grid velocity on to zonal direction |
| 2814 |
|
(similar to AngleCosC & -AngleSinC but at U and V point location) and |
| 2815 |
|
compute them in S/R CALC_GRID_ANGLES. |
| 2816 |
|
o pkg/seaice: replace a hard coded parameter by a runtime parameter |
| 2817 |
|
SEAICE_JFNK_tolIter |
| 2818 |
|
o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in |
| 2819 |
|
preconditioner for JFNK (run LSR into the overlaps as far as possible, |
| 2820 |
|
i.e OLx/y-2, but overwrite the solution in the overlaps) |
| 2821 |
|
- extend loop range in seaice_calc_viscosity |
| 2822 |
|
- add new parameters SEAICE_OLx/y (default = OLx/y-2) |
| 2823 |
|
- add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs |
| 2824 |
|
- slightly modify loops in tridiagonal solver lsr-preconditioner |
| 2825 |
|
- by default remove the extra exchange in seaice_preconditioner with a |
| 2826 |
|
replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE |
| 2827 |
|
- modify offline_exf_seaice so that old results without RAS are reproduced |
| 2828 |
|
for output.dyn_jfnk.txt |
| 2829 |
|
in seaice_fgmres.F (unrelated to RAS) |
| 2830 |
|
- add a cpp-flag option for a re-ordered mapping (potentially more |
| 2831 |
|
efficient), but because this changes the results, turn it off by |
| 2832 |
|
default |
| 2833 |
|
- replace the save statement by local common blocks |
| 2834 |
|
o utils/matlab: |
| 2835 |
|
- fix tile-offset in rdmnc.m when output was produced using EXCH2. |
| 2836 |
|
- update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab) |
| 2837 |
|
instead of local script "load_cs.m". |
| 2838 |
|
o pkg/seaice: |
| 2839 |
|
- fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected |
| 2840 |
|
to the scalarProductMetric and the unrolling. By chance this does not |
| 2841 |
|
change the verification experiment, because of the particular domain |
| 2842 |
|
decomposition |
| 2843 |
|
o pkg/diagnostics: |
| 2844 |
|
- change default missing_value from UNSET_RL to -999. |
| 2845 |
|
o pkg/layers: improve vectorization of layers_fluxcalc.F |
| 2846 |
|
- step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu |
| 2847 |
|
time spent in this routine by more than a factor of 3 on an NEC-SX8 |
| 2848 |
|
- step 2: replace search algorithm by a bisection algorithm found in |
| 2849 |
|
Press et al. Numerical Recipes in Fortran. This algorithm can be |
| 2850 |
|
vectorized and finds the correct bin in approx. log2(Nlayers) steps. |
| 2851 |
|
For now, use this algorithm only for TARGET_NEC_SX defined. |
| 2852 |
|
- moved the search algorithm into a separate subroutine, that is kept |
| 2853 |
|
within the same file for automatic inlining. |
| 2854 |
|
- modified catching potential errors |
| 2855 |
|
o pkg/ecco: |
| 2856 |
|
- add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY. |
| 2857 |
|
o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk : |
| 2858 |
|
- modifications for ALLOW_GENTIM2D_CONTROL |
| 2859 |
|
-- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes. |
| 2860 |
|
-- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid ) |
| 2861 |
|
-- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc |
| 2862 |
|
-- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F |
| 2863 |
|
o model/src: |
| 2864 |
|
- account for moist thermodynamics in (dry) potential temperature equation; |
| 2865 |
|
update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev) |
| 2866 |
|
and cpl_aim+ocn. |
| 2867 |
|
- also switch to standard compiler (gfortran, was using ifort previously) |
| 2868 |
|
for fizhi-cs experiments reference output. |
| 2869 |
|
o pkg/ctrl: |
| 2870 |
|
- 1st step toward generic time-varying control variable (2D) via CPP option |
| 2871 |
|
ALLOW_GENTIM2D_CONTROL |
| 2872 |
|
- note new namelist ctrl_nml_genarr in data.ctrl |
| 2873 |
|
o verification/global_ocean.cs32x15: |
| 2874 |
|
- switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new |
| 2875 |
|
thsice calling sequence and update "output.icedyn.txt" output file. |
| 2876 |
|
o pkg/ptracers: |
| 2877 |
|
- from Ryan A.: code to allow to restart a tracer at regular time interval |
| 2878 |
|
specifying a reset frequency and a reset-phase (for each tracers). |
| 2879 |
|
o pkg/thsice: |
| 2880 |
|
- implement new sequence of calls for thsice+seaice: |
| 2881 |
|
previously: ice-Dyn,ice-Advect,ice-Thermo(thsice) |
| 2882 |
|
new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect |
| 2883 |
|
- allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE" |
| 2884 |
|
in CPP_OPTIONS.h) to recover old sequence; |
| 2885 |
|
- update diagnostics for Intermediate State thsice diagnostics: now filled |
| 2886 |
|
just before advection (instead of just after advection in old sequence); |
| 2887 |
|
- update output of experiment offline_exf_seaice (standard test); |
| 2888 |
|
- in global_ocean.cs32x15 exp., postpone output.icedyn.txt update |
| 2889 |
|
by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h |
| 2890 |
|
o pkg/aim_v23: |
| 2891 |
|
- use tiled array for aim_CO2 and surface wind speed for export to coupler; |
| 2892 |
|
- use standard pkg/mdsio routines to read & write CO2 pickup file; |
| 2893 |
|
- in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F; |
| 2894 |
|
- Implement new sequence of calls for seaice advection (with thsice and |
| 2895 |
|
seaice diffusion): do ice advection after ice-Thermodynamic (previously |
| 2896 |
|
was done before); change aim_do_physics.F (split the bi,bj loops block); |
| 2897 |
|
- use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence; |
| 2898 |
|
o pkg/thsice: |
| 2899 |
|
- add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case |
| 2900 |
|
where just seaice diffusion is used without seaice-dynamics. |
| 2901 |
|
|
| 2902 |
|
checkpoint64c (2013/01/18) |
| 2903 |
|
o pkg/seaice: |
| 2904 |
|
- add a parameter JFNKres_tFac that can replace JFNKres_t |
| 2905 |
|
(= JFNKres_tFac*JFNKresidual before JFNK solver) |
| 2906 |
|
- add a line search option to the JFNK solver |
| 2907 |
|
- move update of u/vIce and computation of initial residual into a separate |
| 2908 |
|
routine (same file); makes the code a little easier to read (?) |
| 2909 |
|
- the line search requires computation of the residual and for some reason |
| 2910 |
|
I cannot do the update of u/vIce at the beginning of the Newton loop |
| 2911 |
|
without changing the results, so we move computation of the new residual |
| 2912 |
|
also to the end of the Newton loop, even without the line search |
| 2913 |
|
o pkg/mdsio: |
| 2914 |
|
- write missing value (corresponding to undefined array value) to meta files; |
| 2915 |
|
skip this if missing value is one (UNSET_RL would be a better value for the |
| 2916 |
|
case of undefined missing value but it's current the default missing-value); |
| 2917 |
|
Also update mdsio_read_meta.F (reading timeInterval & missing-value). |
| 2918 |
|
o pkg/exf & thsice: |
| 2919 |
|
- for diagnostics purpose, fill-up and update Qsw array (+ fill the |
| 2920 |
|
diagnostics) even when SHORTWAVE_HEATING is #undef; |
| 2921 |
|
o verification/cfc_example: |
| 2922 |
|
- turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to |
| 2923 |
|
illustrate how to use it). |
| 2924 |
|
o verification/offline_exf_seaice: |
| 2925 |
|
in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing |
| 2926 |
|
files to only one time-record. |
| 2927 |
|
in input.thermo: narrow the 2 bands of low initial ice-concentration near |
| 2928 |
|
N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for |
| 2929 |
|
snapshot output; same mcPheePiston value as in thsice with |
| 2930 |
|
surf-current=0.2m/s. |
| 2931 |
|
in input.thsice: similar set-up as in input.thermo (channel with same seaice |
| 2932 |
|
initial conditions). |
| 2933 |
|
o verification/cfc_example: |
| 2934 |
|
- update file "data" with more standard choice (default rotationPeriod, |
| 2935 |
|
exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F, |
| 2936 |
|
set deltaTFreeSurf to deltaTtracer) and update the output. |
| 2937 |
|
o pkg/layers: |
| 2938 |
|
- fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC; |
| 2939 |
|
- ensure that "layers_bolus" is switched to False when useGMRedi=False. |
| 2940 |
|
o verification/offline_exf_seaice: |
| 2941 |
|
- set all {field}period to zero for constant-in-time forcing (not tested |
| 2942 |
|
anywhere else). |
| 2943 |
|
o verification/offline_exf_seaice: |
| 2944 |
|
- dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice; |
| 2945 |
|
- dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice. |
| 2946 |
|
o model/src: |
| 2947 |
|
- implement Finite-Volume method for (hydrostatic) presure gradient |
| 2948 |
|
from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate. |
| 2949 |
|
o pkg/seaice: implement EVP* by Lemieux et al. (2012). |
| 2950 |
|
- In order to be compatible with the default EVP code, this requires changing |
| 2951 |
|
the EVP code around a little; and because any small change immediately |
| 2952 |
|
breaks the lab_sea.hb87 verification experiment, the reference output is |
| 2953 |
|
updated two times (each time the remaining aggrement was only 2 digits): |
| 2954 |
|
- after replacing 1/dt by 1*recip_dt with a precomputed recip_dt |
| 2955 |
|
- after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt |
| 2956 |
|
The adjoint test lab_sea.evp also needed to be updated. |
| 2957 |
|
- Turn on EVP* by setting SEAICE_deltaTevp as before, and setting |
| 2958 |
|
SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be |
| 2959 |
|
a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps |
| 2960 |
|
explicitly with SEAICEnEVPstarSteps (thereby overriding the default of |
| 2961 |
|
INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately |
| 2962 |
|
kept obscure, because I need to test it a little more. |
| 2963 |
|
o pkg/cheapaml: |
| 2964 |
|
- fix few incorrect type (_RL/_RS) in subroutine calls. |
| 2965 |
|
o pkg/seaice: |
| 2966 |
|
- new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays |
| 2967 |
|
to _RL vector; this fixes JFNK code when compiling with "-use_r4" option. |
| 2968 |
|
o model/src: |
| 2969 |
|
- add a warning if using select_rStar=2 with nonlinFreeSurf <> 4; |
| 2970 |
|
change (in input_ad*/data) select_rStar from 2 to 1 for AD verification |
| 2971 |
|
experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output) |
| 2972 |
|
o pkg/cheapaml: |
| 2973 |
|
- replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and |
| 2974 |
|
update output of experiment cheapAML_box. |
| 2975 |
|
- store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity, |
| 2976 |
|
and set them only in one place (cheapaml_readparms.F). |
| 2977 |
|
- replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI" |
| 2978 |
|
- remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms) |
| 2979 |
|
and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia). |
| 2980 |
|
o model/src/the_main_loop.F: |
| 2981 |
|
- fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION. |
| 2982 |
|
o pkg/seaice: |
| 2983 |
|
- remove legacy branch code. |
| 2984 |
|
- retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly. |
| 2985 |
|
o verification/*/code*/SEAICE_OPTIONS.h: |
| 2986 |
|
- remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY, |
| 2987 |
|
SEAICE_CAP_HEFF). |
| 2988 |
|
o pkg/cheapaml: |
| 2989 |
|
- use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time |
| 2990 |
|
to load new forcing fields. |
| 2991 |
|
- add missing "_d 0" where it's needed; + some editing (improve indentation). |
| 2992 |
|
- remove switch to "-r8" compiler option (no longer needed) in verification |
| 2993 |
|
cheapAML_box, keep same output (small trucation error differences). |
| 2994 |
|
o verification/offline_exf_seaice: |
| 2995 |
|
- add thermodynamics only test. |
| 2996 |
|
o verification/cheapAML_box: |
| 2997 |
|
- split the domain in 8 (2x4) tiles; add MPI and multi-threaded test; |
| 2998 |
|
keep same output (same 14 digits for cg2d). |
| 2999 |
|
- switch on "-r8" compiler option (some numerical values are missing |
| 3000 |
|
the "_d 0") and update output (only 6 digits for cg2d were preserved). |
| 3001 |
|
|
| 3002 |
|
checkpoint64b (2012/12/24) |
| 3003 |
|
o pkg/cheapaml: |
| 3004 |
|
- remove un-used variables (Qnet,EmPmR) from pickup files. |
| 3005 |
|
- store tendency of advected variables into cheapaml pickup file |
| 3006 |
|
and fix the AB-2 restart. |
| 3007 |
|
o verification/offline_exf_seaice and lab_sea adjoint: |
| 3008 |
|
- switch to new code (#undef SEAICE_GROWTH_LEGACY). |
| 3009 |
|
- switch to 4 time steps in offline, consistent with lab_sea. |
| 3010 |
|
- match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice. |
| 3011 |
|
- update results after change of experiment seaice. |
| 3012 |
|
o pkg/seaice: |
| 3013 |
|
- remove option SEAICE_MULTICATEGORY; has been replaced with run-time |
| 3014 |
|
parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is |
| 3015 |
|
still defined since SEAICE_multDim needs to be set to MULTDIM value (from |
| 3016 |
|
SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default. |
| 3017 |
|
o model/src: |
| 3018 |
|
- add run-time parameter to select CG2D solver minimum-residual solution |
| 3019 |
|
(in case of a poor convergence). |
| 3020 |
|
o pkg/seaice/seaice_lsr.F |
| 3021 |
|
- move calculation of matrix coefficients into new |
| 3022 |
|
S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same |
| 3023 |
|
file; the main purpose of this change is to be able to reuse the code |
| 3024 |
|
in S/R SEAICE_PRECONDITIONER |
| 3025 |
|
- modify the computation of the residual so that the mass of sea-ice |
| 3026 |
|
is not used twice; this simplifies the calculations, but since |
| 3027 |
|
the residual is never used except when LSR_mixIniGuess.ge.4---and this is |
| 3028 |
|
not tested in testreport---this does not affect the testreport results. |
| 3029 |
|
o verification/seaice_obcs: |
| 3030 |
|
- disable SEAICE_GROWTH_LEGACY; reset input files to match those of |
| 3031 |
|
verification/lab_sea/input.salt_plume; changes results/output.txt* |
| 3032 |
|
o model/src: |
| 3033 |
|
- adapt quasi-hydrostatic formulation to work with p or p* coordinate. |
| 3034 |
|
o pkg/seaice: |
| 3035 |
|
- improve description of parameters in seaice_fgmres.F and start |
| 3036 |
|
cleaning up the code |
| 3037 |
|
- change name of SCALPROD to SEAICE_SCALPROD and modify meaning of |
| 3038 |
|
second argument |
| 3039 |
|
- add a metric based on grid cell area to SEAICE_SCALPROD; update |
| 3040 |
|
results of offline_exf_seaice.dyn_jfnk |
| 3041 |
|
- compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD |
| 3042 |
|
o pkg/aim_v23: |
| 3043 |
|
- fix an other bug in dissipation heating (grid-cell area was missing). |
| 3044 |
|
o model/src + pkg/seaice: |
| 3045 |
|
- add global (multi-tile) linear solver for pair of tri-diagonal system |
| 3046 |
|
along X and Y lines, respectively for U and V component. |
| 3047 |
|
Note: 1) MPI and cube-exchange not yet coded. |
| 3048 |
|
2) probably not accurate for poorly conditioned / large size problem. |
| 3049 |
|
- add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver; |
| 3050 |
|
default: not compiled and not used. |
| 3051 |
|
o pkg/seaice: |
| 3052 |
|
- first attempt at a multi-threaded fgmres solver for the JFNK solver: |
| 3053 |
|
introduce bi/bj loops and use global_sum_tile_rl instead of |
| 3054 |
|
mpi_allreduce in seaice_fgmres.F |
| 3055 |
|
- improve diagnostics output for fgmres solver (seaice_fgmres.F) |
| 3056 |
|
- replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F) |
| 3057 |
|
- add a verification experiment for JFNK in offline_exf_seaice |
| 3058 |
|
o verification: |
| 3059 |
|
- change (for now, only fwd test) offline_exf_seaice experiment: |
| 3060 |
|
use a re-entrant channel with idealized coastline (trapezoidal shape) |
| 3061 |
|
at southern boundary to explore seaice dynamics and thermodynamics |
| 3062 |
|
with simple forcing. Main set-up has dynamics+thermo and SST relaxation; |
| 3063 |
|
secondary test (input.thsice) use thermodynamics only with SST relaxation. |
| 3064 |
|
- add seaice-dynamics only secondary test using LSR and pkg/thsice advection. |
| 3065 |
|
o pkg/exf: |
| 3066 |
|
- disable "sstExtrapol" when Nr=1 |
| 3067 |
|
o verification: |
| 3068 |
|
- add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble) |
| 3069 |
|
to test pkg/cheapaml. |
| 3070 |
|
o pkg/aim_v23 & pkg/shap_filt: |
| 3071 |
|
- fix dissipation heating (erroneous gravity multiplication factor). |
| 3072 |
|
o pkg/seaice: |
| 3073 |
|
- remove unused field pressPre from jfnk solver |
| 3074 |
|
- rename two subroutines in seaice_preconditioner.F |
| 3075 |
|
o eesupp/src: |
| 3076 |
|
- S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...) |
| 3077 |
|
o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again |
| 3078 |
|
- remove wrong parts of the rhs and the lhs (were in there |
| 3079 |
|
because I did not understand the concept of this preconditioner) |
| 3080 |
|
- add an exchange between u- and v-sweep. This increases communication |
| 3081 |
|
by a factor of two but improves the convergence of jfnk. Ideally, |
| 3082 |
|
one would like the u- and v-sweep to be independent. So far within |
| 3083 |
|
undocumented ifdefs |
| 3084 |
|
- reorganize the extra computations for printing the residuals |
| 3085 |
|
o tools/genmake2: |
| 3086 |
|
- comment out the "mpif.h" include in NetCDF test programm (for MPI built) |
| 3087 |
|
since it's not necessary (and was preventing to use MNC in some cases). |
| 3088 |
|
|
| 3089 |
|
checkpoint64a (2012/11/16) |
| 3090 |
|
o pkg/autodiff: |
| 3091 |
|
- improve pkg-internal logical parameter switch (inAd/inFwd mode) so that |
| 3092 |
|
autodiff_readparms.F no longer depends on calling order (within |
| 3093 |
|
packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h): |
| 3094 |
|
rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd |
| 3095 |
|
and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd. |
| 3096 |
|
o pkg/obcs: |
| 3097 |
|
- adding tidal velocity forcing capability to obcs |
| 3098 |
|
for usage example, see verification/seaice_obcs/input.tides |
| 3099 |
|
o pkg/seaice: |
| 3100 |
|
- turn the LSR-relaxation parameters WFAU/V into runtime parameters |
| 3101 |
|
SEAICE_LSRrelaxU/V |
| 3102 |
|
- introduce runtime parameter SEAICEetaZmethod (=0 by default) |
| 3103 |
|
o pkg/aim_v23: |
| 3104 |
|
- implement heating from friction (bottom friction and stratospheric drag). |
| 3105 |
|
o pkg/shap_filt: |
| 3106 |
|
- fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from |
| 3107 |
|
dissipation but only for Shap_funct=2, active when addFrictionHeating=T. |
| 3108 |
|
o model/src: |
| 3109 |
|
- move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in |
| 3110 |
|
time-constant addMass field from file (addMassFile); |
| 3111 |
|
- support for heating due to friction (and Kinetic Energy dissipation): |
| 3112 |
|
add option, run-time switch and 3-D field array + support code ; each pkg |
| 3113 |
|
or S/R can add heating contribution (if there is a sink of KE); the sum is |
| 3114 |
|
accounted for as a Temperature tendency term (EXTERNAL_FORCING_T). |
| 3115 |
|
o pkg/seaice: |
| 3116 |
|
- complete merge of ITD code into seaice_growth.F |
| 3117 |
|
from MITgcm_contrib/torge/itd/code/ |
| 3118 |
|
no verification so far, but Torge Martin tested |
| 3119 |
|
"1-D test case and Beaufort set up; |
| 3120 |
|
deliver okay results after 1 model year." |
| 3121 |
|
- complete merge of SEAICE_SIZE.h into all relevant routines |
| 3122 |
|
- move computation of eta at Z-points into calc_viscosities |
| 3123 |
|
+ introduce global field etaZ |
| 3124 |
|
+ add different methods for computing etaZ, for now the old |
| 3125 |
|
method (simple averages of eta to Z-points) is hardwired |
| 3126 |
|
+ replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual, |
| 3127 |
|
seaice_preconditioner |
| 3128 |
|
- simplify computations for SEAICE_ZETA_SMOOTHREG |
| 3129 |
|
- seaice_preconditioner: |
| 3130 |
|
+ replace one remaining press by pressLoc (mistake) |
| 3131 |
|
+ adjust printing of residuals |
| 3132 |
|
- improve I/O of diagnostics of JFNK in seaice_jfnk.F: |
| 3133 |
|
+ add (SEAICE.h) and rename some counters (initiliased in |
| 3134 |
|
seaice_init_fixed.F) |
| 3135 |
|
+ add _BEGIN/END_MASTER (myThid) around print statements |
| 3136 |
|
+ print total number of iterations and failures over SEAICE_monFreq |
| 3137 |
|
interval to STDOUT |
| 3138 |
|
- move control over output-messages by fgmres to seaice_jfnk to save |
| 3139 |
|
some operations |
| 3140 |
|
- move resetting initial guess for fgmres outside of seaice_fgmres_driver |
| 3141 |
|
in order to make restarts with sol .ne. zero (fgmres with restarts) |
| 3142 |
|
(seaice_jfnk.F, seaice_fgmres.F) |
| 3143 |
|
- seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes |
| 3144 |
|
a serious convergence problem when open boundaries are involved |
| 3145 |
|
o pkg/ggl90: fix computation of control volumes for the case of |
| 3146 |
|
ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes |
| 3147 |
|
up half a grid cell from C-centered to W-centered (pointed out by C. Eden) |
| 3148 |
|
o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC |
| 3149 |
|
o pkg/autodiff |
| 3150 |
|
- Add inAdMode switch for SEAICEuseDYNAMICS: |
| 3151 |
|
SEAICEuseDYNAMICSinAdMode |
| 3152 |
|
(extend logic in ADAUTODIFF_INADMODE_SET) |
| 3153 |
|
o pkg/seaice |
| 3154 |
|
- Step 1 of merging ice-thickness distribution (ITD) code from |
| 3155 |
|
MITgcm_contrib/torge/itd/ (author: Torge Martin) |
| 3156 |
|
The code implements concept laid out in Thorndike et al. (1975); |
| 3157 |
|
code is enabled via CPP flag SEAICE_ITD |
| 3158 |
|
nITD (in SEAICE_SIZE.h) defines number of ice thickness categories; |
| 3159 |
|
code is not complete yet!! |
| 3160 |
|
- SEAICE_SIZE.h now included in almost all seaice routines |
| 3161 |
|
o verification (using seaice): |
| 3162 |
|
- switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp. |
| 3163 |
|
global_ocean.cs32x15.seaice ; update results. |
| 3164 |
|
- compile B-grid dynamics in FW test exp 1D_ocean_ice_column ; |
| 3165 |
|
- compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp |
| 3166 |
|
offline_exf_seaice (previously compiling B-grid). |
| 3167 |
|
o pkg/exf: |
| 3168 |
|
- fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow |
| 3169 |
|
to specify neither just 1 comp of wind or wind-stress, nor no surface momentum |
| 3170 |
|
forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind. |
| 3171 |
|
o pkg/layers (adjust changes from Sept 19): |
| 3172 |
|
- do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F) |
| 3173 |
|
this allows to remove "layers_maxNum" dimension from all layers arrays. |
| 3174 |
|
o pkg/layers (adjust changes from Sept 19): |
| 3175 |
|
- remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ; |
| 3176 |
|
- snap-shot extended to all type of layers (not just the 1rst type); |
| 3177 |
|
- remove layers variables when corresponding CPP option is undef. |
| 3178 |
|
o pkg/layers: |
| 3179 |
|
- rename pkg/layers variable and add new output (layer exist & un-weighted |
| 3180 |
|
velocity in layer) |
| 3181 |
|
o pkg/seaice: |
| 3182 |
|
- simplify (?) ocean-drag coefficent computations by using |
| 3183 |
|
the same routine in all three solvers (saves some code lines) |
| 3184 |
|
- remove global fields DRAGA and DRAGS from C-grid code and |
| 3185 |
|
declare them locally in lsr.F (the only place where they are |
| 3186 |
|
still used) |
| 3187 |
|
- update AD output of lab_sea.evp (very sensitive anyway). |
| 3188 |
|
o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics |
| 3189 |
|
(Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK |
| 3190 |
|
and SEAICEuseJFNK=.true. A few things to note: |
| 3191 |
|
- involves a FGMRES, that is parallel but very inefficient, |
| 3192 |
|
because of many scalar products (global sums) in the Gram-Schmidt |
| 3193 |
|
orthogonalization method. Needs to be replaced. Original code |
| 3194 |
|
from J.-F. Lemieux |
| 3195 |
|
- preconditioner for FGMRES is a stripped down version of LSOR |
| 3196 |
|
- SOLV_MAX_ITERS is now used for LSOR as a solver and as a |
| 3197 |
|
preconditioner. For the preconditioner, the default is set to 10. |
| 3198 |
|
- Jacobian times vector is computed with finite differences |
| 3199 |
|
- marginally related to JFNK-solver: add a smooth regularization for |
| 3200 |
|
zeta with tanh that will improve convergence (Lemieux and Tremblay, |
| 3201 |
|
2009) for any implicit solver (not implemented for EVP because EVP |
| 3202 |
|
does not need this regularization in the first place). Define |
| 3203 |
|
SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use. |
| 3204 |
|
o eesupp/src: |
| 3205 |
|
- check in genmake2 that intrinsic S/R flush is available. |
| 3206 |
|
- add S/R to flush IO unit (if intrinsic S/R flush is available) |
| 3207 |
|
- flush standard & error msg unit before MPI termination |
| 3208 |
|
- if debugMode, flush IO unit after printing msg |
| 3209 |
|
o pkg/ctrl: |
| 3210 |
|
- ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call |
| 3211 |
|
to ctrl_set_unpack_xyz. |
| 3212 |
|
|
| 3213 |
|
checkpoint64 (2012/10/09) |
| 3214 |
|
o pkg/shelfice |
| 3215 |
|
- in mom_fluxform.F, mom_vecinv.F: |
| 3216 |
|
CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid) |
| 3217 |
|
Bug fix KappaRU -> KappaRV |
| 3218 |
|
does not change verification/isomip but may change other setups |
| 3219 |
|
(presumably constant KappaRU=KappaRV) |
| 3220 |
|
- fix diagnostics SHIU/Vdrag (thanks to Tom Millgate) |
| 3221 |
|
o pkg/obcs: |
| 3222 |
|
- fixed some indexing bugs in obcs_seaice_sponge.F |
| 3223 |
|
- added obcs relaxation subroutines for HSALT and HSNOW |
| 3224 |
|
- changes verification/seaice_obcs/results/obcs_seaice_sponge.F |
| 3225 |
|
o pkg/seaice: |
| 3226 |
|
- add "multicategory" parameterization for snow in analogy to ice, |
| 3227 |
|
default is off for now. |
| 3228 |
|
o pkg/obcs: |
| 3229 |
|
- added obcs_seaice_sponge.F for obcs relaxation of seaice variables; |
| 3230 |
|
see verification/seaice_obcs/input.seaiceSponge for example application. |
| 3231 |
|
- remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB |
| 3232 |
|
index setting by master-thread. This fix multi-threads Pb in previous modifs. |
| 3233 |
|
o pkg/layers : |
| 3234 |
|
- add diagnostics to pkg/layers |
| 3235 |
|
- move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F |
| 3236 |
|
(from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly. |
| 3237 |
|
o pkg/generic_advdiff/gad_implicit_r.F : |
| 3238 |
|
- fix ADVr diagnostics in case of both implicit vertical advection and diffusion. |
| 3239 |
|
o pkg/seaice/seaice_growth.F: |
| 3240 |
|
- fix SItflux diagnostics in virtual salt flux + balanceEmpmr case. |
| 3241 |
|
o pkg/obcs: |
| 3242 |
|
- change default setting of OBCS_UVICE_OLD from defined to undef; |
| 3243 |
|
- use new parameter OB_indexNone for null index value (instead of hard-coded 0) |
| 3244 |
|
in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F; |
| 3245 |
|
- pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z; |
| 3246 |
|
- change OB null index value (OB_indexNone) to -99 ; this fix the problem |
| 3247 |
|
with Southern & Western OB at a tile edge (at least in a simple set-up). |
| 3248 |
|
o pkg/obcs: |
| 3249 |
|
- change settings of OB index in case OB coincides with tile edge (shared by |
| 3250 |
|
2 tiles), so that common OB location is registered by both tiles (instead of |
| 3251 |
|
only 1). However, for Southern and Western OB, index value = 0 is not |
| 3252 |
|
recognized as valid OB index (=default null value) and needs to be fixed. |
| 3253 |
|
- modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting) |
| 3254 |
|
- new parameter "OB_indexNone" for null index value (for now, still zero) |
| 3255 |
|
to replace hard-coded null index value of zero. |
| 3256 |
|
o pkg/exch2: |
| 3257 |
|
- improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON: |
| 3258 |
|
always check buffer-size (but outside the loop); move checking for valid |
| 3259 |
|
index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON, |
| 3260 |
|
print each tile and point connection only if |W2_printMsg|>= 2 and 3. |
| 3261 |
|
o pkg/ctrl (pack & unpack): |
| 3262 |
|
- in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable |
| 3263 |
|
(locally defined) for different variables (+ remove the variable-specific |
| 3264 |
|
file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL |
| 3265 |
|
(to be extended to other local file names in ctrl.h). |
| 3266 |
|
o pkg/flt: |
| 3267 |
|
- add a FLT_Iter0 option (similar to PTRACERS_Iter0). |
| 3268 |
|
o pkg/mdsio: |
| 3269 |
|
- fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing |
| 3270 |
|
o tools/genmake2: |
| 3271 |
|
- add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE |
| 3272 |
|
(added by Alistair in version 1.51 for building without make depend); |
| 3273 |
|
- remove Header files list (H_SRC_FILES) from the dependence of targets |
| 3274 |
|
ad_input_code.f & ftl_input_code.f (not clear why it was added in the first |
| 3275 |
|
place in version 1.23): this save going through staf when unrelated header |
| 3276 |
|
file has been modified. |
| 3277 |
|
Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without |
| 3278 |
|
"make depend" step, still need to do "make links" before "make adtaf". |
| 3279 |
|
o eesupp/src (+ few pkg src files) & genmake2: |
| 3280 |
|
- finish to remove ALWAYS_USE_MPI in source code that TAF does not see; |
| 3281 |
|
- no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2). |
| 3282 |
|
- improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish |
| 3283 |
|
upper/lower case ; account for space between "#" and undef/define) |
| 3284 |
|
o pkg/flt (with exch2): |
| 3285 |
|
- cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F; |
| 3286 |
|
- simplify threads synchronisation; fix (many issues) multi-threaded with MPI. |
| 3287 |
|
|
| 3288 |
|
checkpoint63s (2012/09/05) |
| 3289 |
|
o pkg/ecco: |
| 3290 |
|
- remove #ifdef ALLOW_SMOOTH_CORREL3D brackets. |
| 3291 |
|
- add more relevant #ifdef ALLOW_SMOOTH ones. |
| 3292 |
|
- sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D. |
| 3293 |
|
o pkg/ctrl: |
| 3294 |
|
- CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D, |
| 3295 |
|
ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D. |
| 3296 |
|
- ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag, |
| 3297 |
|
doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and |
| 3298 |
|
ctrlSmoothCorrel3D (new). |
| 3299 |
|
The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP. |
| 3300 |
|
- ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist. |
| 3301 |
|
- ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress |
| 3302 |
|
controls when useAtmWind, and vice versa. |
| 3303 |
|
- ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers. |
| 3304 |
|
- ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with |
| 3305 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH. |
| 3306 |
|
- ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with |
| 3307 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH. |
| 3308 |
|
- ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F: |
| 3309 |
|
replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D. |
| 3310 |
|
o pkg/smooth: |
| 3311 |
|
- remove un-necessary includes. |
| 3312 |
|
- remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets. |
| 3313 |
|
Those CPP options were never defined, and not necessary. |
| 3314 |
|
o model/src: |
| 3315 |
|
- fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi). |
| 3316 |
|
- standard treatment of useSMOOTH. |
| 3317 |
|
o pkg/autodiff: |
| 3318 |
|
- add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode, |
| 3319 |
|
useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint. |
| 3320 |
|
o pkg/exch2: |
| 3321 |
|
- add "if usingMPI" where it was missing (in exch2_rx?_cube*.template) |
| 3322 |
|
+ start to remove ALWAYS_USE_MPI in source code that TAF does not see. |
| 3323 |
|
- make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag |
| 3324 |
|
and tiles to process mapping. |
| 3325 |
|
- re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h) |
| 3326 |
|
moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h; |
| 3327 |
|
rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX |
| 3328 |
|
from w2_eeboot.F to w2_readparms.F. |
| 3329 |
|
o eesupp/src: |
| 3330 |
|
- set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of |
| 3331 |
|
ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F; |
| 3332 |
|
also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F |
| 3333 |
|
- in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI |
| 3334 |
|
is defined (remove condition on usingMPI) to match cases where MPI_INIT |
| 3335 |
|
has been called. |
| 3336 |
|
- fix bug I put in previous modif of exch_sm_3d_rx.template (not much used); |
| 3337 |
|
- change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings |
| 3338 |
|
(so that on 1 proc, get same myPid independently of usingMPI) |
| 3339 |
|
- add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and |
| 3340 |
|
useCubedSphereExchange with EXCH-1 (safer). |
| 3341 |
|
- add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI). |
| 3342 |
|
o pkg/ggl90: |
| 3343 |
|
- fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call) |
| 3344 |
|
used in ALLOW_GGL90_SMOOTH code. |
| 3345 |
|
o pkg/flt: |
| 3346 |
|
- fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping |
| 3347 |
|
floats at the Southern end of the domain). |
| 3348 |
|
o eesupp/inc: |
| 3349 |
|
- add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h); |
| 3350 |
|
but not used (and not to be used) anywhere, just for documentation. |
| 3351 |
|
o pkg/autodiff, exf, ptracers & seaice (AD & TL output): |
| 3352 |
|
- comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since: |
| 3353 |
|
a) can damage previously written records in any other multi-record files. |
| 3354 |
|
b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S. |
| 3355 |
|
o tools/genmake2: |
| 3356 |
|
- define variable MAKE within Makefile and use it in place of 'make'; |
| 3357 |
|
- update AD_CONFIG.h (if needed) before building any of the executable |
| 3358 |
|
(forward, adjoint or tangent-lin); this involves a 2nd invocation of make; |
| 3359 |
|
and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h; |
| 3360 |
|
- always print usual warning comment 'this file is automatically generated' |
| 3361 |
|
from script convert_cpp_cmd2defines (+ remove this warning from genmake2). |
| 3362 |
|
o pkg/cheapaml: |
| 3363 |
|
- updated to correspond to the code used in accepted paper (Nico Wienders). |
| 3364 |
|
o pkg/exf: |
| 3365 |
|
added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch. |
| 3366 |
|
ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F) |
| 3367 |
|
and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h). |
| 3368 |
|
o pkg/exf, autodiff, ctrl, ecco and seaice: |
| 3369 |
|
remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones. |
| 3370 |
|
o pkg/ctrl, ecco: |
| 3371 |
|
allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL. |
| 3372 |
|
Depending on useAtmWind, one is inactive, and the other is active (see |
| 3373 |
|
exf_getffields.F/exf_getsurfacefluxes.F). |
| 3374 |
|
o tools/genmake2: |
| 3375 |
|
- improve error msg when failing in 2nd test of check_for_broken_Ff |
| 3376 |
|
- fix option '-makefile' short-name (-mf according to genmake2 -help) |
| 3377 |
|
- source local config file "genmake_local" just after processing the genmake2 |
| 3378 |
|
command arguments (previously done before processing arg). |
| 3379 |
|
o pkg/grdchk: |
| 3380 |
|
- add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call |
| 3381 |
|
to this routine from cost_final has been dropped in g_cost_final) |
| 3382 |
|
- improve printed information (more explicit msg, no longer using "print *," |
| 3383 |
|
fix fcpertminus printed value). |
| 3384 |
|
o model/src: |
| 3385 |
|
- move call to COST_INIT_VARIA out of packages_init_variables.F directly |
| 3386 |
|
into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES): |
| 3387 |
|
this prevents getting cost-funct reset in adinitialise_varia recomputations. |
| 3388 |
|
o pkg/dic: |
| 3389 |
|
- move initialisation of "freefe" array from from dic_biotic_forcing.F to |
| 3390 |
|
fe_chem.F: this prevents TAF from dropping this initialisation in TLM code. |
| 3391 |
|
o pkg/grdchk: |
| 3392 |
|
- grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid ) |
| 3393 |
|
- grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0 |
| 3394 |
|
o pkg/autodiff/ctrl/grdchk : |
| 3395 |
|
- attempt to sort out what works and what does not, |
| 3396 |
|
with regard to I/O, and to warn/stop accordingly. |
| 3397 |
|
o pkg/grdchk: |
| 3398 |
|
- attempt to fix grdchk in the case of useSingleCpuIO. |
| 3399 |
|
- "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )" |
| 3400 |
|
statements were moved from grdchk_main.F and into |
| 3401 |
|
grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F. |
| 3402 |
|
- a global sum is applied to record numbers icvrec/layer |
| 3403 |
|
out of grdchk_loc so that they be passed to I/O routines. |
| 3404 |
|
o pkg/smooth: |
| 3405 |
|
- fix recomputation that appeared with nlfs : use smooth_recip_hFacC, |
| 3406 |
|
smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case. |
| 3407 |
|
o verification/testreport: |
| 3408 |
|
- add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive); |
| 3409 |
|
- can also use compressed (gzip) reference output file; |
| 3410 |
|
- change format (in pkg/grdchk) of TLM output (+ add forward gradient) |
| 3411 |
|
to be easier to collect by testreport. |
| 3412 |
|
- update existing TLM output (half out-of-date by more than 3 yrs). |
| 3413 |
|
- report NETCDF & LAPACK settings (from genmake2) in output dir. |
| 3414 |
|
- report run-time in each individual summary (previously only for AD test); |
| 3415 |
|
for TLM test, add also TAF version. |
| 3416 |
|
- add daily TLM test on (old) aces cluster + weekly test on baudelaire. |
| 3417 |
|
|
| 3418 |
|
checkpoint63r (2012/08/15) |
| 3419 |
|
o tools/genmake2: |
| 3420 |
|
- fix Makefile for target ftlall (+ update files to clean after make ftlall) |
| 3421 |
|
o pkg/ecco/ecco_cost_final.F : |
| 3422 |
|
- fix fc print statements (to stdout and costfunction0000) so |
| 3423 |
|
that the printed value is always after the global sum. |
| 3424 |
|
o pkg/seaice/seaice_dynsolver.F : |
| 3425 |
|
- fix ice strength assymptote at SEAICE_area_max<1 |
| 3426 |
|
(no change for the standard case of SEAICE_area_max=1) |
| 3427 |
|
o some cleaning: |
| 3428 |
|
- pkg source files: ensure that all *.F files from each pkg included the |
| 3429 |
|
corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which |
| 3430 |
|
only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment |
| 3431 |
|
code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding |
| 3432 |
|
includes; |
| 3433 |
|
- model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used. |
| 3434 |
|
- ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR |
| 3435 |
|
is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when |
| 3436 |
|
ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop. |
| 3437 |
|
- update option-file CPP_OPTIONS.h of all AD experiments: |
| 3438 |
|
* no longer include PACKAGES_CONFIG.h ; |
| 3439 |
|
* includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ; |
| 3440 |
|
* def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before |
| 3441 |
|
including ECCO_CPPOPTIONS.h). |
| 3442 |
|
o pkg/cost, pkg/ctrl, pkg/ecco option-file: |
| 3443 |
|
- clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into |
| 3444 |
|
separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h, |
| 3445 |
|
not necessary accurate). |
| 3446 |
|
- add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in |
| 3447 |
|
pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to |
| 3448 |
|
deliberately break compilation (a remainder that it needs to be customized) |
| 3449 |
|
- in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h |
| 3450 |
|
- rename COST_CPPOPTIONS.h to COST_OPTIONS.h |
| 3451 |
|
- rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h |
| 3452 |
|
o tools/genamke2: |
| 3453 |
|
- check for lapack. |
| 3454 |
|
o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies. |
| 3455 |
|
- pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions |
| 3456 |
|
jointly. The exclusive ifdefs were removed, to add costs terms (when defined) |
| 3457 |
|
from both packages. |
| 3458 |
|
- the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly. |
| 3459 |
|
- for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs. |
| 3460 |
|
- pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes |
| 3461 |
|
of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly. |
| 3462 |
|
o pkg/cost : add comments to explain special and/or untested setups. |
| 3463 |
|
o pkg/exf: |
| 3464 |
|
- use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h |
| 3465 |
|
(previously, ALLOW_AUTODIFF_TAMC was controling this switch). |
| 3466 |
|
o verification/*/code_ad: |
| 3467 |
|
mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file: |
| 3468 |
|
- reccord when this file is included (define ECCO_CPPOPTIONS_H) |
| 3469 |
|
- remove the most obvious obsolete features (e.g., #define ALLOW_COST not |
| 3470 |
|
allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h) |
| 3471 |
|
o pkg/seaice : |
| 3472 |
|
- added possibility to change ice strength/PRESS0 relationship to |
| 3473 |
|
HEFF, according to the following run time parameters |
| 3474 |
|
SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0) |
| 3475 |
|
SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0) |
| 3476 |
|
SEAICEpresH0 :: HEFF threshold for ice strength (m) |
| 3477 |
|
o pkg/ggl90 : |
| 3478 |
|
- added run time flag mxlSurfFlag to include the code that ensure |
| 3479 |
|
mixing between first and second level (previously included as a comment) |
| 3480 |
|
o verification/1D_ocean_ice_column/input_ad/data.autodiff : |
| 3481 |
|
- add test of newly added dumpAdByRec=T option where |
| 3482 |
|
we write all records to one file per variable. |
| 3483 |
|
o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h : |
| 3484 |
|
- switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES |
| 3485 |
|
to check that this code is ok with taf and compiles in adjoint. |
| 3486 |
|
o pkg/autodiff : |
| 3487 |
|
- added run time param dumpAdByRec : ad dump format switch. |
| 3488 |
|
If true then write all records to one file per variable. |
| 3489 |
|
Else write one file per record (remains the default). |
| 3490 |
|
- revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly. |
| 3491 |
|
o pkg/seaice: |
| 3492 |
|
- Added SEAICEuseTILT run time switch : if set to |
| 3493 |
|
false then omit the tilt term in seaice dynamics. |
| 3494 |
|
- Fix free drift calculation. |
| 3495 |
|
o pkg/shelfice: |
| 3496 |
|
When initializing SHELFICEDragQuadratic, set default to be |
| 3497 |
|
consistent with shiCdrag in case SHELFICEuseGammaFrict is used, |
| 3498 |
|
but retain option to set it independently |
| 3499 |
|
(inconsistenty spotted by Veronique Dansereau) |
| 3500 |
|
o eesupp/inc: |
| 3501 |
|
- in EEPARAMS.h, add real-type constant for some frequently used simple number |
| 3502 |
|
(0,1,2,1/2), with name explicitly referring to RS/RL type. |
| 3503 |
|
o model/src: |
| 3504 |
|
- move balancing of relaxation terms to new S/R balance_relax.F. |
| 3505 |
|
o pkg/autodiff: |
| 3506 |
|
re-write active I/O high-level (control) S/R: |
| 3507 |
|
- rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL |
| 3508 |
|
- add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R. |
| 3509 |
|
- use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and |
| 3510 |
|
MDS_READ/WRITE_FIELD); change loops to multi-threads. |
| 3511 |
|
- update and merge active_file_control_slice.flow into active_file_control.flow |
| 3512 |
|
- update the calls in lower level S/R (active_file.F, active_file_g.F and |
| 3513 |
|
active_file_ad.F) keeping the argument list and function unchanged. |
| 3514 |
|
- also update lower-level "_LOC" version (call same S/R with "useCurrentDir |
| 3515 |
|
=.TRUE.") and remove high-level (control) _loc version (not called anymore). |
| 3516 |
|
- new low-level active I/O routines, one for each type (RL/RS), for active var |
| 3517 |
|
of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr); |
| 3518 |
|
fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the |
| 3519 |
|
right type. |
| 3520 |
|
o autodiff and RS=real*4: |
| 3521 |
|
- call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf |
| 3522 |
|
ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ; |
| 3523 |
|
- change argument type of 3-D mask argument to _RS to match type in the call |
| 3524 |
|
(in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued. |
| 3525 |
|
o pkg/thsice: |
| 3526 |
|
- re-anable balanceEmPmR when useSEAICE=T with useThSIce=T. |
| 3527 |
|
- option to correct ocean fresh-water flux for imbalance of Atmos+Land |
| 3528 |
|
fresh-water flux: uniform correction or proportional to local precip. |
| 3529 |
|
o pkg/ctrl: |
| 3530 |
|
- new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D |
| 3531 |
|
- redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to |
| 3532 |
|
ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC |
| 3533 |
|
- verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL |
| 3534 |
|
|
| 3535 |
|
checkpoint63q (2012/07/30) |
| 3536 |
|
o pkg/autodiff: |
| 3537 |
|
note about monitor and snap-shot of ad-variables: |
| 3538 |
|
a) need to apply ADEXCH before monitor or output of ad-vars to include |
| 3539 |
|
overlap contributions (was done for adjDump but missing for monitor). |
| 3540 |
|
b) since ADEXCH implies adding overlap values to interior array, machine |
| 3541 |
|
truncation error is expected when adding an ADEXCH call in the middle of |
| 3542 |
|
the time-stepping (although mathematically identical). |
| 3543 |
|
modifs: |
| 3544 |
|
- fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars |
| 3545 |
|
declaration (adEddyPsiX,adEddyPsiY in adcommon.h). |
| 3546 |
|
- add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to |
| 3547 |
|
apply ADEXCH before monitor or snap-shot of ad-variables: |
| 3548 |
|
=0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy. |
| 3549 |
|
- implement new method (copy+adexch) for snap-shot and monitor of main model |
| 3550 |
|
ad-vars (initially not used by default -> output unchanged). |
| 3551 |
|
- change default (set to 2) to use new method and update few output_adm.txt |
| 3552 |
|
with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo |
| 3553 |
|
and both tutorial_tracer_adjsens tests). |
| 3554 |
|
- switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice) |
| 3555 |
|
and turn off momDissip_In_AB in the 2 other (needed for stable AB-3). |
| 3556 |
|
o pkg/ctrl: |
| 3557 |
|
enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of |
| 3558 |
|
generic control variables via |
| 3559 |
|
#define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL |
| 3560 |
|
Only required customization should be S/R ctrl_map_ini_genarr.F |
| 3561 |
|
(routine in repository contains example) |
| 3562 |
|
o pkg/exf: |
| 3563 |
|
- fix and refine checking of surface-relaxation setting when using EXF |
| 3564 |
|
o verification (adjoint exp): |
| 3565 |
|
- reduce length of simulation by half for experiment global_ocean.cs32x15 |
| 3566 |
|
(std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output. |
| 3567 |
|
o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag) |
| 3568 |
|
- replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers |
| 3569 |
|
of KE that can occur with aggressive optimization |
| 3570 |
|
+ put quadratic bottom drag calculation in separated loops (only done if |
| 3571 |
|
using bottomDragQuadratic) |
| 3572 |
|
o model/src: CG2D_NSA |
| 3573 |
|
- clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF |
| 3574 |
|
and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE. |
| 3575 |
|
- in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens), |
| 3576 |
|
change cg2d residual target to be expressed in Wunits (=> do not normalise |
| 3577 |
|
RHS ; this fix global_max Pb with TAF); update output. |
| 3578 |
|
o verification/tutorial_tracer_adjsens: |
| 3579 |
|
improve parameter consistency (and get rid of warnings): |
| 3580 |
|
- use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf); |
| 3581 |
|
- switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical) |
| 3582 |
|
- use staggerTimeStep (for stability) in som81; use default rotation period. |
| 3583 |
|
o pkg/exch2: |
| 3584 |
|
- with empty facet: fix compact-format (W2_mapIO=1) definition (was previously |
| 3585 |
|
reset to 0 = 1 long line in X) |
| 3586 |
|
o pkg/mdsio: |
| 3587 |
|
- fix reading of dimensions from meta file for large-size domain |
| 3588 |
|
o model/src: |
| 3589 |
|
- fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long); |
| 3590 |
|
- to refine CS-grid check, add logical flag "hasWetCSCorners": true if using |
| 3591 |
|
Cubed-Sphere Exch with CS-corners inside the domain; |
| 3592 |
|
make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate |
| 3593 |
|
globalArea and to set hasWetCSCorners. |
| 3594 |
|
- add warning if usingCurvilinearGrid and momAdvection in flux-form (missing |
| 3595 |
|
metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form. |
| 3596 |
|
- re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if |
| 3597 |
|
useCDscheme and useCubedSphereExchange). |
| 3598 |
|
o pkg/seaice/seaice_growth.F : |
| 3599 |
|
- compute the SEAICE_DISABLE_HEATCONSFIX term accordingly |
| 3600 |
|
for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0) |
| 3601 |
|
when the previous code was not correct. |
| 3602 |
|
- in all cases diagnoze the boundary condition mismatch to SIaaflux |
| 3603 |
|
- in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add |
| 3604 |
|
that term to QNET (essentially to set the melt/freeze water to 0degC). |
| 3605 |
|
when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed. |
| 3606 |
|
o verification/global_ocean.cs32x15/input.seaice : |
| 3607 |
|
- add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget. |
| 3608 |
|
- add diagnostics (commented out) for budget test using my matlab codes (gcmfaces). |
| 3609 |
|
- update results (output.seaice.txt) accordingly. |
| 3610 |
|
o verification/lab_sea/input/data.seaice : |
| 3611 |
|
- remove SEAICEheatConsFix, which is now be tested |
| 3612 |
|
in global_ocean.cs32x15. The presently coded fix |
| 3613 |
|
is only consistent with real fresh water + nlfs. |
| 3614 |
|
- update results (output.txt) accordingly. |
| 3615 |
|
o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd). |
| 3616 |
|
o AD_CONFIG.h file: |
| 3617 |
|
- in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h; |
| 3618 |
|
- remove #include "AD_CONFIG.h" from all included OPTIONS files and |
| 3619 |
|
add it explicitly in each fortran src file where it is needed. |
| 3620 |
|
motivation: header file AD_CONFIG.h is generated/modified after "make depend" |
| 3621 |
|
thus introducing potentially wrong dependency; therefore, better to include |
| 3622 |
|
it only where it's really needed, and after any other included OPTIONS file |
| 3623 |
|
(less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN |
| 3624 |
|
or ALLOW_TANGENTLINEAR_RUN). |
| 3625 |
|
|
| 3626 |
|
checkpoint63p (2012/07/06) |
| 3627 |
|
o pkg/autodiff: |
| 3628 |
|
- rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ; |
| 3629 |
|
- create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters |
| 3630 |
|
which are now read from new parameter file "data.autodiff" (inAdExact |
| 3631 |
|
previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg) |
| 3632 |
|
- add file "data.autodiff" in all verification/*/input_ad/ directories. |
| 3633 |
|
- add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward |
| 3634 |
|
mode (used in global_ocean.cs32x15.seaice_dynmix test exp.) |
| 3635 |
|
o verification/tutorial_tracer_adjsens/ |
| 3636 |
|
- add extra sub-verification which uses "SOM" advection scheme |
| 3637 |
|
(2nd Order-Moment Advection Scheme, Prather Limiter) with |
| 3638 |
|
#define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h |
| 3639 |
|
and in data: |
| 3640 |
|
multiDimAdvection=.TRUE., |
| 3641 |
|
tempAdvScheme=81, |
| 3642 |
|
saltAdvScheme=81, |
| 3643 |
|
o model/src: |
| 3644 |
|
- introduce ALLOW_BALANCE_RELAX which allow the removal |
| 3645 |
|
of the global mean of relaxation terms by setting |
| 3646 |
|
balanceThetaClimRelax and balanceSaltClimRelax |
| 3647 |
|
- disable balanceEmPmR and balanceQnet in the case when useSeaice. |
| 3648 |
|
This case is now treated appropriately in seaice_growth.F |
| 3649 |
|
o pkg/seaice: |
| 3650 |
|
- do balanceEmPmR and balanceQnet based on the net fluxes |
| 3651 |
|
(SItflux) that enter the ocean+ice system rather than QNET |
| 3652 |
|
and EMPMR. Works best in real fresh water. |
| 3653 |
|
- SIatmFW, SIatmQnet, and SItflux computations had to be moved |
| 3654 |
|
out of the diagnotics bloc, and stored in global arrays. |
| 3655 |
|
|
| 3656 |
|
checkpoint63o (2012/06/29) |
| 3657 |
|
o vertical mixing schemes: |
| 3658 |
|
- remove unused S/R CALC_BUOYANCY (left from branch-atmos merging) |
| 3659 |
|
- replace computation of density (in Function STATE1, opps_calc.F) by a call |
| 3660 |
|
to S/R FIND_RHO_SCALAR |
| 3661 |
|
- pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC |
| 3662 |
|
and use it for N^2 calculation in ggl90_calc.F (save 2 density computations); |
| 3663 |
|
affects output (vermix.ggl90) at truncation level. |
| 3664 |
|
o testreport: |
| 3665 |
|
- change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles |
| 3666 |
|
(nSx,nSy) for the number of threads (from eedata.mth) |
| 3667 |
|
o model/src: |
| 3668 |
|
- remove 2nd set of calls at the top of initialise_varia.F (Adjoint part) |
| 3669 |
|
related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary). |
| 3670 |
|
o verification/tutorial_tracer_adjsens/ |
| 3671 |
|
- compile with ALLOW_CG2D_NSA |
| 3672 |
|
- run with nonlinFreeSurf=3 |
| 3673 |
|
- update reference output_adm.txt |
| 3674 |
|
o tools/genmake2: |
| 3675 |
|
- add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ; |
| 3676 |
|
refine usePROFILES switching off (only when NetCDF is not available). |
| 3677 |
|
o verification (atmospheric set-up): |
| 3678 |
|
- change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration |
| 3679 |
|
o pkg/profiles : refine profiles and files handling. |
| 3680 |
|
o model/src and pkg/ecco : introduce run-time switch usePROFILES. |
| 3681 |
|
o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h : |
| 3682 |
|
- changes to use model/src/the_main_loop.F rather than the ecco version |
| 3683 |
|
in ecco type adjoint runs. |
| 3684 |
|
o model/src: |
| 3685 |
|
- move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID |
| 3686 |
|
- move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC |
| 3687 |
|
- update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL) |
| 3688 |
|
o model/src: |
| 3689 |
|
- fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before); |
| 3690 |
|
update output of test experiment bottom_ctrl_5x5. |
| 3691 |
|
o pkg/generic_advdiff: |
| 3692 |
|
- implement vertical bi-harmonic diffusion (for now, only for T & S and |
| 3693 |
|
only explicitly). |
| 3694 |
|
o verification/bottom_ctrl_5x5/ |
| 3695 |
|
update reference output (results changed quite some time ago, |
| 3696 |
|
not sure when; but new reference results look ok in terms of grdchk) |
| 3697 |
|
o verification/1D_ocean_ice_column/ |
| 3698 |
|
For verification purposes, the exact adjoint rather than an approx. |
| 3699 |
|
should be used (e.g., to comare against F.D. or TLM). |
| 3700 |
|
removed autodiff_inadmode*_ad.F routines in code_ad/ |
| 3701 |
|
Update results/ accordingly. |
| 3702 |
|
o pkg/cal: |
| 3703 |
|
- change cal_getdate.F so that output date is function of input time only |
| 3704 |
|
(less ambiguous, not mixed up with input iteration number). |
| 3705 |
|
- fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP). |
| 3706 |
|
o pkg/diagnostics: |
| 3707 |
|
- implement calendarDumps also for stats-diags |
| 3708 |
|
- implement calendarDumps also for snap-shot output (negative freq) |
| 3709 |
|
- for now, ignores calendarDumps if non-zero phase-lag. |
| 3710 |
|
|
| 3711 |
|
checkpoint63n (2012/06/04) |
| 3712 |
|
o model/src: |
| 3713 |
|
- recompute rSurfW & S to ensure consistent column thickness (needed for rStar) |
| 3714 |
|
between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice; |
| 3715 |
|
- use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more |
| 3716 |
|
similar to calc_r_star.F); update results of experiment internal_wave and |
| 3717 |
|
tutorial_global_oce_in_p (affected @ truncation level). |
| 3718 |
|
o pkg/shelfice: |
| 3719 |
|
- add parameterisation of advective-diffusive flux into the ice shelf |
| 3720 |
|
according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd |
| 3721 |
|
- simply eps3/3a computation |
| 3722 |
|
o eesupp: |
| 3723 |
|
- add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange |
| 3724 |
|
between tiles, just fill-in edges assuming locally periodic subdomain) and |
| 3725 |
|
add corresponding exchange subroutines (EXCH0); |
| 3726 |
|
- new CG-solver version (_EX0) for disconnected-tiles special case. |
| 3727 |
|
o model/src (CG-solvers): |
| 3728 |
|
- modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached |
| 3729 |
|
(similar final residual output and max-Iter number as with standard version); |
| 3730 |
|
- allows to store and use lowest-residual solution (standard & _SR versions); |
| 3731 |
|
- cleaning up (remove old, commented out code, LETS_MAKE_JAM ...). |
| 3732 |
|
- by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h) |
| 3733 |
|
o eesup/src: |
| 3734 |
|
- global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef |
| 3735 |
|
ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012) |
| 3736 |
|
o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn |
| 3737 |
|
|
| 3738 |
|
checkpoint63m (2012/04/27) |
| 3739 |
|
o pkg/shelfice: |
| 3740 |
|
- account for partical cells in surface level below ice-shelf for hydrostatic |
| 3741 |
|
pressure calculion (set uniformFreeSurfLev to F); update isomip experiments. |
| 3742 |
|
o ad test experiments: |
| 3743 |
|
- update and rename to "ad_optfile.local" local AD-optfile specific to a |
| 3744 |
|
particular adjoint verification experiment (in verification/*/code_ad/) |
| 3745 |
|
o pkg/seaice & pkg/exf: |
| 3746 |
|
- Part two of ECCO-CLIVAR code merges. |
| 3747 |
|
Completes merge of seaice area relax. code. |
| 3748 |
|
Requires unified CPP option EXF_ALLOW_SEAICE_RELAX |
| 3749 |
|
to be set in EXF_OPTIONS.h since this pkg controls its I/O |
| 3750 |
|
(and avoids second CPP option in SEAICE_OPTIONS.h) |
| 3751 |
|
- change default value of costIceStart & costIceEnd to a valid date. |
| 3752 |
|
- add snowPrecip to HSNOW in seaice_growth |
| 3753 |
|
o pkg/ptracers: |
| 3754 |
|
- move ptracers summary and setup check into separated S/R ; add a check for |
| 3755 |
|
valid PTRACERS_Iter0 value (error+stop or just warning). |
| 3756 |
|
o pkg/cal (+ pkg/ecco): |
| 3757 |
|
- avoid calling a S/R with 2 times the same arg (FWD: unless both are only used |
| 3758 |
|
as input; and for AD, unless both are not differentiable (e.g., k index)). |
| 3759 |
|
o model/src: |
| 3760 |
|
- define internal flag "uniformFreeSurfLev" (=T when free-surface level-index |
| 3761 |
|
is everywhere k=1) to speed-up some calculations (by pass kSurf reference); |
| 3762 |
|
temporary set to usingZCoords value (to be changed to F when using shelfice). |
| 3763 |
|
- hydrostatic pressure: implement partial cell near the surface also for |
| 3764 |
|
Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on |
| 3765 |
|
usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code). |
| 3766 |
|
o pkg/ctrl/ctrl_init.F: |
| 3767 |
|
- add a formal parameter to s/r ctrl_init_rec to print |
| 3768 |
|
xx_$(ctrl_valiable)_file for easier debugging |
| 3769 |
|
- move call of cal_* routines into the if-block where they are really |
| 3770 |
|
needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having |
| 3771 |
|
to specify a startdate |
| 3772 |
|
o pkg/seaice: |
| 3773 |
|
- update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and |
| 3774 |
|
global_ocean.cs32x15/code versions). |
| 3775 |
|
- turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for |
| 3776 |
|
verification experiment global_ocean.cs32x15.seaice and update results. |
| 3777 |
|
o pkg/exf: |
| 3778 |
|
- new S/R EXF_GETFIELD_START to return starting-time of a forcing field |
| 3779 |
|
(according to useExfYearlyFields). |
| 3780 |
|
o pkg/cal: |
| 3781 |
|
- move calendar setting & summary (previously in cal_readparams.F) into new |
| 3782 |
|
S/R CAL_INIT_FIXED to be called later in the initialisation process, once |
| 3783 |
|
length of the simulation is set (after SET_PARMS call); This is an attempt |
| 3784 |
|
to fix Pb when, e.g.: pkg/longstep, modifies the length of the run. |
| 3785 |
|
- For safety: keep a record of pkg/cal parameter settings status |
| 3786 |
|
to allow to STOP if one pkg/cal S/R is called too early. |
| 3787 |
|
- add a stop in all basic pkg/cal subroutines if called before setting is done. |
| 3788 |
|
- modify cal_getdate.F: stop when nothing was returned; |
| 3789 |
|
if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2); |
| 3790 |
|
this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F. |
| 3791 |
|
|
| 3792 |
|
checkpoint63l (2012/04/04) |
| 3793 |
|
o pkg/bbl: |
| 3794 |
|
- fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc); |
| 3795 |
|
update global_with_exf output.yearly.txt file. |
| 3796 |
|
o pkg/cal: |
| 3797 |
|
- start to clean-up cal_set.F ; fix for the case where baseTime is non-zero. |
| 3798 |
|
- remove 2 unsused and very short (1 line only) functions ; |
| 3799 |
|
- remove unsused subroutines from AD-Diff list. |
| 3800 |
|
o model/src: |
| 3801 |
|
- start to implement clean wait to stop in initialization S/R (config_check.F, |
| 3802 |
|
packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage) |
| 3803 |
|
o folowing PRINT_MESSAGE changes: |
| 3804 |
|
- remove reminder multiple print to the same file (STDOUT) when multi-threads. |
| 3805 |
|
o pkg/bbl: |
| 3806 |
|
- modification so it can work with z* |
| 3807 |
|
- replace deltaT with dTtracerLev(k) for asynchronous time stepping |
| 3808 |
|
- global_with_exf/input.yearly verification; changes output.yearly.txt |
| 3809 |
|
o eesupp/src: |
| 3810 |
|
- PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR); |
| 3811 |
|
writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1 |
| 3812 |
|
- CHECK_THREADS: specific code if using OpenMP threading: improve checking of |
| 3813 |
|
# of threads across processors (e.g., different env OMP_NUM_THREADS setting) |
| 3814 |
|
- improve special preliminary call to EESET_PARMS (if eedata is read 2 times). |
| 3815 |
|
- when using MPI, always set usingMPI=T ; set default accordingly and stop |
| 3816 |
|
if not consistent. |
| 3817 |
|
- ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread |
| 3818 |
|
argument is zero (in case called within single-thread section). |
| 3819 |
|
o pkg/fizhi: |
| 3820 |
|
clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored |
| 3821 |
|
in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO. |
| 3822 |
|
o pkg/exch2: |
| 3823 |
|
- add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to |
| 3824 |
|
activate EXCH_IGNORE_CORNERS in vector EXCH S/R). |
| 3825 |
|
- switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS) |
| 3826 |
|
but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data |
| 3827 |
|
with bad ones coming from a not-yet-updated halo. |
| 3828 |
|
This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx. |
| 3829 |
|
o pkg/frazil: |
| 3830 |
|
move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F |
| 3831 |
|
http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html |
| 3832 |
|
o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy |
| 3833 |
|
o verification/lab_sea |
| 3834 |
|
* #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING |
| 3835 |
|
* #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL |
| 3836 |
|
* nTimeSteps 3 -> 4 |
| 3837 |
|
* changed reference output accordingly |
| 3838 |
|
o pkg/ctrl: |
| 3839 |
|
* fix ctrl_get_gen for xx_sst, xx_sss |
| 3840 |
|
o pkg/fizhi: |
| 3841 |
|
- fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F |
| 3842 |
|
update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d) |
| 3843 |
|
- by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE); |
| 3844 |
|
fix few out-of-bounds indices in referencing vars (initialise igrd to 1); |
| 3845 |
|
clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array). |
| 3846 |
|
o pkg/gmredi: |
| 3847 |
|
- add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp |
| 3848 |
|
o pkg/fizhi: |
| 3849 |
|
- fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the |
| 3850 |
|
(old)aces open64 tuv test. |
| 3851 |
|
o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F |
| 3852 |
|
o pkg/mom_vecinv: |
| 3853 |
|
- fix 1 loop range in mom_vecinv.F to be like all the other loops which |
| 3854 |
|
set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv |
| 3855 |
|
with non-lin free-surf). |
| 3856 |
|
o model/src: move k-loop outside of i/j-loops when (re-)computing R_low |
| 3857 |
|
in ini/update_masks_etc.F in order to avoid -O3 optimization problems with |
| 3858 |
|
some compilers (gfortran 4.6.0 on MacOS) |
| 3859 |
|
o momentum: |
| 3860 |
|
- separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM |
| 3861 |
|
& MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised |
| 3862 |
|
fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control. |
| 3863 |
|
|
| 3864 |
|
checkpoint63k (2012/03/17) |
| 3865 |
|
o model/src: |
| 3866 |
|
- selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum |
| 3867 |
|
flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations. |
| 3868 |
|
- SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version |
| 3869 |
|
(#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp. |
| 3870 |
|
o model/src: solve_*diagonal.F |
| 3871 |
|
- replace division with multiplication by inverse (similar to original version) |
| 3872 |
|
update output of AD exp. global_ocean.90x40x15. |
| 3873 |
|
- fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F |
| 3874 |
|
to enable the use of the vectorized & differentiable solve_tridiagonal.F |
| 3875 |
|
- test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for |
| 3876 |
|
vertical advection (to get solve_tridiagonal tested in AD mode). |
| 3877 |
|
o pkg/seaice: ECCO-CLIVAR merge: |
| 3878 |
|
1. seaice AREA relaxation |
| 3879 |
|
* CPP option: SEAICE_ALLOW_AREA_RELAXATION |
| 3880 |
|
* runtime flag: SEAICE_tauAreaObsRelax |
| 3881 |
|
2. modified global mean cost imbalance code: CPP option |
| 3882 |
|
ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION |
| 3883 |
|
o another iteration on solve_*diagonal.F |
| 3884 |
|
Make choices independent of AUTODIFF |
| 3885 |
|
Default will be the adjoinable vectorized version. |
| 3886 |
|
Alternative choices are: |
| 3887 |
|
* non-adjoinable original version with low memory footprint: |
| 3888 |
|
#define SOLVE_DIAGONAL_LOWMEMORY |
| 3889 |
|
* still adjoinable but does not vectorize (k as inner-most loop): |
| 3890 |
|
#define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef) |
| 3891 |
|
o testreport |
| 3892 |
|
- add option to use a home made wrapper around "make" |
| 3893 |
|
- remove MITGCM_IEEE env. variable (no longer active) |
| 3894 |
|
o pkg/shelfice |
| 3895 |
|
- improve computation of friction velocity for velocity dependent |
| 3896 |
|
exchange coefficients: include velocities into SHELFICEBoundaryLayer |
| 3897 |
|
block to average velocities vertically |
| 3898 |
|
- add TAF store directives for SHI_ALLOW_GAMMAFRICT |
| 3899 |
|
o Modify diagonal solvers, now three versions (upon request): |
| 3900 |
|
#ifndef SOLVE_DIAGONAL_AUTODIFF |
| 3901 |
|
1. default version (dating back a while ago) |
| 3902 |
|
#else /* def SOLVE_DIAGONAL_AUTODIFF */ |
| 3903 |
|
# ifdef SOLVE_DIAGONAL_KINNER |
| 3904 |
|
2. adjoinable version with k-innermost loop (G. Forget) |
| 3905 |
|
# else |
| 3906 |
|
3. adjoinable vectorized version of 2. |
| 3907 |
|
# endif |
| 3908 |
|
#endif /* SOLVE_DIAGONAL_AUTODIFF */ |
| 3909 |
|
All flags are currently set within routines, but could/should be moved to CPP-options. |
| 3910 |
|
Array bounds for 1. are as before, for 2.,3. cover the entire domain |
| 3911 |
|
(could be changed for 1. too). |
| 3912 |
|
o verification/lab_sea (fwd): |
| 3913 |
|
- update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY, |
| 3914 |
|
use 7 categories (except hb87), new solve4temp params (except salt_plume), |
| 3915 |
|
constant salinity (=4) or variable salinity (salt_plume) done through |
| 3916 |
|
SItracer. |
| 3917 |
|
o pkg/seaice: |
| 3918 |
|
- rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0; |
| 3919 |
|
- remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t, |
| 3920 |
|
SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz) |
| 3921 |
|
from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when |
| 3922 |
|
SEAICE_freeze got retired) but already better than previously with |
| 3923 |
|
SEAICE_freeze=123456.7 deg.C; |
| 3924 |
|
- move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS |
| 3925 |
|
(safer multi-threaded setting); always set SEAICEuseEVP; |
| 3926 |
|
- setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to |
| 3927 |
|
SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report); |
| 3928 |
|
stop if multiple specifications for the same coeff; make sure default |
| 3929 |
|
SEAICE_mcPheePiston is compatible with drF(1) & deltaT. |
| 3930 |
|
o pkg/obcs: |
| 3931 |
|
- allow to switch to upwind 1rst order advection scheme for the advective |
| 3932 |
|
flux computation at the open-boundary; disabled for adjoint built. |
| 3933 |
|
o pkg/ptracers: |
| 3934 |
|
- rename PTRACERS_RESTART.h -> PTRACERS_START.h |
| 3935 |
|
- rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F |
| 3936 |
|
- add parameter to decide when to start a tracer; use internal flag to |
| 3937 |
|
know which tracer to step-forward; switch this internal flag at the top |
| 3938 |
|
of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled |
| 3939 |
|
for adjoint built. |
| 3940 |
|
o pkg/seaice: |
| 3941 |
|
- add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ; |
| 3942 |
|
- move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ; |
| 3943 |
|
- keep experiment offline_exf_seaice truly single category (set MULTDIM=1). |
| 3944 |
|
o pkg/ecco: |
| 3945 |
|
- fix writing of output file DiagnosCost_ClimSalt/Theta |
| 3946 |
|
and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc). |
| 3947 |
|
o pkg/seaice: |
| 3948 |
|
- add missing initialisation of COR_ICE array in dynsolver.F |
| 3949 |
|
- merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is |
| 3950 |
|
compiled either way, and is tested in all exps (multidim was only tested |
| 3951 |
|
in lab_sea ad before). |
| 3952 |
|
- cosmetic change to prepare for future addition of ITD. no change to results. |
| 3953 |
|
no defaults change. |
| 3954 |
|
- added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise). |
| 3955 |
|
- by lack of adequate verification experiments, I further used custom versions |
| 3956 |
|
of global_ocean.cs32x15 to test multicat or not, with pickup or not. All |
| 3957 |
|
should be correct. |
| 3958 |
|
- avoid recomputations in ad. |
| 3959 |
|
o array initialisation in adjoint mode: |
| 3960 |
|
1) pkg/mom_common/mom_calc_ke.F: |
| 3961 |
|
add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC): |
| 3962 |
|
The S/R which calls MOM_CALC_KE initialises KE but in some recomputation |
| 3963 |
|
part this initialisation is gone, resulting in Floating Point Exception |
| 3964 |
|
(caught by open64 compiler with debug option). |
| 3965 |
|
2) model/src/convective_weights.F |
| 3966 |
|
set output convectCount over the full array range (instead of doing |
| 3967 |
|
an update): this fix a similar issue when called within recomputation (adjoint) |
| 3968 |
|
which could by-pass the initialisation (normally done in the caller S/R). |
| 3969 |
|
o pkg/seaice: |
| 3970 |
|
- final version of turbulent flux params, as agreed at MIT ice meet: |
| 3971 |
|
SEAICE_mcPheePiston (default is ~ 0.000875) |
| 3972 |
|
SEAICE_mcPheeTaper (default is 0.) |
| 3973 |
|
SEAICE_frazilFrac (defualt is 1.) |
| 3974 |
|
SEAICE_mcPheeStepFunc (default is false) |
| 3975 |
|
- changes results at trunction error level |
| 3976 |
|
- ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo |
| 3977 |
|
o added pkg/frazil: |
| 3978 |
|
- see frazil_description.tex for details |
| 3979 |
|
- verification experiment is global_with_exf/input.yearly; changes output.yearly.txt |
| 3980 |
|
o pkg/shelfice/shelfice_thermodynamics.F |
| 3981 |
|
- fix exponents for velocity dependent exchange coefficients: change |
| 3982 |
|
from 2/3(=0) to 0.66666666666666667 |
| 3983 |
|
- move computation of velocity dependent exchange coefficients into |
| 3984 |
|
separate loop, so that it applies to both thermodynamics |
| 3985 |
|
- move some divisions by constants out of loops |
| 3986 |
|
|
| 3987 |
|
checkpoint63j (2012/02/16) |
| 3988 |
|
o pkg/seaice: |
| 3989 |
|
- overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc. |
| 3990 |
|
- SItracer: added run time params, and allow coupling to ocn salinity. |
| 3991 |
|
o pkg/seaice: remove (almost) all divisions by constants within loops |
| 3992 |
|
in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d |
| 3993 |
|
results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only |
| 3994 |
|
those, caused by 1/QI -> recip_QI) -> update output.seaice.txt, |
| 3995 |
|
output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt |
| 3996 |
|
o pkg/seaice : |
| 3997 |
|
- simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula |
| 3998 |
|
= 1 or 2, using newly added run time parameter SEAICE_availHeatTaper. |
| 3999 |
|
- fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148. |
| 4000 |
|
- add permanent SItflux diag that corresponds to TFLUX but includes |
| 4001 |
|
ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget. |
| 4002 |
|
- allow activation/testing of a fix for suspected missing term in |
| 4003 |
|
ocn-ice heat budget (to be confirmed). To test this, you want to |
| 4004 |
|
undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param |
| 4005 |
|
SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic. |
| 4006 |
|
- no change in results, fwd or ad. |
| 4007 |
|
o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below: |
| 4008 |
|
- switch to variable freezing point. |
| 4009 |
|
Results change : cg2d -> 1 digits; ad -> 3-6-6 digits. |
| 4010 |
|
- bug fix : the sublimation term that was missing is now activated. |
| 4011 |
|
Results change : cg2d -> 2 digits; ad -> 8-6-6 digits. |
| 4012 |
|
- bug fix : flooding sign term for SIsal0.NE.0. |
| 4013 |
|
Result change : cg2d -> 8 digits; ad -> 11-12-9 digits. |
| 4014 |
|
o pkg/seaice: |
| 4015 |
|
- unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT |
| 4016 |
|
is now the default, and the old default constant freezing point is recovered |
| 4017 |
|
with SEAICE_tempFrz0 = -1.96, |
| 4018 |
|
SEAICE_dTempFrz_dS = 0., |
| 4019 |
|
- retire SEAICE_freeze (= the old way of specifycing the constant freezing point) |
| 4020 |
|
- remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there. |
| 4021 |
|
- bug fix (thanks to M. Losch) : the sublimation term that was missing is now |
| 4022 |
|
activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM. |
| 4023 |
|
- bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211) |
| 4024 |
|
was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail). |
| 4025 |
|
- bug fix (thanks to O. Jahn) : area loss for melting got messed up in |
| 4026 |
|
seaice_growth r149 for legacy branch (no results change). |
| 4027 |
|
- introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code |
| 4028 |
|
from I. Fenty). |
| 4029 |
|
- results did not change except for global_ocean.cs32x15, mostly due to the |
| 4030 |
|
switch to variable freezing point (see above item for detail). |
| 4031 |
|
o pkg/thsice: |
| 4032 |
|
- fix and simplify interface to salt_plume pkg ; diagnose directly amount of |
| 4033 |
|
seawater freezing in thsice_calc_thickn (not used). |
| 4034 |
|
o pkg/seaice: turbulent flux term specification via run time params. |
| 4035 |
|
- replace CPP switches with run time switches to facilitate testing |
| 4036 |
|
- retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, |
| 4037 |
|
GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR |
| 4038 |
|
- added runtime parameter : SEAICEturbFluxFormula |
| 4039 |
|
- move Mcphee constants to SEAICE_PARAMS.h |
| 4040 |
|
- seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula; |
| 4041 |
|
SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); |
| 4042 |
|
remove seaice_summary call (moved to seaice_init_fixed) |
| 4043 |
|
- seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on |
| 4044 |
|
SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms) |
| 4045 |
|
- seaice_summary.F : add missing report of read turbulent flux term set up |
| 4046 |
|
and SITRACER. |
| 4047 |
|
- seaice_check.F : check range; inform and stop if retired CPPs are used |
| 4048 |
|
(incl. SEAICE_AGE). |
| 4049 |
|
- seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without |
| 4050 |
|
CPP switch, same computation as before for the different options. |
| 4051 |
|
- change results at the truncation level. |
| 4052 |
|
o pkg/seaice: |
| 4053 |
|
- remove un-used parameters LAD & MAX_TICE ; add new run-time parameters: |
| 4054 |
|
useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and |
| 4055 |
|
SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY. |
| 4056 |
|
- update verification/*/input*/data.seaice: |
| 4057 |
|
to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY |
| 4058 |
|
code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ; |
| 4059 |
|
and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code, |
| 4060 |
|
set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0. |
| 4061 |
|
o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY): |
| 4062 |
|
- remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same |
| 4063 |
|
algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0); |
| 4064 |
|
difference in results only due to machine truncation. |
| 4065 |
|
- remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using |
| 4066 |
|
MaykutPolySatVap; keep MIN_LWDOWN. |
| 4067 |
|
- adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation. |
| 4068 |
|
- update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87, |
| 4069 |
|
+ 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits). |
| 4070 |
|
o pkg/salt_plume: |
| 4071 |
|
- isolate saltPlumeFlux array exch into a specific S/R called from |
| 4072 |
|
do_oceanic_phys.F |
| 4073 |
|
- add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice. |
| 4074 |
|
o verification: |
| 4075 |
|
- move untested set-up to MITgcm_contrib/verification_other. |
| 4076 |
|
o pkg/seaice: |
| 4077 |
|
- retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER. |
| 4078 |
|
o pkg/seaice: |
| 4079 |
|
- seaice_solve4temp.F (keeping results unchanged): |
| 4080 |
|
* add 2 future run-time params to select which saturation vapor pressure |
| 4081 |
|
formula is used and how post-iteration fluxes are set. |
| 4082 |
|
Temporary set these 2 params according to option SOLVE4TEMP_LEGACY; |
| 4083 |
|
* New piece of code (not used) to update surf. atmos. heat flux F_ia using |
| 4084 |
|
the linearized expression to stay consistent with tsurf finding. |
| 4085 |
|
- seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x |
| 4086 |
|
can be < 0. |
| 4087 |
|
o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef): |
| 4088 |
|
- remove from F_ia (and from it's derivative dFiDTs1) the contribution of |
| 4089 |
|
conductive heat flux F_c , and add it explicitly when updating tsurf as |
| 4090 |
|
solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf |
| 4091 |
|
so that now F_ia has a consistent meaning through the entire routine. |
| 4092 |
|
This causes differences at truncation level: update output of fwd exp. |
| 4093 |
|
global_ocean.cs32x15.seaice. |
| 4094 |
|
o pkg/seaice: |
| 4095 |
|
- lots of editing/cleaning in seaice_solve4temp.F + better documentation |
| 4096 |
|
of arrays, sign/direction of fluxes; no effect on results. |
| 4097 |
|
- replace hard coded 273.16 (=previous value of celsius2K) by celsius2K |
| 4098 |
|
in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part); |
| 4099 |
|
note: this should have been done before changing celsius2K default. |
| 4100 |
|
- to keep results unchanged, add back old value of celsius2K in verification |
| 4101 |
|
exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs |
| 4102 |
|
- replace hard coded seawater freezing temp in seaice_solve4temp.F (part |
| 4103 |
|
SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default |
| 4104 |
|
value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater |
| 4105 |
|
freezing temp is consistent with value in seaice_growth.F ; this causes |
| 4106 |
|
differences at machine truncation level: update lab_sea AD output (3/4). |
| 4107 |
|
o pkg/seaice: |
| 4108 |
|
- mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask |
| 4109 |
|
and climsst/sss even when using seaice (to prevent calculation that might |
| 4110 |
|
use SST on land); does not affect any verification exp. |
| 4111 |
|
- apply mask to taux,tauy (in seaice_get_dynforcing.F); update output |
| 4112 |
|
of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix. |
| 4113 |
|
o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness |
| 4114 |
|
over land (non-legacy code) |
| 4115 |
|
o vectorize salt_plume package: |
| 4116 |
|
- add extra code to salt_plume_frac and salt_plume_tendency_apply_s |
| 4117 |
|
- this code computes plumebk everywhere (also over land), thus requires |
| 4118 |
|
code to avoid divisions by zero and catch the case of kLev=Nr. |
| 4119 |
|
- efficiency of salt_plume_frac is still sub-optimal |
| 4120 |
|
o tools (genmake2): |
| 4121 |
|
- fix makefile NAME specification (option: -makefile NAME) by adding |
| 4122 |
|
"-f $MAKEFILE" in few places where it was missing including makedepend |
| 4123 |
|
command (contribution from Paul). |
| 4124 |
|
|
| 4125 |
|
checkpoint63i (2012/01/24) |
| 4126 |
|
o model/src: |
| 4127 |
|
- add factorized versions of some EOS code to find_rho.F, |
| 4128 |
|
define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX) |
| 4129 |
|
o model/src: |
| 4130 |
|
- add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h; |
| 4131 |
|
- change default celsius2K from 273.16 to 273.15 |
| 4132 |
|
- to keep results unchanged, add back old value of celsius2K in verification |
| 4133 |
|
exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd), |
| 4134 |
|
global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm). |
| 4135 |
|
o model/src: add a little initialisation trick to find_rho.F and find_alpha.F |
| 4136 |
|
to make TAF generate vectorizable code |
| 4137 |
|
o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows. |
| 4138 |
|
Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers |
| 4139 |
|
have flags that do this more efficiently. |
| 4140 |
|
o pkg/diagnostics/diagstats_calc.F |
| 4141 |
|
- for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact |
| 4142 |
|
o pkg/obcs (with exch2): |
| 4143 |
|
- derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F) |
| 4144 |
|
and remove code (in obcs_readparms.F) which was based on EXCH of indices |
| 4145 |
|
(through buffer) and did not account for exch2 (e.g., CS-grid) topology. |
| 4146 |
|
o pkg/exf and seaice exp: |
| 4147 |
|
- change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0) |
| 4148 |
|
so that switching off area & heff advection flags does not affect results. |
| 4149 |
|
- change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h |
| 4150 |
|
- keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef |
| 4151 |
|
EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update |
| 4152 |
|
results of verification experiments: 1D_ocean_ice_column(fwd), |
| 4153 |
|
global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8) |
| 4154 |
|
and offline_exf_seaice (all 4). |
| 4155 |
|
o pkg/seaice: |
| 4156 |
|
- remove array YNEG, RIVER, TMIX (replaced by local var) from common block; |
| 4157 |
|
remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef. |
| 4158 |
|
- fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY) |
| 4159 |
|
but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and |
| 4160 |
|
not multi-dim advection; |
| 4161 |
|
- fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and |
| 4162 |
|
SHORTWAVE_HEATING #undef. |
| 4163 |
|
o optim: make Makefile more robust (?) |
| 4164 |
|
o pkg/obcs: |
| 4165 |
|
* fix treatment of obcs_read_pickup for TAF |
| 4166 |
|
o pkg/shelfice: |
| 4167 |
|
* add missing initialisation of num_shifwflx |
| 4168 |
|
* new adjoint verification exp. for isomip |
| 4169 |
|
* change Prandtl and Schmidt numbers from generic formulations |
| 4170 |
|
(in terms of model diffus. and visc.) to separate runtime |
| 4171 |
|
parameters, with Holland and Jenkins (1999) default values. |
| 4172 |
|
o pkg/exf (interpolation): |
| 4173 |
|
- extended input field (2 rows) near the N & S poles: |
| 4174 |
|
* fill in with the symetric value (when even Nb of data in longitude) |
| 4175 |
|
* add average value at the poles only for scalar quantities ; for vector |
| 4176 |
|
component interpolation, skip the averaging and keep duplicated values, |
| 4177 |
|
unless the 2 components have same location (uvInterp=T) in which case |
| 4178 |
|
interpolate the 2 components together using S/R EXF_INTERP_UV. |
| 4179 |
|
- new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field |
| 4180 |
|
together: this allows to account properly for local orientation when |
| 4181 |
|
averaging at N & S pole. |
| 4182 |
|
- add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding |
| 4183 |
|
exf-interpolation near N & S poles. Undef by default. |
| 4184 |
|
- add debug check/print on 1rst iter if debugLevel >=2. |
| 4185 |
|
o pkg/exf: |
| 4186 |
|
- change masking flags definition (no longer "parameter"), put them in |
| 4187 |
|
common block and set them in S/R EXF_INIT_FIXED. |
| 4188 |
|
- change recognized masking flag from s,u,v to c,w,s since the mask |
| 4189 |
|
to use (maskC,W,S) depends on position on model grid and has little to |
| 4190 |
|
do with scalar/vector difference; fix masking if using P-coordinates. |
| 4191 |
|
- fix masking of wind-stress (was wrong if interpolated or read on A-grid) |
| 4192 |
|
and update results of exp. global_with_exf (x2). |
| 4193 |
|
- fix setting of zenith-angle table when SHORTWAVE_HEATING is undef. |
| 4194 |
|
o pkg/obcs |
| 4195 |
|
- S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate) |
| 4196 |
|
o pkg/exf (interpolation): |
| 4197 |
|
- assume periodicity in X only if input field cover full longitude range. |
| 4198 |
|
- improve search for lat. index (supposed to be faster, in ~log2(ny) steps, |
| 4199 |
|
and should vectorise). |
| 4200 |
|
- fix input lat of the 2 added row (in case we provide N.pole data). |
| 4201 |
|
|
| 4202 |
|
checkpoint63h (2011/12/30) |
| 4203 |
|
o pkg/seaice: |
| 4204 |
|
- change declaration of UVM from _RL to _RS in order to get B-grid |
| 4205 |
|
uIce,vIce monitor when _RS = real*4 |
| 4206 |
|
o pkg/offline: |
| 4207 |
|
- new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags); |
| 4208 |
|
- compute vertical velocity if not read from file (switch on exactConserv |
| 4209 |
|
& staggerTimeStep); |
| 4210 |
|
- fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq. |
| 4211 |
|
o verification: |
| 4212 |
|
- update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input) |
| 4213 |
|
with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m": |
| 4214 |
|
fix Pb in yG definition @ 2 missing corners (previously yG was averaged); |
| 4215 |
|
- update output of exp. global_ocean.cs32x15.viscA4 after changing |
| 4216 |
|
grid-file angles (used here for coriolis-3d); |
| 4217 |
|
- remove (or gzip) few files not needed to run fizhi-cs experiments. |
| 4218 |
|
o pkg/exf (vector interpolation): |
| 4219 |
|
- rotate vector component toward local grid-axis orientation using grid-angles |
| 4220 |
|
(stored in GRID.h) instead of locally computed rotation angle; keep old code |
| 4221 |
|
available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default). |
| 4222 |
|
o pkg/seaice: |
| 4223 |
|
- allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION |
| 4224 |
|
undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined. |
| 4225 |
|
o pkg/PKG_OPTIONS.h files: |
| 4226 |
|
- move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h", |
| 4227 |
|
outside of the #ifdef ALLOW_THISPKG / #endif block. |
| 4228 |
|
- update verification/*/code/PKG_OPTIONS.h files. |
| 4229 |
|
o add a verification experiment (offline_exf_seaice/input.seaice) that test |
| 4230 |
|
the B-grid LSOR solver |
| 4231 |
|
o pkg/seaice: sort out emissivity and long wave radiation step 2: |
| 4232 |
|
- add emissivity for snow and ice as new run-time parameters |
| 4233 |
|
(unfortunately) that default to the corresponding exf values; this |
| 4234 |
|
changes results in most verification experiments so that for backward |
| 4235 |
|
compatibility these parameter have to be set explicitly to inconsistent |
| 4236 |
|
values (ugly); |
| 4237 |
|
- the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired |
| 4238 |
|
emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp |
| 4239 |
|
until we agree how to handle this bug properly |
| 4240 |
|
o pkg/exf (interpolation): |
| 4241 |
|
- add a set of run-time param ({inputfield}_interpMethod), one for |
| 4242 |
|
each interpolated input field, to select the interpolation method |
| 4243 |
|
with a value of zero switching off the interpolation; |
| 4244 |
|
- print interpolation parameters to standard output; |
| 4245 |
|
- refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined |
| 4246 |
|
(to use instead runoff_interpMethod=0 in data.exf). |
| 4247 |
|
- simplify default setting of interpolation parameters (for all fields, |
| 4248 |
|
set position to match model grid cell-center position, leading to trivial |
| 4249 |
|
interpolation in case of regular Lat-Lon grid) and fix for the case of |
| 4250 |
|
non-uniform delY. |
| 4251 |
|
o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for |
| 4252 |
|
within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1. |
| 4253 |
|
this factor is absolutely required, because the lw exitance (= out-going |
| 4254 |
|
long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown, |
| 4255 |
|
where the reflectivity rho = 1-emissivity for conservation reasons. Once |
| 4256 |
|
this is established, we can remove the CPP-Flag (if we want to). |
| 4257 |
|
o pkg/seaice: |
| 4258 |
|
- qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and |
| 4259 |
|
ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined |
| 4260 |
|
- sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity |
| 4261 |
|
what the name implies (and not emissivity*BoltzmannConstant), this means |
| 4262 |
|
the old default value of 5.5e-8 now means |
| 4263 |
|
5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in |
| 4264 |
|
S/R exf_readparms |
| 4265 |
|
- FV-discretization of the B-grid LSOR solver, turn on with |
| 4266 |
|
SEAICE_LSRBNEW. This new solver also involves a slight re-organization |
| 4267 |
|
of the calling routine dynsolver, so that B and C-grid code look a |
| 4268 |
|
little more alike. |
| 4269 |
|
- fix index bugs in ostres.F (B-grid code) |
| 4270 |
|
o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better |
| 4271 |
|
o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the |
| 4272 |
|
default for SEAICE_emissivity, if useEXF; requires setting a wrong |
| 4273 |
|
parameter value in global_ocean.cs32x15/input.seaice/data.seaice for |
| 4274 |
|
backward compatiblity |
| 4275 |
|
o model/src: use sigmaR in calc_ivdc |
| 4276 |
|
|
| 4277 |
|
checkpoint63g (2011/12/16) |
| 4278 |
|
o pkg/seaice/seaice_growth.F: |
| 4279 |
|
fix heat conservation of the coupled ocean-seaice system. |
| 4280 |
|
when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of |
| 4281 |
|
solid vs liquid water treatment is resolved via QNET. |
| 4282 |
|
o pkg/seaice/seaice_growth.F: |
| 4283 |
|
add missing term for sublimation in saltFlux, which was breaking conservation. |
| 4284 |
|
o pkg/seaice/seaice_model.F: |
| 4285 |
|
Remove this patholigical case treatment in evolution branch, |
| 4286 |
|
where it is un-necessary and breaks conservation. |
| 4287 |
|
Update global_ocean.cs32x15/results accordingly for |
| 4288 |
|
output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt |
| 4289 |
|
o model/src: |
| 4290 |
|
useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in |
| 4291 |
|
external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE. |
| 4292 |
|
o pkg/obcs: |
| 4293 |
|
modify Stevens boundary conditions so that S/R obcs_calc_stevens computes |
| 4294 |
|
tendency for temperature and salinity that is then applied to update |
| 4295 |
|
theta and salt in S/R obcs_apply_ts; this requires proper masking of all |
| 4296 |
|
horizontal advection and diffusion contributions on the boundary (in |
| 4297 |
|
S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and |
| 4298 |
|
removing the mask in S/R timestep_tracer. The advantage of this approach is |
| 4299 |
|
that the updated tracer values include contributions from the surface |
| 4300 |
|
forcing and vertical diffusion. |
| 4301 |
|
This modification changes exp4.stevens because of vertical diffusion. |
| 4302 |
|
o model/src: |
| 4303 |
|
change non-curvilinear grid setting to also work with exch2 + blank tiles: |
| 4304 |
|
- move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst |
| 4305 |
|
face dimensions. |
| 4306 |
|
- new S/R INI_LOCAL_GRID to define model tile-local grid (using same units |
| 4307 |
|
as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID |
| 4308 |
|
and INI_SPHERICAL_POLAR_GRID. |
| 4309 |
|
change test-experiment global_ocean.90x40x15: |
| 4310 |
|
- split the domain in many more tiles (9x4 tiles of 10x10 each); |
| 4311 |
|
- switch to exch2 and remove 1 blank-tile (but only for MPI test). |
| 4312 |
|
- update results of both test (std & dwnslp). |
| 4313 |
|
o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in |
| 4314 |
|
tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation |
| 4315 |
|
o model/src: |
| 4316 |
|
- take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS |
| 4317 |
|
and fix initialisation when using sigma-coords. |
| 4318 |
|
o model/src: |
| 4319 |
|
- improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc. |
| 4320 |
|
to their current value at the beginning of forward_step.F": add a new run-time |
| 4321 |
|
switch "doResetHFactors" (default=false) and use it to do (or not) the resetting. |
| 4322 |
|
- set doResetHFactors=T in the following test exp: |
| 4323 |
|
global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS), |
| 4324 |
|
global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS) |
| 4325 |
|
and tutorial_global_oce_in_p (nonLinFS in p) |
| 4326 |
|
o pkg/ecco |
| 4327 |
|
- added IES cost term |
| 4328 |
|
o verification/advect_xz |
| 4329 |
|
- scale down the depth by 1/100 (from 200 km to just 2.km) |
| 4330 |
|
- add secondary test using divergent flow, r-star and implicit vertical advection. |
| 4331 |
|
- add note (check_conserve_TS.txt) and matlab script to check global |
| 4332 |
|
conservation of T & S with NonLin-FreeSurf and Adams-Bashforth. |
| 4333 |
|
o pkg/rbcs: |
| 4334 |
|
- add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F). |
| 4335 |
|
o pkg/obcs (Stevens BCs): |
| 4336 |
|
- fix various problems in the phase speed computations of the Stevens |
| 4337 |
|
boundary conditions: |
| 4338 |
|
- sign error for western and southern boundaries, |
| 4339 |
|
- time tendencies were underestimated by factor of dTracerLev and some just |
| 4340 |
|
zero (for multidim advection schemes) -> now estimate time tendencies |
| 4341 |
|
from difference between previous (n) time level and the one before (n-1); |
| 4342 |
|
this requires storing a field per tracer per boundary, also in the pickup |
| 4343 |
|
files. |
| 4344 |
|
- replace deltaTmom in cflMer/Zon computation with dTracerLev |
| 4345 |
|
- set default phase velocity to cflMer/Zon |
| 4346 |
|
- update verification experiment exp4.stevens |
| 4347 |
|
o pkg/generic_advdiff (implicit_r): |
| 4348 |
|
- fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf |
| 4349 |
|
(remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F); |
| 4350 |
|
- fix implicit vertical diffusion or advection with NonLin FreeSurf |
| 4351 |
|
(was using current recip_hFacC instead of future recip_hFacC): set future |
| 4352 |
|
recip_hFac in thermodynamics.F and pass & use it in all vertical implicit |
| 4353 |
|
solver S/R ; |
| 4354 |
|
- fill diagnostics of vertical advective fluxes (computed from tendency) |
| 4355 |
|
when using implicit vert. advection; |
| 4356 |
|
- update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion: |
| 4357 |
|
global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD), |
| 4358 |
|
tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD) |
| 4359 |
|
and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5. |
| 4360 |
|
o pkg/diagnostics: |
| 4361 |
|
- add diags for T & S tendency which goes through Adams-Bashforth. |
| 4362 |
|
|
| 4363 |
|
checkpoint63f (2011/11/30) |
| 4364 |
|
o pkg/obcs/obcs_calc_stevens.F: |
| 4365 |
|
- join some loops to reduce number of if-statements |
| 4366 |
|
- fix a bug in code for northern and southern boundaries. |
| 4367 |
|
o pkg/seaice/seaice_init_varia.F |
| 4368 |
|
- undo resetting UVM=0 that has slipped in unnoticed in r1.49 and |
| 4369 |
|
caused zero ice-velocities for the B-grid code |
| 4370 |
|
o pkg/seaice/seaice_init_fixed.F |
| 4371 |
|
- fix a bug in the initialisation of the second metric terms |
| 4372 |
|
k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0. |
| 4373 |
|
- this affects all seaice configurations with useCurviLinearGrid = .true. |
| 4374 |
|
and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms |
| 4375 |
|
= .true. (default) |
| 4376 |
|
- the only verification experiment affected is global_ocean.cs32x15: |
| 4377 |
|
icedyn, seaice, and seaice_dynmix (AD) |
| 4378 |
|
o pkg/thsice/thsice_diagnostics_state.F |
| 4379 |
|
- only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does |
| 4380 |
|
not contain garbage that can lead to surprises in diagstats_calc.F |
| 4381 |
|
o model/src: |
| 4382 |
|
- move bi,bj loops inside INTEGR_CONTINUITY ; |
| 4383 |
|
- call INTEGR_CONTINUITY directly from forward_step.F |
| 4384 |
|
(previously called from momentum_correction_step.F) |
| 4385 |
|
- call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F, |
| 4386 |
|
forward_step.F and pkg/ecco/the_main_loop.F |
| 4387 |
|
o model/src/do_oceanic_phys.F: |
| 4388 |
|
- reset addMass to zero only if useICEFRONT ; |
| 4389 |
|
- separated k-loop for rhoInSitu calculation ; |
| 4390 |
|
- add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P) |
| 4391 |
|
and at constant T,S (= WdRHOdP); |
| 4392 |
|
NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport |
| 4393 |
|
of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical |
| 4394 |
|
transport of locally-referenced potential density); |
| 4395 |
|
to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP) |
| 4396 |
|
o gluemnc: |
| 4397 |
|
- replace ncrcat with ncks when adding variables to *.glob.nc |
| 4398 |
|
- change the way variables without record dimensions are handled so that |
| 4399 |
|
files that have variables with and without record variables can be glued: |
| 4400 |
|
add a record dimension with a new unique name to be able to differentiate |
| 4401 |
|
between variable with and without a-prior record dimensions. Remove |
| 4402 |
|
this record dimension before adding the variable to the *.glob.nc file. |
| 4403 |
|
This procedure automatically works also for grid.*.nc files that do not |
| 4404 |
|
have any record dimension. |
| 4405 |
|
o verification/cpl_aim+ocn: |
| 4406 |
|
- generate new reference output on baudelaire (gfortran, mpich2) (previously |
| 4407 |
|
from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script. |
| 4408 |
|
o pkg/obcs/obcs_calc_stevens.F: |
| 4409 |
|
- add code for northern and southern boundaries. |
| 4410 |
|
- reorder some loops to save some operations and so that drFBar can be scalar |
| 4411 |
|
o model/src: |
| 4412 |
|
- re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine |
| 4413 |
|
truncation) and add diagnostics for Adams-Bashforth tendency increment. |
| 4414 |
|
- update test-exp. AD output: |
| 4415 |
|
1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl; |
| 4416 |
|
and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20, |
| 4417 |
|
front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5), |
| 4418 |
|
global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4), |
| 4419 |
|
matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre, |
| 4420 |
|
tutorial_global_oce_in_p, tutorial_global_oce_latlon and |
| 4421 |
|
tutorial_plume_on_slope. |
| 4422 |
|
o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX |
| 4423 |
|
that vectorises. This code uses 3 extra 2D fields, F90 array assignments |
| 4424 |
|
and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX |
| 4425 |
|
does not even come with an F77 compiler anymore, this should not be |
| 4426 |
|
a limitation |
| 4427 |
|
|
| 4428 |
|
checkpoint63e (2011/11/06) |
| 4429 |
|
o pkg/seaice adjoint of LSR: |
| 4430 |
|
- substantially rework STORE dirs. |
| 4431 |
|
- add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED |
| 4432 |
|
this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields |
| 4433 |
|
and only perform SOLV_MAX_FIXED adjoint iters. |
| 4434 |
|
If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration |
| 4435 |
|
always goes to same record, meaning that the last forward field will be |
| 4436 |
|
the one used in the adjoint - an approximation. |
| 4437 |
|
- now produces non-zero LSR-related gradients, and acceptable gradients for |
| 4438 |
|
An's zonal (x-z) test case (to be checked in) |
| 4439 |
|
- lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR |
| 4440 |
|
(but these are screwed up by the thermodynamics in the first place); |
| 4441 |
|
reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution; |
| 4442 |
|
output_adm.txt also reflects changes to seaice_lsr |
| 4443 |
|
- global_ocean.cs32x15: |
| 4444 |
|
* the "default" input_ad.seaice has been re-defined to always exclude dynamics |
| 4445 |
|
(output_adm.seaice.txt was updated) |
| 4446 |
|
* new input_ad.seaice_dynmix tests a forward LSR / backward free-drift |
| 4447 |
|
(output_adm.seaice_dynmix.txt) |
| 4448 |
|
o test-exp. exp4+stevens: |
| 4449 |
|
- switch off pTracers and nonHydrostatic (restart problems with NH); update output |
| 4450 |
|
o pkg/seaice (lsr solver): |
| 4451 |
|
- put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only); |
| 4452 |
|
update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15 |
| 4453 |
|
- fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD) |
| 4454 |
|
- new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution |
| 4455 |
|
into initial guess for linearised solver; use weight ~ (1/err)^2,4. |
| 4456 |
|
- compute (with new S/R) and print initial (+ free-driff sol. if available) |
| 4457 |
|
and final residual of linearised system. |
| 4458 |
|
o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity |
| 4459 |
|
(requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F) |
| 4460 |
|
o pkg/obcs: Stevens BCs (still only for east and west) |
| 4461 |
|
- fix Stevens BCs by using intermediate velocities of previous |
| 4462 |
|
time step as "baroclinic" contribution rather velocity of one grid cell |
| 4463 |
|
inside the boundaries; more consistent but makes the entire treatment |
| 4464 |
|
more complicated, requires new pickup files and two new S/Rs: |
| 4465 |
|
obcs_copy_uv_n and obcs_save_uv_n |
| 4466 |
|
keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY |
| 4467 |
|
(undefined by default) |
| 4468 |
|
- silently move computation of some grid factors into separate loops to |
| 4469 |
|
save some recomputations |
| 4470 |
|
- add a hack for non-linear free surface |
| 4471 |
|
- add a verification experiment to exp4 that tests this code |
| 4472 |
|
o make gluemnc/xplodemnc work with (moron) non-GNU shell tools |
| 4473 |
|
|
| 4474 |
|
checkpoint63d (2011/10/25) |
| 4475 |
|
o pkg/obcs + seaice-dynamics: |
| 4476 |
|
- new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before |
| 4477 |
|
solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB |
| 4478 |
|
values (consistent with an implicit method). |
| 4479 |
|
- add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to |
| 4480 |
|
return to older implementation (same results as before); note that none of |
| 4481 |
|
the "experimental" OBCS_SEAICE options are implemented in the new version. |
| 4482 |
|
- switch test exp. seaice_obcs to use new version (update output). |
| 4483 |
|
o pkg/seaice: |
| 4484 |
|
- add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS) |
| 4485 |
|
- add parenthesis in Water-Ice drag calculations (evp & lsr); |
| 4486 |
|
- in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1; |
| 4487 |
|
and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice) |
| 4488 |
|
- update output of test exp lab_sea that uses evp or lsr (fwd+ad) |
| 4489 |
|
and global_ocean.cs32x15 (icedyn & seaice fwd+ad). |
| 4490 |
|
o pkg/layers: |
| 4491 |
|
- Include potential density as new coordinate (Thanks to David Munday) |
| 4492 |
|
o pkg/dic: |
| 4493 |
|
- Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add |
| 4494 |
|
carbonate computation/output to CALC_PCO2_APPROX |
| 4495 |
|
o pkg/generic_advdiff |
| 4496 |
|
- make TAF generate code that vectorizes: |
| 4497 |
|
gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F |
| 4498 |
|
o model/src: |
| 4499 |
|
- improve vectorization also for adjoint code of |
| 4500 |
|
solve_tridiagonal and solve_pentadiagonal. As this requires up to |
| 4501 |
|
5 new 3D-fields, this code is only turned on for the combination of |
| 4502 |
|
ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message |
| 4503 |
|
for singular matrix check (only for TARGET_NEC_SX). |
| 4504 |
|
- remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to |
| 4505 |
|
ALLOW_AUTODIFF. This flag now needs to be set outside of |
| 4506 |
|
solve_tri/pentadiagonal.F |
| 4507 |
|
o pkg/exf: |
| 4508 |
|
- fix previous modif in exf_readparms.F (revision 1.66: treatment of |
| 4509 |
|
optional namelist EXF_NML_OBCS). |
| 4510 |
|
- add many debug-print (to trace down where pkg/cal error msg comes from) |
| 4511 |
|
o pkg/mom_vecinv/mom_vi_hdissip.F |
| 4512 |
|
- rearrange loops so that vectorization is improved and in particular |
| 4513 |
|
the adjoint routine vectorizes. The code is a little longer now, but I |
| 4514 |
|
think easier to read. |
| 4515 |
|
Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested. |
| 4516 |
|
o pkg/seaice: |
| 4517 |
|
- allow to specify initial seaice velocity from files (uIceFile,vIceFile) |
| 4518 |
|
o pkg/exch2: |
| 4519 |
|
- alternative code (without tile x tile matrix) for cumulated (global) sum; |
| 4520 |
|
used as default; keep using matrix version in adjustment.cs-32x32x1. |
| 4521 |
|
o tools/build_options: |
| 4522 |
|
- after merging some MPI and/or multi-threads specific optfiles so that |
| 4523 |
|
the modified default optfile support both built (using genmake2 -mpi |
| 4524 |
|
for the MPI built, using genmake2 -omp for OpenMP built), |
| 4525 |
|
move now obsolete optfiles to tools/build_options/unsupported/ |
| 4526 |
|
(add copy of email sent to support list in doc/optfiles_changes.txt) |
| 4527 |
|
|
| 4528 |
|
checkpoint63c (2011/09/28) |
| 4529 |
|
o pkg/ebm: |
| 4530 |
|
- fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of |
| 4531 |
|
test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d) |
| 4532 |
|
o pkg/seaice (SItracer pickup) |
| 4533 |
|
* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER) |
| 4534 |
|
To be done: |
| 4535 |
|
- thorough testing of missing fields in S/R seaice_read_pickup |
| 4536 |
|
- thorough matching between generic tracers and specific fields used |
| 4537 |
|
(e.g. volume-weighted age, area-weighted age, salinity, ...) |
| 4538 |
|
o pkg/grdchk: |
| 4539 |
|
- all procs calculate and print finite-difference gradient (for testreport) |
| 4540 |
|
- change description output used by testreport; |
| 4541 |
|
- AD testing: also compare and report Finite-difference gradient; |
| 4542 |
|
=> update all output_adm*.txt |
| 4543 |
|
o test exp. global_ocean_ebm: |
| 4544 |
|
- switch back useRealFreshWaterFlux (no problem anymore with run-off); |
| 4545 |
|
and turn on exactConserve; update (fwd) output. |
| 4546 |
|
o pkg/seaice (LSR): |
| 4547 |
|
- print to STDOUT number of solver iterations at SEAICE_monFreq interval. |
| 4548 |
|
- modify solver to deal cleanly with u/v switch at face edges (CS-grid): |
| 4549 |
|
* identical results with non-CS topology (but save up to half of EXCH calls) |
| 4550 |
|
* no much changes in cs-32 verification tests since no ice at face edges |
| 4551 |
|
(differences due to convergence criteria, since nb of iterations changed) |
| 4552 |
|
* expect some differences on lat-lon-cap grid. |
| 4553 |
|
update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice) |
| 4554 |
|
o pkg/exch2: |
| 4555 |
|
- add new CPP option to disable Cumul-Sum matrix (to save storage when using |
| 4556 |
|
many tiles); until alternative coding is added, just add a stop. |
| 4557 |
|
o pkg/kpp: |
| 4558 |
|
- move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F |
| 4559 |
|
to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list). |
| 4560 |
|
o optfiles: |
| 4561 |
|
- merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles |
| 4562 |
|
into corresponding standard one, which now support different build: |
| 4563 |
|
(when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built) |
| 4564 |
|
- add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael) |
| 4565 |
|
o pkg/obcs (seaice): |
| 4566 |
|
- add missing EXCH for uIce,vIce after applying OBCS; |
| 4567 |
|
- remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding |
| 4568 |
|
argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R |
| 4569 |
|
EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F; |
| 4570 |
|
- fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared) |
| 4571 |
|
- verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi |
| 4572 |
|
and eedata.mth for MPI and mutlti-threaded testing. |
| 4573 |
|
o pkg/flt: |
| 4574 |
|
- make FLT EXCH working with multi-threads (and MPI + multi-threads); |
| 4575 |
|
- use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h; |
| 4576 |
|
- fix pickup and trajectories + profiles output with multi-threads; |
| 4577 |
|
- add parameter to select group of fields to write along trajectory and |
| 4578 |
|
profile (default unchanged); |
| 4579 |
|
- only call PORT_RAND* function when flt_noise <> 0; |
| 4580 |
|
- add multi-threaded test for verification exp. flt_example. |
| 4581 |
|
o eesupp/src: |
| 4582 |
|
- fix S/R ALL_PROC_DIE for MPI+multi-threads. |
| 4583 |
|
- USE_OMP_THREADING: check that number of threads (from eedata) matches |
| 4584 |
|
actual number (from env.var. setting). |
| 4585 |
|
o pkg/ebm: |
| 4586 |
|
- fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file. |
| 4587 |
|
- add multi-threaded test for verification exp. global_ocean_ebm |
| 4588 |
|
|
| 4589 |
|
checkpoint63b (2011/08/29) |
| 4590 |
|
o pkg/ebm: |
| 4591 |
|
- fix sign of runoff; |
| 4592 |
|
- update directly forcing fields (Qnet,EmPmR) to use standard |
| 4593 |
|
external_forcing_surf.F (remove ebm_forcing_surf.F); |
| 4594 |
|
- avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F); |
| 4595 |
|
- set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm) |
| 4596 |
|
and apply relaxation towards corresponding SST field (2-D map or ZonAver). |
| 4597 |
|
- update global_ocean_ebm parameters file data and update output (fwd+ad). |
| 4598 |
|
o verification/matrix_example: |
| 4599 |
|
- split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for |
| 4600 |
|
MPI and mutlti-threaded testing. |
| 4601 |
|
o pkg/matrix: |
| 4602 |
|
- change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ; |
| 4603 |
|
- fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter); |
| 4604 |
|
- fix for multi-threaded (remove DATA statement); |
| 4605 |
|
- use standard DIFFERENT_MULTIPLE function; |
| 4606 |
|
- add MATRIX_OPTIONS.h |
| 4607 |
|
o verification/matrix_example: |
| 4608 |
|
To allow to split the domain in several tiles, change the domain size |
| 4609 |
|
from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on |
| 4610 |
|
Western side) of land points. |
| 4611 |
|
o (*_)write_pickup: |
| 4612 |
|
- fix few bugs in mypackage_read/write_pickup.F |
| 4613 |
|
- in MDS_WR_METAFILES calls, replace "myTime" by a local copy into |
| 4614 |
|
array of length 1 (was caught by compiler syntax-check). |
| 4615 |
|
o pkg/diagnostics (velocity potential solver): |
| 4616 |
|
- fix initialisation of main diagonal matrix (for overlap values) |
| 4617 |
|
o tools/build_options: |
| 4618 |
|
- towards single optfile for MPI and non-MPI built: merge few +mpi optfile |
| 4619 |
|
into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11) |
| 4620 |
|
- linux_amd64_gfortran: merge +mpi_generic version into standard optfile: |
| 4621 |
|
* move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ; |
| 4622 |
|
* FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list; |
| 4623 |
|
and use "-devel" testreport option for standard testing on baudelaire. |
| 4624 |
|
o pkg/grdchk: |
| 4625 |
|
- Assume that all gradient-check position are within the same tile |
| 4626 |
|
corresponding to global indices (iGloTile,jGloTile) and that |
| 4627 |
|
positions (i,j indices or nbeg) are local to this tile; |
| 4628 |
|
- set tile local-indices and proc. number according to tile global-indices; |
| 4629 |
|
- remove grdchkwhichproc from namelist (retired param); |
| 4630 |
|
- send adjoint gradient to all procs so that all procs print it to STDOUT; |
| 4631 |
|
- switch on MPI test for global_ocean.90x40x15 AD test experiment. |
| 4632 |
|
o adding package bbl (Bottom Boundary Layer) |
| 4633 |
|
description in MITgcm/pkg/bbl/bbl_description.tex |
| 4634 |
|
example/test experiment in MITgcm_contrib/bbl |
| 4635 |
|
o adjoint verifications |
| 4636 |
|
- changed 5 experiments to multi-tiles |
| 4637 |
|
* global_ocean.90x40x15 |
| 4638 |
|
* obcs_ctrl |
| 4639 |
|
* offline_exf_seaice |
| 4640 |
|
* tutorial_dic_adjoffline |
| 4641 |
|
* tutorial_tracer_adjsens |
| 4642 |
|
changed reference output for those that crossed tile boundaries |
| 4643 |
|
(changed choices of gradient check positions) |
| 4644 |
|
- with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi) |
| 4645 |
|
- temporary bug fix in grdchk_loc.F for obcs |
| 4646 |
|
o genmake2 & testreport |
| 4647 |
|
- add target "obj" (just for OBJFILES files) to Makefile; |
| 4648 |
|
- add option to specify FEXTRAFLAGS on command line. |
| 4649 |
|
o pkg/mypackage: |
| 4650 |
|
- remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS |
| 4651 |
|
|
| 4652 |
|
checkpoint63a (2011/08/02) |
| 4653 |
|
o pkg/diagnostics (velocity potential): |
| 4654 |
|
- fix velocity-potential calculation when using OBCS: balance net inflow |
| 4655 |
|
at each level (new S/R OBCS_DIAG_BALANCE). |
| 4656 |
|
- fix some of the problems with OBCS in stream-function calculation. |
| 4657 |
|
o pkg/exf/exf_readparms.F |
| 4658 |
|
- make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF, |
| 4659 |
|
EXF_NML_OBCS) more consistent, so that you need not have these lists |
| 4660 |
|
in data.exf when they are not used. |
| 4661 |
|
o optim/optim_readdata.F: |
| 4662 |
|
- add some output about obcs variables that might help debugging |
| 4663 |
|
- add a check about nvarlength |
| 4664 |
|
o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec |
| 4665 |
|
o pkg/diagnostics (velocity potential): |
| 4666 |
|
- fix mask for OBCS (still problems in stream-function with OBCS); |
| 4667 |
|
- add specific parameter (default = main code CG2D params) for solver; |
| 4668 |
|
- in case of poor convergence, use solution corresponding to lowest residual. |
| 4669 |
|
o pkg/seaice/seaice_growth.F: small changes that permit vectorizable |
| 4670 |
|
adjoint code. In general statements like tmpscal=fld(i,j) are problematic |
| 4671 |
|
and should be avoided where possible. |
| 4672 |
|
o model/src (rStar): |
| 4673 |
|
- include r* effect on reference-state (PhiRef) in totPhiHyd |
| 4674 |
|
(so that it's really the potential anomaly at the cell center); |
| 4675 |
|
affect solution only if z* with full pressure in EOS. |
| 4676 |
|
- test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and |
| 4677 |
|
update output (because of z* in totPhiHyd and viscA4 changes); |
| 4678 |
|
- keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly |
| 4679 |
|
@ constant r) until interpolation at constant r is implemented. |
| 4680 |
|
o pkg/diagnostics |
| 4681 |
|
- fix RCENTER diagnostics in case cell center is not at interface middle |
| 4682 |
|
o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use |
| 4683 |
|
this eos with eosType = 'TEOS10', in data (PARM01). This eos implies |
| 4684 |
|
that THETA and SALT are "conservative temperature" and "absolute |
| 4685 |
|
salinity" |
| 4686 |
|
o pkg/ctrl |
| 4687 |
|
- fix computation of endrec in s/r ctrl_init_rec |
| 4688 |
|
- ctrl_pack/unpack_*: remove unused variables and some obsolete code |
| 4689 |
|
o pkg/seaice/seaice_growth.F |
| 4690 |
|
- fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code, |
| 4691 |
|
remove then obsolete STORE directives |
| 4692 |
|
- fix STORE directives for tice and tices, so that only the |
| 4693 |
|
appropriate part of the fields are stored (and not the entire |
| 4694 |
|
field); update global_ocean.cs32x15.seaice AD output. |
| 4695 |
|
- cosmetic changes: adjust CPP flags and indentation for better |
| 4696 |
|
legibilty |
| 4697 |
|
o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by |
| 4698 |
|
Chris Wilson) |
| 4699 |
|
o pkg/gmredi: |
| 4700 |
|
Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF), |
| 4701 |
|
and test it in verification exp. "front_relax.bvp" (update output.bvp.txt) |
| 4702 |
|
|
| 4703 |
|
checkpoint63 (2011/07/11) |
| 4704 |
|
o pkg/exch2: |
| 4705 |
|
- rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h |
| 4706 |
|
- exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the |
| 4707 |
|
(2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y |
| 4708 |
|
increments, calculates Cumul-Sum @ tile origin and sends results to each tile. |
| 4709 |
|
o pkg/diagnostics: |
| 4710 |
|
- deal with pairs of post-processed diags which are computed together; in |
| 4711 |
|
particular, re-order list of diags within 1 file to save 2nd computation. |
| 4712 |
|
- add S/R to compute velocity stream-function (called after velocity-potential |
| 4713 |
|
calculation) from divergence free transport -> new diagnostics "PsiVEL". |
| 4714 |
|
- add parameter to select grid-point location where PsiVEL == 0. |
| 4715 |
|
o eesupp/src: |
| 4716 |
|
new S/R to calculate cumulated sum on tiled array, corner grid-cell location |
| 4717 |
|
(specific S/R needed with exch2 topology - for now, just print an error msg) |
| 4718 |
|
o pkg/shelfice |
| 4719 |
|
- Implement friction velocity-dependent transfer coefficients following |
| 4720 |
|
Holland and Jenkins, JPO, 1999 |
| 4721 |
|
Original code by M. Losch with small modifs. |
| 4722 |
|
Enable with CPP option SHI_ALLOW_GAMMAFRICT |
| 4723 |
|
and runtime flag SHELFICEuseGammaFrict |
| 4724 |
|
o verification lab_sea & global_ocean.cs32x15: |
| 4725 |
|
- use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local): |
| 4726 |
|
does not miss some dependencies (but is slower) and also works with many files |
| 4727 |
|
(default makedepend limitation for AD built). |
| 4728 |
|
- use cyrus_makedepend in adjustment.128x64x1 (so that it still tested). |
| 4729 |
|
o pkg/diagnostics: |
| 4730 |
|
- add run-time parameter "useMissingValue" (def=False) to fill land-point |
| 4731 |
|
(i.e., where mask=0) with MissingValue ; used only in MNC output file. |
| 4732 |
|
This replaces CPP-option DIAGNOSTICS_MISSING_VALUE. |
| 4733 |
|
- Extend the use of "missing_value" setting from data.diagnostics for the case |
| 4734 |
|
of counter-diagnostics (where fraction-weight is zero). This applies both to |
| 4735 |
|
MNC and MDS output files. |
| 4736 |
|
o pkg/seaice/seaice_growth.F: |
| 4737 |
|
- add 'a priori' cap of latent heat flux based on actual mass considerations |
| 4738 |
|
when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the |
| 4739 |
|
non-legacy seaice_solve4temp. |
| 4740 |
|
- add diagnostic of the residual sublimation freshwater flux (the freshwater |
| 4741 |
|
flux taken from the ocean if the total actual latent heat fluxes exceed |
| 4742 |
|
the maximum) |
| 4743 |
|
- remove the CPP switch around the *_FWbySublim unit change and move diagnostic |
| 4744 |
|
fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F. |
| 4745 |
|
- add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef |
| 4746 |
|
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim). |
| 4747 |
|
- bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET. |
| 4748 |
|
- bug fix : missing part to Martin's r_FWbySublim pathological case fix. |
| 4749 |
|
o verification 1D_ocean_ice_column: |
| 4750 |
|
made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet |
| 4751 |
|
update results |
| 4752 |
|
o pkg/diagnostics: |
| 4753 |
|
- Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P') |
| 4754 |
|
which are not filled-up but computed from other diags ; In this case, the mate |
| 4755 |
|
diag points to the primary (filled-up) diag to used for post processing. |
| 4756 |
|
- Update Velocity-potential computation using post-processed diag framework. |
| 4757 |
|
==> Change the ordering of fields and time-periods in MDS output file |
| 4758 |
|
when using periodic averaging: now writes one time record with the full set |
| 4759 |
|
of fields for this time period, then the next time reccord (it used to be |
| 4760 |
|
one field with the full set of time records then the next field). |
| 4761 |
|
Note: this is now similar to NetCDF (MNC) output file. <== |
| 4762 |
|
|
| 4763 |
|
checkpoint62z (2011/06/21) |
| 4764 |
|
o adjoint monitor: |
| 4765 |
|
- Add adjoint monitor output for packages exf, seaice |
| 4766 |
|
and update relevant testreport output |
| 4767 |
|
o pkg/seaice: |
| 4768 |
|
- re-order diags inits so that they appear in order in available_diagnostics.log |
| 4769 |
|
- added diags: hsnow thermo. rates of change, area preceeding ridiging process, |
| 4770 |
|
area/heff/hsnow preceeding thermodynamic growth/melt. |
| 4771 |
|
- modified diag: SIdA; output actual effect, as the description states. |
| 4772 |
|
- modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. |
| 4773 |
|
- retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. |
| 4774 |
|
(SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; |
| 4775 |
|
and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) |
| 4776 |
|
- modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. |
| 4777 |
|
- added diagnostics for seaice generic tracers (SItr*). |
| 4778 |
|
- added SItrUnit and SItrNameLong run time param (for SItr* diags). |
| 4779 |
|
- in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. |
| 4780 |
|
I. Fenty: 18-Jun-2011: |
| 4781 |
|
Minor changes to seaice package: |
| 4782 |
|
1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and |
| 4783 |
|
added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) |
| 4784 |
|
- Differentiated "regularization variables" from "floor variables" |
| 4785 |
|
* areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor |
| 4786 |
|
* hiceMin became SEAICE_hice_reg (old hiceMin) |
| 4787 |
|
(with _reg meaning regularization variable) |
| 4788 |
|
- SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion |
| 4789 |
|
so as to ensure energy conservation when going between phases |
| 4790 |
|
- A22 was not used anywhere |
| 4791 |
|
2) Changed regularization procedure for heffActual and hsnowActual to ensure |
| 4792 |
|
well-boundedness and smooth adjoint in seaice_growth.F |
| 4793 |
|
3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells |
| 4794 |
|
because the old regularization always set heffActual >= 0.05 cm |
| 4795 |
|
4) Changed the model so that the default behavior is to put a small (10^-5) "floor" |
| 4796 |
|
on AREA when HEFF > 0. |
| 4797 |
|
- went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to |
| 4798 |
|
requiring that DISABLE_AREA_FLOOR *not* be defined |
| 4799 |
|
Affected verifications: |
| 4800 |
|
- 1D_ocean_ice_column (output.txt output_adm.txt) |
| 4801 |
|
- global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) |
| 4802 |
|
o pkg/diagnostics: |
| 4803 |
|
- move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). |
| 4804 |
|
- rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument |
| 4805 |
|
(was _RL, now integer) with option = 0 to retrieve all levels. |
| 4806 |
|
- add pieces of code to compute velocity potential at each level (new diagnostics |
| 4807 |
|
PhiVEL, works only when UVELMASS & VVELMASS are also turned on); |
| 4808 |
|
for now, using same params as CG2D (target-resisual, max Nb of iter ...). |
| 4809 |
|
- fix few issues with counter diagnostics in diagnostics_setdiag.F & |
| 4810 |
|
diagstats_setdiag.F (if diagnostic counter is itself a counter diag) |
| 4811 |
|
and in diagnostics_fract_fill.F (do not need a valid pointer for the |
| 4812 |
|
diagnostics counter-mate); check that definition of counter-diagnostic |
| 4813 |
|
includes a valid counter-mate (in diagnostics_set_levels.F). |
| 4814 |
|
o model/src (rStar): |
| 4815 |
|
- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
| 4816 |
|
affect solution only if z* with full pressure in EOS; |
| 4817 |
|
update output of test-exp global_ocean.90x40x15. |
| 4818 |
|
o pkg/seaice: |
| 4819 |
|
- introduce siEps=1e-5 parameter |
| 4820 |
|
- use areaMax in AREA update (part 4), consistent with ridging step (part 2.5). |
| 4821 |
|
- re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code. |
| 4822 |
|
- introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer. |
| 4823 |
|
For now it covers, and was tested for, ice salinity and age (attached to HEFF), |
| 4824 |
|
as well as ice cover age and ridging index (attached to AREA). |
| 4825 |
|
For now the run time parameters (in data.seaice/SEAICE_PARM03) are |
| 4826 |
|
SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA'). |
| 4827 |
|
Up to SItrMaxNum=3 tracers can be used simultaneously. |
| 4828 |
|
o pkg/salt_plume: |
| 4829 |
|
-introduce SPsalFRAC run time parameter that sets the fraction of the |
| 4830 |
|
salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically) |
| 4831 |
|
that gets vertically redistributed (fluxed down) by pkg/salt_plume. |
| 4832 |
|
o model debug options: |
| 4833 |
|
- Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored |
| 4834 |
|
in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h). |
| 4835 |
|
- Refine debug-msg printing selection (3 new levels): |
| 4836 |
|
debugMode : controls printing of debug messages (sequence of S/R calls). |
| 4837 |
|
debugLevel : controls printing of algorithm-relevant auxiliary/debug messages |
| 4838 |
|
debLevZero = 0 ; /* level of disabled aux. msg printing */ |
| 4839 |
|
debLevA = 1 ; /* level of minimum aux. msg printing */ |
| 4840 |
|
debLevB = 2 ; /* level of low aux. print (report read-file opening)*/ |
| 4841 |
|
debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */ |
| 4842 |
|
debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */ |
| 4843 |
|
debLevE = 5 ; /* level of extensive debug printing */ |
| 4844 |
|
New debugLevel default: with default debugMode value (=F), |
| 4845 |
|
= 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.; |
| 4846 |
|
and if debugMode=T, default debugLevel = 4 (debLevD). |
| 4847 |
|
Relation with previous settings: |
| 4848 |
|
debLevB (=2) corresponds to former debLevA (=1) |
| 4849 |
|
debLevD (=4) corresponds to former debLevB (=2) |
| 4850 |
|
Note: |
| 4851 |
|
a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before); |
| 4852 |
|
b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs); |
| 4853 |
|
to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5) |
| 4854 |
|
- Add new parameter (printResidualFreq, read from PARM02 namelist) to print |
| 4855 |
|
detailed CG solvers convergence; off (=0) by default, except if debugLevel=5. |
| 4856 |
|
o pkg/obcs: |
| 4857 |
|
- change OBCSfixTopo default from True to False (should not change the results); |
| 4858 |
|
keep OBCSfixTopo=T in verification-exp. seaice_obcs. |
| 4859 |
|
o pkg/thsice: |
| 4860 |
|
- fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in |
| 4861 |
|
2nd layer seaice sublimation (unlikely to happen) |
| 4862 |
|
- use Interior mask for OBCS in thsice_advection.F (similar to what is |
| 4863 |
|
done in gad_advection & seaice_advection). |
| 4864 |
|
o adjoint: |
| 4865 |
|
bug fix spotted by Gael Forget: |
| 4866 |
|
seaice_advection and thsice_advection still had |
| 4867 |
|
legacy CPP options to avoid CS corner updates for adjoint |
| 4868 |
|
o pkg/seaice: |
| 4869 |
|
=> Change some of the defaults (2011/05/29): |
| 4870 |
|
- change SEAICEuseFluxForm default (from False to True) |
| 4871 |
|
- change DIFF1 default (from 0.004 m/s to 0. m/s) |
| 4872 |
|
And print warnings if DIFF1 is not set in data.seaice and centered |
| 4873 |
|
avection scheme is used without any diffusion. |
| 4874 |
|
also: |
| 4875 |
|
- fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F; |
| 4876 |
|
- set SEAICEdiffKh[] default in the same way as SEAICEadvSch[] |
| 4877 |
|
- stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any |
| 4878 |
|
other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with |
| 4879 |
|
#undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE. |
| 4880 |
|
update results of test exp.: |
| 4881 |
|
lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20) |
| 4882 |
|
output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200) |
| 4883 |
|
output_adm.noseaicedyn (SEAICEuseFluxForm=T) |
| 4884 |
|
offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T) |
| 4885 |
|
seaice_obcs: output (SEAICEuseFluxForm=T) |
| 4886 |
|
and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004) |
| 4887 |
|
for standard fwd & AD lab_sea tests (to keep the same output). |
| 4888 |
|
o pkg/seaice/seaice_growth.F: |
| 4889 |
|
- use Ian Fenty's capping formulas for actual ice |
| 4890 |
|
thickness thoughout EVOLUTION branch. |
| 4891 |
|
- put treatment pathological case #2) in CPP brackets |
| 4892 |
|
(ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). |
| 4893 |
|
- update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. |
| 4894 |
|
o pkg/seaice: |
| 4895 |
|
- seaice_diffusion.F : remove the min(DX,DY) factor permanently; |
| 4896 |
|
pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter; |
| 4897 |
|
also pass fac as a param, which can be 1. (to update the tendency |
| 4898 |
|
field) or the time step (to update the field itself). |
| 4899 |
|
- seaice_advdiff.F: for multidim, call seaice_diffusion with |
| 4900 |
|
e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call |
| 4901 |
|
seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. |
| 4902 |
|
- SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : |
| 4903 |
|
hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
| 4904 |
|
o pkg/seaice: |
| 4905 |
|
diffusion with centered advection scheme (diffus.F & advect.F): |
| 4906 |
|
- simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) |
| 4907 |
|
to just compute the laplacian of input-field. |
| 4908 |
|
- unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call. |
| 4909 |
|
- fix flux-form version in diffus.F to conserve tracer. |
| 4910 |
|
update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects |
| 4911 |
|
machine truncation) and lab_sea.salt_plume (conservative flux-form modif) |
| 4912 |
|
|
| 4913 |
|
checkpoint62y (2011/05/26) |
| 4914 |
|
o pkg/seaice: |
| 4915 |
|
- seaice_growth.F : in EVOLUTION branch, always include |
| 4916 |
|
a_QSWbyATM_cover in qnet (as it should be). |
| 4917 |
|
- verification/global_ocean.cs32x15 : update results accordingly |
| 4918 |
|
(output.seaice.txt output_adm.seaice.txt). |
| 4919 |
|
o pkg/seaice + obcs: |
| 4920 |
|
- use maskInW & maskInS in multi-dim advection and biharmonic diffusion: |
| 4921 |
|
equivalent of assuming no tracer gradient outside the OB region. |
| 4922 |
|
update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion) |
| 4923 |
|
- remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed |
| 4924 |
|
after changes above); |
| 4925 |
|
- obcs+seaice cleaning: apply seaice-tracer OB values to tracer field |
| 4926 |
|
only at OB location (instead of over a band of OLx width). |
| 4927 |
|
o pkg/seaice: |
| 4928 |
|
- fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F |
| 4929 |
|
(dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid) |
| 4930 |
|
o pkg/obcs: |
| 4931 |
|
- split header file "OBCS.h" into 4 separated files: |
| 4932 |
|
OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h |
| 4933 |
|
Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h |
| 4934 |
|
(contain no conditional statement which depends on OBCS options). |
| 4935 |
|
- move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h) |
| 4936 |
|
to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h). |
| 4937 |
|
o ctrl, cost, grdchk & autodiff pkgs: |
| 4938 |
|
- make options file more standard (like other {PKG}_OPTIONS.h file but |
| 4939 |
|
with AD_CONFIG.h); clean-up some of the included header files. |
| 4940 |
|
o pkg/obcs: |
| 4941 |
|
- do not mask tracer when applying OB (tracer == 0 could generate problems) |
| 4942 |
|
- apply tracer OB values to tracer field only at OB location (instead of |
| 4943 |
|
over a band of OLx width) |
| 4944 |
|
- clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R) |
| 4945 |
|
- remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove |
| 4946 |
|
obcs_apply_tloc.F & obcs_apply_sloc.F |
| 4947 |
|
o obcs in model/src: |
| 4948 |
|
- call OBCS_APPLY_W only if NonHydrostatic. |
| 4949 |
|
- call OBCS_APPLY_ETA only if NonLinFreeSurf. |
| 4950 |
|
- reset dEtaHdt and wVel to zero outside OB interior region ; |
| 4951 |
|
- leave tracer unchanged outside OB interior region: This has no effect |
| 4952 |
|
on the solution but just to prevent unrealistic tracer value outside OB. |
| 4953 |
|
- zero out velocity outside OB interior region: This has no effect on |
| 4954 |
|
the solution but just to prevent unrealistic velocity outside OB. |
| 4955 |
|
o obcs and non-lin free-surf: |
| 4956 |
|
move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F |
| 4957 |
|
and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F |
| 4958 |
|
+ add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR: |
| 4959 |
|
this fixes missing EXCH + get consistent eta OB value (+ fix restart). |
| 4960 |
|
update results of test-exp. exp4(nlfs). |
| 4961 |
|
o exp4 (nlfs) test-exp: |
| 4962 |
|
use OBC for Eta at Western & Eastern OB (to test prescribing Eta |
| 4963 |
|
with NonLin-FreeSurf); update output.nlfs.txt |
| 4964 |
|
o obcs and 2d/3d solver norm: |
| 4965 |
|
use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB |
| 4966 |
|
and outside OB interior region (will allow to place OB further inside the |
| 4967 |
|
domain). Depending on the domain, can affects cg2d-Norm (previous |
| 4968 |
|
cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl, |
| 4969 |
|
and cg3d-Norm (previous Norm was computed before canceling OB terms), |
| 4970 |
|
e.g. in tutorial_plume_on_slope. |
| 4971 |
|
- update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope. |
| 4972 |
|
o pkg rbcs: |
| 4973 |
|
- split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h |
| 4974 |
|
- add capability to apply relaxation to horizontal velocity uVel & vVel. |
| 4975 |
|
o pkg/grdchk: add gradient check for control variable xx_shifwflx |
| 4976 |
|
o pkg/shelfice/shelfice_init_fixed.F |
| 4977 |
|
fix CPP-flag combinations |
| 4978 |
|
o pkg/seaice: Merge iceage code of Pierre Rampal |
| 4979 |
|
* update/change/correct ice age calculations |
| 4980 |
|
* add age updates for pathological cases |
| 4981 |
|
Probably needs more testing... |
| 4982 |
|
|
| 4983 |
|
checkpoint62x (2011/05/13) |
| 4984 |
|
o pkg/mom_vecinv: |
| 4985 |
|
high-order vorticity scheme: use interior masks (maskInW & S) |
| 4986 |
|
to zero-out (outside OB) gradient of vorticity. |
| 4987 |
|
o verification exp.: |
| 4988 |
|
turn on "useEnergyConservingCoriolis" (better discretisation) in exp. |
| 4989 |
|
hs94.128x64x5 and seaice_obcs ; update results. |
| 4990 |
|
o pkg/obcs: |
| 4991 |
|
fix bug in OBeta for YZ sections in obcs_exf_load.F |
| 4992 |
|
o pkg/ctrl, pkg/shelfice, and optim: |
| 4993 |
|
- add new control variable xx_shifwflx (fresh water flux underneath ice |
| 4994 |
|
shelves). This is almost as tedious as obcs-ctrl, because the |
| 4995 |
|
variables needs its own mask. |
| 4996 |
|
- add a cost function term that penalizes the deviation of xx_shifwflx |
| 4997 |
|
from the first guess (zero) in analogy to other control variables |
| 4998 |
|
o pkg/shelfice: |
| 4999 |
|
- start basic adjoint |
| 5000 |
|
o pkg/ctrl: |
| 5001 |
|
- remove extra 2D field "for good measure" when initializing in |
| 5002 |
|
ctrl_set_globfld_[xy/xz/yz].F |
| 5003 |
|
- replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec |
| 5004 |
|
- improve error messages in ctrl_set_unpack_* |
| 5005 |
|
o OBC implementation in momentum: |
| 5006 |
|
use interior masks (maskInC,W & S) in momentum S/R: |
| 5007 |
|
- multiply divergence, tension and some del^i.u or del^j.v by maskInC |
| 5008 |
|
- multiply del2u,del2v by maskInW/S (biharmonic viscosity) |
| 5009 |
|
- multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) |
| 5010 |
|
- multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) |
| 5011 |
|
Motivation: fix/clean implementation of OBC with biharmonic-viscosity |
| 5012 |
|
(and also with Leith/Smagorinsky harmonic-viscosity). |
| 5013 |
|
Update output of experiment dome and exp4 (+nlfs). |
| 5014 |
|
o exp4 test-exp: |
| 5015 |
|
- turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) |
| 5016 |
|
and prescribe time-varying OB (without pkg/exf) for zonal-velocity |
| 5017 |
|
at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
| 5018 |
|
time-varying OB at Western-side for wVel (NonHyd); update output. |
| 5019 |
|
- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
| 5020 |
|
and biharmonic-viscosity ; also use prescribed time varying OB. |
| 5021 |
|
o pkg/obcs: |
| 5022 |
|
fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
| 5023 |
|
o model/src: |
| 5024 |
|
- fix startTime setting when baseTime<>0 & nIter0=0 are specified ; |
| 5025 |
|
- initialise startTime & nIter0 with unlikely values: allows to set one |
| 5026 |
|
from the other without ambiguity. |
| 5027 |
|
o seaice_obcs test-exp.: |
| 5028 |
|
add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output. |
| 5029 |
|
o pkg/obcs: |
| 5030 |
|
- remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: |
| 5031 |
|
no longer needed with maskInC,W,S in pkg/generic_advdiff. |
| 5032 |
|
o pkg/seaice: |
| 5033 |
|
- retired SEAICE_SALINITY and SEAICE_salinity in favor of |
| 5034 |
|
SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively. |
| 5035 |
|
- fixed bug in the initialization of sea ice salinity variable HSALT |
| 5036 |
|
in seaice_init_varia.F (removed dependence on ICE2WATR) |
| 5037 |
|
o fizhi-cs test exp.: |
| 5038 |
|
switch reference output convention for these 2 non-standard test-exp, |
| 5039 |
|
from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5) |
| 5040 |
|
to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11) |
| 5041 |
|
reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran |
| 5042 |
|
o model/inc: |
| 5043 |
|
- change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4") |
| 5044 |
|
of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS) |
| 5045 |
|
o pkg/seaice: |
| 5046 |
|
- fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY |
| 5047 |
|
o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15 |
| 5048 |
|
- updated output*.txt files due to bug fixes in salt, saltPlumeFlux, |
| 5049 |
|
and initial HSALT |
| 5050 |
|
|
| 5051 |
|
checkpoint62w (2011/04/26) |
| 5052 |
|
o pkg/mom_fluxform: |
| 5053 |
|
- fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf. |
| 5054 |
|
- use parameter "sideDragFactor" in no-slip BC side-drag part. |
| 5055 |
|
- update output of exp. global_ocean.90x40x15 |
| 5056 |
|
o pkg/mom_vecinv: |
| 5057 |
|
mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform) |
| 5058 |
|
o update seaice exp.: |
| 5059 |
|
use more consistent parameter values (remove "backward compatability only": |
| 5060 |
|
ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh) |
| 5061 |
|
related to thermodynamics seaice. Update output (fwd+AD) of exp.: |
| 5062 |
|
1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs |
| 5063 |
|
o update test-exp global_ocean.90x40x15: |
| 5064 |
|
o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis). |
| 5065 |
|
o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.) |
| 5066 |
|
o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params) |
| 5067 |
|
o turn on zStar & viscA4 in standard set-up (dir input/) |
| 5068 |
|
and update output files: output.txt & output.dwnslp.txt |
| 5069 |
|
o new AD-test experiment: obcs_ctrl |
| 5070 |
|
(From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector. |
| 5071 |
|
o pkg/dic: |
| 5072 |
|
fix two bugs in handling water vapour pressure in carbonate chemistry |
| 5073 |
|
and air-sea fluxes. Found by Val Bennington and Galen McKinley |
| 5074 |
|
(add DIC Option = WATERVAP_BUG to recover old results) |
| 5075 |
|
update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline |
| 5076 |
|
o adding allowInteriorFreezing option to check for water below freezing point |
| 5077 |
|
at depth and bring the negative heat anomaly to the surface level |
| 5078 |
|
o pkgs _fields_load: |
| 5079 |
|
- extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs) |
| 5080 |
|
- use new S/R GET_PERIODIC_INTERVAL in pkgs: |
| 5081 |
|
bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and |
| 5082 |
|
rbcs to get interpolation weights and time reccord number. |
| 5083 |
|
- fix multi-threading in aim_fields_load.F |
| 5084 |
|
- apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F |
| 5085 |
|
o external_fields_load: |
| 5086 |
|
new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear |
| 5087 |
|
interpolation weights) to use in a periodic time-series ; do not divide by |
| 5088 |
|
time-step to convert to integer: |
| 5089 |
|
- this fixes case where externForcingPeriod is not multiple of time-step |
| 5090 |
|
(Thanks to Christopher L. Wolfe) |
| 5091 |
|
- this fixes case where externForcingPeriod is an odd multiple of time-step |
| 5092 |
|
(was wrong by half of time-step); update results of tutorial_global_oce_in_p. |
| 5093 |
|
store index of time-record which is currently loaded: |
| 5094 |
|
- works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ; |
| 5095 |
|
- needed for the adjoint but not yet used because of extensive recomputations; |
| 5096 |
|
(to be fixed soon) |
| 5097 |
|
|
| 5098 |
|
checkpoint62v (2011/04/02) |
| 5099 |
|
o verification/1D_ocean_ice_column added to test Ian Fenty's |
| 5100 |
|
pkg/seaice_growth.F modifications for improving sea ice code differentiability |
| 5101 |
|
o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope |
| 5102 |
|
(new velocity statistics after changing maskInW & maskInS definition) |
| 5103 |
|
o pkg/generic_advdiff with OBCS: |
| 5104 |
|
use maksInW & maskInS in advective flux and in biharmonic diffusion calculation: |
| 5105 |
|
equivalent to assumption of no tracer gradient outside the OB region. |
| 5106 |
|
This will affect the results if using obcs+biharmonic diffusion. |
| 5107 |
|
update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc) |
| 5108 |
|
o pkg/obcs: |
| 5109 |
|
change definition of maskInW & maskInS: leave OB edges inside (maskIn=1) |
| 5110 |
|
(e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still |
| 5111 |
|
in Interior region. No impact on solution but affects Velocity monitor stats. |
| 5112 |
|
o pkg/ptracers (adjoint) |
| 5113 |
|
New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate |
| 5114 |
|
tape file for each tracer |
| 5115 |
|
o model/inc/src and pkg/autodiff: add parameters that allow to turn |
| 5116 |
|
of parts of the adjoint code at run time. For now, there are only |
| 5117 |
|
useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These |
| 5118 |
|
parameters are set in data.pkg. |
| 5119 |
|
This is the lazy coward's version of doing this, but still useful for |
| 5120 |
|
debugging. In order to do it right, everything needs to be moved to |
| 5121 |
|
pkg/autodiff. |
| 5122 |
|
o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at |
| 5123 |
|
the end; this fixes the adjoint balancing code for open boundaries. |
| 5124 |
|
o pkg/ctrl: |
| 5125 |
|
- change behavior of xx_${varname}period to be analogous to exf-conventions: |
| 5126 |
|
xx_${varname}period = 0., means time-independent control part |
| 5127 |
|
xx_${varname}period = -12., means one-year-periodic monthly control part |
| 5128 |
|
- introduce helper routine ctrl_init_rec (part of ctrl_init.F) to |
| 5129 |
|
clean up ctrl_init a little, remove unused variables |
| 5130 |
|
- ctrl_init: fixed the handling of the start/endrec for obcs-variables |
| 5131 |
|
- move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec |
| 5132 |
|
|
| 5133 |
|
checkpoint62u (2011/03/15) |
| 5134 |
|
o model/src: |
| 5135 |
|
- for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in |
| 5136 |
|
h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ; |
| 5137 |
|
- in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to |
| 5138 |
|
INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF. |
| 5139 |
|
o pkg/ctrl/obcs/ecco: |
| 5140 |
|
- remove obsolete, unused, and partially broken code: |
| 5141 |
|
ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within |
| 5142 |
|
ALLOW_CTRL_OBCS_BALANCE |
| 5143 |
|
- put a stop statement into ecco/cost_obcsvol.F, but also add |
| 5144 |
|
cost_obcsvol to ecco_ad_diff.list |
| 5145 |
|
o pkg/ecco: fix counting cost function contributions for obcs (code |
| 5146 |
|
by Matt M.) and diffkr for diagnostics |
| 5147 |
|
o pkg/ecco, pkg/ctrl, pkg/grdchk: |
| 5148 |
|
add cost penalty terms for initial uvel, vvel, eta controls |
| 5149 |
|
and I/O for prior error files |
| 5150 |
|
o pkg/mdsio: |
| 5151 |
|
move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option |
| 5152 |
|
(new argument) to check for tiled file in mdsioLocalDir : this fix the |
| 5153 |
|
restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir. |
| 5154 |
|
o pkg/ctrl: |
| 5155 |
|
- ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by |
| 5156 |
|
ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove |
| 5157 |
|
unused and superfluous variables |
| 5158 |
|
- ctrl_get_gen_rec.F: catch the case of xx_genperiod=0. |
| 5159 |
|
o pkg/ecco |
| 5160 |
|
- enable adjoint of Stevens OB |
| 5161 |
|
o pkg/ctrl/ecco/grdchk: |
| 5162 |
|
- remove global declaration of tmpfldx/yz and tmpfldx/yz2. |
| 5163 |
|
Fortunately, we do not have any tests for the numerous cpp-flagged |
| 5164 |
|
option of "obcs as control parameters" so we will never know |
| 5165 |
|
if this is an improvement (but at least now things compile). |
| 5166 |
|
- remove an obsolete initialization from ecco_cost_init_barfiles.F |
| 5167 |
|
- fix some problems within never used ifdefs to make the code compile |
| 5168 |
|
o pkg/obcs: |
| 5169 |
|
- Refine Interior mask definition to work with more complex OB (e.g. |
| 5170 |
|
if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to |
| 5171 |
|
read in Interior mask from file. Check if Interior mask is consistent |
| 5172 |
|
with OB list of indices. |
| 5173 |
|
o pkg/seaice |
| 5174 |
|
- beginning code for a seaice tracer package, |
| 5175 |
|
but currently only used for seaice age: SEAICE_AGE |
| 5176 |
|
SEAICE_num = 4 |
| 5177 |
|
iTracer = 1: area-weighted ice age |
| 5178 |
|
= 2: volume-weighted ice age |
| 5179 |
|
= 3, 4: template for one-year vs. multi-year ice |
| 5180 |
|
data.seaice has new namelist SEAICE_PARM03 for arrays related to |
| 5181 |
|
SEAICE_num |
| 5182 |
|
|
| 5183 |
|
checkpoint62t (2011/03/05) |
| 5184 |
|
o pkg/obcs: |
| 5185 |
|
- obcs_apply_uv.F: change to a 2 steps method, first tangential component; |
| 5186 |
|
then normal component. This ensures that the normal component is set |
| 5187 |
|
correctly even when it conficts with tangential setting from an other OB. |
| 5188 |
|
Affects results of test-experiment seaice_obcs: update the output.txt |
| 5189 |
|
o pkg/obcs: |
| 5190 |
|
- add code to monitor statistics of dynamical fields at OB. |
| 5191 |
|
- take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW : |
| 5192 |
|
- fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection). |
| 5193 |
|
- change default: balance the Net inflow through all OB (instead of balancing |
| 5194 |
|
each OB separately); keep the old method if setting OBC_balanceFacX < 0. |
| 5195 |
|
- switch on useOBCSbalance in dome experiment: only correct Western OB outflow |
| 5196 |
|
to match Nortern OB inflow (OBCS_balanceFacN=0). |
| 5197 |
|
o pkg/seaice: |
| 5198 |
|
- redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL |
| 5199 |
|
o pkg/seaice (seaice_growth v 1.113): |
| 5200 |
|
- reverting seaice_growth to v 1.111 in order to have code with exact bit |
| 5201 |
|
compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge |
| 5202 |
|
CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced |
| 5203 |
|
runtime flag SEAICEareaFormula is kept but is inactive |
| 5204 |
|
o model/src: |
| 5205 |
|
- add new param to scale curvilinear grid distance and area when using |
| 5206 |
|
a different sphere radius from the grid-files. |
| 5207 |
|
- test/check multi-threads EXCH applied to local variable (cg2d_x) |
| 5208 |
|
o adjoint: |
| 5209 |
|
- enable adjoint of Stevens OB |
| 5210 |
|
- add dummy_in_dynamics to enable extraction of ADJrhoinsitu |
| 5211 |
|
(a bit delicate because of potentially modified adj. common block structure; |
| 5212 |
|
current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later) |
| 5213 |
|
|
| 5214 |
|
checkpoint62s (2011/02/15) |
| 5215 |
|
o pkg/seaice (seaice_growth v 1.112): |
| 5216 |
|
- introduce SEAICEareaFormula run time parameter, which selects the recipe for |
| 5217 |
|
computing the ice cover tendency from effective thickness tendencies. Include |
| 5218 |
|
Ian Fenty's formula. |
| 5219 |
|
- remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using |
| 5220 |
|
SEAICEareaFormula. |
| 5221 |
|
- simplify notations for the various d_HEFF/d_AREA terms. |
| 5222 |
|
o pkg/gmredi: |
| 5223 |
|
- add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code |
| 5224 |
|
from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative; |
| 5225 |
|
add a verification test-run (front_relax.bvp) to test GM_useBVP. |
| 5226 |
|
o pkg/seaice (seaice_growth v 1.111): |
| 5227 |
|
- for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's. |
| 5228 |
|
- the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to |
| 5229 |
|
also melt ice. |
| 5230 |
|
o pkg/seaice: |
| 5231 |
|
- McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty). |
| 5232 |
|
- can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h |
| 5233 |
|
o pkg/cheapaml: |
| 5234 |
|
- from Nico Wienders: New version of this package. |
| 5235 |
|
o pkg/flt: |
| 5236 |
|
- add CPP options to prevent floats to re-enter the opposite side of |
| 5237 |
|
a periodic domain (default: keep periodicity) |
| 5238 |
|
o pkg/gmredi: |
| 5239 |
|
- apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners |
| 5240 |
|
(needed for multi-dim advection). |
| 5241 |
|
- switch on GM Advective form in global_ocean.cs32x15 and update output.txt |
| 5242 |
|
o model/src: |
| 5243 |
|
- fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run. |
| 5244 |
|
o tutorial_tracer_adjsens |
| 5245 |
|
- extend to NLFS and replace maskC by hFacC |
| 5246 |
|
(change reference output accordingly) |
| 5247 |
|
|
| 5248 |
|
checkpoint62r (2011/01/24) |
| 5249 |
|
o testreport: |
| 5250 |
|
- add option -deloutp (-do) to remove output file after successful run |
| 5251 |
|
- add option -mfile (-mf) for MPI machile-file and for each test-exp, |
| 5252 |
|
extract exact list of procs from this file ; adjust COMMAND by |
| 5253 |
|
replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs. |
| 5254 |
|
o pkg/ecco: replace old ineffective way of penalizing deviations from |
| 5255 |
|
first guess (of obcs) with code by Matt Mazloff |
| 5256 |
|
o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without |
| 5257 |
|
exf/cal |
| 5258 |
|
- ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl |
| 5259 |
|
and handle case of obcs?period == 0 |
| 5260 |
|
Not affected by these changes: There is still an inconsistency in |
| 5261 |
|
the computation of start/endrec for the obcs variables for ALLOW_CAL |
| 5262 |
|
defined (see comment by Menemenlis, 7-Mar-2003) |
| 5263 |
|
- make S/R ctrl_get_gen_rec return something meaningful even if |
| 5264 |
|
ALLOW_CAL is not defined |
| 5265 |
|
- ctrl_getobcs?: simplify code so that it does not need to use |
| 5266 |
|
S/R exf_swapfields |
| 5267 |
|
o testreport: |
| 5268 |
|
allow to test MPI with different number of processors for each experiment: |
| 5269 |
|
create file "SIZE.h.mpi" in each build dir. |
| 5270 |
|
Note: update of "-command" argument not yet implemented. |
| 5271 |
|
o model/src, pkg/autodiff, pkg/ecco, pkg/seaice: |
| 5272 |
|
alleviate the need for additional 3D tapes when using |
| 5273 |
|
the non-inear free surface in the adjoint. This is done |
| 5274 |
|
by adding an 'update' of hfacc etc. to their current |
| 5275 |
|
value at the beginning of forward_step.F. |
| 5276 |
|
o pkg/seaice |
| 5277 |
|
seaice_lsr: move stress-divergence computations out of outer pseudo- |
| 5278 |
|
timestepping loop |
| 5279 |
|
o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD' |
| 5280 |
|
up, so that the calls of the ctrl_* subroutines are really at the end |
| 5281 |
|
of the routine. |
| 5282 |
|
o pkg/gmredi: |
| 5283 |
|
allow to specify a 2-D horizontal map and a 1-D vertical profil |
| 5284 |
|
as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity. |
| 5285 |
|
o pkg/seaice: |
| 5286 |
|
move lsr iterations from seaice_dynsolver to seaice_lsr. |
| 5287 |
|
o pkg/seaice: |
| 5288 |
|
reduce memory footprint of seaice mutldim advection tapes, |
| 5289 |
|
by using a 2D tape independent of the generic_advdiff ones, |
| 5290 |
|
and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc. |
| 5291 |
|
|
| 5292 |
|
checkpoint62q (2010/12/29) |
| 5293 |
|
o model/src: |
| 5294 |
|
- check horizontal grid-spacing for unset or zero/negative values. |
| 5295 |
|
- change AD test hs94.1x64x5 to be truly a 2-D set-up. |
| 5296 |
|
o pkg/flt: |
| 5297 |
|
- use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR |
| 5298 |
|
- precision of input and output files set according to readBinaryPrec |
| 5299 |
|
and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits. |
| 5300 |
|
- initial float position from tiled file was not converted to index space |
| 5301 |
|
(looks like a bug): fixed to make it similar to initial pos. global file. |
| 5302 |
|
o global_ocean.cs32x15: |
| 5303 |
|
change SIZE.h of AD set-up to get same tiling as with MPI. |
| 5304 |
|
Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11) |
| 5305 |
|
o model/src: |
| 5306 |
|
add flag to control printing of domain fields (bathymetry, hFac ...) in |
| 5307 |
|
ini_mask_etc (call to plot_fieds_xy*). |
| 5308 |
|
o pkg/thsice: |
| 5309 |
|
if useEXF, some forcing fields are not valid in overlap: fixed by computing |
| 5310 |
|
over the interior only + apply EXCH at the end (like with SEAICE advection). |
| 5311 |
|
o pkg/mdsio: |
| 5312 |
|
- add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer |
| 5313 |
|
to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS. |
| 5314 |
|
- change barrier call for safe multi-threads access to 3-D shared buffer. |
| 5315 |
|
- MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones) |
| 5316 |
|
- replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and |
| 5317 |
|
remove the 4 S/R MDS_PASS_WH_R4/8toRL/S. |
| 5318 |
|
o pkg/flt: |
| 5319 |
|
- add fourth-order Runge-Kutta integration |
| 5320 |
|
- add basic exch2 support (only 1 facet supported so far!) |
| 5321 |
|
o pkg/mdsio+rw: |
| 5322 |
|
new S/R to read local (or tile independent) vector (read counterpart of |
| 5323 |
|
mds_writevec_loc, and front-end write_glvec_rl/rs). |
| 5324 |
|
o global_ocean.cs32x15: additional input_ad.seaice experiment |
| 5325 |
|
that uses pkg/seaice rather than pkg/thsice. |
| 5326 |
|
(using multidim advection for seaice) |
| 5327 |
|
o towards more F95 syntax for array specification in namelist: |
| 5328 |
|
- change "data.diagnostics" (data.ptracers was changed before checkpoint62p) |
| 5329 |
|
of all verification experiments. |
| 5330 |
|
e.g.: line: fields(1,3)='ETAN ','ETANSQ ', |
| 5331 |
|
was changed to: fields(1:2,3)='ETAN ','ETANSQ ', |
| 5332 |
|
- finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles |
| 5333 |
|
o global_ocean.cs32x15: additional input.seaice experiment |
| 5334 |
|
that uses pkg/seaice rather than pkg/thsice. |
| 5335 |
|
|
| 5336 |
|
checkpoint62p (2010/12/17) |
| 5337 |
|
o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it |
| 5338 |
|
to THSICE_SIZE.h to avoid conflict with pkg/seaice. |
| 5339 |
|
o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint. |
| 5340 |
|
allow for use of multim. advection in seaice adjoint. |
| 5341 |
|
o pkg/seaice: add diagnostics for snow precipitation and sublimation flux |
| 5342 |
|
- first attempt to close budgets by taking into account the freshwater |
| 5343 |
|
flux implied by the sublimation of snow and ice. So far only the |
| 5344 |
|
volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag |
| 5345 |
|
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET |
| 5346 |
|
o eesupp/src: |
| 5347 |
|
new S/R with new option (NML_EXTENDED_F77) to change array specification |
| 5348 |
|
from F95 standard to commonly accepted extended F77 form. |
| 5349 |
|
This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5) |
| 5350 |
|
and to revert back to the original syntax (with -DNML_EXTENDED_F77) |
| 5351 |
|
for less tolerant f77 compiler (e.g., pgf77, g77). |
| 5352 |
|
o globalFiles: |
| 5353 |
|
commented out in parameter file "data" since it's not safe with MPI |
| 5354 |
|
(e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much |
| 5355 |
|
in this case); no longer commented out in restart test (tst_2+2). |
| 5356 |
|
o add adTapeDir to specify a special directory where adjoint tapes are |
| 5357 |
|
written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05 |
| 5358 |
|
and cannot be used together with mdsioLocalDir. |
| 5359 |
|
o nesting pkgs: |
| 5360 |
|
- packages_init_variables : put call to OBCS_INIT_VARIABLES in last position |
| 5361 |
|
- update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) |
| 5362 |
|
- add parameter files + utils dir + output from short run on beagle. |
| 5363 |
|
o pkg/seaice: |
| 5364 |
|
fix seaice_growth.F store directives; update results of exp. lab_sea.ad |
| 5365 |
|
o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid |
| 5366 |
|
unnecessary copying in adjoint code, requires new parameter NMAX_ITER |
| 5367 |
|
|
| 5368 |
|
checkpoint62o (2010/11/25) |
| 5369 |
|
o pkg/exf: |
| 5370 |
|
- change CPP option EXF_VERBOSE to run-time logical param exf_verbose. |
| 5371 |
|
o pkg/seaice: |
| 5372 |
|
- seaice_ocean_stress: split a loop for better vectorization of the |
| 5373 |
|
adjoint code |
| 5374 |
|
- seaice_growth.F: fix bug in conservation of freshwater connected to |
| 5375 |
|
capping of heff, put contribution into d_HEFFbyNEG |
| 5376 |
|
- replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat |
| 5377 |
|
by something more sensible (parameters that are what their name implies) |
| 5378 |
|
- change some defaults, so that by default exf-parameters are used for |
| 5379 |
|
things like rhoAir, cpAir,latent/sensible heat parameters, in order |
| 5380 |
|
to reproduce the old results, many data.seaice now contain funny values |
| 5381 |
|
for cpAir and latent heat of sublimation |
| 5382 |
|
o packages_readparms.F: move exf_readparms up in line so that |
| 5383 |
|
exf-parameters are visible for other packages (e.g. seaice) |
| 5384 |
|
o debugMode & debugLevel=2: |
| 5385 |
|
- differentiate between debugMode & debugLevel=2: |
| 5386 |
|
debugMode: controls printing of debug messages (sequence of S/R calls). |
| 5387 |
|
debugLevel: controls printing of algorithm intermediate results and stats. |
| 5388 |
|
- remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2"; |
| 5389 |
|
=> allows to print debug-stats without all sequence of call messages. |
| 5390 |
|
- switch control of debug print from debugLevel to debugMode in many S/R. |
| 5391 |
|
o pkg/obcs (obcs-sponge): |
| 5392 |
|
fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the |
| 5393 |
|
call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge) |
| 5394 |
|
o pkg/generic_advdiff: |
| 5395 |
|
- record overlap minimum size for each advection scheme; |
| 5396 |
|
- refine criteria on overlap minimum size; |
| 5397 |
|
- check and stop (in gad_check) if overlap size is too small. |
| 5398 |
|
o pkg/obcs: |
| 5399 |
|
- with ptracers: remove multiple calls to obcs_apply_ptracer (only done |
| 5400 |
|
once, in ptracers_implicit.F) |
| 5401 |
|
- with seaice: remove test on empty file name in obcs_apply_seaice (always |
| 5402 |
|
apply OB values when tile has OB) |
| 5403 |
|
o model/src, coriolis setting: |
| 5404 |
|
- integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical |
| 5405 |
|
useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from |
| 5406 |
|
files (selectCoriMap=3) with any grid. |
| 5407 |
|
- add parameter "fPrime" for constant second Coriolis coeff (default=0). |
| 5408 |
|
o pkg/seaice/seaice_growth.F: |
| 5409 |
|
a few cosmetic changes that reduce the number of lines of code |
| 5410 |
|
o pkg/obcs: add boundary conditions following Stevens (1990) |
| 5411 |
|
- the code follows old MOM/NAOSIM code |
| 5412 |
|
- so far it is only implemented for the eastern and western boundaries |
| 5413 |
|
and NOT for pTracers |
| 5414 |
|
o pkg/rbcs: |
| 5415 |
|
- replace rbcsInIter by rbcsForcingOffset, the time in seconds at the |
| 5416 |
|
beginning of the first rbcs forcing period. |
| 5417 |
|
- add option rbcsSingleTimeFiles that makes rbcs read forcing data like the |
| 5418 |
|
offline package, i.e., one file per time, labeled by iteration number; |
| 5419 |
|
deltaTrbcs sets the timestep with which the data was generated; |
| 5420 |
|
rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset. |
| 5421 |
|
- rbcsForcingCycle=0 makes forcing non-cyclic. |
| 5422 |
|
- make arithmetic safe for negative times and odd forcing periods. |
| 5423 |
|
|
| 5424 |
|
checkpoint62n (2010/11/09) |
| 5425 |
|
o pkg/seaice: |
| 5426 |
|
fix masking in free-drift S/R ; update results of exp. lab_sea.fd |
| 5427 |
|
o pkg/obcs: |
| 5428 |
|
New S/R to copy tracer value from the OB location to narrow band region |
| 5429 |
|
(width = same as overlap) beyond the OB: preserve OB value (needed for |
| 5430 |
|
high-order scheme) which were overwritten by EXCH call if in overlap |
| 5431 |
|
region. Applied to theta, salt, ptracer and advected seaice variables. |
| 5432 |
|
With seaice: use maskInC in similar way as in gad_advection.F, |
| 5433 |
|
in seaice_advection.F and advect.F. |
| 5434 |
|
Update output of experiment seaice_obcs and change exp4 to test OBCS with |
| 5435 |
|
4th order Adv.Scheme. for pasive salt and ptracer. |
| 5436 |
|
o tools/genmake2: |
| 5437 |
|
- when looking for an optfile (not specified), only search for Fortran compiler |
| 5438 |
|
(remove sym-link test + setting of CPP + makedepend check + C-compiler check) |
| 5439 |
|
- in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm |
| 5440 |
|
(instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong) |
| 5441 |
|
- set default for CPP to "cpp -traditional -P" (was the case without specifying |
| 5442 |
|
an optfile, but otherwise default was just "cpp". |
| 5443 |
|
- comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from) |
| 5444 |
|
- when "CC" is not set in the optfile, look for possible C compiler |
| 5445 |
|
(instead of just setting CC=cc) |
| 5446 |
|
- put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes: |
| 5447 |
|
=> add a ".F" to ".o" rule for source files with no "#include" (such as |
| 5448 |
|
port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS. |
| 5449 |
|
- move gfortran before g77 in list of possible Fortran compiler (consistent |
| 5450 |
|
with reference compiler switch from g77 to gfortran) |
| 5451 |
|
o pkg/seaice: |
| 5452 |
|
o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to |
| 5453 |
|
seaice_check that stops the model, when the CPP flag is used. |
| 5454 |
|
o seaice_growth.F: make capping of ice volume conserving by returning the |
| 5455 |
|
capped ice as freshwater to EmPmR. This does not change the verification |
| 5456 |
|
experiments but will change runs where the capping is acutally active |
| 5457 |
|
o change reference platform+compiler from faulks+g77 to baudelaire+gfortran |
| 5458 |
|
(except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5, |
| 5459 |
|
global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD), |
| 5460 |
|
lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd) |
| 5461 |
|
o tools/genmake2: |
| 5462 |
|
- merge genmake_warnings & genmake_errors into 1 log file: "genmake.log") |
| 5463 |
|
- change DUMPSTATE default to false (can use "-ds" option to switch it to T) |
| 5464 |
|
- clean previous genmake log files before anything else. |
| 5465 |
|
- change Makefile to remove testreport log files (*.tr_log) and genmake log |
| 5466 |
|
files only with "CLEAN" target (instead of "Clean"); |
| 5467 |
|
o pkg/generic_advdiff: |
| 5468 |
|
Change OBCS in multiDim advection (gad_advection.F): |
| 5469 |
|
Use maskInC to prevent intermediate update of tracer-field in OB regions, |
| 5470 |
|
thus keeping current-time-step OB values; and remove the call to OBCS_APPLY |
| 5471 |
|
which were applying future time-step OB values. |
| 5472 |
|
This way, all explicit calculations use current-time-step OB values |
| 5473 |
|
(simpler and more consistent). |
| 5474 |
|
Affects results when set-up uses time-varying OBC and multi-dim advection; |
| 5475 |
|
update output of experiment seaice_obcs. |
| 5476 |
|
o pkg/seaice: |
| 5477 |
|
move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h: |
| 5478 |
|
this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH & |
| 5479 |
|
SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY. |
| 5480 |
|
Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY |
| 5481 |
|
but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp |
| 5482 |
|
unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h) |
| 5483 |
|
o pkg aim (2010/10/26): |
| 5484 |
|
- Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation |
| 5485 |
|
formulation with obliquity, eccentricity, ... as run-time parameters, |
| 5486 |
|
- Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and |
| 5487 |
|
upward shortwave radition at the surface (all-sky and clear-sky). |
| 5488 |
|
o pkg/obcs: |
| 5489 |
|
- writing sections with globalFiles=T does not work: switch to tiled-files |
| 5490 |
|
when writing sections for OBCS (change pkg/rw/write_rec.F accordingly). |
| 5491 |
|
- fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F |
| 5492 |
|
- apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs |
| 5493 |
|
|
| 5494 |
|
checkpoint62m (2010/10/21) |
| 5495 |
|
o pkg/seaice: vectorize seaice_solve4temp.F |
| 5496 |
|
- move iterations loops outside of i/j-loops |
| 5497 |
|
- requires 2D arrays for TB and effConduct |
| 5498 |
|
- add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is |
| 5499 |
|
modified in this routine |
| 5500 |
|
- a little bit of clean up, adjusting indentation, etc. |
| 5501 |
|
- replaced a few TEN**a by exp(a*log(10.)) in new code for better |
| 5502 |
|
performance and '**TWO' by '**2' (because TWO is a float), |
| 5503 |
|
replaced ONE, ZERO |
| 5504 |
|
o eesupp/src: |
| 5505 |
|
fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube |
| 5506 |
|
o pkg/seaice/seaice_growth.F |
| 5507 |
|
Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and |
| 5508 |
|
merging process. The merged routine has two branches, and one activates the 'evolution' |
| 5509 |
|
branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now). |
| 5510 |
|
In summary, here is what the '10/10 revision' did consist of |
| 5511 |
|
part 1: seaice_growth.F revisions 1.71 to 1.75 |
| 5512 |
|
- Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged. |
| 5513 |
|
The emphasis here was on improving readability (e.g. by trying to use meaningful |
| 5514 |
|
variable names) and modularity (e.g. by adding arrays to store heff etc. updates). |
| 5515 |
|
part 1.5: |
| 5516 |
|
- revising the lab_sea experiment to make it a more useful (i.e. stable |
| 5517 |
|
and representative of an actual model run). This was done by generating a |
| 5518 |
|
(winter) pickup to start from, switching back the main experiment dynamic |
| 5519 |
|
solver from evp to lsr, having one of the experiments use the free drift solution. |
| 5520 |
|
part 2: seaice_growth.F revisions 1.76 to 1.85 |
| 5521 |
|
- Sorting out hard-coded constants that prevented heat and fresh water conservation. |
| 5522 |
|
- Sorting out the various fields units and sign (set early on and reset at the end) |
| 5523 |
|
to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and |
| 5524 |
|
fresh water stock is 'effective ice meters', and >0 implies more ice/snow. |
| 5525 |
|
- Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks, |
| 5526 |
|
and simplifying logical expressions to further improve readibility. |
| 5527 |
|
part 3: seaice_growth.F revisions 1.86 to 1.89 |
| 5528 |
|
- Re-organize the blocks of code more logically. |
| 5529 |
|
- Merging the '_if.F' pieces that add something new. |
| 5530 |
|
o pkg/thsice: |
| 5531 |
|
- vectorize thsice_solve4temp and thsice_get_exf. |
| 5532 |
|
Problem: thsice_solve4temp has an unvectorizable statement that |
| 5533 |
|
might also be problematic for TAF |
| 5534 |
|
- thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This |
| 5535 |
|
does not change the verifcation experiment, but will change all |
| 5536 |
|
experiments that have this flag undefined (not tested in verification); |
| 5537 |
|
a little reorganization to save a few 2D fields and recomputations |
| 5538 |
|
- 1st step of revisiting thsice adjoint (major recomp. sorted out) |
| 5539 |
|
- 2nd step: fix some store dirs |
| 5540 |
|
o seems to work somewhat, i.e. using ifort but not g77 |
| 5541 |
|
o likely cause are incomplete init. or recomputation |
| 5542 |
|
o start verification/global_ocean.cs32x15/input_ad.thsice |
| 5543 |
|
o pkg/obcs: add support for exch2 |
| 5544 |
|
- the position of the boundary and prescribed values are specified using |
| 5545 |
|
a global domain with exch2 facets stacked |
| 5546 |
|
- in x for N,S boundaries (like W2_mapIO=-1) |
| 5547 |
|
- in y for E,W boundaries (so E,W boundaries do not overlap) |
| 5548 |
|
o pkg/mdsio: add support for writing global sections with exch2 |
| 5549 |
|
file layout is as for obcs described above: |
| 5550 |
|
- for x-z sections, facets are stacked in x (like W2_mapIO=-1) |
| 5551 |
|
- for y-z sections, facets are stacked in y |
| 5552 |
|
o pkg/thsice: |
| 5553 |
|
- change a few routines for better vectorization: thsice_albedo.F, |
| 5554 |
|
thsice_step_temp.F, and in thsice_calc_thickn.F. Results are |
| 5555 |
|
not affected, but in particular the latter routine has changed |
| 5556 |
|
dramatically (not necessarily easier to read now). |
| 5557 |
|
- re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops |
| 5558 |
|
iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF. |
| 5559 |
|
o verification/lab_sea: |
| 5560 |
|
- overhaul of the forward model experiments. The main motivation |
| 5561 |
|
for this revision is that lab_sea has proven quite fragile (when |
| 5562 |
|
changing the sea-ice code, and switching platforms) to a point |
| 5563 |
|
when failures were very hard to attribute to specific code problems. |
| 5564 |
|
- the suspected reason for this fragility is noise amplification by evp so, |
| 5565 |
|
to start with, we decided to replace evp with lsr in the main experiment. |
| 5566 |
|
- the input.lsr experiment thus became obsolete and was removed. |
| 5567 |
|
- it was replaced with the input.fd experiment that uses an |
| 5568 |
|
analytical "free drift" solution as the ice velocity field. |
| 5569 |
|
- Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp) |
| 5570 |
|
will hopefully allow us to discriminate problems due to dynamic solvers |
| 5571 |
|
from problems due to the thermodynamic code. input.salt_plume (lsr) allows |
| 5572 |
|
us to test additional options, along with the salt plume package. |
| 5573 |
|
- Finally a pickup was generated (at the end of a one year run) to |
| 5574 |
|
make the tests more representative of an actual model run. Previously |
| 5575 |
|
the tests starting point was a 1m thickness of ice everywhere. |
| 5576 |
|
o pkg/seaice: |
| 5577 |
|
- introducing S\R seaice_freedrift.F that compute the |
| 5578 |
|
analytical solution to an approximate ice momentum |
| 5579 |
|
equation (i.e. the simple stress/coriolis balance). |
| 5580 |
|
- define SEAICE_ALLOW_FREEDRIFT to trigger the computation |
| 5581 |
|
of the free drift velocity field, and enable its use. |
| 5582 |
|
To actually use the free drift solution as the model ice |
| 5583 |
|
velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice. |
| 5584 |
|
o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata" |
| 5585 |
|
|
| 5586 |
|
checkpoint62l (2010/10/04) |
| 5587 |
|
o pkg/seaice: |
| 5588 |
|
-fix the USE_ORIGINAL_SBI version (for variable freezing point); |
| 5589 |
|
-use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new |
| 5590 |
|
version (with USE_ORIGINAL_SBI undef); |
| 5591 |
|
o add hooks for new packages OASIS, the package will follow |
| 5592 |
|
(hooks exclude the seaice pkg for now) |
| 5593 |
|
o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO |
| 5594 |
|
Option to use mdsio_read_whalos.F/mdsio_write_whalos.F, |
| 5595 |
|
rather than mdsio_readvector.F/mdsio_writevector.F, within |
| 5596 |
|
adread_adwrite.F to read/write adjoint-related tapes to disk. |
| 5597 |
|
o eesupp and pkg/mdsio: ALLOW_WHIO |
| 5598 |
|
Option to write/read 2D fields to files including tiles halos. |
| 5599 |
|
The main purpose is for adjoint related "tape I/O". |
| 5600 |
|
The secondary purpose is for debugging phases. |
| 5601 |
|
A word on those rather specifically intended purposes. |
| 5602 |
|
The code was meant to be stripped down to the bare minimum. |
| 5603 |
|
Typically, there is a unique and basic mapping to the global |
| 5604 |
|
buffer (tile by tile, then proc by proc, then level by level), and |
| 5605 |
|
byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not |
| 5606 |
|
meant to generate user friendly outputs of various shapes and forms. |
| 5607 |
|
Rather it is intended, for the knowledgeabale developers, |
| 5608 |
|
to be largely independent of the many mdsio options, to allow |
| 5609 |
|
outputs of tiles+halos in debugging phases and in adjoint runs, |
| 5610 |
|
and to allow some flexibility in tuning (adoint) I/O depending on each |
| 5611 |
|
file system behavior. With regard to tuning, most of the potential knobs |
| 5612 |
|
(to leave files open, to allocate the I/O indep. of usesinglecpuio, |
| 5613 |
|
to specify directories, to specify the typical size of I/O calls, etc.) |
| 5614 |
|
are not yet included, and will be added if they prove useful. |
| 5615 |
|
o pkg/seaice: |
| 5616 |
|
fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F |
| 5617 |
|
o pkg/seaice: |
| 5618 |
|
new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty |
| 5619 |
|
code (seaice_budget_ice_if.F) which enable to recover old standard |
| 5620 |
|
code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined. |
| 5621 |
|
temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F. |
| 5622 |
|
o model/src (rStar): |
| 5623 |
|
use simple average (not area weighted) of rStarFac at U,V point when using |
| 5624 |
|
vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection) |
| 5625 |
|
update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20. |
| 5626 |
|
|
| 5627 |
|
checkpoint62k (2010/09/17) |
| 5628 |
|
o adjoint |
| 5629 |
|
* changed verification/global_ocean.cs32x15 ; adjoint now tests |
| 5630 |
|
Adams-Bashforth 3 + NLFS + RSTAR |
| 5631 |
|
* some more modifs required for ECCO-GODAE v4 |
| 5632 |
|
o pkg/seaice |
| 5633 |
|
add SEAICE_AGE_VOL option to use volume instead of area for |
| 5634 |
|
integrating SEAICE_AGE |
| 5635 |
|
o model/src: |
| 5636 |
|
first check-in of sigma & hybrid-sigma coordinate code ; also includes |
| 5637 |
|
non-linear free-surface parts ; but pressure-gradient not yet coded. |
| 5638 |
|
o pkg/ptracers: |
| 5639 |
|
option for ptracer to convert Salt Relax into additional EmP. |
| 5640 |
|
tested in exp. global_ocean.90x40x15.dwnslp (update output) |
| 5641 |
|
|
| 5642 |
|
checkpoint62j (2010/08/25) |
| 5643 |
|
o pkg/ggl90: |
| 5644 |
|
other minor changes: remove 3-D temp array gTKE (+ add argument myIter) |
| 5645 |
|
o pkg/dic: car_flux.F, phos_flux.F |
| 5646 |
|
- reduce number of exp-calls in order to improve performance |
| 5647 |
|
- clean up a little (replace fields by their macros, etc., fix |
| 5648 |
|
typo in CPP-flag) |
| 5649 |
|
o pkg/ggl90: minor changes |
| 5650 |
|
- GGL90diffKrS was removed --> always use GGL90diffKr |
| 5651 |
|
- GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV |
| 5652 |
|
- hack of mxlMaxFlag=2 --> ensure mixing between first and second level |
| 5653 |
|
(commented out for now) |
| 5654 |
|
- change in max/min operations to ensure that smoothing is ok |
| 5655 |
|
- smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr) |
| 5656 |
|
- always use diffKrNrT as background profile (i.e. never use diffKr field) |
| 5657 |
|
o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj) |
| 5658 |
|
o pkg/dic: |
| 5659 |
|
- model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better |
| 5660 |
|
vectorization |
| 5661 |
|
- small bug fix in insol for the unlikely case of a cartesian grid |
| 5662 |
|
- towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F |
| 5663 |
|
+ now vectorize, which also removes adjoint recomputations; |
| 5664 |
|
+ replace integer maksp1 by _RL maskp1 |
| 5665 |
|
+ replace a**x by exp(x*log(a)) in phos_flux.F for speed |
| 5666 |
|
|
| 5667 |
|
checkpoint62i (2010/07/21) |
| 5668 |
|
o pkg/flt: |
| 5669 |
|
- with OBCS: stop floats which enter the OB region |
| 5670 |
|
o model/src: |
| 5671 |
|
- use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones) |
| 5672 |
|
for implicit vertical advection. |
| 5673 |
|
o pkg/seaice: |
| 5674 |
|
- account for melting in seaice age evolution. |
| 5675 |
|
- remove double counting of seaice ridging effect on seaice age. |
| 5676 |
|
|
| 5677 |
|
checkpoint62h (2010/06/18) |
| 5678 |
|
o pkg/exch2: |
| 5679 |
|
- remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1). |
| 5680 |
|
o tools/genmake2 |
| 5681 |
|
- remove "-pdefault" option: redundant with the use of "packages.conf"; |
| 5682 |
|
- remove file pkg/pkg_default : set the default as a pkg group |
| 5683 |
|
("default_pkg_list") defined in pkg/pkg_groups; |
| 5684 |
|
- fix for case pkg/pkg_depend is missing (was hanging before); |
| 5685 |
|
- add option "-pgroups" to specify a different pkg_groups than the default. |
| 5686 |
|
o verification/adjustment.cs-32x32x1: |
| 5687 |
|
add a "minimal" set-up test (code_min & input_min) which only compiles |
| 5688 |
|
eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc. |
| 5689 |
|
o tools/genmake2 |
| 5690 |
|
- extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg])) |
| 5691 |
|
- fix details of checking for mnc & profile pkg when NetCDF is unavailable. |
| 5692 |
|
o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these |
| 5693 |
|
files are nearly the same anyway. |
| 5694 |
|
Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04: |
| 5695 |
|
- redefinition of tau(i,i) (by a factor of ustar) |
| 5696 |
|
- 1./exf(Const/T) -> exf(-Const/T) (big change in the results) |
| 5697 |
|
- replace rhonil by rhoConstFresh in computation of evap (bug fix) |
| 5698 |
|
- replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results) |
| 5699 |
|
- replace |
| 5700 |
|
rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh ) |
| 5701 |
|
shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j) |
| 5702 |
|
by |
| 5703 |
|
shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh ) |
| 5704 |
|
(changes results) |
| 5705 |
|
-> exf_bulkformulae v1.22, |
| 5706 |
|
update verification experiments lab_sea, offline_exf_seaice, seaice_obcs |
| 5707 |
|
(lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13, |
| 5708 |
|
output.txt 1.63 |
| 5709 |
|
offline_exf_seaice: output.seaicetd.txt 1.7 |
| 5710 |
|
seaice_obcs: output.txt 1.10) |
| 5711 |
|
Step 2: do the actual merge and remove exf_bulk_largeyeager04.F |
| 5712 |
|
-> exf_bulkformulae v1.23, |
| 5713 |
|
unfortunately requires updating lab_sea.salt_plume (6 matching digits), |
| 5714 |
|
and global_ocean.cs32x15.icedyn (only 11 matching digits) |
| 5715 |
|
Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice. |
| 5716 |
|
o adjoint of exch-1: |
| 5717 |
|
- pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list) |
| 5718 |
|
(note: was already like this when using EXCH-2) and remove flow dir |
| 5719 |
|
and hand-written AD version of high-level EXCH S/R (pkg/autodiff); |
| 5720 |
|
- provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow); |
| 5721 |
|
- update pkg/exch2 diff list. |
| 5722 |
|
|
| 5723 |
|
checkpoint62g (2010/05/19) |
| 5724 |
|
o eesupp/src (exch-1): |
| 5725 |
|
- split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F) |
| 5726 |
|
and remove argument "simulationMode"; same thing for all exch_*rx_cube.F |
| 5727 |
|
(renamed to exch1_*rx_cube.F). |
| 5728 |
|
- change accordingly exch_*_rx.template and AD version in pkg/autodiff |
| 5729 |
|
to call new exch1 S/R ; update Makefile and .cvsignore. |
| 5730 |
|
- replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove |
| 5731 |
|
exch2_xy_rx later) |
| 5732 |
|
Note: after updating your code, need to run "make clean" in eesupp/src |
| 5733 |
|
o test experiment bottom_ctrl_5x5: |
| 5734 |
|
new output_adm.txt with fewer grdchk & less monitor output. |
| 5735 |
|
o model/src: |
| 5736 |
|
remove the call to ini_cori in initialise_varia.F (just keep the usual one |
| 5737 |
|
in initialise_fixed.F). More consistent with coriolis & horizontal grid |
| 5738 |
|
beeing treated in the same way (ini_grid is not called a 2nd time). |
| 5739 |
|
o pkg/exf: |
| 5740 |
|
- rewrite exf_bulk_largeyeager04.F for better vectorization, changes |
| 5741 |
|
global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated |
| 5742 |
|
- fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now) |
| 5743 |
|
- cosmetic changes to exf_bulkformulae.F to make it look more like |
| 5744 |
|
exf_bulk_largeyeager04.F |
| 5745 |
|
o eesupp/src (exch-1): |
| 5746 |
|
- Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1). |
| 5747 |
|
- Separate buffer filling and MPI sending: allow EXCH-1 to work for local |
| 5748 |
|
array (non-shared) when using MPI+MTH. Also reduces number of BARRIER |
| 5749 |
|
(even without using MPI). |
| 5750 |
|
- Message mode: move RecvAck setting (indicator of buffer being ready) |
| 5751 |
|
from send_put to recv_get S/R (was useless before, but not sure if |
| 5752 |
|
it's much more useful now); |
| 5753 |
|
- Switch the order of sync: MPI-proc 1rst and then threads; |
| 5754 |
|
- take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead. |
| 5755 |
|
- fix AD code for communication mode ='get' (but not used). |
| 5756 |
|
o model/src: |
| 5757 |
|
initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does |
| 5758 |
|
not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp). |
| 5759 |
|
o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API |
| 5760 |
|
o pkg/ctrl: require a specific set of control variables and exf-flags for |
| 5761 |
|
adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied) |
| 5762 |
|
o model/src: |
| 5763 |
|
a) 1rst version of a new driver S/R to turn-off output freq and flags after the |
| 5764 |
|
1rst forward sweep, to avoid over-writing output files during recomputations |
| 5765 |
|
recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?) |
| 5766 |
|
b) 2nd version: |
| 5767 |
|
- add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO); |
| 5768 |
|
- switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast, |
| 5769 |
|
writePickupAtEnd) + seaice & ptracers output; |
| 5770 |
|
- do not switch off MNC flags (otherwise, won't get admonitor netcdf file) |
| 5771 |
|
o model/src: |
| 5772 |
|
- new S/R rotate_uv2en_rl (..._rs) that rotates vector fields. |
| 5773 |
|
o pkg/exch2: |
| 5774 |
|
- remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ; |
| 5775 |
|
- add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch). |
| 5776 |
|
o pkg/autodiff & exch2: |
| 5777 |
|
process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF |
| 5778 |
|
(for now, only if ALLOW_EXCH2 is defined). |
| 5779 |
|
o pkg/autodiff: |
| 5780 |
|
- include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F |
| 5781 |
|
(not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly. |
| 5782 |
|
+ clean-up comments (_RS is not always real*4) |
| 5783 |
|
- fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R) |
| 5784 |
|
- add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2: |
| 5785 |
|
was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs. |
| 5786 |
|
o testreport (AD-tests): |
| 5787 |
|
no longer link files from dir "../input" (1rst link files from |
| 5788 |
|
"../input_ad.[xx]" if secondary test "xx" and then from "../input_ad") |
| 5789 |
|
|
| 5790 |
|
checkpoint62f (2010/04/29) |
| 5791 |
|
o model/src/the_main_loop.F: |
| 5792 |
|
adjust store directives for seaice evp and multicategory according to |
| 5793 |
|
pkg/ecco/the_main_loop.F |
| 5794 |
|
o adjoint: |
| 5795 |
|
global_sum_ad was incomplete (noted many times by many people ;) |
| 5796 |
|
nice description by Jean U. as follows: |
| 5797 |
|
* allreduce(var) in global_sum.F can be interpreted as |
| 5798 |
|
reduce(sum) followed by broadcast of sum. |
| 5799 |
|
* The adjoint of that is |
| 5800 |
|
sum(adjoint) followed by broadcast(summed adjoint value) |
| 5801 |
|
or in other words, allreduce(sum, adjoint vars) |
| 5802 |
|
We were missing the sum(adjoint)! |
| 5803 |
|
Benign, except(!) for "global" scalars appearing in tile loops (bi,bj) |
| 5804 |
|
(noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset). |
| 5805 |
|
The fix should produce 16-digit accuracy between |
| 5806 |
|
single-CPU multi-tile (e.g. nSx=2, nPx=1) and |
| 5807 |
|
multi-CPU single-tile (e.g. nSx=1, nPx-2) |
| 5808 |
|
We'll probably change this yet again shortly |
| 5809 |
|
o eesupp/src: |
| 5810 |
|
- fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?) |
| 5811 |
|
o pkg/icefront |
| 5812 |
|
- ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving |
| 5813 |
|
specification of addmass array based on a 2D field, which is added |
| 5814 |
|
at bottommost wet level at each horizontal location. |
| 5815 |
|
o model/src: |
| 5816 |
|
horizontal grid initialisation (other than curvilinear): add code for Exch2 IO |
| 5817 |
|
layout; (not always compatible with delX,delY setting; commented out for now). |
| 5818 |
|
o pkg/exch2: |
| 5819 |
|
change tile to processor setting (case nSy*nPy > 1): allows default model mapping |
| 5820 |
|
(myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config. |
| 5821 |
|
|
| 5822 |
|
checkpoint62e (2010/04/15) |
| 5823 |
|
o pkg/obcs: |
| 5824 |
|
- fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert). |
| 5825 |
|
o pkg/dic: |
| 5826 |
|
-fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up; |
| 5827 |
|
(note: not presently tested in any forward verification exp.) |
| 5828 |
|
update tutorial_global_oce_biogeo AD output file. |
| 5829 |
|
o pkg/exf: |
| 5830 |
|
- account for the variation of albedo as a function of zenith angle |
| 5831 |
|
by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h |
| 5832 |
|
o build_options: |
| 5833 |
|
- rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas" |
| 5834 |
|
o pkg/dic: |
| 5835 |
|
change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart: |
| 5836 |
|
- use binary pickup file for restart; |
| 5837 |
|
- initialise atmos-CO2 box from dic_pCO2 parameter; |
| 5838 |
|
- fix multi-threaded. |
| 5839 |
|
o pkg/rbcs: |
| 5840 |
|
- clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ; |
| 5841 |
|
change (+ fix IO calls) type of array RBC_mask from _RL to _RS. |
| 5842 |
|
- add RBCS to exp4 passive tracer 01 (rbcs was previously untested) |
| 5843 |
|
and update output.txt |
| 5844 |
|
o pkg/kpp: |
| 5845 |
|
- add diagnostics for KPP non-local flux of Temp, Salinity and pTracers; |
| 5846 |
|
- change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS |
| 5847 |
|
(= ratio of KPP non-local (salt) flux relative to surface-flux) when |
| 5848 |
|
using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat '); |
| 5849 |
|
- change pkg/offline to read-in average KPPghat*KPPdiffKzS from file |
| 5850 |
|
KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile). |
| 5851 |
|
o pkg/offline: |
| 5852 |
|
fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor |
| 5853 |
|
(bug was added in version 1.10 on 2007-08-23). |
| 5854 |
|
o pkg/offline: |
| 5855 |
|
- no need to specify periodicExternalForcing, etc ... to use offline pack |
| 5856 |
|
- offline input files no longer just single prec --> parameter offlineLoadPrec |
| 5857 |
|
o verification/lab_sea: |
| 5858 |
|
change AD test to multi-tile setup and update all 4 AD output. |
| 5859 |
|
NOTE: while cost function values remain very similar, |
| 5860 |
|
gradients are very different, although gradient checks are self-consistent |
| 5861 |
|
Should try to get to the bottom of this (cost function summation order?) |
| 5862 |
|
o pkg/dic: |
| 5863 |
|
in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid |
| 5864 |
|
a weakness of TAF that drops part of double precision in log10 derivative. |
| 5865 |
|
<= changes removed since problem has been fixed in current TAF version 1.9.71 |
| 5866 |
|
update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo. |
| 5867 |
|
o pkg/ecco: |
| 5868 |
|
add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F |
| 5869 |
|
update all 4 lab_sea AD output. |
| 5870 |
|
|
| 5871 |
|
checkpoint62d (2010/03/22) |
| 5872 |
|
o build_options: |
| 5873 |
|
remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles. |
| 5874 |
|
o remove unbalanced quote (single or double) in commented line of source code |
| 5875 |
|
(may cause some warning with some preprocessor/makedepend versions). |
| 5876 |
|
o pkg/seaice: |
| 5877 |
|
fix seaice_model.F for adjoint (gael) and update AD results of experiments |
| 5878 |
|
lab_sea (std + evp + noseaicedyn) and offline_exf_seaice. |
| 5879 |
|
o testreport: |
| 5880 |
|
add option '-runonly' (short: '-ro') to just do the run part (without make). |
| 5881 |
|
o eesupp: remove JAM communication code (obsolete). |
| 5882 |
|
o add option to genmake2 & testreport to switch "_RS" type to "real*4" |
| 5883 |
|
(if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return |
| 5884 |
|
to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1 |
| 5885 |
|
(update also the output). |
| 5886 |
|
|
| 5887 |
|
checkpoint62c (2010/03/02) |
| 5888 |
|
o tools/build_options : |
| 5889 |
|
move (some) old optfiles from build_options/ to build_options/unsupported/ |
| 5890 |
|
o model/src and pkg/exf |
| 5891 |
|
surface relaxation -- separating data and data.exf options |
| 5892 |
|
The point is to ensure that we specify the surface relaxation |
| 5893 |
|
either in data or in data.exf (but not half and half) and to |
| 5894 |
|
avoid an accidental relaxation to 0 (which happened if a time |
| 5895 |
|
scale was specified but the file name was left empty) |
| 5896 |
|
o model/src model/inc and pkg/mom_common |
| 5897 |
|
ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity |
| 5898 |
|
=> addition to the viscosity field as computed by others schemes |
| 5899 |
|
o tools/build_options: |
| 5900 |
|
- rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile) |
| 5901 |
|
but keep the former optfile for few weeks for smooth transition |
| 5902 |
|
o pkg/ecco |
| 5903 |
|
- allow user defined cost function contributions |
| 5904 |
|
CPP: ALLOW_USERCOST_CONTRIBUTION |
| 5905 |
|
USAGE: compute contributions in cost_usercost_all.F |
| 5906 |
|
- note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. |
| 5907 |
|
the two options are complementary. |
| 5908 |
|
o pkg/smooth |
| 5909 |
|
- migration from contrib to the main repository |
| 5910 |
|
|
| 5911 |
|
checkpoint62b (2010/01/26) |
| 5912 |
|
o pkg/monitor: |
| 5913 |
|
- change back mon_printstats_rl.F & mon_stats_rl.F and add a stop |
| 5914 |
|
(in case someone forgot to update customized pieces of code) |
| 5915 |
|
o nonHydrostatic: |
| 5916 |
|
- add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested); |
| 5917 |
|
- add a simple 2-D experiment (short_surf_wave) to test it. |
| 5918 |
|
o pkg/icefront: |
| 5919 |
|
adding the shell of, and the hooks to, a new package that |
| 5920 |
|
will model melting and freezing of vertical glacier ice fronts |
| 5921 |
|
o momentum: |
| 5922 |
|
add diagnostics of momentum tendency from Hydrostatic pressure gradient |
| 5923 |
|
(without surf.pressure term: would need a 2nd filling since implicit term). |
| 5924 |
|
o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace |
| 5925 |
|
two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR |
| 5926 |
|
cannot deal with the former |
| 5927 |
|
o cleaning: |
| 5928 |
|
- remove all (except OpenAD) old TLM output from results_ad dirs. |
| 5929 |
|
- remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R) |
| 5930 |
|
- comment out maskH definition (replaced by maskInC) |
| 5931 |
|
o pkg/monitor: |
| 5932 |
|
- change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl |
| 5933 |
|
& mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs. |
| 5934 |
|
|
| 5935 |
|
checkpoint62a (2010/01/15) |
| 5936 |
|
o model/src: |
| 5937 |
|
- bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4) |
| 5938 |
|
o pkg/diagnostics: |
| 5939 |
|
- add optional level number diagnostics (i.e., level number to be define |
| 5940 |
|
explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X". |
| 5941 |
|
- strictly check for valid parser-code(10) ; |
| 5942 |
|
- check if adding diag to the list from the right place. |
| 5943 |
|
o pkg/longstep: |
| 5944 |
|
- change parameters and fix tracer conservation with rstar/nonlinear free surface |
| 5945 |
|
o diagnostics: |
| 5946 |
|
- in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer |
| 5947 |
|
S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics. |
| 5948 |
|
o pkg/diagnostics: |
| 5949 |
|
- Add option for writing vertical integral (sum of selected levels) of an output |
| 5950 |
|
field instead of writing output field levels. Activate this option on a per |
| 5951 |
|
output-file basis, by setting the 2nd character of fileflag to 'I'. |
| 5952 |
|
- Add field-specific information relative to level integral in 3rd postion |
| 5953 |
|
of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate |
| 5954 |
|
vertically (x level-thickness x hFac), "r"=same but without hFac. |
| 5955 |
|
o do_the_model_io: |
| 5956 |
|
- pass end-of-model-run flag as argument, from forward_step to diagnostics_write: |
| 5957 |
|
in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before |
| 5958 |
|
writing pickups and stopping. |
| 5959 |
|
o pkg/diagnostics (for now, only with mdsio): |
| 5960 |
|
- write time information to meta file (and modify accordingly rdmds.m) : |
| 5961 |
|
time-averaged diagnostics output: write starting and ending time of the |
| 5962 |
|
time-averaging interval ; snap-shot diagnostics output remains unchanged; |
| 5963 |
|
o pkg/timeave: |
| 5964 |
|
- S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously |
| 5965 |
|
always Nr), now assumed to be equal to number of levels of averaged field; |
| 5966 |
|
only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F |
| 5967 |
|
o pkg/sbo: |
| 5968 |
|
- fix ocean bottom pressure global-average & 2-D time-ave output (was |
| 5969 |
|
neither initialised nor filled). |
| 5970 |
|
- add starting iteration in suffix of global-average output file |
| 5971 |
|
(to avoid over-writing the file after a restart) |
| 5972 |
|
- use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb). |
| 5973 |
|
o time-average: |
| 5974 |
|
- use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj) |
| 5975 |
|
(pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf, |
| 5976 |
|
ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice) |
| 5977 |
|
this fix DIC_COST cumulative-time array (previously: bi,bj,k) |
| 5978 |
|
- fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice) |
| 5979 |
|
- fix missing accumulation for pkg/opps. |
| 5980 |
|
- cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0) |
| 5981 |
|
(pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81); |
| 5982 |
|
- fix initialisation of time-ave vars and do only full time-step increment |
| 5983 |
|
(i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81); |
| 5984 |
|
o pkg/layers: |
| 5985 |
|
- use standard RW pkg S/R to write the output |
| 5986 |
|
and remove local write_fld version (which had a problem). |
| 5987 |
|
- use simple cumulative-time array (no level index) to fix time-ave S/R calls. |
| 5988 |
|
- fix LAYERS_CALC argument list. |
| 5989 |
|
o pkg/timeave: |
| 5990 |
|
- store cumulative-time in a simple tiled array (drop the level index) |
| 5991 |
|
- add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array. |
| 5992 |
|
o pkg/ocn,aim_compon_interf |
| 5993 |
|
- changes for multi-threaded coupled run. (tested with ifort-11 on danton) |
| 5994 |
|
|
| 5995 |
|
checkpoint62 (2009/12/23) |
| 5996 |
|
o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output. |
| 5997 |
|
(was not previously tested in any other exp.) |
| 5998 |
|
o pkg/monitor: |
| 5999 |
|
- clean-up _RL/_RS version: add specific S/R for statistics with mask & volume: |
| 6000 |
|
mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one |
| 6001 |
|
(mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics. |
| 6002 |
|
- use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F). |
| 6003 |
|
- change del2 calculation. |
| 6004 |
|
- use interior masks (instead of maskH, <- to be remove). |
| 6005 |
|
- shorter monitor suffix for forcing stats ("forcing" instead of "extforcing"). |
| 6006 |
|
o mask & obcs: |
| 6007 |
|
- define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S). |
| 6008 |
|
- move global area computation from ini_masks_etc.F to ini_linear_phisurf.F |
| 6009 |
|
(called after packages_init_fixed) |
| 6010 |
|
o pkg/obcs: |
| 6011 |
|
- move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once. |
| 6012 |
|
Fixes bug in obcs+exf with nSx*nSy.GT.1 |
| 6013 |
|
- fix multi-tile handling in obcs balance code |
| 6014 |
|
o nonHydrostatic: |
| 6015 |
|
- Implement AB-3 for non-hydrostatic vertical momentum ; |
| 6016 |
|
(change ordering of var. stored in pickup file when using NH) |
| 6017 |
|
- move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D. |
| 6018 |
|
- add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x |
| 6019 |
|
(in prep. for new NH free surface form). |
| 6020 |
|
o pkg/obcs: |
| 6021 |
|
add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe |
| 6022 |
|
o model/src: |
| 6023 |
|
fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography |
| 6024 |
|
|
| 6025 |
|
checkpoint61z (2009/12/01) |
| 6026 |
|
o nonHydrostatic: |
| 6027 |
|
Fix missing vertical flux of vert. momentum near surface (k=1). This fixes |
| 6028 |
|
a spurious source of energy in simple baroclinic adjusment test case. |
| 6029 |
|
Update all non-hydrostatic exp output. |
| 6030 |
|
o model/src (3-d solver): |
| 6031 |
|
Change again 3-D solver free-surface RHS term when exactConserv=T: |
| 6032 |
|
simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1 |
| 6033 |
|
(which was not the case with previous formulation). |
| 6034 |
|
To recover previous version, just reset "oldFreeSurfTerm" to previous value. |
| 6035 |
|
Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW. |
| 6036 |
|
o nonHydrostatic: |
| 6037 |
|
- compatible with implicDiv2Dflow < 1 ; + implement implicit factor |
| 6038 |
|
for Non-Hydrostatic pressure gradient (similar to implicSurfPress). |
| 6039 |
|
- change 3-D solver to work with r* (for now, only with linear free-surf.) |
| 6040 |
|
- add few debug diagnostics (cg3d_x, residual) |
| 6041 |
|
o model/src: |
| 6042 |
|
fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b). |
| 6043 |
|
update output of exp. global_ocean.cs32x15.viscA4 |
| 6044 |
|
o update output of exp. global_ocean.cs32x15.icedyn after removing |
| 6045 |
|
#define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h |
| 6046 |
|
o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) |
| 6047 |
|
o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output |
| 6048 |
|
for complex grids, for now only to "state", "adstate", "adexf", "adseaice" |
| 6049 |
|
o model: add Christopher Wolfe's implemetation of the single reduction cg2d |
| 6050 |
|
(d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and |
| 6051 |
|
runtime flag useSRCGSolver. Modify verification experiment global_with_exf |
| 6052 |
|
to test this code |
| 6053 |
|
o pkg/cd_code: |
| 6054 |
|
Change defaut D-grid time-stepping to get the same for D-grid momentum as for |
| 6055 |
|
C-grid momentum. D-grid velocity used to be stepped forward in time with |
| 6056 |
|
Adams-Bashforth only on surface pressure term. Tests show that using AB on |
| 6057 |
|
D-grid coriolis term improves stability (as expected from CD-scheme paper). |
| 6058 |
|
To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h). |
| 6059 |
|
Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2), |
| 6060 |
|
lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD), |
| 6061 |
|
tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens. |
| 6062 |
|
Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2, |
| 6063 |
|
global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD. |
| 6064 |
|
o pkg/obcs: |
| 6065 |
|
- fix bug in initialisation (broken since Oct 1rst modification) |
| 6066 |
|
for useOBCSprescribe without useEXF. |
| 6067 |
|
|
| 6068 |
|
checkpoint61y (2009/11/15) |
| 6069 |
|
o pkg/seaice |
| 6070 |
|
- change (once again) the discretization for the evp solver: rather than |
| 6071 |
|
squaring the averages of strain rates, average the squares to give |
| 6072 |
|
a better approximation to VP behavior (in simple test); this breaks |
| 6073 |
|
verification experiments that use EVP (lab_sea and lab_sea.hb87) |
| 6074 |
|
--> update outputs |
| 6075 |
|
o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit) |
| 6076 |
|
to improve vectorization of adjoint code on TARGET_NEC_SX |
| 6077 |
|
o verification/vermix: |
| 6078 |
|
- change vermix to a more "classical" 1d column with high vertical |
| 6079 |
|
resolution, seasonal heat flux forcing and constant wind forcing |
| 6080 |
|
--> update outputs |
| 6081 |
|
o pkg/seaice |
| 6082 |
|
- fix diagnostics of principal stress components for EVP |
| 6083 |
|
- add optional diagnostics of non-linear convergence for LSOR solver |
| 6084 |
|
- make maximum zeta a runtime parameter |
| 6085 |
|
o model/src (3-d solver): |
| 6086 |
|
Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49), |
| 6087 |
|
which consisted in removing the Surf. Non-Hydrostatic pressure from the |
| 6088 |
|
whole column and adding it to Eta (inspired from Casualli, 1999): |
| 6089 |
|
Only affects 3-D solver initial guess and only if using ExactConserv, |
| 6090 |
|
but tests did show a degradation of solver convergence. For this reason, |
| 6091 |
|
decide to disable this piece of code. |
| 6092 |
|
to recover previous version, just set zeroPsNH = exactConserv (line 78). |
| 6093 |
|
Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW |
| 6094 |
|
o pkg/ggl90: |
| 6095 |
|
- fix previous modif (unfortunatly has not been documented here). |
| 6096 |
|
o pkg/seaice/autodiff: |
| 6097 |
|
- add CPP flag to include clipping of zeta in EVP code; |
| 6098 |
|
although clipping of zeta is not necessary for EVP and not recommended |
| 6099 |
|
it was done by default, now clipping is disabled by default |
| 6100 |
|
- modify computation and store zetaC/Z in seaice_evp for TAF |
| 6101 |
|
- add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default) |
| 6102 |
|
- change seaice_calc_viscosities/strainrates for better |
| 6103 |
|
vectorization after AD by TAF |
| 6104 |
|
- rearrange common blocks in SEAICE.h once again for easier dumps of |
| 6105 |
|
adjoint output, adjust adcommon.h and g_common.h |
| 6106 |
|
- change flux form of default advection scheme for better vectorization |
| 6107 |
|
of adjoint code |
| 6108 |
|
- modify lab_sea/input.lsr to test the flux form of default advection |
| 6109 |
|
scheme |
| 6110 |
|
o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level |
| 6111 |
|
transition in checkpoint61r) |
| 6112 |
|
|
| 6113 |
|
checkpoint61x (2009/10/19) |
| 6114 |
|
o adjoint: adding two new verification experiments |
| 6115 |
|
* tutorial_global_biogeo: an online dic sensitivity experiment |
| 6116 |
|
(work with G. Forget) |
| 6117 |
|
* tutorial_dic_adjoffline: an offline dic sensitivity experiment |
| 6118 |
|
(an update of the Dutkiewicz et al., 2006 paper) |
| 6119 |
|
Both use the same CO2FLUX cost function, but different controls |
| 6120 |
|
Gradient checks look good, but some recomp. could still be traightened out |
| 6121 |
|
Should add xx_dic control variable to test at some point |
| 6122 |
|
o model/src: |
| 6123 |
|
add run-time parameters to check and/or mask initial Temp & Salt |
| 6124 |
|
o pkg/ptracers: |
| 6125 |
|
apply zonal filter (if used) to all passive tracers |
| 6126 |
|
|
| 6127 |
|
checkpoint61w (2009/10/12) |
| 6128 |
|
o adjoint: |
| 6129 |
|
* update and finish work on adjoint of dic package (G. Forget) |
| 6130 |
|
* start adjoint of offline package |
| 6131 |
|
* bug fix for cube-sphere TLM code (active_file_g.F) |
| 6132 |
|
o tutorial_global_oce_optim: |
| 6133 |
|
now tested with 4 tiles (change data.grdchk and update output_adm.txt) |
| 6134 |
|
and add SIZE.h_mpi for MPI testing |
| 6135 |
|
o pkg autodiff |
| 6136 |
|
- fix bug in autodiff_restore |
| 6137 |
|
- make genmake2 remove comments and empty lines from ad_input_code.f in |
| 6138 |
|
order to reduce file size (new script file remove_comments_sed) |
| 6139 |
|
o allows to specify vertical profile of vertical viscosity (viscArNr) |
| 6140 |
|
o pkg autodiff |
| 6141 |
|
autodiff_ini_model_io: comment out writing of grid information to netcdf |
| 6142 |
|
files, because at this time the grid fields are a bunch of zeros |
| 6143 |
|
(this is analogous to ini_mnc_vars.F) |
| 6144 |
|
o pkg seaice/autodiff: |
| 6145 |
|
left-over from removing the 3-time-level fields: |
| 6146 |
|
- small rearrangement of common blocks (SEAICE.h) |
| 6147 |
|
- fix field declaration in order to get meaningful output in |
| 6148 |
|
adseaice.*.nc (adcommon.h) |
| 6149 |
|
o pkg obcs: |
| 6150 |
|
- go through NH code only if nonHydrostatic=T |
| 6151 |
|
- fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart) |
| 6152 |
|
- move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields |
| 6153 |
|
=> Update output of experiment seaice_obcs |
| 6154 |
|
- useOBCSbalance: code is wrong with multi-tile / proc: add a stop. |
| 6155 |
|
- fix NH+Orlanski restart (add wvel OBC value in pickup file) |
| 6156 |
|
- fix restart for useOBCSprescribe + useEXF |
| 6157 |
|
o pkg ctrl |
| 6158 |
|
- make obcs as control parameter work also with useSingleCPUio |
| 6159 |
|
- replace a few sny and snx by Ny and Nx to be consistent with |
| 6160 |
|
ctrl_set_globfld_x/yz.F |
| 6161 |
|
o pkg seaice |
| 6162 |
|
- re-introduce global field frWtrAtm for the case of |
| 6163 |
|
ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F) |
| 6164 |
|
- catch the case of an empty filename in seaice_cost_init_fixed.F |
| 6165 |
|
o pkg ecco: |
| 6166 |
|
- small bug fixes in the_main_loop |
| 6167 |
|
. fix order of monitor arguments |
| 6168 |
|
. change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY |
| 6169 |
|
. move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so |
| 6170 |
|
that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF |
| 6171 |
|
- replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the |
| 6172 |
|
imbalance diagnostics for wmean_h/sflux = 0 |
| 6173 |
|
- add actual values to f_obcsn/s/w/e in ecco_cost_final.F |
| 6174 |
|
- catch the case of empty filenames in ecco_cost_init_fixed.F |
| 6175 |
|
and ecco_readparms.F |
| 6176 |
|
- fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta) |
| 6177 |
|
to make this statement meaningfull in ecco_cost_weights.F |
| 6178 |
|
o pkg zonal_filt: |
| 6179 |
|
- change ZONAL_FILTER S/R interface (allows to filter 2-D fields) |
| 6180 |
|
- when using rStar, filter uVel*hFacW instead of uVel |
| 6181 |
|
(tested without topography: fix a Pb of growing instability with NLFS) |
| 6182 |
|
o pkg/aim/thsice: |
| 6183 |
|
-Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F |
| 6184 |
|
(works as SST restoring) |
| 6185 |
|
o pkg/thsice: |
| 6186 |
|
-add specific parameter for salt restoring in slab mixed-layer |
| 6187 |
|
(by default equal to the temperature restoring) |
| 6188 |
|
|
| 6189 |
|
checkpoint61v (2009/09/21) |
| 6190 |
|
o pkg/kpp: |
| 6191 |
|
-add double diffusive contributions as a hack, turned off by default |
| 6192 |
|
for now, and the code can be excluded with a CPP-flag |
| 6193 |
|
EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX |
| 6194 |
|
-add a verification experiments to "vermix" to test this code |
| 6195 |
|
o pkg/mom_common: |
| 6196 |
|
Move computation of length scales to mom_init_fixed.F (avoid recomputation |
| 6197 |
|
at each time-steps*levels). |
| 6198 |
|
o pkg/layers: |
| 6199 |
|
Created a new package for computing volume fluxes in temperature or |
| 6200 |
|
[not yet implemented] density layers, e.g. for calculating residual |
| 6201 |
|
overturning circulations. |
| 6202 |
|
o pkg/diagnostics: |
| 6203 |
|
implement a RS type version for the set of DIAGNOSTICS-FILL subroutines |
| 6204 |
|
o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option) |
| 6205 |
|
o pkg/mdsio (& pkg/rw): rework high level S/R interface: |
| 6206 |
|
To avoid mixing type (RS/RL) of input/output array argument, |
| 6207 |
|
replace single mixed-type array with a pair from each type (RS/RL). |
| 6208 |
|
o setting pickupSuff force to start from a pickup (even if nIter0=0): this |
| 6209 |
|
is now implemented for all pkgs (previously only done for the main pickup) |
| 6210 |
|
|
| 6211 |
|
checkpoint61u (2009/08/25) |
| 6212 |
|
o pkg/obcs: |
| 6213 |
|
- change OB?eta from _RS to _RL and put them into a separate commen block |
| 6214 |
|
- add code to read OB?eta from a file via obcs_prescribe_read: the code |
| 6215 |
|
compiles and does not destroy any other experiments, the data is read |
| 6216 |
|
properly, but the code is not tested in actual applications |
| 6217 |
|
o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to |
| 6218 |
|
create a meaningful unit attribute for the time coordinate variable |
| 6219 |
|
o pkg/ebm: add plenty of missing "_d 0" ; |
| 6220 |
|
update results of experiment global_ocean_ebm (fwd + adjoint tests) |
| 6221 |
|
Notes: several pieces of code only works for (very) specific set up |
| 6222 |
|
(domain size, lat range, etc ...); should be documented & stop if one |
| 6223 |
|
of those assumptions is not meet. |
| 6224 |
|
o pkg/seaice: add missing "_d 0" in HSNOW initialisation |
| 6225 |
|
update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests) |
| 6226 |
|
and offline_exf_seaice (seaicetd + adjoint). |
| 6227 |
|
o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC): |
| 6228 |
|
update results of experiments: lab_sea (4 fwd tests + 3 adjoint), |
| 6229 |
|
seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2). |
| 6230 |
|
o few changes to pass when compiling with strick checking of arguments |
| 6231 |
|
across S/R (allow to find few bugs in S/R calls). |
| 6232 |
|
o pkg/seaice: |
| 6233 |
|
- seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new |
| 6234 |
|
2d-fields, for slightly better performance |
| 6235 |
|
|
| 6236 |
|
checkpoint61t (2009/07/22) |
| 6237 |
|
o pkg/seaice: |
| 6238 |
|
- remove unused variables in seaice_evp |
| 6239 |
|
- reduce number of SQRT in seaice_evp and seaice_calc_viscosities |
| 6240 |
|
o eeset_parms.F, open_copy_data_file.F & ini_parms.F: |
| 6241 |
|
named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT): |
| 6242 |
|
each processor opens a different file (a fix from Matt). |
| 6243 |
|
o cg2d: |
| 6244 |
|
use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F : |
| 6245 |
|
this reduces number of EXCH calls by 2 when using exch2. |
| 6246 |
|
For now, keep previous size array for gc2d_nsa.F to avoid Pb with store |
| 6247 |
|
directives and missing simple EXCH (exch_s3d_rx) adjoint code. |
| 6248 |
|
o pkg/thsice: |
| 6249 |
|
add code for Near Infra-Red albedo (from Jeff) |
| 6250 |
|
(turned on with run-time flag: thSIce_calc_albNIR, in data.ice). |
| 6251 |
|
o ini_model_io: |
| 6252 |
|
move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F |
| 6253 |
|
MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F |
| 6254 |
|
to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice. |
| 6255 |
|
|
| 6256 |
|
checkpoint61s (2009/06/30) |
| 6257 |
|
o pkg/exch2 (exch2_rxN_cube*): |
| 6258 |
|
remove last BARRIER (no need to synchronise after getting data from shared |
| 6259 |
|
buffer (get) as long as any change to buffer (put,recv) is between BARRIER) |
| 6260 |
|
o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH |
| 6261 |
|
and generate new output (for the 2 tests) using default rotationPeriod. |
| 6262 |
|
o pkg/exch2: |
| 6263 |
|
- always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F |
| 6264 |
|
(was already the case with AUTODIFF_EXCH2 defined) |
| 6265 |
|
- add bj in exch2 arrays and S/R. |
| 6266 |
|
- can now use pkg/exch2 for regular (non CS) set-up; switch test experiment |
| 6267 |
|
MLAdjust to exch2 (identical results except with MPI -> truncation diff); |
| 6268 |
|
o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep |
| 6269 |
|
- adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY |
| 6270 |
|
GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT |
| 6271 |
|
- verification experiment natl_box.longstep |
| 6272 |
|
o build_options: ifort+mpi_aces optfile (following Constantinos advise): |
| 6273 |
|
allow different versions of ifort (8 or 9) and different versions |
| 6274 |
|
of mpi (mpich or mpich2) to be used with the same optfile. |
| 6275 |
|
requires to load a netcdf module and set MPI_INC_DIR (see comments inside |
| 6276 |
|
optfile). Change testing scripts (example_scripts/ACESgrid) accordingly. |
| 6277 |
|
o pkg/seaice: |
| 6278 |
|
fix previous modif (3-level field removed) for old-pickup reading |
| 6279 |
|
|
| 6280 |
|
checkpoint61r (2009/06/25) |
| 6281 |
|
o pkg/seaice: |
| 6282 |
|
- clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps: |
| 6283 |
|
1. introduce fields for time step (N-1) |
| 6284 |
|
2. do not use levels 2 and 3 anymore (but keep them) |
| 6285 |
|
3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This |
| 6286 |
|
includes changes to pkg/thsice/thsice_get_velocity.F, |
| 6287 |
|
model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and |
| 6288 |
|
pkg/obcs/obcs_apply_uvice.F. |
| 6289 |
|
- completely remove code for leap-frog time stepping for second order |
| 6290 |
|
advection |
| 6291 |
|
- adjusted adjoint accordingly; |
| 6292 |
|
gradient checks have improved by an order of magnitude! |
| 6293 |
|
|
| 6294 |
|
checkpoint61q (2009/06/22) |
| 6295 |
|
o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver |
| 6296 |
|
- the boundary conditions along open boundaries are unclear, because the |
| 6297 |
|
associated masks are set to zero and are thus treated as closed when |
| 6298 |
|
applying the slip-boundary conditions. |
| 6299 |
|
- move initialisation of grid variables from seaice_init_varia to _fixed |
| 6300 |
|
o adding doc/diags_changes.txt |
| 6301 |
|
o model/src: |
| 6302 |
|
do_the_model_io: rename few pkg S/R which are called from do_the_model_io, |
| 6303 |
|
to avoid "_diags" naming if no relation to pkg/diagnostics. |
| 6304 |
|
ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF |
| 6305 |
|
file and only call PLOT_FIELD_XYZ if debugMode=T. |
| 6306 |
|
remove few PLOT_FIELD_XY calls outside initialisation. |
| 6307 |
|
remove few unnecessary BARRIER. |
| 6308 |
|
o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling |
| 6309 |
|
of salt_plume package in Southern Ocean |
| 6310 |
|
o pkg/thsice: |
| 6311 |
|
- fix hOceMxL in overlap (needed for sea-ice advection); |
| 6312 |
|
update output of experiment global_ocean.cs32x15.icedyn. |
| 6313 |
|
o pkg/seaice: |
| 6314 |
|
- make the (placeholder-)tracer IceAge a little more meaningful |
| 6315 |
|
by avoiding ridging of age due to convergent ice flow |
| 6316 |
|
- add diagnostics for surface temperature, atmospheric and oceanic |
| 6317 |
|
heat flux, and atmospheric and oceanic ice growth |
| 6318 |
|
|
| 6319 |
|
checkpoint61p (2009/06/10) |
| 6320 |
|
o eesupp (global_max & global_sum): |
| 6321 |
|
- add one more element to buffer (start at index 0) for GL_MAX/SUM output; |
| 6322 |
|
- remove starting & endding barrier (no longer needed) |
| 6323 |
|
o pkg/mdsio, writelocal: |
| 6324 |
|
works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined |
| 6325 |
|
(remove the STOP): uses shared buffer IO to store data from all threads |
| 6326 |
|
and then let master-thread write nThreads tiles. |
| 6327 |
|
o pkg/mdsio (read/write field): |
| 6328 |
|
- tiled IO done in 1 piece (all levels at a time); |
| 6329 |
|
- new header file "MDSIO_BUFF_3D.h" with 3-D buffers. |
| 6330 |
|
- multi-threaded: allow to read/write local (non-shared) array |
| 6331 |
|
(was already working with singleCpuIO ; now works also without); |
| 6332 |
|
=> no longer needs barrier call after reading a file (added inside |
| 6333 |
|
mds_read/write field). |
| 6334 |
|
- move barrier calls outside gather/scatter_2d to mds_read/write_field |
| 6335 |
|
o pkg/obcs/exf |
| 6336 |
|
- exf_getffieldrec.F: add a few ". _d 0" and |
| 6337 |
|
add code to catch the case fldperiod = 0. |
| 6338 |
|
- obcs_precribe_read.F: change if statements so that they match |
| 6339 |
|
the variable type (_RL) |
| 6340 |
|
- add a separate exf_iprec_obcs to exf_set_obcs (by default equal to |
| 6341 |
|
exf_iprec) as part of namelist EXF_NML_01 |
| 6342 |
|
o pkg/mdsio: |
| 6343 |
|
- read/write tiled (local) files: read/write 1-level tile chunk at a time |
| 6344 |
|
(instead of segment of length sNx); expected to speed up tiled IO. |
| 6345 |
|
o pkg/exch2: |
| 6346 |
|
- take buffer copy from/to array out of S/R exch2_send/recv into new |
| 6347 |
|
S/R exch2_put/get ; Exch of local variable now works with MPI+MTH |
| 6348 |
|
(tested by removing commom block statement in SOLVE_FOR_PRESSURE.h). |
| 6349 |
|
- ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get) |
| 6350 |
|
- simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds |
| 6351 |
|
(which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by |
| 6352 |
|
including Topology header file (and common blocks). |
| 6353 |
|
- implement EXCH_IGNORE_CORNERS in scalar exchange (rx1); |
| 6354 |
|
remove 2nd exch call in exch2_s3d_rx (no longer needed). |
| 6355 |
|
- document S/R arg. list (+ update some comments) |
| 6356 |
|
o pkg/seaice: |
| 6357 |
|
- added SEAICE_CLIM_AIR code, which permits modulation of surface air |
| 6358 |
|
temperature and humidity over sea ice based on climatological values. |
| 6359 |
|
- clean up computation of Hibler+Bryan (1987) stress coupling for the case |
| 6360 |
|
of LSR (this change is expected to change the results slightly because now |
| 6361 |
|
it uses slightly difference moduli from the second last LSR solution, but |
| 6362 |
|
that is more consistent with the stress computations; this part of the code |
| 6363 |
|
is not tested in the verification experiments) |
| 6364 |
|
- fix diagnostics for flux of ice in case of B-grid |
| 6365 |
|
- turn strain rates eij and press into global fields within global |
| 6366 |
|
common block in SEAICE.h for more straighforward diagnostics |
| 6367 |
|
- fix diagnostics for principal stress components, press, zeta, eta |
| 6368 |
|
to give something meaning full |
| 6369 |
|
o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate |
| 6370 |
|
new output (all 4 tests) using default rotationPeriod. |
| 6371 |
|
o pkg KPP: |
| 6372 |
|
- add flag (LimitHblStable) to avoid limiting BL depth under stable conditions |
| 6373 |
|
- fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1 |
| 6374 |
|
and normal grid from 1 to Nr) |
| 6375 |
|
o Fix computations of L4rdt in mom_calc_visc.F |
| 6376 |
|
o eesupp: |
| 6377 |
|
new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg): |
| 6378 |
|
should be called before a "stop" if we know that all process are going |
| 6379 |
|
to stop; if one Proc does call this S/R, will hang in MPI_FINALISE. |
| 6380 |
|
|
| 6381 |
|
checkpoint61o (2009/05/26) |
| 6382 |
|
o pkg/exch2: change check_depths to issue just a warning (instead of error+stop) |
| 6383 |
|
o model/src/ini_curvilinear_grid.F: |
| 6384 |
|
compute angleSin/CosC when they are not read from a file |
| 6385 |
|
o pkg/seaice: |
| 6386 |
|
add pseudo time stepping for LSOR |
| 6387 |
|
o pkg/exch2: |
| 6388 |
|
temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW |
| 6389 |
|
o pkg/seaice: |
| 6390 |
|
Adding separate sea ice albedo, drag coefficients, and HO in Southern |
| 6391 |
|
Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h |
| 6392 |
|
o SingleCpuIO: |
| 6393 |
|
fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used. |
| 6394 |
|
o pkg/seaice: |
| 6395 |
|
put exchanged variable in (local) common block for MPI+Multi-Threads |
| 6396 |
|
to work (necessary with exch1, and for now with exch2 too). |
| 6397 |
|
o verification: to get more experiments tested with mpi, mth and mpi+mth, |
| 6398 |
|
change tiling of: |
| 6399 |
|
aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15, |
| 6400 |
|
hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope |
| 6401 |
|
update output of exp: |
| 6402 |
|
exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5), |
| 6403 |
|
tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod) |
| 6404 |
|
+ ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU |
| 6405 |
|
(note: output.txt generated on faulks using only 1 tile) |
| 6406 |
|
o eesupp & mdsio (SingleCpuIO): |
| 6407 |
|
- remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time |
| 6408 |
|
parameter "W2_useE2ioLayOut" (read from file "data.exch2"). |
| 6409 |
|
Note: was not effective for globalFile & useSingleCpuIO=F; now fixed. |
| 6410 |
|
- move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc). |
| 6411 |
|
- fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same |
| 6412 |
|
gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array). |
| 6413 |
|
o pkg/exch2: |
| 6414 |
|
- new code to set-up W2-Exch2 topology (replace matlab-topology-generator): |
| 6415 |
|
read parameter file "data.exch2" if it exists; otherwise try default regular |
| 6416 |
|
cube without blank-tile; new header file "W2_EXCH2_SIZE.h"; |
| 6417 |
|
- update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible |
| 6418 |
|
with new code (not to be used, just as a backup solution). |
| 6419 |
|
- add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2" |
| 6420 |
|
in utils/exch2/input. |
| 6421 |
|
|
| 6422 |
|
checkpoint61n (2009/05/12) |
| 6423 |
|
o eesupp & mdsio (SingleCpuIO): |
| 6424 |
|
- move mapping to global io-buffer inside gather_2d/scater_2d: this save |
| 6425 |
|
memory (1 less 2D global RL array); skip 1 buffer copy; and only send/ |
| 6426 |
|
receive real*4 array (instead of real*8) to read/write 32.bit files. |
| 6427 |
|
(new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S |
| 6428 |
|
and remove new mapping S/R) |
| 6429 |
|
o pkg/mdsio: in preparation for topology-generator within pkg/exch2: |
| 6430 |
|
- Change declaration of SingleCpuIO buffer, reduced to only 1 dim.: |
| 6431 |
|
xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h |
| 6432 |
|
when using exch2. Add S/R to map global io-buffer to global model array. |
| 6433 |
|
- uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt. |
| 6434 |
|
|
| 6435 |
|
checkpoint61m (2009/04/29) |
| 6436 |
|
o write_utils : change WRITE_1D_R8 to WRITE_1D_RL |
| 6437 |
|
and add 3 other S/R for other types (R4,R8,RS). |
| 6438 |
|
Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument. |
| 6439 |
|
o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros): |
| 6440 |
|
- ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ; |
| 6441 |
|
- reduce number of macro definitions (keep only those which are used); |
| 6442 |
|
can always call directly the corrresponding S/R if needed. |
| 6443 |
|
- everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix |
| 6444 |
|
_R4/_R8 to _RS/_RL when applied to _RS/_RL variable. |
| 6445 |
|
Fixed wrong type of arg in: |
| 6446 |
|
atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F |
| 6447 |
|
ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F |
| 6448 |
|
To fix: global_sum of var in common block is wrong (multi-threaded) in: |
| 6449 |
|
dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F |
| 6450 |
|
To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops) |
| 6451 |
|
o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd |
| 6452 |
|
"nlfs" mpi test is going to stop when checking for unconnected tile egdes. |
| 6453 |
|
o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error |
| 6454 |
|
o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile |
| 6455 |
|
edges are closed (zero depth); might happen with "blank tiles"; |
| 6456 |
|
for now, disabled if using OBCS. |
| 6457 |
|
o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi": |
| 6458 |
|
link *_mpi files from "MODS" dir) to return to a strait-forward behavior. |
| 6459 |
|
o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D) |
| 6460 |
|
to reduce length of 1.D array print in STDOUT. |
| 6461 |
|
o adjustment.cs-32x32x1: changed to oceanic test with 1 continent |
| 6462 |
|
+ use 48 tiles (16x8): this will allow to test "blank tiles". |
| 6463 |
|
o start to test MPI + multi-threaded (change testreport to skip tests |
| 6464 |
|
where number of tiles do not match). |
| 6465 |
|
o genmake2: add option "-omp" to turn on Open-MP ; |
| 6466 |
|
passed to testreport (if using -mth) ; merge few (*+mth) optfiles. |
| 6467 |
|
o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them) |
| 6468 |
|
and keep the original tile numbering. Note: compatible with old |
| 6469 |
|
W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files. |
| 6470 |
|
|
| 6471 |
|
checkpoint61l (2009/04/07) |
| 6472 |
|
o Overlaps had been forgotten in calculating ijk keys : fixed |
| 6473 |
|
o fix cyrus makedepend for gcc 4.4 |
| 6474 |
|
o experiment fizhi-cs-aqualev20: |
| 6475 |
|
switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE) |
| 6476 |
|
and generate new output. Note: new output is much closer to the old |
| 6477 |
|
one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from |
| 6478 |
|
the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007. |
| 6479 |
|
o pkg/fizhi: |
| 6480 |
|
- change to avoid indices going deliberately over array-bounds |
| 6481 |
|
- remove unnecessary MPI stuff |
| 6482 |
|
- perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY" |
| 6483 |
|
- new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE: |
| 6484 |
|
does not go over array-bounds and therefore returns reliable output. |
| 6485 |
|
- in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls: |
| 6486 |
|
this S/R has 4 output arguments, which are used inside "get_alarm"; |
| 6487 |
|
when it is called with the same variable "ndum" in place of several |
| 6488 |
|
output arguments, this produces weird side effect inside "get_alarm" |
| 6489 |
|
(e.g., datein=dates(n) is overwritten by timein=times(n) since both |
| 6490 |
|
datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum" |
| 6491 |
|
address) and produces error. |
| 6492 |
|
o tools/gemake2: (March 27-29 2009) |
| 6493 |
|
with option "-mpi": link *_mpi files from "MODS" dir (this is what |
| 6494 |
|
testreport does). |
| 6495 |
|
o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output |
| 6496 |
|
o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F: |
| 6497 |
|
update lab_sea.lsr & lab_sea.salt_plume results |
| 6498 |
|
o pkg/seaice: |
| 6499 |
|
Major overhaul of the LSOR solver: change discretization from original |
| 6500 |
|
finite differences to finite volume. The old routine is still in the |
| 6501 |
|
file seaice_lsr.F and can be turned on with the CPP-flag |
| 6502 |
|
SEAICE_OLD_AND_BAD_DISCRETIZATION |
| 6503 |
|
Along with this change, the discretization of the strain rates is changed. |
| 6504 |
|
The same flag turns on the old discretization in seaice_calc_strainrates.F |
| 6505 |
|
All verification experiments with seaice are affected (except for |
| 6506 |
|
seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old |
| 6507 |
|
results by setting the above flag. |
| 6508 |
|
Further changes involve changes in defaults: |
| 6509 |
|
- ALLOW_FLOODING is defined and turned on by default |
| 6510 |
|
- SEAICEadvSnow = .true. is now the default |
| 6511 |
|
- SEAICEadvSalt = .true. is now the default |
| 6512 |
|
- SEAICEadvAge = .true. is now the default |
| 6513 |
|
- SEAICE_clipVelocities = .false. is now the default |
| 6514 |
|
(as per J. Zhang's recommendation) |
| 6515 |
|
- B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE |
| 6516 |
|
is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS |
| 6517 |
|
- seaice_growth: replace computation of UG by a simple copy from wspeed |
| 6518 |
|
|
| 6519 |
|
checkpoint61k (2009/03/18) |
| 6520 |
|
o pkg/seaice: a few bug fixes mostly concerning the metric terms: |
| 6521 |
|
seaice_lsr: fixed a few metric terms, |
| 6522 |
|
affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs |
| 6523 |
|
add more debugging diagnostics |
| 6524 |
|
seaice_evp: removed superfluous many metric terms of FV discretization |
| 6525 |
|
of stress divergence |
| 6526 |
|
affects lab_sea, lab_sea.hb87 |
| 6527 |
|
seaice_ocean_stress: removed superfluous many metric terms of FV discretization |
| 6528 |
|
of stress divergence for non-evp solver |
| 6529 |
|
(this part is not tested anywhere) |
| 6530 |
|
seaice_calc_strainrates: fixed a bug in no-slip boundary conditions, |
| 6531 |
|
they were effectively only half slip |
| 6532 |
|
affects lab_sea.hb87 |
| 6533 |
|
updated all relevant verification experiments (except lab_sea//output_adm.txt |
| 6534 |
|
which was left over, but fails at level 7 & 6) |
| 6535 |
|
|
| 6536 |
|
checkpoint61j (2009/03/17) |
| 6537 |
|
o pkg/seaice: turn a few hard wired parameters into run time parameters |
| 6538 |
|
o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model |
| 6539 |
|
time in seconds as promised by the usints in seaice_monitor and exf_monitor |
| 6540 |
|
o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids |
| 6541 |
|
that are not cubed-sphere grids |
| 6542 |
|
o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR |
| 6543 |
|
o pkg/ctrl: |
| 6544 |
|
fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low) |
| 6545 |
|
o non-hydrostatic (calc_gw.F): |
| 6546 |
|
fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec |
| 6547 |
|
update output of exp. global_ocean.cs32x15.viscA4 |
| 6548 |
|
o remove backward compatibility for thetaMin,phiMin |
| 6549 |
|
(replaced by xgOrigin,ygOrigin on Jan 27, 2009) |
| 6550 |
|
o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the |
| 6551 |
|
interpolated wind field not only for curvilineargrid=.true., but also |
| 6552 |
|
for a rotated grid (rotateGrid=.true.) |
| 6553 |
|
o pkg/exf: add capability to bypass interpolation for runoff |
| 6554 |
|
by setting yet another CPP-flag |
| 6555 |
|
o eesupp/src, B-grid exchange: |
| 6556 |
|
add simple (6 tiles, non MPI) CS exch + standard interface S/R. |
| 6557 |
|
o autodiff |
| 6558 |
|
new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV |
| 6559 |
|
allows to switch to single-prec common blocks; |
| 6560 |
|
corresponding switch occurs in tamc.h, integer isbyte |
| 6561 |
|
TAF store directivs "byte" and "kind" seem equivalent; |
| 6562 |
|
Most tamc.h have been updated correspondingly. |
| 6563 |
|
|
| 6564 |
|
checkpoint61i (2009/02/13) |
| 6565 |
|
o autodiff: |
| 6566 |
|
fix autodiff_sore/_restore indices for obcs |
| 6567 |
|
(spotted by I. Hoteit, M. Mazloff) |
| 6568 |
|
o pkg/autodiff, pkg/ctrl: |
| 6569 |
|
Add flag to reduce all tapelev I/O to single-prec. |
| 6570 |
|
In data.ctrl set |
| 6571 |
|
doSinglePrecTapelev = .TRUE. |
| 6572 |
|
o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2: |
| 6573 |
|
check in hack for SX8 compiler (for dxV, dyU); remove it afterwards. |
| 6574 |
|
o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for |
| 6575 |
|
real fresh water flux (not yet) |
| 6576 |
|
o pkg/mdsio & rw: |
| 6577 |
|
- add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta) |
| 6578 |
|
- add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX. |
| 6579 |
|
o pkg/flt: |
| 6580 |
|
- replace FLT_INIT by 3-steps standard initialization S/R: readparms, |
| 6581 |
|
init_fixed & ini_varia. |
| 6582 |
|
- clean-up & simplify linear interpolation S/R: |
| 6583 |
|
move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid. |
| 6584 |
|
- fix some indices (mainly vertical index) ; add IMPLICIT NONE. |
| 6585 |
|
- more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R. |
| 6586 |
|
- add vert. coordinate & horiz. indices to output files. |
| 6587 |
|
- change vertical position in initial condition, from index to depth [m]. |
| 6588 |
|
- store horizontal (decimal) indices i,j in common block (instead of coord. x,y) |
| 6589 |
|
(easier to get to a curvilinear grid) ; delX,delY no longer used. |
| 6590 |
|
o pkg/ggl90: a few modifications: |
| 6591 |
|
- fix bottom boundary condition, and interpolation of KappaE |
| 6592 |
|
near top and bottom |
| 6593 |
|
- use same set of viscosity/diffusivity for TKE/momnetum/tracer |
| 6594 |
|
- add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH) |
| 6595 |
|
- add a few options for mixing-length upper limit (--> mxlMaxFlag) |
| 6596 |
|
o rename thetaMin,phiMin -> xgOrigin,ygOrigin |
| 6597 |
|
(maintain temporary backward compatibility, until next checkpoint) |
| 6598 |
|
|
| 6599 |
|
checkpoint61h (2009/01/27) |
| 6600 |
|
o pkg/diagnostics with "periodic averaging diagnostics": |
| 6601 |
|
fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. |
| 6602 |
|
o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82 |
| 6603 |
|
o pkg/obcs: fix loop ranges for balancing code |
| 6604 |
|
o pkg/flt: |
| 6605 |
|
- improve criteria for finding which tile owns a float. |
| 6606 |
|
- fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case. |
| 6607 |
|
o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg |
| 6608 |
|
aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling |
| 6609 |
|
with ocean biogeo) |
| 6610 |
|
o pkg/flt: |
| 6611 |
|
- do some cleaning and fix the restart ; |
| 6612 |
|
- add output.txt in flt_example/results to get this pkg tested. |
| 6613 |
|
o genmake2: add an EXTENDED_SRC option and flag. |
| 6614 |
|
for now, cannot be turned on on command line (only through genmake_local) |
| 6615 |
|
o pkg/mdsio: read/write vector: |
| 6616 |
|
- singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS |
| 6617 |
|
- singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR |
| 6618 |
|
& MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. |
| 6619 |
|
- affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) |
| 6620 |
|
(drop to 4 digits matching for grad). But this test does not look very |
| 6621 |
|
reliable (was already failling on eddy, fc5, at 6.digits). Update output. |
| 6622 |
|
|
| 6623 |
|
checkpoint61g (2008/12/29) |
| 6624 |
|
o pkg/flt: |
| 6625 |
|
- move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) |
| 6626 |
|
+ make OPTIONS file more standard. |
| 6627 |
|
- rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) |
| 6628 |
|
- fix _BYTESWAPIO CPP-Flag |
| 6629 |
|
- standard reading of file-parameter "data.flt" |
| 6630 |
|
- fix argument list of S/R FLT_RESTART |
| 6631 |
|
still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F |
| 6632 |
|
o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell |
| 6633 |
|
o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to |
| 6634 |
|
a still unfixed compiler/optimization bug |
| 6635 |
|
|
| 6636 |
|
checkpoint61f (2008/11/21) |
| 6637 |
|
o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; |
| 6638 |
|
update results of global_ocean.cs32x15.icedyn test. |
| 6639 |
|
o move getcon.F from model/src to pkg/fizhi. |
| 6640 |
|
o pkg/exf: add parameter for extrapolation of temp up to the surface |
| 6641 |
|
and option to prevent negative evap (in bulk_largeyeager04 only). |
| 6642 |
|
o Prather Advection scheme: fix tracer conservation for divergent flow |
| 6643 |
|
(e.g., when using NonLin Free-Surface). |
| 6644 |
|
o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead |
| 6645 |
|
o gmredi (Visbeck-variable-K): |
| 6646 |
|
- add more parameters to Visbeck-variable-K. |
| 6647 |
|
- use a 5 points average for dSigmaR in Visbeck-K calculation |
| 6648 |
|
(more "homogenous": same stencil and same weights as in dSigmaH) |
| 6649 |
|
- update output of ideal_2D_oce experiment. |
| 6650 |
|
o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 |
| 6651 |
|
(#undef REAL4_IS_SLOW) |
| 6652 |
|
- pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 |
| 6653 |
|
coordinate variable |
| 6654 |
|
- pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables |
| 6655 |
|
(surface forcing fields), removes some of the functionality |
| 6656 |
|
- model/src/write_grid.F: write _RS variables as RS-netcdf variables |
| 6657 |
|
- model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but |
| 6658 |
|
probably not all: copy _RS surface flux fields to RL field before |
| 6659 |
|
calling DIAGNOSTICS_FILL |
| 6660 |
|
- model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into |
| 6661 |
|
real*4 (CALL EXCH_*_RS) versions. |
| 6662 |
|
- tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 |
| 6663 |
|
(generate new output). |
| 6664 |
|
|
| 6665 |
|
checkpoint61e (2008/10/23) |
| 6666 |
|
o gmredi (Visbeck-variable-K): |
| 6667 |
|
- fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h |
| 6668 |
|
- change computation of Visbeck-K where Slope > Smax : |
| 6669 |
|
now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct) |
| 6670 |
|
previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output. |
| 6671 |
|
o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic |
| 6672 |
|
to be the same as with Z-coord. (i.e., m/s & no-units respectively). |
| 6673 |
|
o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc) |
| 6674 |
|
o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz |
| 6675 |
|
does not become too large (to avoid precision problems in implicit-diffusion |
| 6676 |
|
solver); update ideal_2D_oce output. |
| 6677 |
|
o pkg ggl90: |
| 6678 |
|
- in ggl90_cal.F: compute only one set of visc/diff, used to |
| 6679 |
|
step forward TKE/T/S/momentum |
| 6680 |
|
- default value of GGL90viscMax/GGL90diffMax larger and equal (to |
| 6681 |
|
have Prandlt =1) |
| 6682 |
|
o gmredi (fm07): |
| 6683 |
|
- add lower limit on Transition layer thickness + lower limit on 1/lambda |
| 6684 |
|
- allow to set few more params from data.gmredi |
| 6685 |
|
o pkg ggl90: |
| 6686 |
|
- add missing sqrt(2) factor in computation of mixing length |
| 6687 |
|
scale in ggl90_calc.F |
| 6688 |
|
(see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) |
| 6689 |
|
|
| 6690 |
|
checkpoint61d (2008/09/25) |
| 6691 |
|
o adjoint modifs |
| 6692 |
|
- adapt to new field rhoInSitu |
| 6693 |
|
- allow to revert from StoreDynVars2D, StoreDynVars3D |
| 6694 |
|
to individual fields |
| 6695 |
|
(switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) |
| 6696 |
|
o store 3-D (in-situ) density in commom block (DYNVARS.h) |
| 6697 |
|
- save 1 rho computation. |
| 6698 |
|
- no longer modify T & S inland when using down_slope pkg. |
| 6699 |
|
o gad_som : allow to switch to SOM advection for T & S without corresponding |
| 6700 |
|
pickup files (using new S/R: MDS_CHECK4FILE). |
| 6701 |
|
o keep removing _BEGIN/_END_MASTER between MDSIO S/R call |
| 6702 |
|
(for useSingleCpuIO to work in multi-threaded) |
| 6703 |
|
o pkg/shelfice: |
| 6704 |
|
- disentangle parameters: retire shelfIceFile in data/PARM05 and substitute |
| 6705 |
|
with SHELFICEtopoFile in data.shelfice |
| 6706 |
|
- move code for reading ice shelf topography and modifying hFacC into separate |
| 6707 |
|
subroutines of the shelfice package |
| 6708 |
|
- separate initialisation of "fixed" and "variable" variables |
| 6709 |
|
- kTopC is not (yet) replaced by kSurfC, although this is possible |
| 6710 |
|
o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
| 6711 |
|
o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
| 6712 |
|
and rename: |
| 6713 |
|
ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
| 6714 |
|
ini_reference_state.F --> load_ref_files.F (- set anelastic factors) |
| 6715 |
|
o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) |
| 6716 |
|
|
| 6717 |
|
checkpoint61c (2008/08/30) |
| 6718 |
|
o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" |
| 6719 |
|
to add mass source/sink of fluid in the interior (3-D generalisation |
| 6720 |
|
of oceanic real-fresh water flux). |
| 6721 |
|
o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) |
| 6722 |
|
o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) |
| 6723 |
|
o new pkg: down_slope |
| 6724 |
|
density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). |
| 6725 |
|
- presently, modify T & S inland (dwnslp_calc_rho.F). |
| 6726 |
|
can be avoided if rho was stored in common bloc and used in calc_phi_hyd. |
| 6727 |
|
- implementation for ocean in P-coords not tested. |
| 6728 |
|
- add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. |
| 6729 |
|
o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) |
| 6730 |
|
(to facilitate conversion of oceanic pkg to p-coordinate). |
| 6731 |
|
o change FIND_RHO to FIND_RHO_2D : |
| 6732 |
|
pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. |
| 6733 |
|
o new pkg: cheapaml |
| 6734 |
|
|
| 6735 |
|
checkpoint61b (2008/08/05) |
| 6736 |
|
o exch2: |
| 6737 |
|
change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) |
| 6738 |
|
- no longer depend on the order sequence (N,S,E,W). |
| 6739 |
|
- 3rd exchange no longer needed (tested with 24 tiles). |
| 6740 |
|
- same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) |
| 6741 |
|
- exch_UV_A-grid readily available (but not yet tested). |
| 6742 |
|
comment out 3rd exch call and remove copy of V to U at SE & NE face-corners |
| 6743 |
|
(both are no longer needed) in exch_uv: no effect in forward run; but |
| 6744 |
|
get truncation error differences with adjoint exch. |
| 6745 |
|
o exch2: |
| 6746 |
|
- change index-bounds storage (moved from target to local tile, |
| 6747 |
|
more intuitive this way) ; rename/remove some variables. |
| 6748 |
|
- change utils/exch2/matlab-topology-generator & code_mods accordingly. |
| 6749 |
|
|
| 6750 |
|
checkpoint61a (2008/07/29) |
| 6751 |
|
o exch2/matlab-topology-generator: |
| 6752 |
|
fix bug in index bounds for N-S internal exchange (hard to tell if this |
| 6753 |
|
had any effect on the solution). |
| 6754 |
|
o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf |
| 6755 |
|
is exceeded |
| 6756 |
|
o testreport: modify syntax of awk, so that it works also with |
| 6757 |
|
awk, and not only with nawk and gawk |
| 6758 |
|
|
| 6759 |
|
checkpoint61 (2008/06/24) |
| 6760 |
|
o autodiff |
| 6761 |
|
Change default for TAF usage by removing argument '-nonew_arg' |
| 6762 |
|
This changes TAF subroutine argument list (ordering of active var.) |
| 6763 |
|
Omission of this flag leads to incompatibility w.r.t. TAMC |
| 6764 |
|
To restore TAMC-compatibility, need following modifs: |
| 6765 |
|
* use adoptfile tools/adjoint_options/adjoint_tamc_compatibility |
| 6766 |
|
* use CPP option #define AUTODIFF_TAMC_COMPATIBILITY |
| 6767 |
|
Tested TAF version is 1.9.22 |
| 6768 |
|
N.B.: exch2 hand-written adjoint code currently not TAMC compatible |
| 6769 |
|
|
| 6770 |
|
checkpoint60 (2008/06/19) |
| 6771 |
|
--->>> This is the last checkpoint for which generating the adjoint |
| 6772 |
|
--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" |
| 6773 |
|
--->>> by default. |
| 6774 |
|
--->>> Future checkpoints will ommit this flag by default. |
| 6775 |
|
o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. |
| 6776 |
|
o pkg/grdchk: Add gradient check to etan0 perturbations. |
| 6777 |
|
o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). |
| 6778 |
|
o pkg/autodiff: more flexibility in zeroadj. |
| 6779 |
|
model/src: modifying do_oceanic_phys.F accordingly. |
| 6780 |
|
o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. |
| 6781 |
|
o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option |
| 6782 |
|
special setup of gmredi for which the adjoint is stable |
| 6783 |
|
enough for parameter optimization. |
| 6784 |
|
o bridging the gap between eddy stress and GM. |
| 6785 |
|
-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) |
| 6786 |
|
along with a change in CPP option (now ALLOW_EDDYPSI). |
| 6787 |
|
-> when using GM w/ GM_AdvForm: |
| 6788 |
|
The total eddy streamfunction (Psi = eddyPsi + K x Slope) |
| 6789 |
|
is applied either in the tracer Eq. or in momentum Eq. |
| 6790 |
|
depending on data.gmredi (intro. GM_InMomAsStress). |
| 6791 |
|
-> ALLOW_EDDYPSI_CONTROL for estimation purpose. |
| 6792 |
|
The key modifications are in model/src/taueddy_external_forcing.F |
| 6793 |
|
pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F |
| 6794 |
|
|
| 6795 |
|
checkpoint59r (2008/05/29) |
| 6796 |
|
o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array |
| 6797 |
|
from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); |
| 6798 |
|
fix option to read coriolis(@ cell-corner) from files with CS-grid. |
| 6799 |
|
o pkg/mnc: add some attributes to standard 1D-coordinate variables |
| 6800 |
|
o pkg/diagnostics: enforce missing_value attribute for scalar variables at |
| 6801 |
|
mass points, when using mnc for output |
| 6802 |
|
- add runtime parameter (missing_value, missing_value_int) to override |
| 6803 |
|
default (which is the value of getcon('UNDEF')) |
| 6804 |
|
o pkg/mnc: prepare mnc for the actual use of missing values with the |
| 6805 |
|
diagnostics package: small fix in mnc_cw_readwrite.template and more |
| 6806 |
|
initialisation of never used fields |
| 6807 |
|
- replace mnc_common.h and mnc_id_header.h with corresponding upper case |
| 6808 |
|
versions |
| 6809 |
|
o pkg/thsice/thsice_ini_vars.F added default initial values so that |
| 6810 |
|
thermodynamics sea ice solver does not blow up when some initial fields |
| 6811 |
|
are missing. |
| 6812 |
|
o move from external_forcing_surf.F to ini_forcing.F |
| 6813 |
|
the p-coord. hack consisting in using pLoad to set phi0surf ; |
| 6814 |
|
update output of tutorial_global_oce_in_p (affected @ truncation level). |
| 6815 |
|
o Freshen up a bit hs94.1x64x5, notably: |
| 6816 |
|
remove rotationPeriod and tRef=5*0. (adjoint only), and add |
| 6817 |
|
exactConserv=.TRUE. |
| 6818 |
|
o pkg/generic_advdiff: |
| 6819 |
|
change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
| 6820 |
|
applies to files where Temperature & Salinity 2nd Order moments are used. |
| 6821 |
|
o pkg/ptracers: add second-order moment advection schemes (80 and 81); |
| 6822 |
|
this uses a dynamically allocated internal state data structure |
| 6823 |
|
(#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) |
| 6824 |
|
and requires a fortran 90 compiler |
| 6825 |
|
|
| 6826 |
|
checkpoint59q (2008/05/06) |
| 6827 |
|
o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) |
| 6828 |
|
(from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) |
| 6829 |
|
o Refresh tutorial_global_oce_biogeo, notably: |
| 6830 |
|
- change bathymetry (put back seamounts in ACC, use hFacs) |
| 6831 |
|
- change EOS (POLY3 --> JMD95Z) |
| 6832 |
|
- use Bryan-Lewis vertical diffusivity |
| 6833 |
|
- use multidimensional advection |
| 6834 |
|
- remove old virtual virtual in dic pkg, now done through ptracer pkg |
| 6835 |
|
- change a couple of parameters in dic pkg |
| 6836 |
|
o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F |
| 6837 |
|
o pkg/obcs: change default to OBCSfixTopo = .true., |
| 6838 |
|
- set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result |
| 6839 |
|
- replace "debugMode" with "debugLevel .GE. debLevB" |
| 6840 |
|
o implementation of TAF directives for gchem,cfc,dic |
| 6841 |
|
o remove "exp5" (replaced by tutorial_deep_convection). |
| 6842 |
|
o pkg/obcs: add code to fix topography gradients normal to open boundaries; |
| 6843 |
|
this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; |
| 6844 |
|
the code can be turned on by setting OBCSfixTopo = .true. in data.obcs |
| 6845 |
|
--> changes results in exp4, seaice_obcs |
| 6846 |
|
o tutorial_deep_convection : |
| 6847 |
|
update the set-up and increase resolution and domain size ; start |
| 6848 |
|
from pseudo initial conditions = output at t=120mn in order to see |
| 6849 |
|
something happening when running testreport. |
| 6850 |
|
o pkg/seaice: add os7mp as an advection scheme |
| 6851 |
|
add check for advection schemes |
| 6852 |
|
add a flag for restoring T and S underneath sea ice |
| 6853 |
|
o pkg/my82: add netcdf-support and diagnostics |
| 6854 |
|
o thsice pkg: |
| 6855 |
|
- Now hsMax limits snow height by turning it into ice following |
| 6856 |
|
flooding scheme (and now conserving energy) |
| 6857 |
|
- Slight rewriting of the formula in thsice_calc_thick.F |
| 6858 |
|
- Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos |
| 6859 |
|
--> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice |
| 6860 |
|
|
| 6861 |
|
checkpoint59p (2008/04/10) |
| 6862 |
|
o gchem / dic / cfc : |
| 6863 |
|
- add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); |
| 6864 |
|
- add new parameter files: "data.dic" & "data.cfc" ; |
| 6865 |
|
- various re-arrangement in initialisation & header file ; |
| 6866 |
|
- fix tutorial_global_oce_biogeo for multi-threaded test. |
| 6867 |
|
o pkg/dic: test for "pickup_dic" file when restarting ; |
| 6868 |
|
if no pickup-file, can restart with a re-initialised pH (same as it did |
| 6869 |
|
before) providing pickupStrictlyMatch is set to False. |
| 6870 |
|
o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP |
| 6871 |
|
+ fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP |
| 6872 |
|
o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2 |
| 6873 |
|
and staggerTimeStep is off (needed for stability of Internal-wave dynamics). |
| 6874 |
|
o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax, |
| 6875 |
|
& lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers |
| 6876 |
|
(note: not clear to me what lambdaTr1ClimRelax is still used for ...) |
| 6877 |
|
o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which |
| 6878 |
|
scheme to use for vorticty-term ; |
| 6879 |
|
- compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F |
| 6880 |
|
(with default selectVortScheme, return to original discretisation) |
| 6881 |
|
- remove weird combination (e.g.: upwindVorticity & highOrderVorticity) |
| 6882 |
|
o pkg/seaice: add a line to the summary to indicate grid type (B/C) |
| 6883 |
|
o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the |
| 6884 |
|
bottom ; only used with variable horizontal viscosity and non-hydrostatic. |
| 6885 |
|
also fix diagnostics VISCAHW & VISCA4W. |
| 6886 |
|
|
| 6887 |
|
checkpoint59o (2008/03/07) |
| 6888 |
|
o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). |
| 6889 |
|
o change the loop ordering in most gad_*_adv_x.F to improve vectorization: |
| 6890 |
|
move a few statemens out the main loop into separate loops |
| 6891 |
|
o pkg/shelfice: |
| 6892 |
|
- sort out freshwater flux; convert freshwater fluxes to mass fluxes |
| 6893 |
|
(kg/m^2/s), does not break tests, because in verification/isomip, |
| 6894 |
|
rhoConstFresh=rhoConst (by accident) |
| 6895 |
|
- rearrange computation of tLoc, sLoc, pLoc to make code more efficient |
| 6896 |
|
- move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into |
| 6897 |
|
new file model/src/seawater.F, so that they are available for all pkgs. |
| 6898 |
|
- convert potential temperature into in-situ temperature. This changes the |
| 6899 |
|
isomip tests => update tests |
| 6900 |
|
o add a flag writePickupAtEnd (default=true) to be able to suppress |
| 6901 |
|
writing a pickup at the last timestep |
| 6902 |
|
o tools/mpack-1.6 : |
| 6903 |
|
- disable automake (not working) and autoconf (not needed). |
| 6904 |
|
- update to version 1.6.4 which fix MD5 code on some 64 bits platforms |
| 6905 |
|
also cleaner with much less compilation warnings. |
| 6906 |
|
o pkg/profiles: |
| 6907 |
|
rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg |
| 6908 |
|
(for "less than 32 characters name" compiler requirement) |
| 6909 |
|
o pkg/obcs and pkg/exf: added capability to specify seaice open boundary |
| 6910 |
|
conditions that have a different sampling frequency than S/T/U/V obcs |
| 6911 |
|
o pkg/diagnostics (stats-diags): |
| 6912 |
|
- fix global Min/Max in case 1 processor get only empty tiles |
| 6913 |
|
o genmake2: replace (4 times) |
| 6914 |
|
make genmake_tc_1.o >> genmake_warnings 2>&1 |
| 6915 |
|
with |
| 6916 |
|
COMM="$CC $CFLAGS -c genmake_tc_1.c" |
| 6917 |
|
echo $COMM >> genmake_warnings |
| 6918 |
|
$COMM >> genmake_warnings 2>&1 |
| 6919 |
|
to make genmake2 always see the value of CC as specified in the optfile. |
| 6920 |
|
o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid. |
| 6921 |
|
- add diagnostics for 1srt & 2nd Order moments and sub-grid variance. |
| 6922 |
|
- modify verification advect_cs test to test SOM-advection on CS-grid. |
| 6923 |
|
o pkg/ctrl: |
| 6924 |
|
- Rewrite of ctrl_map_ini_ecco.F, |
| 6925 |
|
introducing a generic routine (ctrl_map_ini_gen.F). |
| 6926 |
|
- Modification of ctrl_bound/adctrl_bound handling control vector bounds. |
| 6927 |
|
|
| 6928 |
|
checkpoint59n (2008/02/09) |
| 6929 |
|
o pkg/diagnostics: for large number of diagnostics, store diagnostic mate |
| 6930 |
|
number in dedicate array "hdiag": |
| 6931 |
|
- new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST |
| 6932 |
|
with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST. |
| 6933 |
|
- many small changes (integer format) for large number of diagnostics |
| 6934 |
|
- start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with |
| 6935 |
|
a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23. |
| 6936 |
|
o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For |
| 6937 |
|
usingSphericalGrid, this allows to define the rotated grid coordinates |
| 6938 |
|
via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the |
| 6939 |
|
geographical coordinates according to the inverse of the rotation defined |
| 6940 |
|
by the Euler angles, so that Coriolis parameter and online-interpolation by |
| 6941 |
|
exf works with the geographical coordinates on XC/YC/XG/YG. |
| 6942 |
|
Naturally, this feature does not work with all packages, so some |
| 6943 |
|
combinations are prohibited in config_summary (flt, flt_zonal, ecco, |
| 6944 |
|
profiles), because there the coordinates are assumed to be regular |
| 6945 |
|
spherical grid coordinates. |
| 6946 |
|
o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc: |
| 6947 |
|
- introduce isopycnal diffusion coefficient control. |
| 6948 |
|
o tools/adjoint_options: |
| 6949 |
|
- additional control vector components. |
| 6950 |
|
o pkg/mnc: have mnc create marginally meaning full coordinate variables |
| 6951 |
|
(that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 |
| 6952 |
|
o pkg/mypackage: |
| 6953 |
|
- add example of read/write pickup for state-var ; |
| 6954 |
|
- add entry points to the main code for state-vars diags & write-pickup. |
| 6955 |
|
o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year |
| 6956 |
|
transitions for useExfYearlyFields |
| 6957 |
|
- add new subroutine that determines the file to read from for |
| 6958 |
|
use*YearlyFields = .TRUE. and .FALSE. |
| 6959 |
|
- add a verification experiment to global_with_exf that tests |
| 6960 |
|
useExfYearlyFields with USE_EXF_INTERPOLATION defined |
| 6961 |
|
o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in |
| 6962 |
|
analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new |
| 6963 |
|
subroutines (which could be generated from a template, because they are |
| 6964 |
|
almost identical), for now they are included in obcs_prescribe_read.F for |
| 6965 |
|
simplicity |
| 6966 |
|
o pkg/exf: |
| 6967 |
|
- add a little more diagnostic to exf_interp_read (in analogy to |
| 6968 |
|
mds_read_field, can be turned off with debugLevel < debugLevA=1) |
| 6969 |
|
- improve vectorizability of exf_interp for TARGET_NEC_SX, makes code |
| 6970 |
|
ugly but fast by unrolling short inner loops, inserting a unroll=8 |
| 6971 |
|
directive in routine lagran, and splitting a loop and making do while the |
| 6972 |
|
outermost loop (the latter requires the intoduction of index arrays) |
| 6973 |
|
o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice |
| 6974 |
|
o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver |
| 6975 |
|
http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html |
| 6976 |
|
o verification/seaice_obcs: updated for restart test and latest options |
| 6977 |
|
o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different |
| 6978 |
|
ice rheology (so-called truncated ellipse, that gets rid of tensile stress); |
| 6979 |
|
for now this is only available for the C-grid code and also within |
| 6980 |
|
#ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code |
| 6981 |
|
|
| 6982 |
|
checkpoint59m (2008/01/14) |
| 6983 |
|
o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) |
| 6984 |
|
and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature |
| 6985 |
|
o gad_som : fix flux output (& diagnostics) to have same units as other |
| 6986 |
|
advection scheme fluxes (was previously multiplied by deltaT). |
| 6987 |
|
o added verification/seaice_obcs both to test seaice open boundaries |
| 6988 |
|
and to provide an example matlab scrpt for generating them |
| 6989 |
|
o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume |
| 6990 |
|
o pkg/salt_plume: clean up salt_plume_frac.F to |
| 6991 |
|
remove redundancy in PlumeMethod 1 and 4 |
| 6992 |
|
o pkg/kpp: added saltplume diagnostics |
| 6993 |
|
o pkg/obcs and pkg/seaice: |
| 6994 |
|
- do not set uice and vice to zero when OB*icefile are unspecified |
| 6995 |
|
- OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default |
| 6996 |
|
- moved seaice tracer obcs after call to seaice_growth |
| 6997 |
|
o pkg/salt_plume: added various options for salt plume depth |
| 6998 |
|
criterion and for vertical distribution of the salt |
| 6999 |
|
|
| 7000 |
|
checkpoint59l (2007/12/18) |
| 7001 |
|
o pkg/ptracers: new version of ptracers pickup: |
| 7002 |
|
read meta file and write only fields which are needed to restart. |
| 7003 |
|
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
| 7004 |
|
o pkg/seaice: |
| 7005 |
|
- add timescale for melting due to warm mixed layer as a means of |
| 7006 |
|
setting SEAICE_availHeatFrac more conveniently |
| 7007 |
|
- add a CPP-flag/runtime parameter check for flooding algorithm |
| 7008 |
|
- reformulated availHeat in seaice_growth.F to be independent of AREA |
| 7009 |
|
o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent |
| 7010 |
|
unit changes |
| 7011 |
|
o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint |
| 7012 |
|
o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC |
| 7013 |
|
SX vector computer. |
| 7014 |
|
o pkg/seaice: |
| 7015 |
|
- removed SEAICE_FFIELDS.h and seaice_get_forcing.F |
| 7016 |
|
seaice forcing fields can now be read only through pkg/exf |
| 7017 |
|
- removed some unused halos |
| 7018 |
|
o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP |
| 7019 |
|
o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL |
| 7020 |
|
or U/VICE from U/VWIND before computing U/VSTRESS |
| 7021 |
|
|
| 7022 |
|
checkpoint59k (2007/11/30) |
| 7023 |
|
o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between |
| 7024 |
|
dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. |
| 7025 |
|
o fix un-initialised variable problem (in mom_vecinv & shap_filt): |
| 7026 |
|
all experiments pass when compile with un-initialised var. checking option. |
| 7027 |
|
o added pkg/salt_plume |
| 7028 |
|
o script to test restart (for now, in MITgcm_contrib/jmc_script) |
| 7029 |
|
o pkg/seaice: new read/write pickup version. |
| 7030 |
|
read meta file and write only fields which are needed to restart. |
| 7031 |
|
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
| 7032 |
|
o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) |
| 7033 |
|
o lab_sea.hb87: modify the domain & update output.hb87.txt : |
| 7034 |
|
lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 |
| 7035 |
|
at j=1 & j=Ny+1 : this case is not treated correctly in the restart |
| 7036 |
|
process. Fixed here by closing the domain at the Northern boundary. |
| 7037 |
|
o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. |
| 7038 |
|
o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing |
| 7039 |
|
a set of consecutive levels in/from a 3-D array. |
| 7040 |
|
o pkg/ptracers: |
| 7041 |
|
use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). |
| 7042 |
|
to-do: fix pkg/diagnostics when large number of diagnostics are defined. |
| 7043 |
|
|
| 7044 |
|
checkpoint59j (2007/11/09) |
| 7045 |
|
o in pkgs: dic, obcs, offline, rbcs: |
| 7046 |
|
standard way to compute coeff. for time interpolation between 2 time reccords |
| 7047 |
|
which retains full precision (& make results less dependent on compiler). |
| 7048 |
|
update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. |
| 7049 |
|
o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those |
| 7050 |
|
packages instead of reading ice cover and wind speed separately |
| 7051 |
|
o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h |
| 7052 |
|
(keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad |
| 7053 |
|
to allow to compile customized code before the update) |
| 7054 |
|
o cleaning-up: |
| 7055 |
|
- fix CPP instruction syntax in pkg/obcs |
| 7056 |
|
- replace (some) call to MDSIO S/R with call to RW interface S/R ; and |
| 7057 |
|
add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio) |
| 7058 |
|
- fix some threads issue in IO parts. |
| 7059 |
|
o pkg/dic: |
| 7060 |
|
- add tons of "_d 0" (--> much better testreports !) |
| 7061 |
|
and then update outputs of tutorial_global_oce_biogeo |
| 7062 |
|
o pkg/mom_fluxform: |
| 7063 |
|
add a special version of momentum advection intended to conserve momentum |
| 7064 |
|
next to a bathymetry step or a coastline edge. (default = off = #undef) |
| 7065 |
|
o new read/write pickup version: |
| 7066 |
|
- for now, only implemented for main (mdsio) pickup file. |
| 7067 |
|
- write out only what is needed to restart; merge pickup_nh , pickup_ph |
| 7068 |
|
and main pickup together. |
| 7069 |
|
- read meta file; read only what is needed to restart; stop if a field |
| 7070 |
|
is missing (if pickupStrictlyMatch=T, = the default) or try to restart |
| 7071 |
|
if it make sense (even if the restart is not perfect). |
| 7072 |
|
- if no meta file, assume that pickup to read corresponds exactly to |
| 7073 |
|
a pickup that would currently be written. |
| 7074 |
|
- read pickup written in the old format (until checkpoint59i) if it |
| 7075 |
|
recognizes an old meta file (no field-list). |
| 7076 |
|
- add a meta file in exp. which starts from a pickup: 2 cases: |
| 7077 |
|
a) minimal meta file (with just file precision) + pickupStrictlyMatch=F |
| 7078 |
|
e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta |
| 7079 |
|
b) a meta file describing the content of the associated pickup file |
| 7080 |
|
e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta |
| 7081 |
|
o pkg/mdsio & pkg/rw: |
| 7082 |
|
- new routine to read a meta file ; new set of routine to read |
| 7083 |
|
Multiple-fields file (with meta file). |
| 7084 |
|
o added open boundary conditions capability for seaice |
| 7085 |
|
HSNOW, HSALT, UICE, and VICE |
| 7086 |
|
|
| 7087 |
|
checkpoint59i (2007/10/21) |
| 7088 |
|
o adjoint: |
| 7089 |
|
* fix multiDimAdvection adjoint |
| 7090 |
|
(partial recomputation problem by TAF for fVerT(:,:,kDown) |
| 7091 |
|
and comlev1 size definition (maxpass vs. max. number of tracers) |
| 7092 |
|
* verification/global_ocean.90x45x15 adjoint now tests |
| 7093 |
|
NLFS and multiDimAdvection using DST3 (=30) |
| 7094 |
|
* verification/lab_sea now tests multiDimAdvection using DST3 (=30) |
| 7095 |
|
o pkg/kpp: add "_d 0" to real constant (if missing); |
| 7096 |
|
update output of exp: natl_box (10.digits); vermix (std, 7.digits) |
| 7097 |
|
and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). |
| 7098 |
|
o prepare for "clever pickup" implementation: add new header file "RESTART.h" |
| 7099 |
|
for internal parameters related to restart process (formerly from PARAMS.h) |
| 7100 |
|
and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. |
| 7101 |
|
o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed |
| 7102 |
|
as argument. (only atm2d & obcs write_pickup have not yet been updated) |
| 7103 |
|
o pkg/monitor: |
| 7104 |
|
- use GLOBAL_SUM_TILE instead of _GLOBAL_SUM |
| 7105 |
|
- fix mon_stats_rs (statistics over the full domain, even where field is zero) |
| 7106 |
|
- account for deep Atmosphere factor and density factor (anelastic) |
| 7107 |
|
o added open boundary conditions capability for seaice HEFF and AREA |
| 7108 |
|
o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) |
| 7109 |
|
thermodynamics |
| 7110 |
|
- requires a little reorganization, which affects the testreport results |
| 7111 |
|
of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, |
| 7112 |
|
so that now the conservative form is tested |
| 7113 |
|
- add a few comments |
| 7114 |
|
o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* |
| 7115 |
|
o add a little bit of code to gad_os7mp_adv_?.F to help vectorization |
| 7116 |
|
o add new diagnostics to seaice: advective, diffusive fluxes (only for |
| 7117 |
|
multidim-advection, for scheme 2 they are not filled) and transports, |
| 7118 |
|
thermodynamic growth rates |
| 7119 |
|
o change units of EmPmR (inside the code, + within coupling interface) |
| 7120 |
|
from m/s to kg/m2/s (mass flux) but leave input file unchanged. |
| 7121 |
|
Affects results @ truncation level (cg2d match) and update output of |
| 7122 |
|
experiments: lab_sea(6), global_ocean.90x40x15(10), |
| 7123 |
|
global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) |
| 7124 |
|
+ adjoint results: global_ocean_ebm(11) and lab_sea (12). |
| 7125 |
|
Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). |
| 7126 |
|
Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). |
| 7127 |
|
|
| 7128 |
|
checkpoint59h (2007/09/29) |
| 7129 |
|
o pkg/exf: |
| 7130 |
|
- improve vectorization by moving if-statement out of loops in |
| 7131 |
|
exf_mapfields, exf_radiation |
| 7132 |
|
- exf_bulkformulae.F: introduce 2D fields and vectorize code |
| 7133 |
|
o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package |
| 7134 |
|
o testreport: |
| 7135 |
|
- allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE |
| 7136 |
|
monitor & update offline_exf_seaice exp. output. |
| 7137 |
|
- AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) |
| 7138 |
|
o pkg/seaice: |
| 7139 |
|
- bug fix in the evp solver: boundary conditions were affected be |
| 7140 |
|
masking of zMax/zMin (changes results) |
| 7141 |
|
- minor bug fix in boundary conditions in seaice_calc_strainrates |
| 7142 |
|
(changes results for no_slip) |
| 7143 |
|
- seaice_lsr.F: make interpolation of eta dependent on boundaries |
| 7144 |
|
- replace hardcoded lower limit for zeta (zMin) by runtime parameter |
| 7145 |
|
- add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean |
| 7146 |
|
stress formulation and no-slip boundary conditions |
| 7147 |
|
o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP |
| 7148 |
|
in gad_calc_rhs.F ; add few safety stops in initialisation phase. |
| 7149 |
|
o pkg/seaice: a first HSALT time stepping equation has been checked in |
| 7150 |
|
o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV |
| 7151 |
|
in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem |
| 7152 |
|
without requiring DO-IF statements |
| 7153 |
|
o pkg/thsice: |
| 7154 |
|
use continuous power-law function for partition of energy between lateral |
| 7155 |
|
melting/freezing and thinning/thickening ; old code using step function |
| 7156 |
|
still available with #undef THSICE_FRACEN_POWERLAW |
| 7157 |
|
update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice |
| 7158 |
|
o testreport: change AD testing : check against results/output_adm.txt |
| 7159 |
|
using same scripts as for forward test. |
| 7160 |
|
|
| 7161 |
|
checkpoint59g (2007/09/17) |
| 7162 |
|
o adjoint testing: in preparation for changing testreport: |
| 7163 |
|
- output format: cost and grad written on separated lines |
| 7164 |
|
- ad output results in directory "results" (instead of "results_ad") |
| 7165 |
|
o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
| 7166 |
|
o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
| 7167 |
|
o pkg/ecco: allow user defined cost function contributions |
| 7168 |
|
o testreport: |
| 7169 |
|
Allow to choose (per experiment) the list of tested output variables |
| 7170 |
|
and the main variable (used to issue a pass/FAIL ) ; |
| 7171 |
|
- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
| 7172 |
|
- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
| 7173 |
|
Also modify printing of summary: |
| 7174 |
|
a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
| 7175 |
|
b) echo the list of tested variables in the individual summary.txt of |
| 7176 |
|
each experiment. |
| 7177 |
|
o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
| 7178 |
|
threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
| 7179 |
|
(but still depend on the tile decompostion of the domain). |
| 7180 |
|
o pkg/seaice: change a discretization detail to make the B-grid code |
| 7181 |
|
"more symmetric". This change is likely to remove all "ridges/leads" that |
| 7182 |
|
where quasi-aligned with the grid in B-grid solutions. It may also be |
| 7183 |
|
the solution to the stress coupling issues with the B-grid. |
| 7184 |
|
o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
| 7185 |
|
remove .cvsignore from input dir. (since testreport no longer run here). |
| 7186 |
|
o pkg/thsice: |
| 7187 |
|
- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
| 7188 |
|
- fix reshaping of sea-ice just after advection: |
| 7189 |
|
melt all the ice only if ice-volume is too small. |
| 7190 |
|
- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
| 7191 |
|
prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
| 7192 |
|
and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
| 7193 |
|
o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
| 7194 |
|
tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
| 7195 |
|
o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
| 7196 |
|
forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
| 7197 |
|
(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
| 7198 |
|
and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
| 7199 |
|
of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
| 7200 |
|
-> update output.txt |
| 7201 |
|
o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
| 7202 |
|
this affects truncation error: -> update output.txt of exp: |
| 7203 |
|
global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
| 7204 |
|
ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
| 7205 |
|
|
| 7206 |
|
checkpoint59f (2007/08/21) |
| 7207 |
|
o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
| 7208 |
|
o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
| 7209 |
|
a bounded range (in forward mode) |
| 7210 |
|
o pkg/ecco, ctrl, autodiff and mom_common: |
| 7211 |
|
internal parameter controls, completements of implementations |
| 7212 |
|
o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
| 7213 |
|
o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
| 7214 |
|
(not seem any difference in testing results). |
| 7215 |
|
o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
| 7216 |
|
at face corners. |
| 7217 |
|
o pkg/generic_advdiff: |
| 7218 |
|
- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
| 7219 |
|
loop range indices for computing vertical advection tendency |
| 7220 |
|
and do the calculation in the interior only (no overlap) ; |
| 7221 |
|
for now, only implemented for SOM advection (to save CPU time). |
| 7222 |
|
- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
| 7223 |
|
o exch2 adjoint |
| 7224 |
|
First set of changes: |
| 7225 |
|
- add exch2 hand-written adjoint templates |
| 7226 |
|
- exch2 hand-written no longer use TAF-flag 'nownew_arg' |
| 7227 |
|
This will require cleanup in pkg/autodiff/*.F |
| 7228 |
|
(changed routines currently kept separate in verif. code/) |
| 7229 |
|
- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
| 7230 |
|
that used to hide exch2 or cubed-sphere specific code |
| 7231 |
|
(commented via 'cph-exch2') |
| 7232 |
|
o pkg/seaice |
| 7233 |
|
- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
| 7234 |
|
o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
| 7235 |
|
output of global_ocean.cs32x15.thsice . |
| 7236 |
|
|
| 7237 |
|
checkpoint59e (2007/07/26) |
| 7238 |
|
o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
| 7239 |
|
for B-grid vector (not yet tested) and C-grid vector (<- only used |
| 7240 |
|
when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). |
| 7241 |
|
o starting implementation of Duffy et al. (GRL 1999) salt plume scheme |
| 7242 |
|
(#ifdef ALLOW_SALT_PLUME) |
| 7243 |
|
o gather_2d/scatter_2d: removed halo regions |
| 7244 |
|
o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
| 7245 |
|
scheme and the corresponding test case (under front_relax dir). For now, |
| 7246 |
|
only available with Skew-flux form and not yet tested in realistic set-up. |
| 7247 |
|
adjoint: store directives updated, but gradient checks deteriorated, |
| 7248 |
|
so maybe GM/Redi adjoint is now broken. |
| 7249 |
|
o seaice adjoint |
| 7250 |
|
* add AREA, HEFF, HSNOW as control variable |
| 7251 |
|
(should not change lab_sea results) |
| 7252 |
|
* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
| 7253 |
|
o pkg/seaice: |
| 7254 |
|
* added computation of saltFlux in seaice_growth; |
| 7255 |
|
For time being, sea ice salinity is assumed constant |
| 7256 |
|
contribution of snow flooding to freshening of sea ice is neglected. |
| 7257 |
|
SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
| 7258 |
|
defaults to 0.0 in order to maintain backward compatibility. |
| 7259 |
|
Typical values for SEAICE_salinity are 4 to 10 g/kg. |
| 7260 |
|
* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
| 7261 |
|
* added SEAICE_availHeatFrac, which specifies fraction of surface level |
| 7262 |
|
heat content used to melt or grow ice |
| 7263 |
|
* commented out cap of HICE: it helps keep ice thinner |
| 7264 |
|
* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
| 7265 |
|
* applied OBCS T/S mask to HEFFM sea ice mask |
| 7266 |
|
|
| 7267 |
|
checkpoint59d (2007/06/21) |
| 7268 |
|
o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
| 7269 |
|
for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
| 7270 |
|
(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
| 7271 |
|
o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
| 7272 |
|
and change default value of parameter "GM_Small_Number"; |
| 7273 |
|
update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
| 7274 |
|
global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
| 7275 |
|
tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
| 7276 |
|
o pkg/ecco: cost function when applying pkg/smooth to controls |
| 7277 |
|
o pkg/ctrl: add forcingPrecond run time parameter |
| 7278 |
|
o pkg/seaice: |
| 7279 |
|
- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
| 7280 |
|
- fix bug in metric terms of u-equation in LSR solver (implicit part), |
| 7281 |
|
changes verification/lab_sea |
| 7282 |
|
- rearrange implicit part of u-equation in LSR solver to make it easier to |
| 7283 |
|
read, understand, and debug. This causes changes at the truncation level. |
| 7284 |
|
- fix (serious) bug in the boundary conditions (sign error in the implicit |
| 7285 |
|
part) of the LSR solver. Changes all LSR results. |
| 7286 |
|
- fixed problem with HSNOW initialization to avoid thick snow when AREA |
| 7287 |
|
is initilized with small values - does not change lab_sea results. |
| 7288 |
|
- added HsnowFile initialization capability |
| 7289 |
|
o pkg/smooth: addition to model/src and pkg/ctrl so allow |
| 7290 |
|
initialization of pkg/smooth and application to control vector |
| 7291 |
|
o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
| 7292 |
|
o dependencies: pkg/profiles requires pkg/cal |
| 7293 |
|
o pkg/profiles: |
| 7294 |
|
- added option ALLOW_PROFILES_GENERICGRID |
| 7295 |
|
-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
| 7296 |
|
that interpolation information (grid points and coefficients) is provided |
| 7297 |
|
within the netcdf input files. |
| 7298 |
|
-> sample matlab scripts can be found in MITgcm_contrib/gael |
| 7299 |
|
that allow you to prepare netcdf input files. |
| 7300 |
|
- also modified: cleaner include statements, cleaner error print statements, |
| 7301 |
|
cleaner stops when error, and more tests of the netcdf input files consistency. |
| 7302 |
|
o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
| 7303 |
|
o pkg/seaice: |
| 7304 |
|
- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
| 7305 |
|
requires a new routine: seaice_diagnostics_fill.F |
| 7306 |
|
- make sure that seaice does not move if not forced (pressure replacement |
| 7307 |
|
method, Hibler and Ip, 1995), changes results |
| 7308 |
|
- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
| 7309 |
|
- SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). |
| 7310 |
|
It is turned off by default (=-1.), because it changes the results. |
| 7311 |
|
- make it possible to read AREA from a file, too. |
| 7312 |
|
|
| 7313 |
|
checkpoint59c (2007/06/04) |
| 7314 |
|
o add S/R and diagnostics for oceanic mixed-layer depth |
| 7315 |
|
o move GMRedi call after all vertical mixing schemes (including KPP) |
| 7316 |
|
o pkg/thsice: |
| 7317 |
|
- ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs |
| 7318 |
|
(melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice |
| 7319 |
|
o pkg/obcs: |
| 7320 |
|
- bug fix for balance code |
| 7321 |
|
o pkg/seaice: |
| 7322 |
|
- allow values of SEAICE_elasticParm > 1 |
| 7323 |
|
- add new parameter SEAICE_evpTauRelax as an alternative |
| 7324 |
|
to SEAICE_elasticParm |
| 7325 |
|
- make lsr boundary conditions free slip (by default), changes result |
| 7326 |
|
- add code for no slip boundary conditions for lsr |
| 7327 |
|
- set minimum of zeta to zero (and not 4e8) (changes results) |
| 7328 |
|
- add a cap on AREA after advecting AREA if seaice_growth is not called |
| 7329 |
|
o change calculation of Visbeck K: |
| 7330 |
|
- no longer depend on tapering scheme; instead, compute slope (limited |
| 7331 |
|
by GM_maxSlope). this is equivalent to what was comuted before with |
| 7332 |
|
clipping or linear tappering. |
| 7333 |
|
- fix vertical averaging (wrong by 1/2 level) |
| 7334 |
|
- leave the old version (but will not be maintained) within |
| 7335 |
|
#ifdef OLD_VISBECK_CALC / #endif |
| 7336 |
|
- update output of exp. ideal_2D_oce |
| 7337 |
|
o change error catch in calc_r_star to improve vectorization |
| 7338 |
|
o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
| 7339 |
|
add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
| 7340 |
|
o adjoint: |
| 7341 |
|
Re-organized adjoint checkpointing according to Matt Mazloff |
| 7342 |
|
(but with modifs/completions/cleanups) |
| 7343 |
|
Storing is now bundled into large arrays to optimized I/O |
| 7344 |
|
(and second step in cleanup of the_main_loop) |
| 7345 |
|
|
| 7346 |
|
checkpoint59b (2007/05/16) |
| 7347 |
|
o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
| 7348 |
|
- export/import (between ocean & coupler) fields needed for ocean DIC. |
| 7349 |
|
o pkg/seaice: |
| 7350 |
|
- get rid of three more exchanges seaice_calc_viscosities (required |
| 7351 |
|
different loop boundaries in seaice_lsr and seaice_ocean_stress) |
| 7352 |
|
- bug fix in seaice_ocean_stress (update of lab_sea required) |
| 7353 |
|
- reduce loop boundaries to necessary minimum also in seaice_evp |
| 7354 |
|
- go back to the old way of computing deltaC/Z as the adjoint likes that |
| 7355 |
|
better |
| 7356 |
|
o Refresh of tutorial_global_oce_latlon (includes changing salinity-like |
| 7357 |
|
passive tracer to an Age Tracer) + update output.txt |
| 7358 |
|
o pkg/exf: |
| 7359 |
|
- implement A-grid / C-grid selection for wind-stress input files. |
| 7360 |
|
- clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) |
| 7361 |
|
for now, in exf_bulk_largeyeager04.F only : |
| 7362 |
|
- change implementation for case where windspeed + 2. components wind-stress |
| 7363 |
|
are read-in. AND use rhoConstFresh to convert evap. |
| 7364 |
|
o pkg/seaice: |
| 7365 |
|
- use correct EXCH_UV for wind-forcing (on A-grid). |
| 7366 |
|
- change SEAICE_OPTIONS.h to limit the number of option combinations (regarding |
| 7367 |
|
SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops. |
| 7368 |
|
o pkg/exf: |
| 7369 |
|
- default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC) |
| 7370 |
|
EXF_INTERPOLATION: |
| 7371 |
|
- merge global_with_exf/code version of exf_interp_read.F |
| 7372 |
|
to the main code ; |
| 7373 |
|
- Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when |
| 7374 |
|
reading the file ; Important: This options needs to be defined to recover |
| 7375 |
|
previous code. |
| 7376 |
|
otherwise, use fixed size array to read in (size=exf_interp_bufferSize). |
| 7377 |
|
- no longer loose real*8 precision along the way when using exf_iprec=64. |
| 7378 |
|
o pkg/seaice: rearrangement of common blocks (really needs more cleaning up) |
| 7379 |
|
- change discretisation of evp-solver in order to avoid another exchange |
| 7380 |
|
(changes lab_sea) and clean up a little |
| 7381 |
|
- replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS) |
| 7382 |
|
help the adjoint (this also changes the results slightly) |
| 7383 |
|
- add a few "_d 0" where they had been missing in seaice_evp.F |
| 7384 |
|
- cleaning up: remove unused seaice_calc_rhs.F |
| 7385 |
|
o pkg/exf: some cleaning-up: |
| 7386 |
|
- change various "constants" into runtime parameters |
| 7387 |
|
- cleaned-up Large&Yeager04 routine which should eventually |
| 7388 |
|
replace exf_bulkformulae.F (changed names of S/R and CPP) |
| 7389 |
|
and merged various ALLOW_ATM_WIND options |
| 7390 |
|
only used with thsice pkg (in thsice_get_exf.F): |
| 7391 |
|
- implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04) |
| 7392 |
|
which are used when useStabilityFct_overIce=TRUE (= the default) |
| 7393 |
|
- change default values of ice & snow emissivity and scale downward LW |
| 7394 |
|
by ice & snow emissivity. |
| 7395 |
|
o pkg/thsice: |
| 7396 |
|
fix few little problems, in thsice_calc_thickn.F: |
| 7397 |
|
- growth vertically (and not laterally) if iceFrac == iceMaskMax |
| 7398 |
|
- melt only laterally if hIce < hThinIce (as the comments say) |
| 7399 |
|
and in thsice_extend.F: |
| 7400 |
|
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
| 7401 |
|
- start to form ice as soon as the minimum ice-volume is reachable. |
| 7402 |
|
update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice), |
| 7403 |
|
and cpl_aim+ocn |
| 7404 |
|
o pkg/kpp |
| 7405 |
|
- move computation of surface related input fields to KPP into a new |
| 7406 |
|
subroutine kpp_forcing_surf.F |
| 7407 |
|
- remove wrong (within bi,bj loops) EXCH calls. |
| 7408 |
|
- little cleaning (add argument myThid in last position, cvs header ...) |
| 7409 |
|
- for now, fix conservation problem by exchanging KPPviscAz (may not |
| 7410 |
|
be the best fix) |
| 7411 |
|
o pkg/seaice |
| 7412 |
|
- check for inconsistent evp parameter/cpp-flag combination |
| 7413 |
|
- remove leftover errIO flat for obsolete name list error handling |
| 7414 |
|
o OpenAD |
| 7415 |
|
- changed verification/OpenAD to full baroclinic setup (including GM/Redi) |
| 7416 |
|
|
| 7417 |
|
checkpoint59a (2007/05/01) |
| 7418 |
|
o pkg/seaice: some parameter clarifications and a little bit of clean up |
| 7419 |
|
o pkg/thsice: rename run-time parameters: |
| 7420 |
|
himin -> hIceMin |
| 7421 |
|
himin0 -> hThinIce |
| 7422 |
|
hihig -> hThickIce |
| 7423 |
|
i0 -> i0swFrac |
| 7424 |
|
transCoef -> bMeltCoef |
| 7425 |
|
frac_energy -> fracMelting |
| 7426 |
|
add new parameters: hNewIceMax, fracFreezing, dhSnowLin |
| 7427 |
|
with default values (for now) that do not change the results. |
| 7428 |
|
remove old version of thsice vars advection in pkg/seaice. |
| 7429 |
|
o in FFIELDS.h: |
| 7430 |
|
- replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD |
| 7431 |
|
- make pLoad & sIceLoad always available (but still only used if |
| 7432 |
|
ATMOSPHERIC_LOADING is #define). |
| 7433 |
|
o pkg/kpp: replaced _KPP_RL with _RL |
| 7434 |
|
o bug fixes for vertical diffusivity computations when both KPP and |
| 7435 |
|
3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F |
| 7436 |
|
are no longer updating the vertical diffusivity array |
| 7437 |
|
(passed as argument) but are (re-) setting those arrays. |
| 7438 |
|
o pkg/seaice: fix bug in evp solver, while doing that |
| 7439 |
|
- change (improve?) discretization of stress computations for both |
| 7440 |
|
cgrid-lsr and evp solver |
| 7441 |
|
- add a new routine to compute strain rates |
| 7442 |
|
- the above changes lab_sea results |
| 7443 |
|
- add no slip conditions for evp solver (off by default), lsr-version |
| 7444 |
|
may follow |
| 7445 |
|
- fix exchange for shear at Z-points (does not change lab_sea) |
| 7446 |
|
- retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp |
| 7447 |
|
(to force the user to pick a time step since there is not "safe" way |
| 7448 |
|
of choosing it) |
| 7449 |
|
- add principal stress diagnostics |
| 7450 |
|
- rearrange fields for evp a little to avoid having to call a: too many |
| 7451 |
|
exchanges and b: exchanges for stress trensor components which we do |
| 7452 |
|
not have. |
| 7453 |
|
- modify Hibler+Bryan (1987) stress coupling so that it reuses information |
| 7454 |
|
of evp, complete rewrite for lsr case (latter is does not yet work |
| 7455 |
|
in all cases) |
| 7456 |
|
o pkg/kpp: add code to have mixing in shelf ice caverns |
| 7457 |
|
- add myThid to all kpp routines (long overdue) |
| 7458 |
|
|
| 7459 |
|
checkpoint59 (2007/04/19) |
| 7460 |
|
o pkg/exf: |
| 7461 |
|
- fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND & |
| 7462 |
|
ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid |
| 7463 |
|
- move exf header files from lower_case.h to UPPER_CASE.h ; |
| 7464 |
|
add missing cvs Header & Name |
| 7465 |
|
- add adjoint routines and flow dirs for newly used exch_uv_agrid routines |
| 7466 |
|
- add namelist param. selectStressGridPosition, exf_monFreq |
| 7467 |
|
- retire many _CLIM routines, and remove data.exf_clim |
| 7468 |
|
+ params moved to data.exf |
| 7469 |
|
+ climsst, climsss now handled by exf_set_gen, i.e. |
| 7470 |
|
climss?period=0 refers to constant field, |
| 7471 |
|
climss?period=-12 to monthly forcing |
| 7472 |
|
- split up namelists in data.exf |
| 7473 |
|
o pkg/seaice: |
| 7474 |
|
- remove seaice_exch and seaice_exch_uv |
| 7475 |
|
- remove superfluous exchange of theta |
| 7476 |
|
- add myThid to seaice_budget_ocean/ice |
| 7477 |
|
- add new interface for atmospheric wind forcing (C-grid only) |
| 7478 |
|
+ new routine |
| 7479 |
|
+ two new field (taux, tauy for stress over ice) |
| 7480 |
|
+ removed one global field (DAIRN) for C-grid case only |
| 7481 |
|
o pkg/thsise |
| 7482 |
|
- 2nd set of modifs for thsice adjoint in conjunction with exf |
| 7483 |
|
o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.) |
| 7484 |
|
|
| 7485 |
|
checkpoint58y_post (2007/04/15) |
| 7486 |
|
o Added capability for latitudinal dependence of Bryan and Lewis, 1979 |
| 7487 |
|
vertical diffusivity, similar to that in MOM4; turned on using |
| 7488 |
|
#define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using |
| 7489 |
|
diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file. |
| 7490 |
|
o Added capability for 3D specification of background vertical diffusion |
| 7491 |
|
coefficient. This is done by (i) #define ALLOW_3D_DIFFKR |
| 7492 |
|
in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime |
| 7493 |
|
"data" file that contains the 3D vertical diffusivity coefficients. |
| 7494 |
|
o ice dynamics (pkg/seaice) with thsice thermodynamics: |
| 7495 |
|
- add code within pkg thsice to advect & diffuse sea-ice fields |
| 7496 |
|
similar to (and will replace) what has been added in seaice_advdiff.F, |
| 7497 |
|
but: - conserving Mass, Heat & Salt. |
| 7498 |
|
- better when using non-linear advection scheme (not yet fully tested) |
| 7499 |
|
- can also be used in atmospheric set-up (for now, only the diffusion). |
| 7500 |
|
|
| 7501 |
|
checkpoint58x_post (2007/04/04) |
| 7502 |
|
o IO option for global-file compact format: |
| 7503 |
|
- add options when generating topology (utils/exch2/matlab-topology-generator) |
| 7504 |
|
- add I/O capability (pkg/mdsio). |
| 7505 |
|
- adapt utils/matlab/rdmds.m to read this format. |
| 7506 |
|
for now long-line format not yet supported by pkg/mdsio (& exch2). |
| 7507 |
|
o shelfice: add a few diagnostics |
| 7508 |
|
|
| 7509 |
|
checkpoint58w_post (2007/03/13) |
| 7510 |
|
o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: |
| 7511 |
|
rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref |
| 7512 |
|
(and replace horiVertRatio in NH code). |
| 7513 |
|
Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) |
| 7514 |
|
and tutorial_plume_on_slope (sensitive to truncation) |
| 7515 |
|
o seaice: if ALLOW_ATM_WIND is undefined use wind stress |
| 7516 |
|
directly to drive seaice model (C-grid only) |
| 7517 |
|
o exf: when input wind-stress (#undef ALLOW_ATM_WIND): |
| 7518 |
|
- reintroduce computation of wind from stress, |
| 7519 |
|
- compute tau (in exf_bulkformulae.F) from windstress averaged to |
| 7520 |
|
mass points to avoid tau = 0 |
| 7521 |
|
- fix serious bug: (1/3) in Fortran is not the same as (1./3.) |
| 7522 |
|
o rdmnc.m: make it work with "global" files created with gluemnc |
| 7523 |
|
o rdmnc.m : some improvements in dealing with singleton dimension |
| 7524 |
|
(tested on all testreport mnc output files). |
| 7525 |
|
o genmake2: disable pkg/profiles if netcdf test fails. |
| 7526 |
|
o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output. |
| 7527 |
|
o move call to cal_readparms up to make calendar parameters/variable available |
| 7528 |
|
to all packages |
| 7529 |
|
|
| 7530 |
|
checkpoint58v_post (2007/02/08) |
| 7531 |
|
o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get |
| 7532 |
|
useDynP_inEos_Zc tested. |
| 7533 |
|
o pkg/exf: changes to properly interpolate/mask/scale initial fields |
| 7534 |
|
o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields |
| 7535 |
|
and portions thereof. See read_cs.txt for description and examples. |
| 7536 |
|
o utils/matlab/cs_grid/bk_line: to compute transport through passages, |
| 7537 |
|
add a script (grt_circ_bkl.m) to generate broken-line between 2 points, |
| 7538 |
|
following the great-circle arc between those 2 points. |
| 7539 |
|
o trap un-initialized variable with pathscale compiler on weddell.mit.edu |
| 7540 |
|
(thanks to Constantinos): fix few problems and get (almost) all exp to pass. |
| 7541 |
|
o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in |
| 7542 |
|
- enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) |
| 7543 |
|
- used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81) |
| 7544 |
|
- still needs work (not working with some options ; efficiency to improve) |
| 7545 |
|
and serious testing. |
| 7546 |
|
- use this scheme for temperature & salinity in 2 advection test exp.: |
| 7547 |
|
advect_xy & advect_xz, respectively. |
| 7548 |
|
|
| 7549 |
|
checkpoint58u_post (2007/01/12) |
| 7550 |
|
o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. |
| 7551 |
|
o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. |
| 7552 |
|
o testreport: add option "-skipdir" to skip some test. |
| 7553 |
|
o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent |
| 7554 |
|
momentum calculation. |
| 7555 |
|
o gad_advection: fix vertAdvecScheme (if different from advectionScheme) |
| 7556 |
|
o some cleaning: usePickupBeforeC35 no longer supported ; remove this option. |
| 7557 |
|
remove checkpoint.F and the_correction_step.F (no longer used); |
| 7558 |
|
do the k loop inside CYCLE_TRACER (supposed to be more efficient). |
| 7559 |
|
o add option (linFSConserveTr) to correct for tracer source/sink due to |
| 7560 |
|
Linear Free surface |
| 7561 |
|
o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine |
| 7562 |
|
o pkg/thsice: fix reading mnc-pickups |
| 7563 |
|
|
| 7564 |
|
checkpoint58t_post (2006/12/30) |
| 7565 |
|
o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) |
| 7566 |
|
o pkg/mdsio: |
| 7567 |
|
- clean-up mdsio_readfield.F & mdsio_writefield_new.F and |
| 7568 |
|
move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & |
| 7569 |
|
mdsio_write_field.F (S/R MDS_WRITE_FIELD); |
| 7570 |
|
- fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD |
| 7571 |
|
- collect old S/R in one file: mdsio_rw_field.F (now just a call to |
| 7572 |
|
either MDS_READ_FIELD or MDS_WRITE_FIELD ) |
| 7573 |
|
- new S/R (to replace MDSWRITEMETA), which allows to write more |
| 7574 |
|
informations (variable names, time ...) to meta files. |
| 7575 |
|
- modify rdmds.m to give back the meta file content. |
| 7576 |
|
o pkg/diagnostics: change vertical interpolation to be safer, and more |
| 7577 |
|
flexible (define p-levels to interpolate to in data.diagnostics); |
| 7578 |
|
add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right |
| 7579 |
|
diagnostic pointer. |
| 7580 |
|
o pkg/seaice: more cleaning up of seaice_growth, added many comments |
| 7581 |
|
o pkg/exf: put runoff0 and runoff1 into the appropriate common block |
| 7582 |
|
o fix multi-category seaice: |
| 7583 |
|
- change cpp flag SEAICE_MULTILEVEL to more meaningful name: |
| 7584 |
|
SEAICE_MULTICATEGORY |
| 7585 |
|
- fix short wave heat flux |
| 7586 |
|
o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics |
| 7587 |
|
and allow to use EVP solver. Change forward lab_sea: test both EVP |
| 7588 |
|
solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) |
| 7589 |
|
o Initial check-in of lab_sea adjoint |
| 7590 |
|
(very similar to natl_box_adjoint/code_seaice) |
| 7591 |
|
* used C-grid and EVP solver |
| 7592 |
|
* used KPP, GM/Redi |
| 7593 |
|
* uses inAdExact=.TRUE. |
| 7594 |
|
* gradient checks fail for both ADM and TLM |
| 7595 |
|
due to sensitive snow melt code in seaice_grwoth (look for "JZ") |
| 7596 |
|
f.d. gradients actually seem more problematic than ADM, TLM gradients; |
| 7597 |
|
issue is related to forward mismatch between g77 an ifort |
| 7598 |
|
o pkg/seaice: overhaul of thermodynamics |
| 7599 |
|
- growth.F and groatb.F are replaced by new routine seaice_growth.F |
| 7600 |
|
- budget.F is replaced by two new routines seaice_budget_ocean/ice.F |
| 7601 |
|
- move a few global fields out of SEAICE.h into seaice_growth.F and |
| 7602 |
|
make them 2D (FICE/QNETO/ ...) |
| 7603 |
|
- remove FO (it is the same as QNETO) |
| 7604 |
|
- introduce a few local fields to avoid modifying external fields such |
| 7605 |
|
as atemp, etc. |
| 7606 |
|
|
| 7607 |
|
checkpoint58s_post (2006/12/11) |
| 7608 |
|
o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F |
| 7609 |
|
changed exf_set_gen.F so that |
| 7610 |
|
genperiod=0 means input file is one time-constant field and |
| 7611 |
|
genperiod=-12 means input file contains 12 monthly means |
| 7612 |
|
o CG2D: use pre-computed solver main-diagonal (stored in common block); |
| 7613 |
|
this affects truncation error ; generate new output file for exp. which |
| 7614 |
|
fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), |
| 7615 |
|
global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), |
| 7616 |
|
ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), |
| 7617 |
|
MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), |
| 7618 |
|
tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), |
| 7619 |
|
vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) |
| 7620 |
|
o start implementation of deep-atmosphere and anelastic formulation |
| 7621 |
|
o verification: remove 2nd copy of input files and use script "prepare_run" |
| 7622 |
|
to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) |
| 7623 |
|
o mom_common/vecinv/fluxform: fix a few initialisation isssues |
| 7624 |
|
o profiles: fix for multithreaded case |
| 7625 |
|
|
| 7626 |
|
o diagnostics: rename few diags: |
| 7627 |
|
s/'PRESSURE'/'RCENTER '/g |
| 7628 |
|
s/'TICE '/'oceFreez'/g |
| 7629 |
|
s/'TAUX '/'oceTAUX '/g |
| 7630 |
|
s/'TAUY '/'oceTAUY '/g |
| 7631 |
|
s/'SWFLUX '/'oceQsw '/g |
| 7632 |
|
s/DIFx/DFxE/g |
| 7633 |
|
s/DIFy/DFyE/g |
| 7634 |
|
and add few ocean-forcing diagnostics: |
| 7635 |
|
atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS |
| 7636 |
|
o modifications to pkg/seaice/growth.F and budget.F, which change results of |
| 7637 |
|
lab_sea experiment: HSNOW was sometimes treated as effective and sometimes |
| 7638 |
|
as actual snow thickness. It now refers everywhere to effective snow |
| 7639 |
|
thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. |
| 7640 |
|
|
| 7641 |
|
checkpoint58r_post (2006/11/17) |
| 7642 |
|
o modifications to pkg/seaice/growth.F, which change results of |
| 7643 |
|
lab_sea experiment: fixes pertain to melting snow over open water, to |
| 7644 |
|
masking EVAP under sea ice, and to using the correct AREA variable for |
| 7645 |
|
computations of EVAP, PRECIP, HSNOW, and GHEFF |
| 7646 |
|
o add ability to read bathy, salt, and theta using MNC (off by def) |
| 7647 |
|
o add flooding algorithm and advection of HSNOW for pkg/seaice; |
| 7648 |
|
both are turned off by default and do no change any results |
| 7649 |
|
o seaice advection with pkg/thsice: a step toward the use of non-linear |
| 7650 |
|
advection scheme, but #ifdef or commented out for now (requires more EXCH). |
| 7651 |
|
o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens |
| 7652 |
|
(identical results) and the standard version of EXTERNAL_FIELDS_LOAD |
| 7653 |
|
in natl_box (affects results @ truncation level: update output.txt) |
| 7654 |
|
o multi-threading and IO: |
| 7655 |
|
- replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. |
| 7656 |
|
- remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls |
| 7657 |
|
(needed to work with SingleCpuIO): tested in all verif. exp. |
| 7658 |
|
o GAD: use simpler DST3 formulation as default (old version left within #ifdef) |
| 7659 |
|
affects the results (but none of the verification test uses this scheme). |
| 7660 |
|
o Adding some pkg/diagnostics capability to pkg/seaice |
| 7661 |
|
(will certainly be subject to changes) |
| 7662 |
|
o ctrl: adding new control variables: |
| 7663 |
|
lwflux, lwdown, evap, snowprecip, apressure, runoff |
| 7664 |
|
|
| 7665 |
|
checkpoint58q_post (2006/10/20) |
| 7666 |
|
o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up |
| 7667 |
|
1/6-deg Southern Ocean configuration by 8% on IBM Datastar and |
| 7668 |
|
high_res_cube configuration by 4% on Columbia. |
| 7669 |
|
o clean-up multi-threaded problems (reported by debugger tcheck on ACES); |
| 7670 |
|
add (in global_with_exf/code) a version of EXF_INTERP_READ without |
| 7671 |
|
dynamical allocation (seems to work in multi-threaded). |
| 7672 |
|
o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using |
| 7673 |
|
single CPU io) so that TAF does not have to see EESUPPORT.h |
| 7674 |
|
o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
| 7675 |
|
|
| 7676 |
|
checkpoint58p_post (2006/09/08) |
| 7677 |
|
o obcs: stop if obcs is used with useCDscheme = .true. |
| 7678 |
|
o shelfice: |
| 7679 |
|
- fix a sign error so that no slip at shelfice interface works |
| 7680 |
|
- remove stop for combination non-hydrostatic code and shelfice. That does |
| 7681 |
|
not mean, that the results are correct, but at least they are numerically |
| 7682 |
|
stable |
| 7683 |
|
o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) |
| 7684 |
|
o added adjoint exch routined for all exch*3d* routines |
| 7685 |
|
and updated flow directives |
| 7686 |
|
|
| 7687 |
|
checkpoint58o_post (2006/08/28) |
| 7688 |
|
o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; |
| 7689 |
|
remove old subroutines (_XY_ & _XYZ_); update the adjoint version. |
| 7690 |
|
o change controling S/R for writing pickup file (new S/R do_write_pickup) |
| 7691 |
|
and clean-up reading/writing of pickup files. |
| 7692 |
|
o fix local version of read/write pickup (NH part) in rotating_tank/code |
| 7693 |
|
o simplify EXCH interface: |
| 7694 |
|
- change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) |
| 7695 |
|
- not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version |
| 7696 |
|
o added the regrid package |
| 7697 |
|
o shelfice: |
| 7698 |
|
- add a simple boundary layer scheme to reduce noise |
| 7699 |
|
- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
| 7700 |
|
|
| 7701 |
|
checkpoint58n_post (2006/08/14) |
| 7702 |
|
o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
| 7703 |
|
local variable (not in common block). |
| 7704 |
|
o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
| 7705 |
|
- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
| 7706 |
|
- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
| 7707 |
|
to work with SingleCpuIO. |
| 7708 |
|
o add "_d 0" to real constant of pkg/cfc subroutines ; |
| 7709 |
|
update exp. cfc_exemple & tutorial_cfc_offline output files. |
| 7710 |
|
o multi-threading and IO: |
| 7711 |
|
- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
| 7712 |
|
(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
| 7713 |
|
- barrier before and after reading. |
| 7714 |
|
- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
| 7715 |
|
- avoid using MDS_WRITELOCAL for LAND pkg output. |
| 7716 |
|
- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
| 7717 |
|
common-block variables ; Allows multi-threading with master-thread IO. |
| 7718 |
|
o change default MAX_NO_THREADS from 32 to 4 ; |
| 7719 |
|
and stop cleanly when MAX_NO_THREADS is too small. |
| 7720 |
|
o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
| 7721 |
|
|
| 7722 |
|
checkpoint58m_post (2006/07/17) |
| 7723 |
|
o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
| 7724 |
|
and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
| 7725 |
|
o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
| 7726 |
|
keep global_ocean.90x40x15 (for AD testing) with former secondary test |
| 7727 |
|
(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
| 7728 |
|
o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
| 7729 |
|
add MITgcm_tutorials (= code + all the tutorials) |
| 7730 |
|
o ecco, option to compute cost for total ssh (mean+anom) |
| 7731 |
|
o consistent with addition of ptracer and ssh in pkg/profiles |
| 7732 |
|
o profiles: adding ptracer and ssh |
| 7733 |
|
o testreport: change multi-test output-file name |
| 7734 |
|
(from output.txt.{name} to output.{name}.txt) |
| 7735 |
|
o profiles: now ok for mutli-tiles case |
| 7736 |
|
o seaice: add 4 parameters for different advection schemes for area, |
| 7737 |
|
(effective) seaice thickness, enthalphy, and snow height. Their default |
| 7738 |
|
is the standard parameter SEAICEadvScheme |
| 7739 |
|
o calc_gw: |
| 7740 |
|
- add cosFacU in zonal viscous flux (harmonic.visc.). |
| 7741 |
|
- put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. |
| 7742 |
|
of tutorial_plume_on_slope. |
| 7743 |
|
o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). |
| 7744 |
|
o calc_gw: true flux-form, account for horizontal grid spacing. |
| 7745 |
|
update rotating_tank results, but not plume_on_slope (affected at |
| 7746 |
|
truncation level, 11 digits). |
| 7747 |
|
|
| 7748 |
|
checkpoint58l_post (2006/07/12) |
| 7749 |
|
o calc_gw: |
| 7750 |
|
- take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V |
| 7751 |
|
- remove side-drag for now (need to fix it); update plume_on_slope results. |
| 7752 |
|
- fix for partial-cell & non-uniform dz; update plume_on_slope results. |
| 7753 |
|
o commit code to make SST/SSS weights spatially variable |
| 7754 |
|
(based on either variable in-situ or variable initial T/S weights) |
| 7755 |
|
o pkg/ecco: |
| 7756 |
|
* commit code to relax deviations of xx_theta, xx_salt to 5*sigma, |
| 7757 |
|
now based on horizontally varying weights wthetaLev, wsaltLev |
| 7758 |
|
* cost_averagesflags now returns year indices in addition to day, month |
| 7759 |
|
* sflux balance is performed on annual basis |
| 7760 |
|
(sflxumm, sfluxmm2, bal_sfluxmm) |
| 7761 |
|
* for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, |
| 7762 |
|
including separate counting and multipliers |
| 7763 |
|
o pkg/rbcs |
| 7764 |
|
* add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing |
| 7765 |
|
|
| 7766 |
|
checkpoint58k_post (2006/07/06) |
| 7767 |
|
o testreport: |
| 7768 |
|
- always build in dir. "build" (if not there, mkdir build instead of building |
| 7769 |
|
& running in input) |
| 7770 |
|
- run in dir run (if it exists), in build otherwise. |
| 7771 |
|
- call prepare_run (if input/prepare_run exists) |
| 7772 |
|
- run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. |
| 7773 |
|
o pkg/exf modifications to interpolation and rotation routines for more |
| 7774 |
|
reasonable treatment of North Pole singularity: for tracers North Pole |
| 7775 |
|
value is set to northernmost zonal-mean value, for zonal velocity it is |
| 7776 |
|
set to zero, and for meridional velocity it is set to northernmost value. |
| 7777 |
|
o pkg/exf/exf_check_range.F |
| 7778 |
|
- add tile index to diagnostics and move stop statement to the very |
| 7779 |
|
end of the routine. |
| 7780 |
|
o pkg/diagnostics: (diagnostics_main_init.F) |
| 7781 |
|
define title of isomorphic variables according to the current config. |
| 7782 |
|
o pkg/thsice with pkg/seaice dynamics: |
| 7783 |
|
- fix domain of computation (interior only, required for exf) and do exchanges |
| 7784 |
|
- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient |
| 7785 |
|
o towards a standard way of dealing with multi-threading in MONITOR |
| 7786 |
|
and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. |
| 7787 |
|
o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) |
| 7788 |
|
to W momentum equation in nonhydrostatic and quasihydrostatic runs. |
| 7789 |
|
o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. |
| 7790 |
|
o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) |
| 7791 |
|
o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL |
| 7792 |
|
(problems ? with gradient check in bottom_ctrl_5x5 adjoint test) |
| 7793 |
|
o tracer advection: |
| 7794 |
|
- clean-up and simplify calc_common_factors.F |
| 7795 |
|
- make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer |
| 7796 |
|
advection subroutine (but still not used within DST advection S/R) |
| 7797 |
|
o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
| 7798 |
|
|
| 7799 |
|
checkpoint58j_post (2006/06/15) |
| 7800 |
|
o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
| 7801 |
|
from file (collects calls previously in FORWARD_STEP) |
| 7802 |
|
o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS |
| 7803 |
|
o adjoint store dir. adjusted accordingly |
| 7804 |
|
o genmake2 |
| 7805 |
|
replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. |
| 7806 |
|
|
| 7807 |
|
checkpoint58i_post (2006/06/14) |
| 7808 |
|
o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
| 7809 |
|
on wind stress (SEAICEstressFactor defaults to 1.) |
| 7810 |
|
o Total number of Timers is finite (<=40): comment out 2 non-essential one |
| 7811 |
|
in the_main_loop.F to avoid Pb (e.g., when running fizhi test) |
| 7812 |
|
o vector_invariant: fix highOrderVorticity(=4.th.Order) advection |
| 7813 |
|
on CS-grid: no longer loosing mass. |
| 7814 |
|
o exf & curvilinear-grid: no longer modify longitude xC & xG. |
| 7815 |
|
o pkg/ggl90: fix sloppy output and fix a bug |
| 7816 |
|
o pkg/seaice: added SEAICEuseEVPpickup parameter |
| 7817 |
|
- Set to false in order to start EVP solver with |
| 7818 |
|
non-EVP pickup files when using SEAICEuseEVP |
| 7819 |
|
- fix sign error in diffusion in seaice_calc_rhs |
| 7820 |
|
|
| 7821 |
|
checkpoint58h_post (2006/06/07) |
| 7822 |
|
* Modifications for bottom topography control |
| 7823 |
|
o replace hFacC by _hFacC at various places |
| 7824 |
|
o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL |
| 7825 |
|
o add non-self-adjoint cg2d_nsa |
| 7826 |
|
o update autodiff support routines |
| 7827 |
|
o re-initialise hfac after ctrl_depth_ini |
| 7828 |
|
o works for 5x5 box, doesnt work for global_ocean.90x40x15 |
| 7829 |
|
* Adding verification for 5x5 box (4-layer) bottom topography control |
| 7830 |
|
|
| 7831 |
|
checkpoint58g_post (2006/06/07) |
| 7832 |
|
o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., |
| 7833 |
|
used for mean seasonal cycle, mean diurnal cycle); add an example |
| 7834 |
|
in verification/global_ocean.cs32x15/input.thsice/data.diagnostics |
| 7835 |
|
o pkg/ggl90: |
| 7836 |
|
- add parameter (minimum surface kinetic energy) |
| 7837 |
|
- fix bug (avoiding division by zero) |
| 7838 |
|
o couple pkg/thsice to pkg/seaice: |
| 7839 |
|
- modify advection in seaice to accomodate new scalar fields to be advected |
| 7840 |
|
- only muliDimAdection scheme work with seaice/thsice |
| 7841 |
|
- mapping of thsice-variables to seaice-variables, back and forth |
| 7842 |
|
- does not break the verification experiments, but does not give the |
| 7843 |
|
desired results either |
| 7844 |
|
o pkg/seaice |
| 7845 |
|
- make (default) second order advection a bit less confusing? |
| 7846 |
|
|
| 7847 |
|
checkpoint58f_post (2006/06/05) |
| 7848 |
|
o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice |
| 7849 |
|
to pkg/seaice): |
| 7850 |
|
- new routines thsice_map_exf and thsice_get_exf provide the interface |
| 7851 |
|
- add an additional formal parameter to thsice_solve4temp |
| 7852 |
|
o pkg/exf: |
| 7853 |
|
- add new fields wspeed, snowprecip (to be able to couple to thsice) |
| 7854 |
|
- correct Stefan-Boltzmann constant |
| 7855 |
|
- new parameter for longwave surface emittance |
| 7856 |
|
- separate some stuff from exf_bulkformulae into new routines |
| 7857 |
|
exf_radiation, exf_wind |
| 7858 |
|
- add new parameters and constants: longwave emissivity for ocean, ice |
| 7859 |
|
and snow, evaporation parameters over ice |
| 7860 |
|
- decouple wind/stress computation from ALLOW_BULKFORMULA: always compute |
| 7861 |
|
either wind from stress or stress from wind |
| 7862 |
|
o pkg/thSIce: |
| 7863 |
|
- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F |
| 7864 |
|
- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND |
| 7865 |
|
and THSICE_CALC_THICKN |
| 7866 |
|
- for now, call to THSICE_GET_BULKF remains inside i,j loops. |
| 7867 |
|
- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h |
| 7868 |
|
to make debugging easier. |
| 7869 |
|
- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output |
| 7870 |
|
o pkg/bulk_force: |
| 7871 |
|
- clean-up comments and parameters ; |
| 7872 |
|
- add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; |
| 7873 |
|
o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; |
| 7874 |
|
generate new output for test-experiment: aim.5l_cs.thSI |
| 7875 |
|
o results_ad : rename "output.txt_adm" to "output_adm.txt" and change |
| 7876 |
|
testreport accordingly |
| 7877 |
|
|
| 7878 |
|
checkpoint58e_post (2006/05/17) |
| 7879 |
|
o SEAICE_CGRID adjoint done |
| 7880 |
|
o R_STAR adjoint implemented. |
| 7881 |
|
* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
| 7882 |
|
* need to sort out init. of h0facc, etc. |
| 7883 |
|
o Make pkg/profile fully independent of ecco,cost, etc. stuff |
| 7884 |
|
to be able to use it in pure forward. |
| 7885 |
|
|
| 7886 |
|
checkpoint58d_post (2006/04/21) |
| 7887 |
|
o upgrade simple test-experiment to tutorial example: |
| 7888 |
|
step.1: duplicate the experiment and (step.2) will remove the old copy. |
| 7889 |
|
tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
| 7890 |
|
tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) |
| 7891 |
|
tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
| 7892 |
|
tutorial_global_oce_biogeo <- copy of dic_example |
| 7893 |
|
tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
| 7894 |
|
tutorial_plume_on_slope <- copy of plume_on_slope |
| 7895 |
|
tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) |
| 7896 |
|
tutorial_global_oce_optim <- empty for now (David ?) |
| 7897 |
|
tutorial_global_oce_in_p <- copy of global_ocean_pressure |
| 7898 |
|
some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
| 7899 |
|
o correct a sign problem in cost_scat.F |
| 7900 |
|
o obcs and ptracers: fix boundary conditions for advections schemes |
| 7901 |
|
with larger stencil |
| 7902 |
|
o thsice adjoint: start |
| 7903 |
|
o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for |
| 7904 |
|
completeness |
| 7905 |
|
o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING |
| 7906 |
|
and COSINEMETH_III, add comments in default CPP_OPTIONS.h |
| 7907 |
|
o ptracers adjoint: |
| 7908 |
|
* avoid extensive recomputatations |
| 7909 |
|
* fix missing re-init. of gptr (missed by TAF) |
| 7910 |
|
o obcs: add a flag (OBCSprintDiags, defaults is true) that allows |
| 7911 |
|
me to turn off the excessive output to STDOUT that this package produces |
| 7912 |
|
o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common |
| 7913 |
|
and add those terms in Vector-Invariant formulation. |
| 7914 |
|
o in ctrl pkg, if ALLOW_CAL, use monthly mean controls |
| 7915 |
|
if the control period (xx_hfluxperiod etc) is 0 |
| 7916 |
|
o in profiles pkg, clean routines and fix details |
| 7917 |
|
o in ecco pkg, reading ssh data: |
| 7918 |
|
fix problem in case the model does not start at iter0=0 |
| 7919 |
|
o fix mnc-pickup/restart for ptracers |
| 7920 |
|
o new package prifiles: |
| 7921 |
|
code to compute profile-based cost by Gael Forget |
| 7922 |
|
(modifs in ecco, ctrl, autodiff) |
| 7923 |
|
o Benign bug fix in initialization (spotted by M. Mazloff) of |
| 7924 |
|
ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F |
| 7925 |
|
|
| 7926 |
|
checkpoint58c_post (2006/03/23) |
| 7927 |
|
o adjoint: finish NLFS adjoint and provide reference output in |
| 7928 |
|
verification/global_ocean.90x40x15/results_ad_nlfs |
| 7929 |
|
o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the |
| 7930 |
|
documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in |
| 7931 |
|
SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only |
| 7932 |
|
with SEAICE_CGRID defined. |
| 7933 |
|
o move calendarDumps from "data" to "data.cal" and clean-up the code |
| 7934 |
|
with a simple call to pkg/cal S/R: CAL_TIME2WRITE |
| 7935 |
|
o add useEXF & useCAL flags (for now, set in hard-coded way) |
| 7936 |
|
o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum |
| 7937 |
|
(were missing in NH mode, and wrong in quasihydrostatic mode). |
| 7938 |
|
waiting for Chris updated version of calc_gw to add those CALLs. |
| 7939 |
|
o fix bug in quasihydrostatic S/R ; |
| 7940 |
|
add a test for this option: global_ocean.90x40x15.qshyd |
| 7941 |
|
o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs. |
| 7942 |
|
(called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS) |
| 7943 |
|
o add on/off flag useOffLine for package OFFLINE |
| 7944 |
|
o seaice: |
| 7945 |
|
- modify advection so that it works also on the C-grid |
| 7946 |
|
- extend loop ranges in seaice_lsr and seaice_dynsolver; fixes |
| 7947 |
|
problem in multi-tile runs with C-grid |
| 7948 |
|
- add flags for clipping ice velocities and/or masking solver forcing |
| 7949 |
|
- fix drag (ocean on ice) formulation and a bug that caused noise in the |
| 7950 |
|
C-grid solver |
| 7951 |
|
- added a few comments to seaice_diffusion.F |
| 7952 |
|
- separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V |
| 7953 |
|
are now exclusive) |
| 7954 |
|
- add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which |
| 7955 |
|
required re-ordering the code a little: |
| 7956 |
|
+ make DAIRN global variable (defined in SEAICE) |
| 7957 |
|
+ move computation of the viscosities eta and zeta into a new separate |
| 7958 |
|
routine (because I need to recompute them in seaice_ocean_stress.F) |
| 7959 |
|
|
| 7960 |
|
checkpoint58b_post (2006/03/13) |
| 7961 |
|
o AIM+thSIce: fix sign of Short-Wave through the Ice ; |
| 7962 |
|
update output.txt of exp. aim.5l_cs.thSI |
| 7963 |
|
o various mnc cleanups and improvements: |
| 7964 |
|
+ shrink lookup tables by factor of ~4 |
| 7965 |
|
+ better error reporting when running out of lookup space |
| 7966 |
|
+ able to handle longer path/file names (up to 500 chars) |
| 7967 |
|
o adjoint: |
| 7968 |
|
- Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. |
| 7969 |
|
- TBD: "hidden" mom_vecinv recomp. in dynamics |
| 7970 |
|
o change forcing_In_AB to affects both T,S forcing and Momentum forcing |
| 7971 |
|
(allow to differentiate between forcing components using new integer flags: |
| 7972 |
|
momForcingOutAB=1/0 & tracForcingOutAB=1/0) |
| 7973 |
|
and add new flag to put Dissipation tendency out of Adams-Bashforth. |
| 7974 |
|
o ecco |
| 7975 |
|
- enable trend removal from SSH anomaly obs. |
| 7976 |
|
o adjoint |
| 7977 |
|
- a fix for PmEpR when #undef EXACT_CONSERV |
| 7978 |
|
- fix of "hidden" recomp. in thermodynamics (no TAF warnings) |
| 7979 |
|
- try to fix "hidden" recomp. in forward_step for NLFS |
| 7980 |
|
(NLFS seems broken sometimes after I checked it in) |
| 7981 |
|
o seaice: |
| 7982 |
|
- add c-grid version of the dynamic solver: |
| 7983 |
|
+ three new routines that are the c-grid substitute lsr, dynsolver |
| 7984 |
|
and ostres |
| 7985 |
|
+ put a few fields that were local to dynsolver into global common |
| 7986 |
|
blocks, so that I can move the computation of stresses etc into |
| 7987 |
|
seaice_lsr (saves coding but may break the adjoint). |
| 7988 |
|
- replace more hardwired parameters by runtime parameters |
| 7989 |
|
- add ice masks that mask the rhs of the implicit solvers where there |
| 7990 |
|
is no ice (commented out in seaice_dynsolver, because i am not sure |
| 7991 |
|
if this works properly), eventually this should replace the clipping |
| 7992 |
|
of ice velocities in seaice_dynsolver to +/-40cm/s. |
| 7993 |
|
o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly |
| 7994 |
|
include it only where its needed |
| 7995 |
|
o move balancing of fluxes before the call of external_forcing_surf |
| 7996 |
|
o seaice: |
| 7997 |
|
- correct units of turning angles (now they are really in degrees) |
| 7998 |
|
- move computation of GWATX/Y out of main routine into dynsolver |
| 7999 |
|
- initialize GWATX/Y in seaice_init |
| 8000 |
|
o Apply mask on Fresh-Water flux (needed for SSH forcing). |
| 8001 |
|
update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) |
| 8002 |
|
o seaice: add runtime flags for turning angles (default to zero) |
| 8003 |
|
o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean |
| 8004 |
|
and trend from exf forcing and ctrl control adjustments |
| 8005 |
|
o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF |
| 8006 |
|
(since checkpoint57x_post) |
| 8007 |
|
o change the default rotation period to 86164.s = the Earth rotation |
| 8008 |
|
o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) |
| 8009 |
|
and based on a reference stratification. Tested within hs94.cs-32x32x5. |
| 8010 |
|
o seaice advection: add code for choosing between the default (2nd order |
| 8011 |
|
central differences) and multiDim advection schemes provided by |
| 8012 |
|
pkg/generic_advdiff |
| 8013 |
|
o seaice: |
| 8014 |
|
- removed all references to SEAICE_GRID.h fields from |
| 8015 |
|
dynsolver, advect, diffus, lsr, without changing the results of lab_sea |
| 8016 |
|
(cubed-sphere configuration will change a little) |
| 8017 |
|
- grid computations in seaice_init are obsolete now. |
| 8018 |
|
- cleaned up code a little so that is easier to read (hopefully). |
| 8019 |
|
- added new (better?) discretizations of default advection and diffusion |
| 8020 |
|
(turn on with SEAICEuseFluxForm) |
| 8021 |
|
- replace 1 in 3d global fields by kSurface in growth.F |
| 8022 |
|
|
| 8023 |
|
checkpoint58a_post (2006/02/13) |
| 8024 |
|
o seaice: |
| 8025 |
|
- bug fix in advect.F |
| 8026 |
|
o shelfice: |
| 8027 |
|
- separate shelfice load anomaly from pload (breaks with time |
| 8028 |
|
dependent forcing), => introduce constant field shelficeLoadAnomaly. |
| 8029 |
|
Its default is 0., but it may be computed more cleverly from (unknown) |
| 8030 |
|
t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be |
| 8031 |
|
done offline. A good approximation of the pressure load anomaly is |
| 8032 |
|
necessary to avoid large initial adjustment processes underneath |
| 8033 |
|
deep-reaching shelfice. |
| 8034 |
|
- small fix in ISOMIP shelfice_thermodynamics |
| 8035 |
|
- add more sophisticated thermodynamics of Hellmer (1989), this is |
| 8036 |
|
now the default |
| 8037 |
|
- give a few constants more intuitive names |
| 8038 |
|
o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful |
| 8039 |
|
if bulk formulae are used in long integration (especially EmPmR). Turn |
| 8040 |
|
on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01 |
| 8041 |
|
if balancePrintMean, the imbalance that is substracted is printed to |
| 8042 |
|
STDOUT. |
| 8043 |
|
o fix bug (typo) in obcs_apply_eta.F |
| 8044 |
|
o add a new package shelfice which enables us to model the circulation |
| 8045 |
|
underneath shelf-ice with draughts of hundreds of meters. |
| 8046 |
|
- works |
| 8047 |
|
- to do: + include improved thermodynamics |
| 8048 |
|
+ check whether kSurfC (from model/inc/SURFACE.h) can be used |
| 8049 |
|
instead of new field kTopC |
| 8050 |
|
+ can we use topoFile, Ro_surf and existing code in ini_depth.F |
| 8051 |
|
instead of new field R_shelfIce and new code in ini_depth.F |
| 8052 |
|
and ini_mask_etc.F? |
| 8053 |
|
+ adjust vertical mixing schemes? |
| 8054 |
|
o seaice pkg: |
| 8055 |
|
- add a cpp-flag to include a simple formula for a salinity dependent |
| 8056 |
|
freezing point of sea water at the surface |
| 8057 |
|
- change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and |
| 8058 |
|
meridional stresses are now different (and hopefully correct) |
| 8059 |
|
o AIM pkg: change threshold on large-scale condensation to conserve Heat. |
| 8060 |
|
update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics |
| 8061 |
|
and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG) |
| 8062 |
|
o pkg/diagnostics: add options and parameters for regional-statistics |
| 8063 |
|
diagnostics ; define regions by reading a region-mask from a file |
| 8064 |
|
(might add other options later) |
| 8065 |
|
o pkg/bulk_force: |
| 8066 |
|
- add option and parameters to use AIM surface-flux formulae. |
| 8067 |
|
- Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ; |
| 8068 |
|
others forcing fields (defined in PARM05, parameter file "data") are loaded |
| 8069 |
|
from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F). |
| 8070 |
|
- initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F |
| 8071 |
|
- use the right EXCH call for uwind,vwind (to work on CS-grid). |
| 8072 |
|
- re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h) |
| 8073 |
|
and parameters (note: calcWindStress replaces .NOT.readwindstress). |
| 8074 |
|
- cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). |
| 8075 |
|
|
| 8076 |
|
checkpoint58 (2006/01/12) |
| 8077 |
|
o add "--embed-source" option to genmake2 which, when the supporting |
| 8078 |
|
tools can be compiled (as determined by genmake2) will turn on the |
| 8079 |
|
embed_files package which then embeds the entire MITgcm source code |
| 8080 |
|
(*.[fFhc] + Makefile) used for the build within the executable |
| 8081 |
|
- requested by CNH but off by default |
| 8082 |
|
- adds a paltry <9MB to the mitgcmuv executable in most cases |
| 8083 |
|
- only writes the output when useEMBEDSRC in eedata is true |
| 8084 |
|
o clean up 3-dim. relaxation codes: |
| 8085 |
|
* Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec |
| 8086 |
|
* Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) |
| 8087 |
|
* Thanks to Tom Haine for testing! |
| 8088 |
|
|
| 8089 |
|
checkpoint57z_post (2005/12/31) |
| 8090 |
|
o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): |
| 8091 |
|
affects output (@ truncation level) of exp. plume_on_slope ; updated. |
| 8092 |
|
o fix the pickup behavior for obcs in combination with ptracers |
| 8093 |
|
o fix a bug in ptracers_external_fields_load |
| 8094 |
|
o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...) |
| 8095 |
|
affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) |
| 8096 |
|
o transfered surface NH pressure to eta field (if exactConserv). |
| 8097 |
|
o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign) |
| 8098 |
|
and update lab_sea output.txt file. |
| 8099 |
|
o completing 3-dim. relaxation code: additional term |
| 8100 |
|
1/tau*( theta(i,j,k) - thetaStar(i,j,k) ) |
| 8101 |
|
in S/R EXTERNAL_FORCING_T (file external_forcing.F) |
| 8102 |
|
* At compile time, in "EXF_OPTIONS.h" set |
| 8103 |
|
#define ALLOW_CLIMTEMP_RELAXATION |
| 8104 |
|
#define ALLOW_CLIMSALT_RELAXATION |
| 8105 |
|
* At runtime in "data", under &PARM03 set (e.g., units in seconds) |
| 8106 |
|
tauThetaClimRelax3Dim = 15552000.0, |
| 8107 |
|
tauSaltClimRelax3Dim = 15552000.0, |
| 8108 |
|
* 3 cases: |
| 8109 |
|
1) Use a constant-in-time 3-dim. field |
| 8110 |
|
2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec. |
| 8111 |
|
3) Real-time relax. to time-evolving prescribed field |
| 8112 |
|
o Adding Laplacian-type smoothness constraint on |
| 8113 |
|
initial and boundary (forcing) controls (ic, bc) |
| 8114 |
|
* enable at compile-time via |
| 8115 |
|
ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION |
| 8116 |
|
* enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1 |
| 8117 |
|
* Absolute scale somewhat unclear so far |
| 8118 |
|
* no area weighting was included since no other cost term does so far |
| 8119 |
|
|
| 8120 |
|
checkpoint57y_post (2005/12/08) |
| 8121 |
|
First step for a NLFS adjoint |
| 8122 |
|
o initially suppress rStar (new flag DISABLE_RSTAR_CODE) |
| 8123 |
|
o new init. routines for calc_r_star, calc_surf_dr |
| 8124 |
|
o still need to deal with ini_masks_etc |
| 8125 |
|
o testreport seemed happy |
| 8126 |
|
checkpoint57y_pre (2005/12/08) |
| 8127 |
|
|
| 8128 |
|
o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
| 8129 |
|
o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) |
| 8130 |
|
o add new offset feature to offline pkg (plus minor cleanup) |
| 8131 |
|
o cfc fixes for final year of integration |
| 8132 |
|
o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should |
| 8133 |
|
be in GCHEM_OPTIONS). |
| 8134 |
|
|
| 8135 |
|
checkpoint57x_post (2005/12/04) |
| 8136 |
|
o fix testreport Pb in multiple test experiment. |
| 8137 |
|
o cleanup our namelist syntax in verification: |
| 8138 |
|
- make it more F95 standards compliant (some work still needed) |
| 8139 |
|
- allows the vast majority of our tests to work with gfortran |
| 8140 |
|
o Non-Hydrostatic: |
| 8141 |
|
- put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h |
| 8142 |
|
- fix exchange calls for CS-grid using the new EXCH_S3D_RL. |
| 8143 |
|
o Allow to apply AB on T,S rather than on AB(gT,gS): |
| 8144 |
|
- implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 |
| 8145 |
|
- use the same arrays (gtNm,gsNm) to hold tracer field at previous |
| 8146 |
|
time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). |
| 8147 |
|
- need a "clever" read_pickup to restart from the other AB formulation |
| 8148 |
|
o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h |
| 8149 |
|
o remove some unused variables (reduces number of compiler warnings) |
| 8150 |
|
o adjoint |
| 8151 |
|
* Disable useVariableViscosity for adjoint for time being |
| 8152 |
|
(there are a number of extensive recomputations) |
| 8153 |
|
* Initialize certain variables needed for adjoint |
| 8154 |
|
|
| 8155 |
|
checkpoint57w_post (2005/11/03) |
| 8156 |
|
o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names |
| 8157 |
|
fix the singleCpuIO RS version of MDSWRITEFIELD |
| 8158 |
|
and add a WARNING if using globalFiles=T with multi-processors. |
| 8159 |
|
o write grid-file(s) in only one format (MDS or MNC): default=MNC (if |
| 8160 |
|
using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc |
| 8161 |
|
o tracer advection scheme: |
| 8162 |
|
add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get |
| 8163 |
|
those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, |
| 8164 |
|
was not very convenient). |
| 8165 |
|
add implicit version for DST-3 & DST3_Flux_Limit vertical advection; |
| 8166 |
|
(further tests needed for the implicit DST & Flux-Limiter schemes). |
| 8167 |
|
o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef |
| 8168 |
|
and sRef for convenience, handy, when you want to initialize |
| 8169 |
|
ptracers in a large domain with a constant non-zero value. Also, |
| 8170 |
|
untangle ptracers_init.F a little. |
| 8171 |
|
|
| 8172 |
|
checkpoint57v_post (2005/10/13) |
| 8173 |
|
o change dome exp. to use variable viscosity in side-drag terms. |
| 8174 |
|
o remove all the files from the cfc_offline test since they are now |
| 8175 |
|
incorporated into tutorial_cfc_offline which has been producing |
| 8176 |
|
identical results for a few days of testing |
| 8177 |
|
o add new parameter: sideDragFactor to enable half-slip-side BC |
| 8178 |
|
and change side-drag S/R to use viscosity from mom_calc_visc |
| 8179 |
|
(can switch back by setting sideDragFactor=0.); affects results at |
| 8180 |
|
truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), |
| 8181 |
|
global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). |
| 8182 |
|
o vorticity & strain are now computed without masking, to account for |
| 8183 |
|
no-slip-side BC in variable viscosity calculation ; mask is applied |
| 8184 |
|
anyway later on, before computing advection/coriolis terms. |
| 8185 |
|
o modify exp4 to test new obcs support for reading from external files |
| 8186 |
|
and for passive tracers |
| 8187 |
|
o fix behavior of ptracers_monitor when monitor output is written to a |
| 8188 |
|
netcdf-file; still not independent of monitor.F (writes in the same |
| 8189 |
|
file). |
| 8190 |
|
o change default value of tRef (put a uniform, meaningful value for ocean |
| 8191 |
|
& atmos) and initialize sRef (was missing, as Martin mentioned). |
| 8192 |
|
o Redefine viscC?Leith*. Change the coefficients of Leith viscosity |
| 8193 |
|
to be proportional to enstrophy dissipation length. Thus, |
| 8194 |
|
viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) |
| 8195 |
|
This is now consistent with Smagorinsky and with the manual. |
| 8196 |
|
|
| 8197 |
|
checkpoint57u_post |
| 8198 |
|
o OBCS and PTRACERS: add open boundary support for passive tracers |
| 8199 |
|
- either use homogenous (pseudo) v.Neumann conditions or prescribe |
| 8200 |
|
OB-values from file; this is not different from the way theta and salinity |
| 8201 |
|
are treated |
| 8202 |
|
- however, Orlanski-radiation conditions are not supported, and the model |
| 8203 |
|
will stop if you use pTracers and Orlanski at the same time. |
| 8204 |
|
- beefed up the rountine obcs_external_fields_load: now only those open |
| 8205 |
|
boundary values are overwritten with values from files for which there |
| 8206 |
|
are really files, otherwise the OB-fields remain untouched. This makes |
| 8207 |
|
it possible to use different OBs at different ends of the domain (as |
| 8208 |
|
with EXF) |
| 8209 |
|
o reduce number of exch calls in shap_filt (s2). |
| 8210 |
|
o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ |
| 8211 |
|
truncation level) 4/5 MLAdjust test results (11&12 digits match). |
| 8212 |
|
|
| 8213 |
|
checkpoint57t_post (2005/10/03) |
| 8214 |
|
o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
| 8215 |
|
o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
| 8216 |
|
same truncation, independent of the face number: affects affects several |
| 8217 |
|
test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). |
| 8218 |
|
o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); |
| 8219 |
|
note that biharmonic viscosity + no-slip was not tested in any experiment. |
| 8220 |
|
o fix bug in non-linear free-surf side-drag ; generate new output for |
| 8221 |
|
global_ocean.cs32x15(+.thsice) & global_ocean_pressure. |
| 8222 |
|
o make mnc honor the writeBinaryPrec flag for most kinds of output |
| 8223 |
|
o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
| 8224 |
|
o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
| 8225 |
|
error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
| 8226 |
|
o add brackets in multi-terms sum to get same truncation, independent of |
| 8227 |
|
the face number (manage to get exactly same value of gU,gV at the cs-edge) |
| 8228 |
|
affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
| 8229 |
|
o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
| 8230 |
|
and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
| 8231 |
|
a maximum grid-scale Reynolds number. Also, changes all length calculations |
| 8232 |
|
in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
| 8233 |
|
Suggested values of viscosity parameters found in mom_calc_visc. |
| 8234 |
|
Many new viscosity diagnostics available. |
| 8235 |
|
|
| 8236 |
|
checkpoint57s_post (2005/09/20) |
| 8237 |
|
o Add clearing-house for viscosity calculations, mom_calc_visc and |
| 8238 |
|
correct numerous bugs in LeithD and Smagorinsky discretizations. |
| 8239 |
|
mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
| 8240 |
|
used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
| 8241 |
|
Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
| 8242 |
|
and with Strain-Tension viscous term calculation (mom_hdissip.F). |
| 8243 |
|
The Strain-Tension form is now called with useStrainTensonVisc=.true. |
| 8244 |
|
ViscAhStrain and viscAhTension are now retired. |
| 8245 |
|
o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
| 8246 |
|
o In response to JMC's bug report, genmake2 now ignores any soft-links |
| 8247 |
|
that it finds in the *current* directory when searching for files. |
| 8248 |
|
Soft-links found in any other source directories will still work as |
| 8249 |
|
they did before. |
| 8250 |
|
o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
| 8251 |
|
a C routine to unlimit the stack size |
| 8252 |
|
o mnc-ify pkg/aim snapshot vars |
| 8253 |
|
o mnc-ify pkg/land as requested by Daniel |
| 8254 |
|
o various changes to mnc including: |
| 8255 |
|
- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
| 8256 |
|
- output can now be grouped so that all files within a group |
| 8257 |
|
change the ITER portion of their names in lock-step together |
| 8258 |
|
- can now read ("global") PER-FACE (in addition to PER-TILE) files |
| 8259 |
|
and works with both EXCH1 and EXCH2 (but needs more testing) |
| 8260 |
|
- writing works for all verification test cases w/ g77 on Linux |
| 8261 |
|
|
| 8262 |
|
checkpoint57r_post (2005/09/07) |
| 8263 |
|
o make MNC variable initialization happen earlier |
| 8264 |
|
o add diagnostics for (almost) each term of the momentum Eq. |
| 8265 |
|
o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
| 8266 |
|
o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
| 8267 |
|
o remove MINIMAL_TAVE_OUTPUT option ; |
| 8268 |
|
add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
| 8269 |
|
o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
| 8270 |
|
allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
| 8271 |
|
o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
| 8272 |
|
o add time-dependent SST, SSS control |
| 8273 |
|
o cost terms in ecco/ modularized (new cost_generic.F) |
| 8274 |
|
o cost_averages routines are modularized (new cost_averagesgeneric.F) |
| 8275 |
|
o new infrastructure for seaice model vs. obs misfits in seaice/ |
| 8276 |
|
* driver from the_main_loop.F is seaice_cost_driver.F |
| 8277 |
|
* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
| 8278 |
|
* gradient check in Exp. 6a of natl_box_adjoint/ |
| 8279 |
|
o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
| 8280 |
|
(see README file) |
| 8281 |
|
|
| 8282 |
|
checkpoint57q_post (2005/08/19) |
| 8283 |
|
o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
| 8284 |
|
o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
| 8285 |
|
- bug was reported by Jean-Michel and Ian Fenty |
| 8286 |
|
o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
| 8287 |
|
update exp. cpl_aim+ocn output. |
| 8288 |
|
o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
| 8289 |
|
Needed for high-res. runs with large global files |
| 8290 |
|
to be able to limit tapelev size |
| 8291 |
|
o Changed some tests for adjoint: |
| 8292 |
|
* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
| 8293 |
|
* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
| 8294 |
|
* global_ocean.90x40x15/ back to default 3-level checkpointing |
| 8295 |
|
o Modifications to enable scripted COMMON to MODULE conversion |
| 8296 |
|
* verification/OpenAD/code/ has necessary scripts and description; |
| 8297 |
|
* converts, compiles and runs successfully; |
| 8298 |
|
|
| 8299 |
|
checkpoint57p_post (2005/08/01) |
| 8300 |
|
o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
| 8301 |
|
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
| 8302 |
|
(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
| 8303 |
|
o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
| 8304 |
|
o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
| 8305 |
|
(was already the case for dissipation with mom_vecinv, |
| 8306 |
|
and also the case for grad.PhiHyd when staggered-timeStep) |
| 8307 |
|
This will allow to put dissipation out-off the AB time-stepping. |
| 8308 |
|
Unfortunately, affects truncation error. Update output of exp. that "fails" |
| 8309 |
|
(cg2d matching number) and leave the others for later: front_relax(10), |
| 8310 |
|
global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
| 8311 |
|
matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
| 8312 |
|
|
| 8313 |
|
checkpoint57o_post (2005/07/30) |
| 8314 |
|
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
| 8315 |
|
(2) its ready to be documented during the 20050801 DocFest |
| 8316 |
|
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
| 8317 |
|
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
| 8318 |
|
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
| 8319 |
|
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
| 8320 |
|
(worth another tag) |
| 8321 |
|
|
| 8322 |
|
checkpoint57n_post (2005/07/29) |
| 8323 |
|
o adding precip control xx_precip 32 |
| 8324 |
|
o adding swflux control xx_swflux 33 |
| 8325 |
|
o Replacing 10 forcing penalty cost routines by 1 generic. |
| 8326 |
|
o Implementing partitioning in time-mean and variable adjustment |
| 8327 |
|
for atmos. state. |
| 8328 |
|
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
| 8329 |
|
o in natl_box_adjoint: |
| 8330 |
|
* updated exp 1 to 10 |
| 8331 |
|
(but does not have time-mean vs. variable split results yet) |
| 8332 |
|
o updated global1x1/*_seaice_adj/ |
| 8333 |
|
to incorporate latest changes |
| 8334 |
|
o enable useSingleCpuIO for mdsio vector routines |
| 8335 |
|
(applies in particular to tapelev I/O) |
| 8336 |
|
o removed inefficient K-loop in all active_file*control*.F |
| 8337 |
|
|
| 8338 |
|
checkpoint57m_post (2005/07/28) |
| 8339 |
|
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
| 8340 |
|
and advect_cs (use EXCH-2 and standard cs-32 grid files). |
| 8341 |
|
o pkg/exch2: filling of face-corner halo regions is optional |
| 8342 |
|
(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
| 8343 |
|
|
| 8344 |
|
checkpoint57l_post (2005/07/14) |
| 8345 |
|
tag before updating tutorials (pre-release-2) |
| 8346 |
|
o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
| 8347 |
|
for output and interpolation of input fields onto model grid) |
| 8348 |
|
o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
| 8349 |
|
Affects results of exp. rotating_tank ; update output.txt. |
| 8350 |
|
o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
| 8351 |
|
and taking the square quantity and/or using a fraction-weight field. |
| 8352 |
|
o fix aim_diagnostics_init.F mate numbers. |
| 8353 |
|
o add mnc output capability to diagnostics/diagstat and update |
| 8354 |
|
our cvsignore files for the ACSII output generated |
| 8355 |
|
|
| 8356 |
|
checkpoint57k_post (2005/07/02) |
| 8357 |
|
o lab_sea now uses diagnostics package and provides a suite of |
| 8358 |
|
new EXF diagnostics output. |
| 8359 |
|
|
| 8360 |
|
checkpoint57j_post (2005/06/30) |
| 8361 |
|
o exf |
| 8362 |
|
* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
| 8363 |
|
Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
| 8364 |
|
terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
| 8365 |
|
* extended diagnostics output |
| 8366 |
|
- now includes all EXF variables |
| 8367 |
|
- hs, hl moved to common block |
| 8368 |
|
- separate S/R for diagnostics, called after ctrl vector is added |
| 8369 |
|
- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
| 8370 |
|
- EXFqnet contains true Qnet (i.e. includes qsw) |
| 8371 |
|
* updated verif. lab_sea, global_with_exf |
| 8372 |
|
* Rearranging hflux (exf_mapfields -> exf_getforcing) |
| 8373 |
|
to ensure that diagnostics sees a true EXFqnet |
| 8374 |
|
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
| 8375 |
|
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
| 8376 |
|
several times with different frequencies. |
| 8377 |
|
o mnc-ify the thsice package as requested by Daniel Enderton |
| 8378 |
|
- the monitor--MNC output needs work |
| 8379 |
|
- many attributes need to be added (most are currently blank) |
| 8380 |
|
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
| 8381 |
|
- many attributes need to be added (most are currently blank) |
| 8382 |
|
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
| 8383 |
|
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
| 8384 |
|
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
| 8385 |
|
update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
| 8386 |
|
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
| 8387 |
|
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
| 8388 |
|
(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
| 8389 |
|
|
| 8390 |
|
checkpoint57i_post (2005/06/19) |
| 8391 |
|
o Diagnostics package was changed: diagnostic allocation is now deactivated |
| 8392 |
|
by setting an empty file name in the namelist (used to be by setting 0 frequency) |
| 8393 |
|
o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
| 8394 |
|
add 1rst Order upwind vertical Shear. |
| 8395 |
|
o add a quick fix for A/B checkpointing in OFFLINE mode |
| 8396 |
|
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
| 8397 |
|
end-run around the C/Fortran linking horror in eesup/src/timers.F |
| 8398 |
|
o added pkg/runclock: allows user to terminate run based on wall clock |
| 8399 |
|
o added non-hydrostatic scaling parameter: nh_am2 |
| 8400 |
|
o pkg/my82: futile attempt to make results compiler-independent by adding |
| 8401 |
|
some "_d 0", etc. no effect. |
| 8402 |
|
o for mnc output, fill the 'T' coordinate var with myTime and create a |
| 8403 |
|
separate 'iter' variable for iteration count |
| 8404 |
|
o pkg/diagnostics: |
| 8405 |
|
add new capability: output of Global/Regional & per-level statistics ; |
| 8406 |
|
tested against monitor output (including land & thSIce) on various exp. |
| 8407 |
|
o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
| 8408 |
|
|
| 8409 |
|
checkpoint57h_done (2005/05/19) |
| 8410 |
|
tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
| 8411 |
|
data.diagnostics, data.gchem, data.ptracers) is done. |
| 8412 |
|
|
| 8413 |
|
o pkg/diagnostics: prepare for Global/Regional statistics. |
| 8414 |
|
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
| 8415 |
|
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
| 8416 |
|
and rename it: DIFFERENT_MULTIPLE |
| 8417 |
|
|
| 8418 |
|
checkpoint57h_post (2005/05/14) |
| 8419 |
|
o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
| 8420 |
|
o pkg/diagnostics: change output frequency, now in seconds (instead |
| 8421 |
|
of Nb of iterations). This requires to change data.diagnostics. |
| 8422 |
|
checkpoint57h_pre (2005/05/12) |
| 8423 |
|
|
| 8424 |
|
o in mnc, let the user create the output dir if both mnc_outdir_date |
| 8425 |
|
and mnc_outdir_num are false |
| 8426 |
|
o add fflags() to pkg/diagnostics which allows one to specify, on a |
| 8427 |
|
per-file basis, the file precision [default behavior is unchanged] |
| 8428 |
|
o added diagnostics to pkg/kpp, including computation of mixed layer |
| 8429 |
|
depth based on a temperature/density criterion |
| 8430 |
|
o updated verification/natl_box to test the new pkg/kpp diagnostics |
| 8431 |
|
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
| 8432 |
|
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
| 8433 |
|
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
| 8434 |
|
not mnc -- this mistake was found by JMC and is now corrected |
| 8435 |
|
|
| 8436 |
|
checkpoint57g_post (2005/04/15) |
| 8437 |
|
o add Adams-Bashforth 3rd Order time stepping: |
| 8438 |
|
- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
| 8439 |
|
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
| 8440 |
|
checkpoint57g_pre (2005/04/15) |
| 8441 |
|
|
| 8442 |
|
o make lambda[Theta,Salt]ClimRelax spatially varying |
| 8443 |
|
(default remains spatially uniform constant based on tau) |
| 8444 |
|
o added new control variables |
| 8445 |
|
* init. uVel, vVel, etanN |
| 8446 |
|
* lambda[Theta,Salt]ClimRelax |
| 8447 |
|
o separate masks used for ctrl_pack/unpack 'from write_grid' output |
| 8448 |
|
(suggested by G. Forget) |
| 8449 |
|
|
| 8450 |
|
checkpoint57f_post (2005/04/06) |
| 8451 |
|
o add parameter "baseTime" = model base time = time at iteration zero |
| 8452 |
|
new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
| 8453 |
|
account for baseTime shift |
| 8454 |
|
o move Coriolis arrays from PARAMS.h to GRID.h |
| 8455 |
|
checkpoint57f_pre (2005/04/06) |
| 8456 |
|
|
| 8457 |
|
o mnc-ifying the seaice package |
| 8458 |
|
o introduced an alternative length scale calculation for use in the limiting |
| 8459 |
|
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
| 8460 |
|
o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
| 8461 |
|
o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
| 8462 |
|
as well as grad(vort3). Made it compatible with both approximate form |
| 8463 |
|
for the cubed sphere and full form of these gradients. Added flag |
| 8464 |
|
useFullLeith to select between approximate and full form. |
| 8465 |
|
o add "d0" in getcon.F to reduce differences between compilers/platforms |
| 8466 |
|
update output.txt of exp. fizhi-gridalt-hs |
| 8467 |
|
o change port_rand funtion to allow to set the seed. |
| 8468 |
|
o fix obscure MNC bug involving conversion between reals and integers |
| 8469 |
|
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
| 8470 |
|
new version is now more standards-compliant |
| 8471 |
|
o adjoint-related modifications |
| 8472 |
|
* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
| 8473 |
|
* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
| 8474 |
|
* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
| 8475 |
|
|
| 8476 |
|
checkpoint57e_post (2005/02/28) |
| 8477 |
|
o Adding eddy stress controls a la Ferreira et al. |
| 8478 |
|
checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
| 8479 |
|
|
| 8480 |
|
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
| 8481 |
|
update output.txt of exp. fizhi-gridalt-hs |
| 8482 |
|
o add more "Z" dimensions and associated coordinate vars to MNC |
| 8483 |
|
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
| 8484 |
|
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
| 8485 |
|
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
| 8486 |
|
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
| 8487 |
|
months and years. Requires pkg/cal. |
| 8488 |
|
o diagnostics: add pickup functionality |
| 8489 |
|
- off by default for backwards compatibility |
| 8490 |
|
- current version only uses MDSIO -- MNC will be added |
| 8491 |
|
o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
| 8492 |
|
o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
| 8493 |
|
|
| 8494 |
|
checkpoint57d_post (2005/02/11) |
| 8495 |
|
o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
| 8496 |
|
o modify verification/ideal_2D_oce so that it tests the creation of mnc |
| 8497 |
|
output from the diagnostics package |
| 8498 |
|
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
| 8499 |
|
o make genmake2 more portable by using ".$FS" instead of ".f" for more |
| 8500 |
|
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
| 8501 |
|
o add coordinate variables to the MNC output from the diagnostics package |
| 8502 |
|
o change MNC-flags default value: true when useMNC=TRUE |
| 8503 |
|
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
| 8504 |
|
the ability (off by default) to read the grid information using MNC |
| 8505 |
|
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
| 8506 |
|
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
| 8507 |
|
o do snap-shot diagnostics at the middle of the time-interval (instead of |
| 8508 |
|
at the end). |
| 8509 |
|
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
| 8510 |
|
new test for AIM with thSIce + slab-ocean |
| 8511 |
|
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
| 8512 |
|
o move state variable diagnostics to the beginning of the time step ; |
| 8513 |
|
(note: still needs some work specially for snap-shot diagnostics) |
| 8514 |
|
duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
| 8515 |
|
|
| 8516 |
|
checkpoint57c_post (2005/01/27) |
| 8517 |
|
o Change testing option (-ieee) to get closer agreement between g77 & ifort |
| 8518 |
|
o generate new output.txt files on faulks with g77 & the new -ieee option |
| 8519 |
|
checkpoint57c_pre (2005/01/27) |
| 8520 |
|
|
| 8521 |
|
o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
| 8522 |
|
update output.txt of exp. global_ocean.90x40x15 |
| 8523 |
|
o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
| 8524 |
|
results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
| 8525 |
|
o add saltFlux(+File) forcing capability with periodicExternalForcing |
| 8526 |
|
o allow to use pkg diagnostics for GM-Redi & ThSIce output |
| 8527 |
|
o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
| 8528 |
|
o improvements for the MNC output from DIAGNOSTICS: |
| 8529 |
|
- correct handling of the unlimitied dimension |
| 8530 |
|
- all dims now have associated coordinate variables |
| 8531 |
|
- variables located at U, V, and Corner ("Z") points are now written |
| 8532 |
|
with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
| 8533 |
|
*all* data points are output |
| 8534 |
|
o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
| 8535 |
|
o added pkg/seaice/seaice_monitor.F |
| 8536 |
|
o mdsio_readfield.F can now read files visible only to master MPI process. |
| 8537 |
|
o pkg/seaice: some test code for ice-modified ocean stress |
| 8538 |
|
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
| 8539 |
|
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
| 8540 |
|
spurious negative numbers for precipitation and humidity. Will cause |
| 8541 |
|
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
| 8542 |
|
o pkg/ctrl/ |
| 8543 |
|
* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
| 8544 |
|
May be enabled via doPackDiag |
| 8545 |
|
* introduce z-scaling of |
| 8546 |
|
+ gradient (doZscalePack) and |
| 8547 |
|
+ control (doZscaleUnpack) |
| 8548 |
|
o pkg/mdsio/ |
| 8549 |
|
* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
| 8550 |
|
* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
| 8551 |
|
|
| 8552 |
|
checkpoint57b_post (2004/12/20) |
| 8553 |
|
o simplify options in diagnostics_fill arguments (remove weird combinations) |
| 8554 |
|
o fix MNC coordinate variables so that they now contain per-face index |
| 8555 |
|
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
| 8556 |
|
general, EXCH2 grids are only aligned to a "local" coordinate system |
| 8557 |
|
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
| 8558 |
|
o Implement instantaneous output within pkg diagnostics: |
| 8559 |
|
setting a negative frequency in data.diagnostics produces |
| 8560 |
|
"snap-shot" output (as opposed to time-average if freq > 0) |
| 8561 |
|
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
| 8562 |
|
NOTE: change ptracer diagnostics name: use 2 characters to work with |
| 8563 |
|
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
| 8564 |
|
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
| 8565 |
|
becomes the coordinate variable for the 'T' dimension |
| 8566 |
|
o add CF-style coordinate variables to MNC |
| 8567 |
|
- just a first cut: numbers are meaningless on the cubesphere and |
| 8568 |
|
missing along the T axis but otherwise it works! |
| 8569 |
|
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
| 8570 |
|
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
| 8571 |
|
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
| 8572 |
|
this is based directly on what the model compute, so that the content of |
| 8573 |
|
each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
| 8574 |
|
o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
| 8575 |
|
o clean up build options files for SunOS, in particular |
| 8576 |
|
- remove -traditional from xmakedepend |
| 8577 |
|
- change -xarch=v9 to -xarch=native for f77 |
| 8578 |
|
- restore use of make (not gmake) |
| 8579 |
|
- add CC=gcc if using g77 |
| 8580 |
|
o changes per discussion of AM, JMC, & EH3 today: |
| 8581 |
|
- move redundant "grid" variables out of "state" -- in preparation of |
| 8582 |
|
creating proper CF-style coordinate variables and in recognition |
| 8583 |
|
that any/all grid variables can be easily copied (eg. w/NCO) from |
| 8584 |
|
the grid files into any of the other NetCDF files |
| 8585 |
|
- *always* output grid variables with MDSIO (this will eventually be |
| 8586 |
|
changed) |
| 8587 |
|
- output MNC grid file if useMNC is true |
| 8588 |
|
o every instance of _END_MASTER() has been found and replaced with |
| 8589 |
|
_END_MASTER( myThid ) in order to satisfy certain picky Sun |
| 8590 |
|
preprocessors |
| 8591 |
|
o re-arrange diagnostics pkg initialisation: |
| 8592 |
|
- allow each package to extend the available diagnostics list |
| 8593 |
|
- add some checking and fix small problems (multi-threaded, ...) |
| 8594 |
|
- new S/R diagnostics_fill (replace fill_diagnostics): |
| 8595 |
|
look through the short list of active diag. (instead of the long list) |
| 8596 |
|
create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
| 8597 |
|
|
| 8598 |
|
checkpoint57a_post (2004/12/10) |
| 8599 |
|
o this set of changes restores TAMC compatibility |
| 8600 |
|
tested for global_ocean.90x40x15 adjoint on trough |
| 8601 |
|
(what a pain) |
| 8602 |
|
|
| 8603 |
|
checkpoint57a_pre (2004/12/10) |
| 8604 |
|
o some modifs in tools/build_options for sunos |
| 8605 |
|
o call ctrl_pack for ctrl at end for optimcycle=0 |
| 8606 |
|
|
| 8607 |
|
checkpoint57 (2004/12/09) |
| 8608 |
|
o add horizontal bi-harmonic viscosity for vertical velocity |
| 8609 |
|
- new parameter viscA4W (defaults to viscA4) |
| 8610 |
|
- affects only non-hydrostatic code |
| 8611 |
|
- to be done: no-slip lateral boundary conditions |
| 8612 |
|
o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
| 8613 |
|
o implement Implicit Vertical advection for pTracers |
| 8614 |
|
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
| 8615 |
|
(implemented also for implicit vertical diffusion & advection) |
| 8616 |
|
o OBCS: extend application of tracer open boundary conditions |
| 8617 |
|
to a strip beyond the boundary of width Olx/Oly |
| 8618 |
|
o add call monitor to TAF set of required calls (flow directives) |
| 8619 |
|
and include in natl_box_adjoint |
| 8620 |
|
o untangle a few ifdefs related to cost, ctrl, autodiff |
| 8621 |
|
untangel a few ALLOW_ECCO_OPTIMIZATION |
| 8622 |
|
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
| 8623 |
|
(theta2, salt2 in ecco_cost_weights) |
| 8624 |
|
|
| 8625 |
|
checkpoint56c_post (2004/12/03) |
| 8626 |
|
o OBCS as control variables |
| 8627 |
|
- update ctrl_ad_diff.list, obcs_ad_diff.list |
| 8628 |
|
- remove balance of obcs controls from default |
| 8629 |
|
- fix index bug nobcs in ctrl_init |
| 8630 |
|
- fix dummy fields filen in ctrl_pack |
| 8631 |
|
- add dummy weights for obcs |
| 8632 |
|
o lsopt: comment out fort.94 output |
| 8633 |
|
o optim: |
| 8634 |
|
- remove unnecessary header files |
| 8635 |
|
- adjusted namelists |
| 8636 |
|
- add xerbla.F to Makefile |
| 8637 |
|
o exf: |
| 8638 |
|
- multiple modifications of exf_check_range |
| 8639 |
|
- unit change in exf_init_runoff from [m/year] to [m/s] |
| 8640 |
|
o mdsio: |
| 8641 |
|
- i/o-vector change debugLevel from debLevA to debLevB |
| 8642 |
|
|
| 8643 |
|
checkpoint56b_post (2004/12/01) |
| 8644 |
|
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
| 8645 |
|
is called from DO_THE_MODEL_IO |
| 8646 |
|
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
| 8647 |
|
- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
| 8648 |
|
- clean up PTRACERS_WRITE_TIMEAVE a little |
| 8649 |
|
o add another verification experiment that tests both the cfc-pkg and |
| 8650 |
|
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
| 8651 |
|
reactive tendencies treated inline with regular timestepping |
| 8652 |
|
o testreport previously did a lousy job of comparing small numbers, so |
| 8653 |
|
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
| 8654 |
|
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
| 8655 |
|
testreport. |
| 8656 |
|
o ptracers_monitor: bug fix for MPI |
| 8657 |
|
|
| 8658 |
|
checkpoint56a_post (2004/11/28) |
| 8659 |
|
o GCHEM: finish reorganizating the package |
| 8660 |
|
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
| 8661 |
|
(introduces another 3D-array for each passive tracer, but only if |
| 8662 |
|
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
| 8663 |
|
gchemTendency is not needed because the timestep is done separately) |
| 8664 |
|
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
| 8665 |
|
- GCHEM is now---more or less cleanly---separate from PTRACERS |
| 8666 |
|
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
| 8667 |
|
so clear to me how that should be done in a general way. |
| 8668 |
|
o CFC: improve formatting of output in CFC_ATMOS |
| 8669 |
|
o PTRACERS: |
| 8670 |
|
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
| 8671 |
|
that ALL experiments with ptracers enable can be checked. This makes |
| 8672 |
|
GCHEM_MONITOR obsolete. |
| 8673 |
|
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
| 8674 |
|
monitorFreq |
| 8675 |
|
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
| 8676 |
|
o add PTRACERS (PTR0[1-5]) to testreport output |
| 8677 |
|
o exf_check_range: |
| 8678 |
|
* default changed to .TRUE. |
| 8679 |
|
* will check values for niter0 if debLevA, every timestep if debLevB |
| 8680 |
|
* STOP in exf_check_range if 'out of range' |
| 8681 |
|
* range chosen generous to allow for potential extema |
| 8682 |
|
TBD: a version with stricter range |
| 8683 |
|
permitted range would be runtime parameters |
| 8684 |
|
o GMredi: |
| 8685 |
|
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
| 8686 |
|
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
| 8687 |
|
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
| 8688 |
|
o GCHEM: |
| 8689 |
|
- move call to GCHEM_FORCING_SEP, so that it is now called before |
| 8690 |
|
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
| 8691 |
|
- introduced a useGCHEM runtime flag and applied it everywhere. |
| 8692 |
|
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
| 8693 |
|
this flag is now only visible within GCHEM-pkg routines. |
| 8694 |
|
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
| 8695 |
|
be replaced by a 3D array that is computed before thermodynamics; for |
| 8696 |
|
this, the tracer ID iTracer had to be included into the parameter list |
| 8697 |
|
of ptracers_forcing |
| 8698 |
|
- set up forward_step to call gchem_forcing, that will replace |
| 8699 |
|
gchem_forcing_int in ptracers_forcing |
| 8700 |
|
- cleaning up |
| 8701 |
|
o small cleaning of exch2: remove files that are also in eesupp/src |
| 8702 |
|
|
| 8703 |
|
checkpoint56 (2004/11/17) |
| 8704 |
|
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
| 8705 |
|
o mnc: cleanup "full" files--fixes out-of-memory problem |
| 8706 |
|
o ECCO-GODAE |
| 8707 |
|
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
| 8708 |
|
* fully merged and updated from SIO code |
| 8709 |
|
windstress sign change affects |
| 8710 |
|
- exf_inscal_[u/v]stress |
| 8711 |
|
- sign of xx_tau[u/v] adjustments |
| 8712 |
|
- signs in cost_scat |
| 8713 |
|
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
| 8714 |
|
* natl_box_adjoint updated and compressed |
| 8715 |
|
* 2-level checkpoint switch added |
| 8716 |
|
(tested in EXP. 1 of natl_box_adjoint) |
| 8717 |
|
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
| 8718 |
|
o SVD |
| 8719 |
|
* first complete, non-hacked version for SVD calculations |
| 8720 |
|
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
| 8721 |
|
performed via direct access files admtlm_vector.it???? |
| 8722 |
|
(via ctrl_[un]pack) |
| 8723 |
|
* optimcycle is used for ARPACK iteration counter |
| 8724 |
|
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
| 8725 |
|
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
| 8726 |
|
and add linear transforms where necessary |
| 8727 |
|
* controls are initial/final SST, SSS (can be extended; need to check |
| 8728 |
|
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
| 8729 |
|
o mdsio: filename info to both stderr, stdout |
| 8730 |
|
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
| 8731 |
|
from sign change |
| 8732 |
|
|
| 8733 |
|
checkpoint55j_post (2004/11/10) |
| 8734 |
|
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
| 8735 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 8736 |
|
o add consistent build directories and .cvsignore files to verification |
| 8737 |
|
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
| 8738 |
|
o make all subroutines 30 or less characters in length for certain older |
| 8739 |
|
compilers to work (a thorough search only turns up two routines in |
| 8740 |
|
pkg/ptracers) |
| 8741 |
|
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
| 8742 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 8743 |
|
|
| 8744 |
|
checkpoint55i_post (2004/10/28) |
| 8745 |
|
o change arrays for total vertical diffusivity (2.D if explicit, |
| 8746 |
|
3.D if implicit) ; each ptracer uses its own background value. |
| 8747 |
|
o added mnc/NetCDF output capability to ocn_compon_interf |
| 8748 |
|
- added bits to verification/cpl_aim+ocn so that it can run on |
| 8749 |
|
ITRDA and other clusters without the mpirun "-wd" option |
| 8750 |
|
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
| 8751 |
|
configuration |
| 8752 |
|
o give MNC the ability to create additional files rather than |
| 8753 |
|
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
| 8754 |
|
- the default is just less than 2GB which is a practical limit |
| 8755 |
|
on many systems |
| 8756 |
|
o Compute the non-local term using either KPP vertical diffusivity (=default) |
| 8757 |
|
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
| 8758 |
|
|
| 8759 |
|
checkpoint55h_post (2004/10/20) |
| 8760 |
|
o add verification test "vermix" |
| 8761 |
|
o remove all the *_ioinc flags and replace with the single global |
| 8762 |
|
outputTypesInclusive flag |
| 8763 |
|
o allow to set a vertical profile of vertical diffusivity for T & S |
| 8764 |
|
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
| 8765 |
|
o useMNC moved from data.mnc to data.pkg |
| 8766 |
|
|
| 8767 |
|
checkpoint55g_post (2004/10/14) |
| 8768 |
|
o Renaming carbon AD experiments to comply with testreport conventions |
| 8769 |
|
o Updating adjoint of Held-Suarez hs94.1x64x5 |
| 8770 |
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
| 8771 |
|
have been fixed to avoid recomp. of do_oceanic_phys |
| 8772 |
|
Works well for global_ocean.90x40x15, |
| 8773 |
|
but recomp. issue remains for carbon |
| 8774 |
|
o Updating adjoint output for natl_box_adjoint after |
| 8775 |
|
pkg/ecco has been modified (see taga c55d_post) |
| 8776 |
|
|
| 8777 |
|
checkpoint55f_post (2004/10/13) |
| 8778 |
|
o rename to timeave_init_fixed |
| 8779 |
|
|
| 8780 |
|
checkpoint55e_post (2004/10/13) |
| 8781 |
|
o some delicate re-shuffle of store directives to avoid one |
| 8782 |
|
extra call of do_oceanic_physics |
| 8783 |
|
affects ecco_the_main_loop.F, do_oceanic_physics.F |
| 8784 |
|
checkpoint_lev1_directives.h |
| 8785 |
|
o NB: this may break global_ocean adjoint temporarily, |
| 8786 |
|
but it is clear how to fix it. Will do later, need this now. |
| 8787 |
|
|
| 8788 |
|
checkpoint55d_post (2004/10/11) |
| 8789 |
|
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
| 8790 |
|
o ecco_cost_weights is modified to 1x1 runs |
| 8791 |
|
o modifs to allow observations to be read in as |
| 8792 |
|
single file or yearly files |
| 8793 |
|
o enable to read exf forcing fields as either |
| 8794 |
|
single file or yearly files (flag useExfYearlyFields) |
| 8795 |
|
checkpoint55d_pre (2004/10/08) |
| 8796 |
|
|
| 8797 |
|
o switch between 2-level and 3-level checkpointing |
| 8798 |
|
o add ability of MNC to write local and "partial" (eg. 2D slices where |
| 8799 |
|
the full 3D field is never actually stored) arrays to NetCDF files |
| 8800 |
|
with the correct (that is, the complete multi-dimensional) set of |
| 8801 |
|
array indicies |
| 8802 |
|
- used in mom_vecinv() to write the diagFreq output |
| 8803 |
|
- tested (demonstrated) in verification/aim.5l_cs |
| 8804 |
|
o further mnc-ification |
| 8805 |
|
- add verification/lab_sea to the list with mnc setups |
| 8806 |
|
- fix undefined mnc v-names in cd_code |
| 8807 |
|
- add kpp to mnc output (both snapshot and timeave) |
| 8808 |
|
o non-hydrostatic code |
| 8809 |
|
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
| 8810 |
|
in calc_gw.F |
| 8811 |
|
- defaults to viscAh |
| 8812 |
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
| 8813 |
|
friction or Leith) in non-hydrostatic mode, as long as there is |
| 8814 |
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
| 8815 |
|
o pkg/cost |
| 8816 |
|
extend simple cost functions to treat time mean quantities |
| 8817 |
|
(T,U,V) via cost_accumulate_state from cost_tile |
| 8818 |
|
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
| 8819 |
|
be 2 times larger than the minimum size the advection scheme requires. |
| 8820 |
|
now get a perfect conservation of salt in advect_cs test-exp (updated) |
| 8821 |
|
o GGL90 (Gaspar's TKE mixed layer) |
| 8822 |
|
- add horizontal diffusion of TKE, requires exchanges in |
| 8823 |
|
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
| 8824 |
|
default. In OPA there is no horizontal diffusion of TKE but the |
| 8825 |
|
mixing coefficients are computed from a horizontal average of TKE of |
| 8826 |
|
6 points or so. I think that diffusion has a little more physical |
| 8827 |
|
justification. |
| 8828 |
|
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
| 8829 |
|
was in vain) |
| 8830 |
|
- mask tke-variable in ggl90_init |
| 8831 |
|
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
| 8832 |
|
o fix biharmonic diffusion on CS-grid. |
| 8833 |
|
o more obcs stuff |
| 8834 |
|
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
| 8835 |
|
for reading boundary values. This routine is called from |
| 8836 |
|
obcs_prescribe_read |
| 8837 |
|
- updated obcs_check |
| 8838 |
|
- changed sponge layer relaxation parameter units for days to seconds |
| 8839 |
|
- turned off sponge layer by default |
| 8840 |
|
- changed argument list of OBCS_CALC to myTime+deltaTclock |
| 8841 |
|
- fixed about 35 bugs in obcs_external_fields_load |
| 8842 |
|
|
| 8843 |
|
checkpoint55c_post (2004/09/23) |
| 8844 |
|
o obcs stuff |
| 8845 |
|
- new runtime flags useOBCSprescribe, useOBCSbalance |
| 8846 |
|
- re-arranged obcs_calc |
| 8847 |
|
- moved exf_getobcs to obcs_prescibe_read |
| 8848 |
|
obcs_prescibe_read is called after ORLANSKI stuff |
| 8849 |
|
and independent of it (executable can contain all). |
| 8850 |
|
- updated obcs_check |
| 8851 |
|
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
| 8852 |
|
These may be necessary only if tangential velocities are |
| 8853 |
|
prescribed at OB, not sure, needs testing. |
| 8854 |
|
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
| 8855 |
|
which simplifies the calls and passes the ifc check-bounds test |
| 8856 |
|
|
| 8857 |
|
checkpoint55b_post (2004/09/22) |
| 8858 |
|
o add a 2D scalar, Z location, exchange_2 routine. |
| 8859 |
|
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
| 8860 |
|
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
| 8861 |
|
affects advect_cs results (for the wrong reason): update output.txt |
| 8862 |
|
o use a more standard discretization for biharmonic viscosity ; |
| 8863 |
|
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
| 8864 |
|
affects results of dome set-up: update output.txt |
| 8865 |
|
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
| 8866 |
|
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
| 8867 |
|
|
| 8868 |
|
checkpoint55a_post (2004/09/20) |
| 8869 |
|
o merged code to |
| 8870 |
|
* prescribe/read time-dependent open boundaries |
| 8871 |
|
(works in conjunction with exf, cal) |
| 8872 |
|
* sponge layer code for open boundaries |
| 8873 |
|
* each boundary N/S/E/W now has its own CPP option |
| 8874 |
|
(healthy for the adjoint) |
| 8875 |
|
|
| 8876 |
|
checkpoint55 (2004/09/17) |
| 8877 |
|
o up-to-date adjoint of previous breaks |
| 8878 |
|
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
| 8879 |
|
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
| 8880 |
|
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
| 8881 |
|
- carbon: * remove tr1-related adjoint verification |
| 8882 |
|
* add ptracer as control variable |
| 8883 |
|
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
| 8884 |
|
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
| 8885 |
|
|
| 8886 |
|
checkpoint54f_post (2004/09/16) |
| 8887 |
|
o in verification/carbin/ remove experiment related to |
| 8888 |
|
ALLOW_PASSIVE_TRACER (array tr1 etc) |
| 8889 |
|
code_ad/ input_ad/ results_ad |
| 8890 |
|
|
| 8891 |
|
o add two new packages |
| 8892 |
|
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
| 8893 |
|
+ subject to optimization (memory) |
| 8894 |
|
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
| 8895 |
|
+ subject to reordering (many GOTOs in the original code) |
| 8896 |
|
+ so far opps is called for every (i,j) point, and then operates in |
| 8897 |
|
the vertical; one may want to reorder the scheme in order operate in |
| 8898 |
|
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
| 8899 |
|
fields) |
| 8900 |
|
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
| 8901 |
|
- all verification tests compile and run with linux_ia32_g77 |
| 8902 |
|
- defaults are compatible with current input files--nothing |
| 8903 |
|
should change if you were not previously using MNC |
| 8904 |
|
- MNC output has been added in numerous places (eg. timeave) |
| 8905 |
|
but there are still a few writes not yet do-able with MNC |
| 8906 |
|
(this is in progress) |
| 8907 |
|
- flags now allow for either/or/both use of MDSIO and MNC and |
| 8908 |
|
documentation will soon follow |
| 8909 |
|
- numerous small formatting cleanups for ProTeX |
| 8910 |
|
o add version info (via BUILD_INFO.h) to MNC and stdout |
| 8911 |
|
|
| 8912 |
|
checkpoint54e_post (2004/09/02) |
| 8913 |
|
o add two new packages |
| 8914 |
|
- pp81 (Packanowski and Philander, 1981), Richardson number and |
| 8915 |
|
stratification dependent mixing |
| 8916 |
|
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
| 8917 |
|
- these scheme operate in a similar manner as KPP (without ghat, of |
| 8918 |
|
course), however there is only one diffusivity that is used for both |
| 8919 |
|
temperature and salinity (and passive tracers) |
| 8920 |
|
o add offline package |
| 8921 |
|
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
| 8922 |
|
provided by Stephanie Dutkiewicz |
| 8923 |
|
o genmake2: add ability to search for C compilers and cleanup test output |
| 8924 |
|
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
| 8925 |
|
|
| 8926 |
|
checkpoint54d_post (2004/07/27) |
| 8927 |
|
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
| 8928 |
|
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
| 8929 |
|
leading to additional shift by 5 days each year of integration |
| 8930 |
|
(i.e. leading to considerable offset over the years) |
| 8931 |
|
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
| 8932 |
|
o start with no AB and no initial filtering (staggerTimeStep): |
| 8933 |
|
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
| 8934 |
|
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
| 8935 |
|
(external loading & cpl import/export stay in forward_step.F) |
| 8936 |
|
o update coupling interface to work with new staggerTimeStep |
| 8937 |
|
o change MDSIO ptracers_pickup. |
| 8938 |
|
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
| 8939 |
|
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
| 8940 |
|
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
| 8941 |
|
|
| 8942 |
|
checkpoint54c_post (2004/07/18) |
| 8943 |
|
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
| 8944 |
|
this affects (truncation error) output.txt of test-exp: |
| 8945 |
|
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
| 8946 |
|
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
| 8947 |
|
o change Qnet to always be the net heat flux, (+upward). |
| 8948 |
|
affects (truncation error) output of natl_box exp.: updated |
| 8949 |
|
o define the max number of passive tracers in PTRACERS_SIZE.h |
| 8950 |
|
o start to test mnc routinely in exp0 |
| 8951 |
|
o add sea-ice loading (sIceLoad) as a new forcing field. |
| 8952 |
|
|
| 8953 |
|
checkpoint54b_post (2004/07/08) |
| 8954 |
|
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
| 8955 |
|
impressive on Altix and Opteron systems) |
| 8956 |
|
o diagnostics can now write NetCDF files through the mnc package |
| 8957 |
|
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
| 8958 |
|
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
| 8959 |
|
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
| 8960 |
|
affects (truncation error) output of lab_sea & natl_box exp.: updated |
| 8961 |
|
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
| 8962 |
|
|
| 8963 |
|
checkpoint54a_post (2004/07/06) |
| 8964 |
|
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
| 8965 |
|
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
| 8966 |
|
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
| 8967 |
|
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
| 8968 |
|
+ internal_wave (shift in writing cg2d_ini_res) |
| 8969 |
|
checkpoint54a_pre (2004/07/05) |
| 8970 |
|
|
| 8971 |
|
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
| 8972 |
|
- modified verification/lab_sea and natl_box_adjoint accordingly |
| 8973 |
|
|
| 8974 |
|
checkpoint54 (2004/07/02) |
| 8975 |
|
checkpoint53g_post (2004/07/02) |
| 8976 |
|
o prepare splitting of thermodynamics: store convect.counter in common block |
| 8977 |
|
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
| 8978 |
|
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
| 8979 |
|
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
| 8980 |
|
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
| 8981 |
|
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
| 8982 |
|
o restore adjointability |
| 8983 |
|
|
| 8984 |
|
checkpoint53f_post (2004/06/25) |
| 8985 |
|
o modifications that affect AIM experiment results (update output.txt): |
| 8986 |
|
- no advection of S at top interface Nr (pkg/generic_advdiff) |
| 8987 |
|
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
| 8988 |
|
o AIM pkg: |
| 8989 |
|
- include stability function into surf.Flux derivative relative to Tsurf |
| 8990 |
|
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
| 8991 |
|
|
| 8992 |
|
checkpoint53e_post |
| 8993 |
|
o merged cylindrical coord configuration |
| 8994 |
|
o added rotating_tank experiment |
| 8995 |
|
checkpoint53e_pre |
| 8996 |
|
|
| 8997 |
|
checkpoint53d_post (2004/06/14) |
| 8998 |
|
o faulks upgraded: re-generate output.txt that have changed: |
| 8999 |
|
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
| 9000 |
|
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
| 9001 |
|
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
| 9002 |
|
o added Sadourny discretization of Coriolis |
| 9003 |
|
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
| 9004 |
|
- re-enabled use of omega3 (useAbsVorticity) |
| 9005 |
|
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
| 9006 |
|
vector-invariant equations |
| 9007 |
|
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
| 9008 |
|
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
| 9009 |
|
hopefully without new bugs |
| 9010 |
|
- still to do: biharmonic friction for non-hydrostatic w |
| 9011 |
|
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
| 9012 |
|
o regenerated output for global_ocean_ebm (using -ieee) |
| 9013 |
|
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
| 9014 |
|
of mom_common/ |
| 9015 |
|
- simple re-arrangement of instructions within computing loop |
| 9016 |
|
checkpoint53d_pre (2004/05/21) |
| 9017 |
|
|
| 9018 |
|
checkpoint53c_post (2004/05/21) |
| 9019 |
|
o new version of coupler for AIM+thSIce and Ocean models |
| 9020 |
|
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
| 9021 |
|
- land: change Evaporation of snow |
| 9022 |
|
- aim with thSIce: fix bug in snow-precip. |
| 9023 |
|
o changes to calc_gw.F |
| 9024 |
|
- bug fix for w^2 term near the bottom boundary |
| 9025 |
|
- (hopefully) improve the lateral slip boundary condtions for use with |
| 9026 |
|
partial/looped cells |
| 9027 |
|
- because the bug fix changes two verification experiments anyway (exp5 |
| 9028 |
|
and plume on slope), change the lateral boundary condition from half slip |
| 9029 |
|
to the value of no_slip_sides |
| 9030 |
|
o ebm package wasnt quite up to the parallel task. Fixed that. |
| 9031 |
|
o Adjoint of EBM package + verification |
| 9032 |
|
* TLM OK |
| 9033 |
|
* ADM not sufficient accuracy yet (needs further testing) |
| 9034 |
|
|
| 9035 |
|
checkpoint53b_post (2004/05/14) |
| 9036 |
|
o Commiting new energy balance model to repository |
| 9037 |
|
* package is pkg/ebm |
| 9038 |
|
* verif. is verification/global_ocean_ebm |
| 9039 |
|
* references are in ebm_driver.F |
| 9040 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
| 9041 |
|
C Global thermohaline circulation. Part I: |
| 9042 |
|
C Sensitivity to atmospheric moisture transport. |
| 9043 |
|
C J. Climate 12(1), 71-82 |
| 9044 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
| 9045 |
|
C Global thermohaline circulation. Part II: |
| 9046 |
|
C Sensitivity with interactive transport. |
| 9047 |
|
C J. Climate 12(1), 83-91 |
| 9048 |
|
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
| 9049 |
|
C Destabilization of the thermohaline circulation |
| 9050 |
|
C by atmospheric eddy transports. |
| 9051 |
|
C J. Climate 7(12), 1870-1882 |
| 9052 |
|
o Will need long integration testing. |
| 9053 |
|
checkpoint53b_pre (2004/05/14) |
| 9054 |
|
|
| 9055 |
|
o created pkg/mom_common in preparation for variable viscosity code |
| 9056 |
|
o renamed and split ini_mnc_io |
| 9057 |
|
o pkg/land: only liquid water can diffuse or run-off |
| 9058 |
|
o AIM using land: soil wetness availability account for snow |
| 9059 |
|
o added printMapIncludesZeros to EEPARMS namelist |
| 9060 |
|
|
| 9061 |
|
checkpoint53a_post (2004/05/11) |
| 9062 |
|
o restore TAMC compatiility for exf_constants.h |
| 9063 |
|
(no usage of _d in .h) |
| 9064 |
|
o Additional storing in KPP in an attempt to fix |
| 9065 |
|
TAMC problem with adjoint of KPP code. |
| 9066 |
|
(no success...) |
| 9067 |
|
Identical code works fine with TAF. |
| 9068 |
|
o Fixed verification/natl_box_adjoint experiments. |
| 9069 |
|
Initial conditions for Experiments 4 and 5 are now |
| 9070 |
|
set to "SEAICE_initialHEFF=0", which is more reasonable, |
| 9071 |
|
and hence gives results closer to that of Experiment 2. |
| 9072 |
|
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
| 9073 |
|
|
| 9074 |
|
checkpoint53 (2004/05/06) |
| 9075 |
|
o stable checkpoint with up to date adjoint |
| 9076 |
|
TLM tests only run for 1st grdchk at the moment. Its unclear if |
| 9077 |
|
this is a code problem or a problem with resetting code for g_ |
| 9078 |
|
variables that is being autogenerated wrong. |
| 9079 |
|
Otherwise: |
| 9080 |
|
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
| 9081 |
|
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
| 9082 |
|
are both still in chaos following their security messes. |
| 9083 |
|
|
| 9084 |
|
checkpoint52n_post (2004/05/06) |
| 9085 |
|
o various build (mostly genmake2) changes including: |
| 9086 |
|
- ability to build/run more easily within Cygwin and MacOS X |
| 9087 |
|
- more complicated Makefiles with a stronger dependence on Gnu Make |
| 9088 |
|
o pkg/seaice modifications |
| 9089 |
|
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
| 9090 |
|
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
| 9091 |
|
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
| 9092 |
|
- changed proxy for geostrophic velocity and updated |
| 9093 |
|
verification/lab_sea/results/* accordingly |
| 9094 |
|
- removed ADI dynamic solver from pkg/seaice |
| 9095 |
|
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
| 9096 |
|
they caused a segmentation fault under certain circumstances |
| 9097 |
|
- removed unused field WATR |
| 9098 |
|
o bug fix in exf-package: |
| 9099 |
|
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
| 9100 |
|
now reflect that. |
| 9101 |
|
o small fixes in the cal-package: |
| 9102 |
|
- set reference date to first of January for the 'model'-calendar |
| 9103 |
|
- failing of cal_CheckDate in cal_FullDate now actually results in a |
| 9104 |
|
warning |
| 9105 |
|
o small modifications in exf-package to increase flexibility: |
| 9106 |
|
- change climtempfreeze from a constant to a runtime parameter that |
| 9107 |
|
is specified in data.exf_clim (default = -1.9) |
| 9108 |
|
- introduce runtime parameter windstressmax (default = 2.0) that is |
| 9109 |
|
specified in data.exf |
| 9110 |
|
o fix in pkg/thsice: |
| 9111 |
|
- update Evap (Tsf changes) to be consistent with Latent heat flux |
| 9112 |
|
- maintain snow precipitation unchanged (even if Tsf >=0). |
| 9113 |
|
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
| 9114 |
|
|
| 9115 |
|
checkpoint52m_post (2004/04/18) |
| 9116 |
|
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
| 9117 |
|
this does not change any of the results, because myIter=0 in swfrac always |
| 9118 |
|
lead to jwtype=2 (the default anyway), but the call makes little sense |
| 9119 |
|
as a default |
| 9120 |
|
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
| 9121 |
|
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
| 9122 |
|
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
| 9123 |
|
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
| 9124 |
|
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
| 9125 |
|
o extending useSingleCpuIO option to work with new exch2 I/O format |
| 9126 |
|
- old-style, missing-tile I/O is still accessible by defining CPP |
| 9127 |
|
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
| 9128 |
|
o monitor package can write to NetCDF files and/or STDOUT |
| 9129 |
|
o fix re-definition bug in MNC_GRID_INIT_ALL() |
| 9130 |
|
o doc/api_reference added |
| 9131 |
|
- a framework for building an API Reference Manual using all |
| 9132 |
|
the "protex" comments embedded in the code |
| 9133 |
|
- see pkg/generic_advdiff, pkg/mnc for examples |
| 9134 |
|
o MNC: |
| 9135 |
|
- make myThid the last argument for all subroutines |
| 9136 |
|
- new default for the grid files: NO halos |
| 9137 |
|
- add useMNC and other run-time flags |
| 9138 |
|
- separate per-file-group handling of the unlimited dimension |
| 9139 |
|
- early initialization of MNC w/ flags read at the eeboot stage |
| 9140 |
|
and lookup tables set in initialize_fixed |
| 9141 |
|
- write all MNC output to a freshly-created directory |
| 9142 |
|
o thermodynamics sea-ice (thsice) is now tested with testreport. |
| 9143 |
|
o test exp. advect_cs: use the standard cs32 grid ; update output. |
| 9144 |
|
o Added functionality to grdchk: |
| 9145 |
|
pick global i,j,k position (or nearest wet) where to perform check. |
| 9146 |
|
|
| 9147 |
|
checkpoint52l_post (2004/03/11) |
| 9148 |
|
o new land formulation: |
| 9149 |
|
a) use ground enthalpy as prognostic variable to ensure exact |
| 9150 |
|
energy conservation. |
| 9151 |
|
b) account for water temperature and for latent heat of freezing |
| 9152 |
|
in all processes (rain, run-off, ground storage) |
| 9153 |
|
c) compute surface and ground temperature implicitly. |
| 9154 |
|
o aim_v23 modification for new land model: |
| 9155 |
|
a) Treat separately land / ocean / sea-ice surface fluxes |
| 9156 |
|
to allow implicit computation of land & sea-ice surface temp. |
| 9157 |
|
b) add snow precipitation. |
| 9158 |
|
checkpoint52l_pre (2004/03/11) |
| 9159 |
|
|
| 9160 |
|
o fix problem (when 1 tile is empty) in min/max monitor. |
| 9161 |
|
o fix bug in timeAve (u,vZetatave in common block) |
| 9162 |
|
o no restoring terms under ice for pkg/seaice |
| 9163 |
|
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
| 9164 |
|
o bug fix for pkg/seaice pickups |
| 9165 |
|
o change MNC call locations and add coordinate attributes |
| 9166 |
|
o mask vorticity at the corner ; affects global_ocean.cs output |
| 9167 |
|
o fix ini_curvilinear_grid ; test CS experiments with mpi |
| 9168 |
|
o aim.5l_cs: modify sea-ice fraction input file ; update output |
| 9169 |
|
o exf: Adding simple range check routine for exf fields after read |
| 9170 |
|
|
| 9171 |
|
checkpoint52k_post (2004/02/23) |
| 9172 |
|
o removed top-level directory "diags" |
| 9173 |
|
- we migrated these functions to pkg/timeave a long time ago |
| 9174 |
|
o fixed bug introduced in pkg/monitor |
| 9175 |
|
o accuracy ctrlprec = 32 insuffient for gradient checks using |
| 9176 |
|
averaged fields (I/O via cost_averages) |
| 9177 |
|
-> use ctrl.h in active_file*.F to control I/O precision. |
| 9178 |
|
o paramter list of CALL ADTHE_MAIN_LOOP |
| 9179 |
|
o added initial do_the_model_io to ecco |
| 9180 |
|
o set all ...Freq to zero after cost_final |
| 9181 |
|
taveFreq, dumpFreq, pChkptFreq |
| 9182 |
|
o MAIN and ECCO differentiability restored |
| 9183 |
|
|
| 9184 |
|
checkpoint52j_post (2004/02/18) |
| 9185 |
|
o fix nchklev in tamc.h for global_ocean... |
| 9186 |
|
o Bringing flow and store directives up-to-date |
| 9187 |
|
o Really weird thing! |
| 9188 |
|
call do_the_model_io from the_main_loop with parameters |
| 9189 |
|
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
| 9190 |
|
TAF places a faulty re-call of initialise_varia |
| 9191 |
|
after cost_final call which should not be there! |
| 9192 |
|
checkpoint52j_pre (2004/02/03) |
| 9193 |
|
|
| 9194 |
|
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
| 9195 |
|
error messages |
| 9196 |
|
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
| 9197 |
|
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
| 9198 |
|
debug output |
| 9199 |
|
o modfied mdsio_writefield.F to handle non-global files under exch2 |
| 9200 |
|
o update AIM Cubed-Sphere exp (aim.5l_cs): |
| 9201 |
|
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
| 9202 |
|
o update AIM Equatorial Channel exp: |
| 9203 |
|
use standard aim_v23 pkg and change the SST fields to be more realistic. |
| 9204 |
|
o globalFile now works with exch2 |
| 9205 |
|
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
| 9206 |
|
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
| 9207 |
|
o limit timeave output for hi-res integrations |
| 9208 |
|
|
| 9209 |
|
checkpoint52i_post (2004/01/21) |
| 9210 |
|
o removed CPP_EEOPTIONS.h from verification/*/code |
| 9211 |
|
o updated the tiling for global_ocean_pressure |
| 9212 |
|
checkpoint52i_pre (2004/01/20) |
| 9213 |
|
|
| 9214 |
|
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
| 9215 |
|
the old pkg/aim). |
| 9216 |
|
|
| 9217 |
|
checkpoint52h_pre (2004/01/20) |
| 9218 |
|
o shortened offending lines in exch2_send_rx?.template |
| 9219 |
|
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
| 9220 |
|
o genmake2: add build & execute test for NetCDF code |
| 9221 |
|
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
| 9222 |
|
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
| 9223 |
|
o added useSingleCPUIO flag to monitor.F and mon_out.F |
| 9224 |
|
o added temporary hack for sea-ice dynamics on the cube: |
| 9225 |
|
metric terms are ignored and it is assumed that |
| 9226 |
|
there is no sea-ice on cube faces 1, 2, 4, and 5. |
| 9227 |
|
|
| 9228 |
|
checkpoint52f_post (2004/01/09) |
| 9229 |
|
o added exch2 cube routines to pkg/exch2 |
| 9230 |
|
o modified hs94.cs-32x32x5 to use it |
| 9231 |
|
o added new grid files to hs94.cs-32x32x5 |
| 9232 |
|
checkpoint52f_pre (2004/01/07) |
| 9233 |
|
|
| 9234 |
|
checkpoint52e_post (2004/01/07) |
| 9235 |
|
o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
| 9236 |
|
for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
| 9237 |
|
o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
| 9238 |
|
to work with implicit vertical advection and AB ; |
| 9239 |
|
o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
| 9240 |
|
o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
| 9241 |
|
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
| 9242 |
|
checkpoint52e_pre (2004/01/02) |
| 9243 |
|
|
| 9244 |
|
o fix bug in impldiff when Nr=1 or Nr=2. |
| 9245 |
|
o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
| 9246 |
|
o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
| 9247 |
|
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
| 9248 |
|
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
| 9249 |
|
o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
| 9250 |
|
o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
| 9251 |
|
o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
| 9252 |
|
|
| 9253 |
|
checkpoint52d_post (2003/12/16) |
| 9254 |
|
o re-tiled many expts to allow comparison in multi-processor mode |
| 9255 |
|
- updated output accordingly |
| 9256 |
|
- changed hs94.128x64x5 to use intial T from file rather than use the |
| 9257 |
|
random number generator |
| 9258 |
|
o add infrastructure in model routines for fizhi and gridalt packages |
| 9259 |
|
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
| 9260 |
|
o changes to permit hi-res, cubed-sphere, configuration |
| 9261 |
|
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
| 9262 |
|
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
| 9263 |
|
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
| 9264 |
|
of surface winds for the cube |
| 9265 |
|
(A verification experiment, based on global_ocean.cs32x15, but with |
| 9266 |
|
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
| 9267 |
|
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
| 9268 |
|
complete with example surface forcing files and matlab scripts to look |
| 9269 |
|
at the output and compare it with that of global_ocean.cs32x15.) |
| 9270 |
|
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
| 9271 |
|
but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
| 9272 |
|
to conform to the common rule. |
| 9273 |
|
o check-in the first version of the coupler + interfaces for multi-components |
| 9274 |
|
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
| 9275 |
|
- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
| 9276 |
|
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
| 9277 |
|
- ocean and atmos. share the same horizontal grid (no interpolation). |
| 9278 |
|
- exchanges between component and coupler is done in forward_step |
| 9279 |
|
o new verification experiment, cpl_aim+ocn: |
| 9280 |
|
coupled ocean - AIM atmosphere on cs32 grid. |
| 9281 |
|
|
| 9282 |
|
checkpoint52d_pre (2003/12/06) |
| 9283 |
|
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
| 9284 |
|
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
| 9285 |
|
|
| 9286 |
|
checkpoint52c_post (2003/11/25) |
| 9287 |
|
o Fixing OPTIONS files for use of exf: |
| 9288 |
|
- ALLOW_ECCO not needed |
| 9289 |
|
- ECCO_CPPOPTIONS.h should not be included from |
| 9290 |
|
EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
| 9291 |
|
as has been the case in the past |
| 9292 |
|
- All cal/exf related options are currently set in |
| 9293 |
|
single header file. Should remain so until we |
| 9294 |
|
agree on a consistent new policy. |
| 9295 |
|
o Removed all CPP options for cal package. |
| 9296 |
|
cal has no more CPP options. |
| 9297 |
|
o modified STOREs in GAD_ADVECTION |
| 9298 |
|
o corrected key comp. for passkey |
| 9299 |
|
|
| 9300 |
|
checkpoint52b_post (2003/11/23) |
| 9301 |
|
o new version: "thsice" of thermodynamic sea-ice pkg: |
| 9302 |
|
- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
| 9303 |
|
- modify fluxes but do not change theta directly; |
| 9304 |
|
- light cleaning of bulk_force pkg (still needed with thsice). |
| 9305 |
|
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
| 9306 |
|
+ output_thsice.txt to test thsice & bulk_force pkgs. |
| 9307 |
|
o put back grid & coriolis monitor output. |
| 9308 |
|
checkpoint52b_pre (2003/11/23) |
| 9309 |
|
|
| 9310 |
|
o call "do_the_model_io" at the beginning (=> dump initial state) |
| 9311 |
|
o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
| 9312 |
|
o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
| 9313 |
|
(need info on NUMBER_OF_PTRACERS) |
| 9314 |
|
o missing PTRACERS headers in some routines |
| 9315 |
|
o default tamc.h in pkg/autodiff supposed to crash |
| 9316 |
|
to ensure proper customization |
| 9317 |
|
|
| 9318 |
|
checkpoint52a_post (2003/11/17) |
| 9319 |
|
o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
| 9320 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
| 9321 |
|
- subroutine FREEZE_SURFACE now limits only surface temperature |
| 9322 |
|
and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
| 9323 |
|
=> new output.txt for global_ocean.cs32x15 & global_with_exf |
| 9324 |
|
- keep the old version of FREEZE for backward compatibility; |
| 9325 |
|
global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
| 9326 |
|
- corresponding modifs for TAF directives |
| 9327 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
| 9328 |
|
o time-averaged output for pkg/ptracers |
| 9329 |
|
o fix problem with ECCO-related divided adjoint |
| 9330 |
|
snapshot file was missing some ad-variables, |
| 9331 |
|
but no warning issued by TAF |
| 9332 |
|
|
| 9333 |
|
checkpoint52a_pre (2003/11/12) |
| 9334 |
|
o some bug fixes for #undef REAL4_IS_SLOW |
| 9335 |
|
|
| 9336 |
|
checkpoint52 = ecco_c52_e35 |
| 9337 |
|
o after testing adjoints of checkpoint51u_post |
| 9338 |
|
|
| 9339 |
|
checkpoint51u_post (2003/11/06) |
| 9340 |
|
o this is the post-merge tag of the ecco-branch |
| 9341 |
|
(needs another clean checkout and re-testing) |
| 9342 |
|
o various natl_box_adjoint configs and results |
| 9343 |
|
but no input fields |
| 9344 |
|
o obcs adjoint not yet merged! |
| 9345 |
|
o adding ECCO global 1x1 and 2x2 degree configs |
| 9346 |
|
o updated/extended some store directives for seaice |
| 9347 |
|
o pkg/ecco now containes ecco-specific part of cost function |
| 9348 |
|
o top level routines the_main_loop, forward_step |
| 9349 |
|
supersede those in model/src/ |
| 9350 |
|
previous input data.cost now in data.ecco |
| 9351 |
|
(new namelist ecco_cost_nml) |
| 9352 |
|
o in ctrl/ cleaned some cross-dependencies and updated CPP options |
| 9353 |
|
|
| 9354 |
|
checkpoint51t_post (2003/11/04) |
| 9355 |
|
o this is the pre-merge tag of the ecco-branch |
| 9356 |
|
|
| 9357 |
|
checkpoint51s_post (2003/11/04) |
| 9358 |
|
o cleanup: removed various obsolete #define-s |
| 9359 |
|
o pkg/grdchk |
| 9360 |
|
- renamed 'ph-grd 3' to 'grad-res' |
| 9361 |
|
- merged from ecco-branch |
| 9362 |
|
(remaining bug fixes for obcs gradient checks) |
| 9363 |
|
- additional high-precision output for testreport |
| 9364 |
|
(grep for 'precision_grdchk_result') |
| 9365 |
|
|
| 9366 |
|
checkpoint51r_post (2003/11/03) |
| 9367 |
|
o cleaned up or removed CPP_OPTIONS.h files |
| 9368 |
|
o updated results for some of the tests to reflect the new |
| 9369 |
|
optfiles (-ieee: -O0 instead of -O3) |
| 9370 |
|
|
| 9371 |
|
checkpoint51q_post (2003/10/30) |
| 9372 |
|
o cd_code: |
| 9373 |
|
- moved cd_scheme.F -> cd_code_scheme.F |
| 9374 |
|
- separate read_checkpoint from cd_code_ini_vars.F |
| 9375 |
|
- separated cd_code part from write_checkpoint |
| 9376 |
|
- updated AD_SOURCE, generated .flow |
| 9377 |
|
- added CD_CODE_VARS.h to the_main_loop |
| 9378 |
|
- Moving cd_code specific store dir.s to pkg/cd_code |
| 9379 |
|
o ctrl package totally restructured |
| 9380 |
|
- pack/unpack now optional and decoupled from |
| 9381 |
|
xx_/adxx_ I/O |
| 9382 |
|
- ctrl_pack/unpack cleaned |
| 9383 |
|
(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
| 9384 |
|
- confined inclusion of AD_CONFIG.h to where necessary. |
| 9385 |
|
o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
| 9386 |
|
|
| 9387 |
|
checkpoint51p_post (2003/10/30) |
| 9388 |
|
o create initial cd_code package |
| 9389 |
|
- WARNING: the initialization of fields within packages |
| 9390 |
|
is broken because INI_FIELDS (where READ_CHECKPOINT is |
| 9391 |
|
called) is called *before* PACKAGES_INIT_VARIABLES. |
| 9392 |
|
This seems to be backwards since |
| 9393 |
|
1) its important to initially zero the entire field including |
| 9394 |
|
the "halo" region |
| 9395 |
|
2) zeroing needs to be done *before* reading pickup info |
| 9396 |
|
and the pickup call might or might not happen in any |
| 9397 |
|
particular run |
| 9398 |
|
- this needs an overhaul for R2 |
| 9399 |
|
o cleanup verification/*/code/GMREDI_OPTIONS.h |
| 9400 |
|
o cleanup testreport |
| 9401 |
|
|
| 9402 |
|
checkpoint51o_post (2003/10/27) |
| 9403 |
|
o bringing AD-related verif's up to date with genmake2 |
| 9404 |
|
- carbon/ |
| 9405 |
|
- global_ocean.90x40x15/ |
| 9406 |
|
- hs.94.1x64x5/ |
| 9407 |
|
- (front_relax/ ) |
| 9408 |
|
o (more) consistent directory structure for AD-related verif.'s |
| 9409 |
|
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
| 9410 |
|
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
| 9411 |
|
o bug fix in find_alpha.F for MDJWF: |
| 9412 |
|
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
| 9413 |
|
change rho -> rho-rhoConst |
| 9414 |
|
- replace call find_rho to find_rhonum |
| 9415 |
|
o initialisation of rFlx extended to full array (required by TAF) |
| 9416 |
|
and shifted to thermodynamics |
| 9417 |
|
o removed PTRACERS.h in ptracers routine |
| 9418 |
|
o added surfacetendencyPtr to S/R parameter list pracers_forcing |
| 9419 |
|
o Correcting initialisations for fVerU, fVerV. |
| 9420 |
|
o helping TAF to recognize dependency on kUp for |
| 9421 |
|
fVerU, fVerV |
| 9422 |
|
o Replacing delZ by delR in pkg/ctrl/ |
| 9423 |
|
checkpoint51o_pre (2003/10/24) |
| 9424 |
|
|
| 9425 |
|
o undid all of cp51 pending some cleanups and discussion |
| 9426 |
|
o added the [#include "AD_CONFIG.h"] statement to all files that need |
| 9427 |
|
it for adjoint/tl #defines |
| 9428 |
|
o re-worked the build logic in genmake2 to support AD_CONFIG.h |
| 9429 |
|
o removed tools/genmake since it no longer works |
| 9430 |
|
|
| 9431 |
|
checkpoint51n_post (2003/10/23) |
| 9432 |
|
o modifications to make FREEZE flux visible to pkg/kpp |
| 9433 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
| 9434 |
|
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
| 9435 |
|
- subroutine FREEZE now limits only surface temperature |
| 9436 |
|
(this means new output.txt for global_ocean.90x40x15, |
| 9437 |
|
global_ocean.cs32x15, and global_with_exf) |
| 9438 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
| 9439 |
|
|
| 9440 |
|
checkpoint51n_pre (2003/10/23) |
| 9441 |
|
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
| 9442 |
|
o added [#include "AD_CONFIG.h"] to all files that use the following |
| 9443 |
|
defines: |
| 9444 |
|
- ALLOW_ADJOINT_RUN |
| 9445 |
|
- ALLOW_TANGENTLINEAR_RUN |
| 9446 |
|
- ALLOW_ECCO_OPTIMIZATION |
| 9447 |
|
|
| 9448 |
|
checkpoint51m_post (2003/10/21) |
| 9449 |
|
o incorporating changes to get TAMC/TAF working in genmake2 |
| 9450 |
|
- added new TAMC/TAF targets to the Makefile |
| 9451 |
|
- various cleanups related to package handling |
| 9452 |
|
- these changes should have no impact on the forward model |
| 9453 |
|
|
| 9454 |
|
checkpoint51l_post (2003/10/20) |
| 9455 |
|
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
| 9456 |
|
- faster algorithm for cal_addtime.F |
| 9457 |
|
- higher precision arithmetic, where needed |
| 9458 |
|
- pkg/exf *startdate variables changed from calendar date to |
| 9459 |
|
model integration time |
| 9460 |
|
|
| 9461 |
|
checkpoint51l_pre (2003/10/17) |
| 9462 |
|
o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
| 9463 |
|
o enable to apply restoring on S & T only in a latitude band. |
| 9464 |
|
o update output (external_forcing_surf modif. change truncation errors) |
| 9465 |
|
global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
| 9466 |
|
|
| 9467 |
|
checkpoint51k_post (2003/10/16) |
| 9468 |
|
o change default to: useNHMTerms=.FALSE. |
| 9469 |
|
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
| 9470 |
|
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
| 9471 |
|
- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
| 9472 |
|
exp1, ideal_2D_oce |
| 9473 |
|
- change data file of oceanic exp (leave the results unchanged for now) |
| 9474 |
|
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
| 9475 |
|
o set gravitySign automatically according to the vertical coordinate used |
| 9476 |
|
(and change sign: back to "logical" value: +1 when R increases downward) |
| 9477 |
|
o added an include barrier to the default CPP_OPTIONS.h and |
| 9478 |
|
removed the #include "PACKAGES_CONFIG.h" from it |
| 9479 |
|
o fix a bug in mom_fluxform (from chk51j_post) |
| 9480 |
|
|
| 9481 |
|
checkpoint51j_post (2003/10/10) |
| 9482 |
|
o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
| 9483 |
|
o adjusted some flow directives (dynamics, thermodynamics) |
| 9484 |
|
o added cubed-sphere case to test cost function |
| 9485 |
|
o heckpoint_lev?_directives.h now include |
| 9486 |
|
pkg-specific directives, whenever those are enabled. |
| 9487 |
|
o Moving pkg-specific flow directives to corresponding pkg |
| 9488 |
|
Moving pkg-specific differentiation list to corresponding pkg |
| 9489 |
|
Moving pkg-specific checkpoint-lev storing to corresponding pkg |
| 9490 |
|
---> conventions are |
| 9491 |
|
- pkg_ad.flow |
| 9492 |
|
- pkg_ad_diff.list |
| 9493 |
|
- pkg_ad_check_lev?_dir.h |
| 9494 |
|
|
| 9495 |
|
checkpoint51i_post (2003/10/09) |
| 9496 |
|
o merge of the branch-genmake2 |
| 9497 |
|
- knowingly breaks the older genmake |
| 9498 |
|
- automatic generation of all ALLOW_${PKG_NAME} defines |
| 9499 |
|
- new testreport supersedes older testscript |
| 9500 |
|
o large number of package inclusion and header cleanups |
| 9501 |
|
checkpoint51i_pre (2003/10/08) |
| 9502 |
|
|
| 9503 |
|
o new output for adjoin of global ocean vector invariant |
| 9504 |
|
o fix for checkpoint of thermodynamic seaice and bulk_force |
| 9505 |
|
o Steph gchem various cleanups |
| 9506 |
|
|
| 9507 |
|
checkpoint 51h_pre |
| 9508 |
|
o fixed some single quotes |
| 9509 |
|
o modify gchem pkg to be more versatile |
| 9510 |
|
o modifications to clean up dic pkg |
| 9511 |
|
o add pkg/cfc |
| 9512 |
|
|
| 9513 |
|
checkpoint51g_post (2003/10/02) |
| 9514 |
|
o provide links for ARPACK and ADM*TLM |
| 9515 |
|
o start removing verification/vero/ |
| 9516 |
|
o update AD-related stuff |
| 9517 |
|
(in particular some IF-statements in model/src/ routines) |
| 9518 |
|
o adding to verification/global_ocean.90x40x15/ adjoint of |
| 9519 |
|
vector invariant setup |
| 9520 |
|
|
| 9521 |
|
checkpoint51f_post (2003/10/02) |
| 9522 |
|
o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
| 9523 |
|
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
| 9524 |
|
of tracer Green's fucntions for ocean inversion project. |
| 9525 |
|
|
| 9526 |
|
checkpoint51f_pre (2003/08/07) |
| 9527 |
|
o Added on-the-fly spatial interpolation capability |
| 9528 |
|
"USE_EXF_INTERPOLATION" to pkg/exf. |
| 9529 |
|
- This is a temporary Cartesian-grid hack until |
| 9530 |
|
the super-duper ESMF coupler becomes available. |
| 9531 |
|
- See verification/global_with_exf/README for usage example. |
| 9532 |
|
- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
| 9533 |
|
flags and modified pkg/seaice accordingly. |
| 9534 |
|
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
| 9535 |
|
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
| 9536 |
|
non-local transport term. |
| 9537 |
|
|
| 9538 |
|
checkpoint51e_post (2003/08/03) |
| 9539 |
|
o pkg/mom_vecinv: |
| 9540 |
|
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
| 9541 |
|
- add time-ave diagnostic of vorticity advection. |
| 9542 |
|
o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. |
| 9543 |
|
o atmospheric geopotential: - include water vapor effect; |
| 9544 |
|
- use p^kappa in p* scaling. |
| 9545 |
|
o land pkg: read initial state from files. |
| 9546 |
|
o AIM : add stratospheric drag in the upper level |
| 9547 |
|
|
| 9548 |
|
checkpoint51d_post (2003/07/18) |
| 9549 |
|
o change function ILNBLNK (=> last non-blank char.) to return zero |
| 9550 |
|
(instead of the string length) when the string. char is empty |
| 9551 |
|
o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) |
| 9552 |
|
o modif's to restore TAMC compatibility |
| 9553 |
|
- avoid "_d" constructs in PARAMETER declarations |
| 9554 |
|
- avoid interrupting lines by comment lines |
| 9555 |
|
o Use cluster local disks for purely local I/O |
| 9556 |
|
vs. globally visible disks needed for ctrl stuff |
| 9557 |
|
(merged from ecco-branch) |
| 9558 |
|
- new active_file_loc... and mdsio_..._loc routines |
| 9559 |
|
- affected packages: autodiff, ctrl, grdchk, mdsio |
| 9560 |
|
|
| 9561 |
|
checkpoint51c_post (2003/07/08) |
| 9562 |
|
o introducing integer flag debugLevel |
| 9563 |
|
- debLevZero: suppress all output |
| 9564 |
|
- debLevA: standard |
| 9565 |
|
- debLevB: equivalent to current debugMode=.TRUE. |
| 9566 |
|
o introducing pathname variable mdsioLocalDir for mdsio |
| 9567 |
|
that can be specified at runtime |
| 9568 |
|
(relevant for cluster I/O to local disk) |
| 9569 |
|
` |
| 9570 |
|
>>>checkpoint51b_post |
| 9571 |
|
adjoint of ptracers |
| 9572 |
|
o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
| 9573 |
|
o extended state in checkpoint_lev?, etc. |
| 9574 |
|
o alternative ctrl/cost with tr1 or ptracer |
| 9575 |
|
o new comlev1_bibj_ptracers |
| 9576 |
|
o new ptracers.flow |
| 9577 |
|
o made ptracers_forcing same as external_forcing_s |
| 9578 |
|
o added verification for adjoint with ptracers |
| 9579 |
|
- adm. grdchk fail so far |
| 9580 |
|
- tlm. grdchk OK |
| 9581 |
|
- checked tapelev/comlev recomputations: OK |
| 9582 |
|
<<<checkpoint51b_pre |
| 9583 |
|
|
| 9584 |
|
checkpoint51a_post (2003/06/25) |
| 9585 |
|
o added code for biogeochemistry package |
| 9586 |
|
- new pkgs: dic, gchem |
| 9587 |
|
- new subroutine in ptracers |
| 9588 |
|
o modify code for biogeo packages |
| 9589 |
|
- in model/src and pkg/ptracers |
| 9590 |
|
|
| 9591 |
|
checkpoint51 (2003/06/24) |
| 9592 |
|
o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN |
| 9593 |
|
- autodiff, ctrl, exf, grdchk, seaice |
| 9594 |
|
kept separate packages |
| 9595 |
|
- cost, ecco, obcs |
| 9596 |
|
o updating verification/internal_wave, verification/lab_sea |
| 9597 |
|
(all verif's pass on faulks.lcs.mit.edu RH7.3, g77) |
| 9598 |
|
|
| 9599 |
|
checkpoint50i_post (2003/06/23) |
| 9600 |
|
o Preparing next differentiable checkpoint and sync |
| 9601 |
|
of MAIN vs. ecco-branch |
| 9602 |
|
- 1st step: this one is differentiable |
| 9603 |
|
- 2nd step: next(! not this) checkpoint will have updated packages |
| 9604 |
|
from ecco-branch) |
| 9605 |
|
|
| 9606 |
|
checkpoint50h_post (2003/06/20) |
| 9607 |
|
o new package "land": provide surface BC for AIM. |
| 9608 |
|
o pkg/ptracers: apply exchange to all tracers after reading a pickup. |
| 9609 |
|
o AIM: use true log-P extrapolation for near surface temp (= as in |
| 9610 |
|
F.Molteni paper) ; update aim.5l_cs output. |
| 9611 |
|
o New variable in PARM03 for more flexible pickups |
| 9612 |
|
o somewhat cleaned package initialisation sequence for |
| 9613 |
|
ctrl/ cost/ ecco/ in packages_... routines |
| 9614 |
|
|
| 9615 |
|
checkpoint50g_post (2003/05/23) |
| 9616 |
|
o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
| 9617 |
|
- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
| 9618 |
|
- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
| 9619 |
|
made the default because of faster convergence than ADI |
| 9620 |
|
|
| 9621 |
|
checkpoint50f_post (2003/05/23) |
| 9622 |
|
o exf totally restructured |
| 9623 |
|
- replaced all exf_set_ routines by one generic exf_set_gen.F |
| 9624 |
|
and made sure it's still differentiable |
| 9625 |
|
- split exf_getffields.F into new exf_bulkformulae.F |
| 9626 |
|
- exf_inscal_/exf_outscal_ suffixes consistent with field names |
| 9627 |
|
- updated adjoint/makefile and relevant verif. accordingly |
| 9628 |
|
|
| 9629 |
|
checkpoint50f_pre (2003/05/23) |
| 9630 |
|
o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; |
| 9631 |
|
+ change Evap over land. (update aim.5l_cs output) |
| 9632 |
|
o added missing .cvsignores and made uniform across expts |
| 9633 |
|
o changed configuration of tidal_basin_2d expt |
| 9634 |
|
o added pkg/debug functions for tracing code in fatal crashes |
| 9635 |
|
o tidied pkg/monitor to use MONITOR_OPTIONS.h |
| 9636 |
|
o new fn in pkg/monitor to stop model if solution grows too big |
| 9637 |
|
o removed lots of single quotes from comments |
| 9638 |
|
|
| 9639 |
|
checkpoint50e_post (2003/05/14) |
| 9640 |
|
o make KPP work with PTRACERS |
| 9641 |
|
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
| 9642 |
|
nearly a copy of kpp_transport_s |
| 9643 |
|
- there is no analogue to SurfaceTendencyS, so I have to use |
| 9644 |
|
gPtr(of the surface layer) instead |
| 9645 |
|
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
| 9646 |
|
checkpoint50e_pre (2003/05/13) |
| 9647 |
|
|
| 9648 |
|
checkpoint50d_post (2003/05/13) |
| 9649 |
|
o change kpp output from multiple-record state files to single-record state |
| 9650 |
|
files analogous to write_state.F |
| 9651 |
|
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
| 9652 |
|
analogous to the cg2d-related output. |
| 9653 |
|
o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
| 9654 |
|
so that writing to internal file fn (with length 512) fails. |
| 9655 |
|
checkpoint50d_pre (2003/05/12) |
| 9656 |
|
|
| 9657 |
|
checkpoint50c_post (2003/05/12) |
| 9658 |
|
o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) |
| 9659 |
|
o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. |
| 9660 |
|
o add time-average diagnostic of U*V and vertical diffusive flux for theta. |
| 9661 |
|
o bug fixed in convective adjustment diagnostic (multi-tile set-up). |
| 9662 |
|
o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. |
| 9663 |
|
|
| 9664 |
|
checkpoint50c_pre (2003/04/30) |
| 9665 |
|
Merging from release1_p13: |
| 9666 |
|
o bug fix for pkg/seaice dynamic solver |
| 9667 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
| 9668 |
|
|
| 9669 |
|
checkpoint50b_post (2003/04/17) |
| 9670 |
|
o store u*,v* in gU,V instead of in guNm1,gvNm1 |
| 9671 |
|
o in order to put the momForcing out of the Adams-Bashforth: |
| 9672 |
|
move forcing & CD-scheme calls from mom_fluxform & mom_vecinv |
| 9673 |
|
to timestep.F |
| 9674 |
|
o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays |
| 9675 |
|
o re-generate output for highly sensitive test-exp: |
| 9676 |
|
global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box |
| 9677 |
|
|
| 9678 |
|
checkpoint50b_pre (2003/04/17) |
| 9679 |
|
o restore the use of momAdvection & useCoriolis flags (mom_vecinv) |
| 9680 |
|
o corrected CPP option mismatch in exf_Bulk... functions for case |
| 9681 |
|
#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
| 9682 |
|
|
| 9683 |
|
checkpoint50a_post (2003/03/21) |
| 9684 |
|
o Bug fix for merging between c50 and KPP. |
| 9685 |
|
ikey was passed from thermodynamics to kpp_calc via |
| 9686 |
|
common block rather than being recomputed in kpp_calc, |
| 9687 |
|
in contradiction with new key itdkey. |
| 9688 |
|
New key ikppkey created, and tamc.h headers updated. |
| 9689 |
|
|
| 9690 |
|
checkpoint50 (2003/03/08) |
| 9691 |
|
- 2nd step of merge with ecco-branch: |
| 9692 |
|
merge changes in ecco-branch back into main trunk |
| 9693 |
|
- bug fix in find_alpha |
| 9694 |
|
- more storing in gmredi_calc_tensor.F, kpp_routines.F |
| 9695 |
|
- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
| 9696 |
|
- merged some sliced AD support routines |
| 9697 |
|
|
| 9698 |
|
checkpoint49 (2003/03/06) |
| 9699 |
|
merged from ecco-branch: |
| 9700 |
|
o exf: |
| 9701 |
|
- Enable initialisation of forcing fields to constant |
| 9702 |
|
(runtime) values. |
| 9703 |
|
- in exf_getffields.F |
| 9704 |
|
Reduce i-/j-loop to interior domain, discarding overlaps. |
| 9705 |
|
That also fixes wrong TAF-key computations for key_1, key_2 |
| 9706 |
|
with bulf formulae. |
| 9707 |
|
- exf_init.F modify #ifdef for exf_init_evap |
| 9708 |
|
- exf_getffieldrec.F, ctrl_getrec.F |
| 9709 |
|
The following INT-usages are not safe: |
| 9710 |
|
fldsecs = int(fldsecs/fldperiod)*fldperiod |
| 9711 |
|
fldcount = int(fldsecs/fldperiod) + 1 |
| 9712 |
|
and were modified. |
| 9713 |
|
o autodiff: checkpoint_lev... |
| 9714 |
|
- updated storing for bulk formulae (some arrays were missing) |
| 9715 |
|
- added state for seaice package |
| 9716 |
|
- synchronized with main branch |
| 9717 |
|
o DIVA: |
| 9718 |
|
Modif.s in |
| 9719 |
|
- the_main_loop.F |
| 9720 |
|
- the_model_main.F |
| 9721 |
|
and added cost_final_restore.F cost_final_store.F |
| 9722 |
|
o With these changes, it is possible to fully separate |
| 9723 |
|
the first forward run to compute the cost function (mdthe_main_loop) |
| 9724 |
|
and adjoint runs over individual DIVA intervals (adthe_main_loop) |
| 9725 |
|
into separate model executions. |
| 9726 |
|
This enables better tuning of DIVA to given queue sizes. |
| 9727 |
|
o Loss of cost function value in consecutive DIVA runs is |
| 9728 |
|
fixed by storing to 'costfinal' file. |
| 9729 |
|
o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
| 9730 |
|
beginning/end of adjoint integration is accounted for. |
| 9731 |
|
The current changes apply to TAF-1.4.26. |
| 9732 |
|
TAF has one remaining bug, requiring one manual change |
| 9733 |
|
(see MITgcm manual). |
| 9734 |
|
o cal: synchronized between MAIN and ecco-branch |
| 9735 |
|
|
| 9736 |
|
checkpoint48i_post (2003/03/05) |
| 9737 |
|
o Changes to restore differentiability of code w.r.t. previous tag |
| 9738 |
|
(mostly adding new routines to make list and replacing |
| 9739 |
|
pressure by totPhiHyd). |
| 9740 |
|
o Updated and merged grdchk package |
| 9741 |
|
- has both ADM and TLM checks |
| 9742 |
|
- works for single- and multi-proc. |
| 9743 |
|
- output cleaned |
| 9744 |
|
- worked successfully for parallel DIVA |
| 9745 |
|
o genmake: |
| 9746 |
|
- Adding -platform=SP4 |
| 9747 |
|
- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
| 9748 |
|
o Modif. for DIVA: |
| 9749 |
|
ctrl_unpack should not be called in intermediate DIVA interval. |
| 9750 |
|
(similar thing would apply for active files such as |
| 9751 |
|
tbar, sbar, psbar, which should not be reinitialised; |
| 9752 |
|
only relevant for ecco-branch) |
| 9753 |
|
|
| 9754 |
|
checkpoint48h_post (2003/02/28) |
| 9755 |
|
o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
| 9756 |
|
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
| 9757 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
| 9758 |
|
o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
| 9759 |
|
|
| 9760 |
|
checkpoint48g_post (2003/02/18) |
| 9761 |
|
--- EOS: |
| 9762 |
|
o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
| 9763 |
|
store total Potential in totPhyHyd for diagnostics & EOS. |
| 9764 |
|
o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
| 9765 |
|
--- Pressure/geopotential gradient: |
| 9766 |
|
o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
| 9767 |
|
o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
| 9768 |
|
( changes results of global_ocean_pressure ) |
| 9769 |
|
o NLFS + z-coord.: add eta*Rho' contribution. |
| 9770 |
|
o accurate phiHyd when using interface-W at the middle between 2 centers |
| 9771 |
|
( changes results of ideal_2D_oce ) |
| 9772 |
|
o includes r* 2nd term in potential gradient. |
| 9773 |
|
|
| 9774 |
|
checkpoint48f_post (2003/02/18) |
| 9775 |
|
Merging from release1_p12: |
| 9776 |
|
o Modifications for using pkg/exf with pkg/seaice |
| 9777 |
|
- improved description of the various forcing configurations |
| 9778 |
|
- added basic radiation bulk formulae to pkg/exf |
| 9779 |
|
- units/sign fix for evap computation in exf_getffields.F |
| 9780 |
|
- updated verification/global_with_exf/results/output.txt |
| 9781 |
|
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
| 9782 |
|
(SBO) core products, including oceanic mass, center-of-mass, |
| 9783 |
|
angular, and bottom pressure (see pkg/sbo/README.sbo). |
| 9784 |
|
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
| 9785 |
|
to avoid negative values in shallow regions. |
| 9786 |
|
- updated verification/natl_box/results/output.txt |
| 9787 |
|
- updated verification/lab_sea/results/output.txt |
| 9788 |
|
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
| 9789 |
|
o Added useSingleCpuIO option (see PARAMS.h). |
| 9790 |
|
o Updated useSingleCpuIO option in mdsio_writefield.F to |
| 9791 |
|
work with multi-field files, e.g., for single-file pickup. |
| 9792 |
|
o pkg/seaice: |
| 9793 |
|
- bug fix in growth.F: QNET for no shortwave case |
| 9794 |
|
- added HeffFile for specifying initial sea-ice thickness |
| 9795 |
|
- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
| 9796 |
|
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
| 9797 |
|
kpp_transport_t.F, forward_step.F, and the_main_loop.F |
| 9798 |
|
o pkg/seaice: |
| 9799 |
|
- adjoint-friendly modifications |
| 9800 |
|
- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
| 9801 |
|
|
| 9802 |
|
checkpoint48e_post (2003/02/12) |
| 9803 |
|
o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) |
| 9804 |
|
o dynamics: change definition of computational domain & adapt mom_fluxform |
| 9805 |
|
accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. |
| 9806 |
|
o following exp works with Olx=Oly=2 (and pass through checkbounds option): |
| 9807 |
|
adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 |
| 9808 |
|
exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 |
| 9809 |
|
global_ocean.90x40x15 global_with_exf global_ocean_pressure |
| 9810 |
|
inverted_barometer solid-body.cs-32x32x1 |
| 9811 |
|
(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) |
| 9812 |
|
|
| 9813 |
|
checkpoint48d_post (2003/02/09) |
| 9814 |
|
o in preparation for r*: |
| 9815 |
|
a) use pre-computed gradient of hydrostatic potential: |
| 9816 |
|
changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce |
| 9817 |
|
b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: |
| 9818 |
|
=> affects results of glob_oce_pressure (different truncation error) |
| 9819 |
|
update output.txt of ideal_2D_oce & global_ocean_pressure |
| 9820 |
|
|
| 9821 |
|
checkpoint48d_pre (2003/02/08) |
| 9822 |
|
o in preparation for r*: |
| 9823 |
|
new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
| 9824 |
|
pass the 2 comp. of the grad. as arguments to momentum S/R. |
| 9825 |
|
but for the moment, only used if it does not change the results. |
| 9826 |
|
o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP |
| 9827 |
|
|
| 9828 |
|
checkpoint48c_post (2003/02/06) |
| 9829 |
|
Modifications in treatment of initial flux forcing controls |
| 9830 |
|
to avoid extra storing of flux fields. |
| 9831 |
|
|
| 9832 |
|
checkpoint48c_pre (2003/01/21) |
| 9833 |
|
o Added tidal_basin_2d experiment (currently 1D!) |
| 9834 |
|
o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) |
| 9835 |
|
|
| 9836 |
|
checkpoint48b_post (2003/01/27) |
| 9837 |
|
o r* coordinate added in #ifdef NONLIN_FRSURF block. |
| 9838 |
|
(modification to pressure gradient not yet implemented) |
| 9839 |
|
o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports |
| 9840 |
|
(for U & V) that are used for vertical advection of momentum. |
| 9841 |
|
|
| 9842 |
|
checkpoint48a_post (2003/01/24) |
| 9843 |
|
o In preparation for r*, use temp. array to compute vertical transport |
| 9844 |
|
in flux-form momentum pkg. => change results of few test-exp. |
| 9845 |
|
Update output of: exp4, exp5, front_relax, global_ocean_pressure, |
| 9846 |
|
lab_sea, natl_box & plume_on_slope |
| 9847 |
|
|
| 9848 |
|
checkpoint48 (2003/01/23) |
| 9849 |
|
o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') |
| 9850 |
|
|
| 9851 |
|
checkpoint47j_post (2003/01/21) |
| 9852 |
|
o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. |
| 9853 |
|
o moved adexch from forward_step to addummy_in_stepping |
| 9854 |
|
o added exch in ctrl_map_... |
| 9855 |
|
o aveFreq.=0. at end of cost_final to avoid overwrite in |
| 9856 |
|
reverse checkpointing loop |
| 9857 |
|
o Yet more changes in gmredi: |
| 9858 |
|
* adgmredi_calc_tensor |
| 9859 |
|
avoiding all recomputation of gmredi_slope_limit |
| 9860 |
|
* adgmredi_x/y/rtransport |
| 9861 |
|
added flag for excessive storing to avoid recomp. of |
| 9862 |
|
u/v/rtans, dTdx/y/z |
| 9863 |
|
-> this is not really necessary and very memory-consuming |
| 9864 |
|
* adgmredi_slope_psi: |
| 9865 |
|
consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff |
| 9866 |
|
* gmredi_slope_limit |
| 9867 |
|
re-activated full calculation of taperfct for case 'ac02' |
| 9868 |
|
o updating verification/ adjoints of carbon, global_ocean.90x40x15 |
| 9869 |
|
|
| 9870 |
|
checkpoint47i_post (2003/01/13) |
| 9871 |
|
o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. |
| 9872 |
|
o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) |
| 9873 |
|
default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) |
| 9874 |
|
o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) |
| 9875 |
|
o gmredi: fix few bugs. |
| 9876 |
|
|
| 9877 |
|
checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) |
| 9878 |
|
This will be a good checkpoint to plug into the ecco-branch. |
| 9879 |
|
o few modif.'s to get latest version adjointed |
| 9880 |
|
(mainly kick out code in ini_linear_phisurf) |
| 9881 |
|
o modif's to run adjoint with exactConserv |
| 9882 |
|
o case GM_BOLUS_ADVEC should be cleaned |
| 9883 |
|
S/R gmredi_slope_psi should be cleaned |
| 9884 |
|
o verification/carbon now has exactConserv=.TRUE. |
| 9885 |
|
|
| 9886 |
|
checkpoint47g_post (2003/01/10) |
| 9887 |
|
o time-average AIM output: becomes independent from statvars time-average |
| 9888 |
|
(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
| 9889 |
|
o After TAF bug fix: |
| 9890 |
|
Tested adjoint of gmredi package. |
| 9891 |
|
Tests were done with checkpoint47 rather than with latest |
| 9892 |
|
checkpoint47f_post since the latter is broken for the adjoint |
| 9893 |
|
verification/carbon/ contains both ADM and TLM gradient checks. |
| 9894 |
|
Here they are, before they get changed/lost/stolen. |
| 9895 |
|
Mostly modif.'s to fix numerical sensitivities. |
| 9896 |
|
Gradient checks OK for |
| 9897 |
|
- GM_taper_scheme: |
| 9898 |
|
* clipping |
| 9899 |
|
* ac02 |
| 9900 |
|
* linear |
| 9901 |
|
* glw91 |
| 9902 |
|
* dm95 |
| 9903 |
|
* ldd97 |
| 9904 |
|
- GMREDI_OPTIONS: |
| 9905 |
|
* GM_VISBECK_VARIABLE_K |
| 9906 |
|
* GM_NON_UNITY_DIAGONAL |
| 9907 |
|
* GM_EXTRA_DIAGONAL |
| 9908 |
|
* GM_BOLUS_ADVEC |
| 9909 |
|
in conjunction with data.gmredi parameters to be checked in |
| 9910 |
|
in a few minutes under verification/carbon/code/ |
| 9911 |
|
|
| 9912 |
|
checkpoint47f_post (2002/12/28) |
| 9913 |
|
Merging from release1_p10: |
| 9914 |
|
o modifications for using pkg/exf with pkg/seaice |
| 9915 |
|
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
| 9916 |
|
and SEAICE_EXTERNAL_FLUXES |
| 9917 |
|
- pkg/exf CPP options EXF_READ_EVAP and |
| 9918 |
|
EXF_NO_BULK_COMPUTATIONS |
| 9919 |
|
- usage examples are Experiments 8 and 9 in |
| 9920 |
|
verification/lab_sea/README |
| 9921 |
|
- verification/lab_sea default experiment now uses |
| 9922 |
|
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf |
| 9923 |
|
|
| 9924 |
|
checkpoint47e_post (2002/12/27) |
| 9925 |
|
o created a tag prior to creating a branch |
| 9926 |
|
|
| 9927 |
|
checkpoint47d_post (2002/12/16) |
| 9928 |
|
o fixed bug in the oceanic pressure coordinates code: vertical viscosity |
| 9929 |
|
at the bottom boundary had an erroneous half slip boundary condition |
| 9930 |
|
o added bottom drag and no slip boundary condition capabilities to |
| 9931 |
|
oceanic pressure coordinates code |
| 9932 |
|
o added new verification experiment global_ocean_pressure, this experiment is |
| 9933 |
|
also described in the tutorial section of the manual |
| 9934 |
|
checkpoint47d_pre (2002/12/16) |
| 9935 |
|
|
| 9936 |
|
checkpoint47c_post (2002/12/16) |
| 9937 |
|
o Added a verification experiment for a global cubed-sphere ocean run |
| 9938 |
|
- verification/global_ocean.cubed32x32x30 |
| 9939 |
|
- uses pkg/therm_seaice and pkg/bulk_forcing |
| 9940 |
|
|
| 9941 |
|
o allow to run AIM physics with SPEEDY input files (from Franco Molteni) |
| 9942 |
|
o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) |
| 9943 |
|
when using P-coordinate; only implemented for atmospheric config. |
| 9944 |
|
o OCEANICP & realFreshWater: include P-E direct effect on wVel ; |
| 9945 |
|
NOTES: requires option NONLIN_FRSURF to be "#define". |
| 9946 |
|
o update advect_xz/results/output.txt (left from checkpoint44g_post) |
| 9947 |
|
|
| 9948 |
|
checkpoint47b_post (2002/12/05) |
| 9949 |
|
Merging from release1_p9: |
| 9950 |
|
o pkg/seaice |
| 9951 |
|
- removed GOTO's and added taf directives |
| 9952 |
|
- double precision constants to reduce the g77 (Linux) |
| 9953 |
|
to F77 (SGI) differences reported in release1_p8 |
| 9954 |
|
o tools/genmake |
| 9955 |
|
- added SGI options |
| 9956 |
|
o verification/testscript |
| 9957 |
|
- updated to that of checkpoint47a_post |
| 9958 |
|
o verification/global_ocean.90x40x15/input/eedata |
| 9959 |
|
- modified for SGI f77 compatibility |
| 9960 |
|
o verification/lab_sea |
| 9961 |
|
- added description of sea-ice model |
| 9962 |
|
- added missing matlab routines |
| 9963 |
|
- added test of thermodynamics parallelization |
| 9964 |
|
|
| 9965 |
|
checkpoint47a_post (2002/11/23) |
| 9966 |
|
o new pkg: aim_v23 |
| 9967 |
|
= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
| 9968 |
|
for now, keep the same surface forcing as before. |
| 9969 |
|
- Part-Cell implemented into AIM; check that Heat & Water are conserved |
| 9970 |
|
- aim.5l_cs: use new aim pkg (run 10yr & get better results than before) |
| 9971 |
|
- aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg |
| 9972 |
|
o add diagnostic of surface correction term in monitor output |
| 9973 |
|
|
| 9974 |
|
o bulk_force and therm_seaice |
| 9975 |
|
- Two packages: bulk_force (Bulk forcing) |
| 9976 |
|
and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 |
| 9977 |
|
- Earlier integration from Stephaine Dutkiewicz |
| 9978 |
|
and Patrick Heimbach. |
| 9979 |
|
- Two ifdef statements for compile time, |
| 9980 |
|
ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE |
| 9981 |
|
|
| 9982 |
|
checkpoint47 (2002/11/15) |
| 9983 |
|
differentiable version of checkpoint46n_post |
| 9984 |
|
o bug fix in quasihydrostaticterms |
| 9985 |
|
o * "clean" adjoint code (in terms of extensive recomputations) |
| 9986 |
|
can now be obtained for all GMREDI options (i.e. for |
| 9987 |
|
- GM_VISBECK_VARIABLE_K |
| 9988 |
|
- GM_NON_UNITY_DIAGONAL |
| 9989 |
|
- GM_EXTRA_DIAGONAL |
| 9990 |
|
- GM_BOLUS_ADVEC ) |
| 9991 |
|
* However, wrong gradient check problem remains unsolved. |
| 9992 |
|
* New CPP options have been introduced for different |
| 9993 |
|
tapering schemes |
| 9994 |
|
o external_fields_load now part of differentiation list |
| 9995 |
|
o pressure needs multiple storing; |
| 9996 |
|
would be nice to have store_pressure at beginning or |
| 9997 |
|
end of forward_step, e.g. by having phiHyd global (5-dim.) |
| 9998 |
|
(NB: pressure is needed for certain cases in find_rho, |
| 9999 |
|
which is also invoked through convective_adjustment). |
| 10000 |
|
o recomputations in find_rho for cases |
| 10001 |
|
'JMD95'/'UNESCO' or 'MDJWF' are OK. |
| 10002 |
|
o #define ATMOSPHERIC_LOADING should be differentiable |
| 10003 |
|
o ini_forcing shifted to begining of initialise_varia |
| 10004 |
|
o Incorporating QNVS line search routines into MITgcm |
| 10005 |
|
(this is separate code, and therefore not under pkg) |
| 10006 |
|
lsopt/, optim/ |
| 10007 |
|
o Updated verification/carbon/ |
| 10008 |
|
- #define GM_VISBECK_VARIABLE_K |
| 10009 |
|
- GM_taper_scheme = 'ldd97' |
| 10010 |
|
|
| 10011 |
|
checkpoint46n_post (2002/11/12) |
| 10012 |
|
Merging from release1_p8: |
| 10013 |
|
o verification/natl_box: |
| 10014 |
|
updating new external_fields_load routine |
| 10015 |
|
o New package: pkg/seaice |
| 10016 |
|
Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). |
| 10017 |
|
The sea-ice code is based on Hibler (1979-1980). |
| 10018 |
|
Two sea-ice dynamic solvers, ADI and LSR, are included. |
| 10019 |
|
In addition to computing prognostic sea-ice variables and diagnosing |
| 10020 |
|
the forcing/external data fields that drive the ocean model, |
| 10021 |
|
SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
| 10022 |
|
The implied surface heat flux is then stored in variable |
| 10023 |
|
surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and |
| 10024 |
|
kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the |
| 10025 |
|
non-local transport term. Because this call precedes model |
| 10026 |
|
thermodynamics, temperature under sea-ice may not be "exactly" at |
| 10027 |
|
the freezing point by the time theta is dumped or time-averaged. |
| 10028 |
|
N.B.: fairly large differences in accuracy occur across |
| 10029 |
|
different platforms/compilers; comparison between |
| 10030 |
|
g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) |
| 10031 |
|
generated output gives: |
| 10032 |
|
T S U V |
| 10033 |
|
C D M c m s m s m s m s |
| 10034 |
|
n p a R g m m e . m m e . m m e . m m e . |
| 10035 |
|
f n k u 2 i a a d i a a d i a a d i a a d |
| 10036 |
|
g d e n d n x n . n x n . n x n . n x n . |
| 10037 |
|
|
| 10038 |
|
Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea |
| 10039 |
|
o GAD: |
| 10040 |
|
- generated new common blocks to account for call of |
| 10041 |
|
same gad routines with differing traceridentities |
| 10042 |
|
(needed to modify tracerIdentity indices in GAD.h) |
| 10043 |
|
- generated separate common blocks for case useCubedSphereExchange |
| 10044 |
|
(Department of Futurology) |
| 10045 |
|
- parameter lists to gmredi_?transport: added tracerIdentity |
| 10046 |
|
- added new key indices to tamc.h |
| 10047 |
|
o external_fields_load: |
| 10048 |
|
- added this routine to TAF list |
| 10049 |
|
- needed to make some common blocks global and additional storing |
| 10050 |
|
along the same lines as exf package (checkpoint_lev?_directives.h) |
| 10051 |
|
o exf: |
| 10052 |
|
updated external forcing package |
| 10053 |
|
- bug fixes carried over from ecco-branch |
| 10054 |
|
(missing OBCS_OPTIONS.h in two routines) |
| 10055 |
|
- enable easy to use "no forcing". |
| 10056 |
|
- added exf I/O for atmospheric loading |
| 10057 |
|
- added exf I/O for runoff data |
| 10058 |
|
- transfered scaling between exf <-> MITgcm to exf namelist |
| 10059 |
|
o Adding new verification experiment global_with_exf. |
| 10060 |
|
This verification experiment is almost identical to the |
| 10061 |
|
global_ocean.90x40x15 experiment, except that it uses |
| 10062 |
|
the exf (and cal) package instead of the |
| 10063 |
|
external_fields_load routine (cf README file). |
| 10064 |
|
|
| 10065 |
|
checkpoint46m_post (2002/11/07) |
| 10066 |
|
o modified testscript to return -- when there are no lines of "%MON" output |
| 10067 |
|
o added new flag "quasiHydrostatic" for QH mode |
| 10068 |
|
and new routine quasihydrostaticterms() |
| 10069 |
|
o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
| 10070 |
|
New routine: mom_u_coriolis_nh() |
| 10071 |
|
o fixed sign of non-hydrostatic metric terms in u and v equations. |
| 10072 |
|
Depend on correct sign of gravitySign. |
| 10073 |
|
o added work.pc* to .cvsignore in aim directories using ifc |
| 10074 |
|
o introduced flag for controllin non-hydrostatic metric terms |
| 10075 |
|
o removed gravitySign from PARM04 |
| 10076 |
|
o switched to g77/ifc from pgf77 in aim experiments |
| 10077 |
|
|
| 10078 |
|
checkpoint46l_post (2002/11/01) |
| 10079 |
|
o made convective adjustment work with pressure coordinates: |
| 10080 |
|
- changed the direction of k-loop in convective_adjustment.F for the |
| 10081 |
|
case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
| 10082 |
|
- adjusted the reference pressure k-index in convective_adjustment.F |
| 10083 |
|
- adjusted the convection condition in convect.F (in analogy to |
| 10084 |
|
calc_ivdc.F) |
| 10085 |
|
- convective_adjustment no longer computes anything on the halos |
| 10086 |
|
- removed the warnings about negative salinity from find_rho.F and |
| 10087 |
|
find_alpha.F; instead the new routine look_for_neg_salinity, called |
| 10088 |
|
at the beginning of find_rho, find_alpha, and find_beta, does a |
| 10089 |
|
check of the entire slice, if CPP-option |
| 10090 |
|
CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined |
| 10091 |
|
checkpoint46l_pre (2002/10/23) |
| 10092 |
|
|
| 10093 |
|
checkpoint46k_post (2002/10/23) |
| 10094 |
|
o fixed the verification/global_ocean.90x40x15 experiment: |
| 10095 |
|
- new bathymetry (the world according to A., JMC, and M.) |
| 10096 |
|
- new initial fields and forcing fields (*.bin files) |
| 10097 |
|
- new POLY3.COEFFS (for the next release one should switch to a full |
| 10098 |
|
equation of state: JMD95P or MDJWF) |
| 10099 |
|
- fixed several errors and redundancies in the data file |
| 10100 |
|
- experiment uses looped cells |
| 10101 |
|
- added matlab directory with diagnostic scripts for plotting of output |
| 10102 |
|
|
| 10103 |
|
o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
| 10104 |
|
- read AIM physics parameters from a file (data.aimphys) |
| 10105 |
|
- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
| 10106 |
|
|
| 10107 |
|
checkpoint46j_post (2002/10/07) |
| 10108 |
|
o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
| 10109 |
|
o move wVel computation at the end of the time step, in S/R integr_continuity |
| 10110 |
|
o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
| 10111 |
|
o update timeave pkg for wVel diagnostic. |
| 10112 |
|
checkpoint46j_pre (2002/09/27) |
| 10113 |
|
|
| 10114 |
|
checkpoint46i_post (2002/09/25) |
| 10115 |
|
o Clean up AIM package (and keep the results unchanged): |
| 10116 |
|
include CPP_OPTION and use IMPLICT NONE in all routines ; |
| 10117 |
|
declare all the variables _RL ; use _d 0 for all numerical constants. |
| 10118 |
|
use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
| 10119 |
|
|
| 10120 |
|
checkpoint46h_post (2002/09/25) |
| 10121 |
|
o cleaned up the use of rhoNil and rhoConst. |
| 10122 |
|
- rhoNil should only appear in the LINEAR equation of state, everywhere |
| 10123 |
|
else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
| 10124 |
|
and the dynamical equations are all divided by rhoConst |
| 10125 |
|
o introduced new parameter rhoConstFresh, a reference density of fresh |
| 10126 |
|
water, to remove the fresh water flux's dependence on rhoNil. The default |
| 10127 |
|
value is 999.8 kg/m^3 |
| 10128 |
|
o cleanup up external_forcing.F and external_forcing_surf.F |
| 10129 |
|
- can now be used by both OCEANIC and OCEANICP |
| 10130 |
|
checkpoint46h_pre (2002/09/18) |
| 10131 |
|
|
| 10132 |
|
Added code to convert surface volume flux (fresh water) into |
| 10133 |
|
a mass flux when using P coordinates in the ocean (OCEANICP). |
| 10134 |
|
Note: It assumes you have set rho0=rhoConst=density of fresh water. |
| 10135 |
|
|
| 10136 |
|
checkpoint46g_post (2002/09/18) |
| 10137 |
|
o Include a new diagnostic variable phiHydLow for the ocean model |
| 10138 |
|
- in z-coordinates, it is the bottom pressure anomaly |
| 10139 |
|
- in p-coordinates, it is the sea surface elevation |
| 10140 |
|
- in both cases, these variable have global drift, reflecting the mass |
| 10141 |
|
drift in z-coordinates and the volume drift in p-coordinates |
| 10142 |
|
- included time averaging for phiHydLow, be aware of the drift! |
| 10143 |
|
o depth-dependent computation of Bo_surf for pressure coordinates |
| 10144 |
|
in the ocean (buoyancyRelation='OCEANICP') |
| 10145 |
|
- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
| 10146 |
|
Theta, Salinity, and Pressure in the parameter list. This routine is |
| 10147 |
|
presently contained in find_rho.F. This routine does not give the |
| 10148 |
|
correct density for 'POLY3', which would be a z-dependent reference |
| 10149 |
|
density. |
| 10150 |
|
o cleaned up find_rho |
| 10151 |
|
- removed obsolete 'eqn' from the parameter list. |
| 10152 |
|
o added two new verification experiments: gop and goz |
| 10153 |
|
(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
| 10154 |
|
checkpoint46g_pre (2002/09/16) |
| 10155 |
|
|
| 10156 |
|
checkpoint46f_post (2002/09/16) |
| 10157 |
|
o Enable tangent linear (forward mode) gradient checks: |
| 10158 |
|
- extended active file handling to g_... files |
| 10159 |
|
- added TANGENT_SIMULATION to theSimulationMode |
| 10160 |
|
- extended grdchk package accordingly |
| 10161 |
|
o added tangent linear setup in verification/carbon/code_ftl |
| 10162 |
|
o added adjoint setup in verification/front_relax/code_ad |
| 10163 |
|
|
| 10164 |
|
checkpoint46e_post (2002/09/05) |
| 10165 |
|
o Added new equation of state -> MDJWF |
| 10166 |
|
- EOS of McDougall et al., 2002, JAOT, submitted |
| 10167 |
|
- caveat: the equation of state is only valid for a smaller (more |
| 10168 |
|
realistic?) range of values than JMD95P/Z and UNESCO |
| 10169 |
|
- added masks to the calculation of pressure in store_pressure |
| 10170 |
|
- added more check values for density in check_eos (ini_eos.F), some of |
| 10171 |
|
the old check values are out of the range of the MDJWF-eos, so don't |
| 10172 |
|
expect perfect matches for those |
| 10173 |
|
checkpoint46e_pre (2002/08/19) |
| 10174 |
|
|
| 10175 |
|
checkpoint46d_post (2002/08/19) |
| 10176 |
|
o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
| 10177 |
|
'OCEANICP', also initialised field pressure correctly in ini_eos in the |
| 10178 |
|
case of pressure coordinates. eosType='JMD95Z' in |
| 10179 |
|
combination with buoyancyRelation='OCEANICP' now causes an error. |
| 10180 |
|
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
| 10181 |
|
in find_alpha/beta. |
| 10182 |
|
checkpoint46d_pre (2002/08/15) |
| 10183 |
|
|
| 10184 |
|
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
| 10185 |
|
so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
| 10186 |
|
|
| 10187 |
|
checkpoint46c_post (2002/08/15) |
| 10188 |
|
o Changes necessary for ocean in p-coordinates |
| 10189 |
|
- Added new buoyancy relation = 'OCEANICP' |
| 10190 |
|
- Added new parameters = gravitySign (this used to be contained inside |
| 10191 |
|
the factor dRdZ which I added when we first switched to R coordinates). |
| 10192 |
|
X GM/Redi is not compatible (yet) |
| 10193 |
|
X bottom drag and no-slip need to be debugged. |
| 10194 |
|
checkpoint46c_pre (2002/08/07) |
| 10195 |
|
|
| 10196 |
|
checkpoint46b_post (2002/08/07) |
| 10197 |
|
o Added new equation of state -> JMD95Z and JMD95P |
| 10198 |
|
- EOS of Jackett and McDougall, 1995, JAOT |
| 10199 |
|
- moved all EOS parameters into EOS.h |
| 10200 |
|
- new routines ini_eos.F, store_pressure.F |
| 10201 |
|
o Added UNESCO EOS, but not recommended because it requires |
| 10202 |
|
in-situ temperature (see JMD95) |
| 10203 |
|
o Modified formatting for knudsen2.f in utils/knudsen2 and added |
| 10204 |
|
unesco.f to be used with POLY3 |
| 10205 |
|
checkpoint46b_pre (2002/07/31) |
| 10206 |
|
|
| 10207 |
|
checkpoint46a_post (2002/07/31) |
| 10208 |
|
o Added (atmospheric) pressure loading |
| 10209 |
|
- new field in FFIELDS.h, etc... |
| 10210 |
|
- new cpp flag ATMOSPHERIC_LOADING |
| 10211 |
|
o Changed hFacC to _hFacC in calc_phi_hyd.F |
| 10212 |
|
o Added SHORTWAVE_HEATING to some files for consistency |
| 10213 |
|
checkpoint46a_pre (2002/07/13) |
| 10214 |
|
|
| 10215 |
|
checkpoint46 (2002/07/13) |
| 10216 |
|
further merges from release1_p5 |
| 10217 |
|
o new ctrl package |
| 10218 |
|
- adopted from ECCO environment to enable optimization |
| 10219 |
|
- added Eliassen Palm fluxes to controls |
| 10220 |
|
o added Eliassen Palm flux controls to gradient check package |
| 10221 |
|
o cost package |
| 10222 |
|
- Compatible with new ctrl package |
| 10223 |
|
- added Eliassen Palm cost hooks |
| 10224 |
|
- modif's of existing cost functions |
| 10225 |
|
o Adjoint-related bug fixes in kpp: |
| 10226 |
|
- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
| 10227 |
|
- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
| 10228 |
|
o autodiff package |
| 10229 |
|
- flow directives: |
| 10230 |
|
+ new for S/R do_the_model_io |
| 10231 |
|
+ enhanced for S/R checkpoint |
| 10232 |
|
+ new gmredi.flow |
| 10233 |
|
- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
| 10234 |
|
disable adcommon.h/g_common.h by default. |
| 10235 |
|
- fixed problem for adjoint of global_max |
| 10236 |
|
o modified verification/carbon/ |
| 10237 |
|
o New setup for adjoint of global_ocean |
| 10238 |
|
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
| 10239 |
|
o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
| 10240 |
|
o incorporated hooks for sponge layer code (external_forcing.F) |
| 10241 |
|
|
| 10242 |
|
checkpoint45d_post (2002/07/12) |
| 10243 |
|
o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
| 10244 |
|
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
| 10245 |
|
(affects plume_on_slope "cg2d" output) |
| 10246 |
|
o add new parameter deltaTfreesurf for free-surface time stepping |
| 10247 |
|
o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
| 10248 |
|
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
| 10249 |
|
o change phiMin in exp1 (to agree with documentation) |
| 10250 |
|
o add new flags: |
| 10251 |
|
- T,S forcing inside/outside Adams-Bashforth |
| 10252 |
|
- turn off temp,salt advection and/or forcing |
| 10253 |
|
- for each tracer, define internal flag for multiDimAdvection & A-B |
| 10254 |
|
o monitor: change definition of KE to check conservation of Energy |
| 10255 |
|
|
| 10256 |
|
checkpoint45c_post (2002/05/30) |
| 10257 |
|
o Removed f90 comments ("!") |
| 10258 |
|
o Modified initialisations to enable exf package for MITgcm |
| 10259 |
|
(without invoking ECCO_PACKAGE). |
| 10260 |
|
o modifications to gradient check package (Martin Losch) |
| 10261 |
|
- enable centered differences |
| 10262 |
|
- modified format of standard output |
| 10263 |
|
|
| 10264 |
|
checkpoint45b_post (2002/05/30) |
| 10265 |
|
o cleaned exchange calls in cg2d |
| 10266 |
|
o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
| 10267 |
|
o included CPP option SINGLE_LAYER_MODE in thermodynamics |
| 10268 |
|
to configure barotropic setup (Martin Losch) |
| 10269 |
|
o moved some initialisations within bi,bj loop in dynamics |
| 10270 |
|
(TAF flow dependency) |
| 10271 |
|
o in initialise_varia, moved call packages_init_variables |
| 10272 |
|
before convective_adjustment_init |
| 10273 |
|
(corresponding adjustment of TAF tape initialisation). |
| 10274 |
|
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
| 10275 |
|
|
| 10276 |
|
checkpoint45a_post (2002/05/01) |
| 10277 |
|
o compute Rho over the whole domain (extend iMin,jMin indices) |
| 10278 |
|
o specific exchange for X-slice domain (case Ny=1) |
| 10279 |
|
o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
| 10280 |
|
o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
| 10281 |
|
|
| 10282 |
|
checkpoint44h_post = checkpoint45 |
| 10283 |
|
o Fix to restore differentiability: |
| 10284 |
|
place at which packages_init_variables is called in |
| 10285 |
|
initialise_varia is crucial for reverse control flow. |
| 10286 |
|
o modifications in GMRedi to enable stable adjoint |
| 10287 |
|
(corresponding modif's in thermodynamics, dynamics) |
| 10288 |
|
o added missing hook for sponge layer code in external_forcing |
| 10289 |
|
o modified test cost functions |
| 10290 |
|
o storing in gad_advection (plus removal of write(0,*)! |
| 10291 |
|
o missing headers TR1.h added in convective_adjustment routines |
| 10292 |
|
o errorMessageUnit set non-equal zero in eeboot |
| 10293 |
|
(conflict on some platforms, e.g. IBM SP3) |
| 10294 |
|
o modified carbon verif. |
| 10295 |
|
|
| 10296 |
|
checkpoint44h_pre (2002/03/14) |
| 10297 |
|
o vertical grid option: allow to put the Interface at the middle between |
| 10298 |
|
2 cell-centers ; replace delZ in pkg/kpp by drF. |
| 10299 |
|
o GM Advective form: Tracers are advected using the residual transport (= |
| 10300 |
|
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
| 10301 |
|
|
| 10302 |
|
checkpoint44g_post (2002/03/05) |
| 10303 |
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
| 10304 |
results) ; ifdef missing in thermodynamics.F |
results) ; ifdef missing in thermodynamics.F |
| 10305 |
|
|
| 10364 |
o check parameters & config (chkpt44a_pre,post) |
o check parameters & config (chkpt44a_pre,post) |
| 10365 |
o OBC and NonLin_FrSurf. |
o OBC and NonLin_FrSurf. |
| 10366 |
|
|
| 10367 |
checkpoint44 |
checkpoint44 (2002/01/18) |
| 10368 |
o fix bug in mom_vi_del2uv |
o fix bug in mom_vi_del2uv |
| 10369 |
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
| 10370 |
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
| 10372 |
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
| 10373 |
o added some stuff for AD |
o added some stuff for AD |
| 10374 |
|
|
| 10375 |
checkpoint43 |
checkpoint43 (2001/09/28) |
| 10376 |
o added two new advection tests |
o added two new advection tests |
| 10377 |
o added global 4x4 degree ocean test |
o added global 4x4 degree ocean test |
| 10378 |
o added test of H&S94 with free surface on cube |
o added test of H&S94 with free surface on cube |
| 10379 |
o some final mods for gradient check, adjoint,... |
o some final mods for gradient check, adjoint,... |
| 10380 |
|
|
| 10381 |
checkpoint42 |
checkpoint42 (2001/09/27) |
| 10382 |
Fixed AD-related problems: |
Fixed AD-related problems: |
| 10383 |
o Store directives up-to-date with re-arranged Adams-Bashforth |
o Store directives up-to-date with re-arranged Adams-Bashforth |
| 10384 |
(mainly thermodynamics.F) |
(mainly thermodynamics.F) |
| 10390 |
for the case ALLOW_KPP |
for the case ALLOW_KPP |
| 10391 |
o Cleaned argument list for timestep_tracer.F |
o Cleaned argument list for timestep_tracer.F |
| 10392 |
|
|
| 10393 |
checkpoint41 |
checkpoint41 (2001/09/27) |
| 10394 |
o re-formatted/added comments in prologues of key subroutines |
o re-formatted/added comments in prologues of key subroutines |
| 10395 |
to work with protex |
to work with protex |
| 10396 |
|
|
| 10397 |
checkpoint40 |
checkpoint40 (2001/09/27) |
| 10398 |
o moved calc_gs, calc_gt and calc_tr1 back to model/src |
o moved calc_gs, calc_gt and calc_tr1 back to model/src |
| 10399 |
o added FLT (floats) package from Arne along with demo. experiment |
o added FLT (floats) package from Arne along with demo. experiment |
| 10400 |
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
| 10403 |
o modified multi-dim method to work on cube |
o modified multi-dim method to work on cube |
| 10404 |
o bug fix in KPP (from DM) |
o bug fix in KPP (from DM) |
| 10405 |
|
|
| 10406 |
checkpoint40pre9 |
checkpoint40pre9 (2001/09/27) |
| 10407 |
o added DST advection schemes |
o added DST advection schemes |
| 10408 |
o fix MPI bug on SGI's |
o fix MPI bug on SGI's |
| 10409 |
o modifications for non-linear free-surface |
o modifications for non-linear free-surface |
| 10413 |
o added/updated many matlab scripts |
o added/updated many matlab scripts |
| 10414 |
o added multi-dimensional advection method for tracers |
o added multi-dimensional advection method for tracers |
| 10415 |
|
|
| 10416 |
checkpoint40pre8 |
checkpoint40pre8 (2001/09/05) |
| 10417 |
o new package rw/ |
o new package rw/ |
| 10418 |
Added method for dumping intermediate local arrays: |
Added method for dumping intermediate local arrays: |
| 10419 |
mdsio_writetile - same as mdsio_writefield except works from inside |
mdsio_writetile - same as mdsio_writefield except works from inside |
| 10432 |
currently nothing implemented to switch this storing off |
currently nothing implemented to switch this storing off |
| 10433 |
in case fluxform is used since no CPP flag available). |
in case fluxform is used since no CPP flag available). |
| 10434 |
|
|
| 10435 |
checkpoint40pre7 |
checkpoint40pre7 (2001/08/14) |
| 10436 |
o bug fix in dynamics.F |
o bug fix in dynamics.F |
| 10437 |
calc_viscosity called before k=1,Nr loop. |
calc_viscosity called before k=1,Nr loop. |
| 10438 |
o added some #ifdef's ALLOW_PASSIVE_TRACER |
o added some #ifdef's ALLOW_PASSIVE_TRACER |
| 10439 |
o cleaned initialisations in ctrl_map_ini |
o cleaned initialisations in ctrl_map_ini |
| 10440 |
related to TAF |
related to TAF |
| 10441 |
|
|
| 10442 |
checkpoint40pre6 |
checkpoint40pre6 (2001/08/13) |
| 10443 |
o split dynamics into thermodynamics & dynamics |
o split dynamics into thermodynamics & dynamics |
| 10444 |
o corresponding split of calc_diffusivity into |
o corresponding split of calc_diffusivity into |
| 10445 |
calc_diffusivity, calc_viscosity |
calc_diffusivity, calc_viscosity |
| 10447 |
o Added diffkr, kapgm to control variables |
o Added diffkr, kapgm to control variables |
| 10448 |
o bug fix in gmredi_slope_limit for ldd97 |
o bug fix in gmredi_slope_limit for ldd97 |
| 10449 |
|
|
| 10450 |
checkpoint40pre5 |
checkpoint40pre5 (2001/07/31) |
| 10451 |
o proper initialization of Adams-Bashforth time stepping |
o proper initialization of Adams-Bashforth time stepping |
| 10452 |
+ uses forward step for very first step of model (iter=0) |
+ uses forward step for very first step of model (iter=0) |
| 10453 |
o re-generated *all* output since almost all output is modified by this |
o re-generated *all* output since almost all output is modified by this |
| 10461 |
+ this uses an alternative form of ini_curvilinear_grid.F which |
+ this uses an alternative form of ini_curvilinear_grid.F which |
| 10462 |
is not necessarily any better than the current one... |
is not necessarily any better than the current one... |
| 10463 |
|
|
| 10464 |
checkpoint40pre4 |
checkpoint40pre4 (2001/07/30) |
| 10465 |
o added re-initialisations of utrans,vtrans,rtrans in |
o added re-initialisations of utrans,vtrans,rtrans in |
| 10466 |
calc_common_factors which are crucial for TAF. |
calc_common_factors which are crucial for TAF. |
| 10467 |
o extended iMin,jMin range for calc_common_factors, |
o extended iMin,jMin range for calc_common_factors, |
| 10469 |
o added option ALLOW_PASSIVE_TRACER |
o added option ALLOW_PASSIVE_TRACER |
| 10470 |
o a few minor updates and fixes |
o a few minor updates and fixes |
| 10471 |
|
|
| 10472 |
checkpoint40pre3 |
checkpoint40pre3 (2001/07/13) |
| 10473 |
o created calc_gtr1.F for gad package |
o created calc_gtr1.F for gad package |
| 10474 |
o split the_main_loop and re-introduced forward_step |
o split the_main_loop and re-introduced forward_step |
| 10475 |
o some recomputations of nIter0 for TAMC |
o some recomputations of nIter0 for TAMC |
| 10476 |
|
|
| 10477 |
checkpoint40pre2 |
checkpoint40pre2 (2001/07/13) |
| 10478 |
o Updated to latest branch of AJA, JMC |
o Updated to latest branch of AJA, JMC |
| 10479 |
o Added gradient check package |
o Added gradient check package |
| 10480 |
o Added routines for passive tracer handling |
o Added routines for passive tracer handling |
| 10481 |
o Added carbon sequestration sensitivity experiment |
o Added carbon sequestration sensitivity experiment |
| 10482 |
|
|
| 10483 |
checkpoint39 |
checkpoint39 (2001/05/14) |
| 10484 |
o Modifications and fixes to support TAMC |
o Modifications and fixes to support TAMC |
| 10485 |
(mainly missing or wrong directives) |
(mainly missing or wrong directives) |
| 10486 |
o Corrected common blocks when fooling TAMC to produce adjoint I/O |
o Corrected common blocks when fooling TAMC to produce adjoint I/O |
| 10494 |
(NB: this is not the full ECCO environment) |
(NB: this is not the full ECCO environment) |
| 10495 |
o disabled some packages by default in genmake |
o disabled some packages by default in genmake |
| 10496 |
|
|
| 10497 |
checkpoint38 |
checkpoint38 (2001/04/10) |
| 10498 |
o see notes_c37_adj.txt |
o see notes_c37_adj.txt |
| 10499 |
o corrected wrong layer index in external_forcing_t |
o corrected wrong layer index in external_forcing_t |
| 10500 |
o replaced the_main_loop/forward_step by the_main_loop |
o replaced the_main_loop/forward_step by the_main_loop |
| 10502 |
(replaced criteria for initial/final state) |
(replaced criteria for initial/final state) |
| 10503 |
o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
| 10504 |
|
|
| 10505 |
checkpoint37 |
checkpoint37 (2001/03/13) |
| 10506 |
o mdsio.F routine split and packaged in pkg/mdsio |
o mdsio.F routine split and packaged in pkg/mdsio |
| 10507 |
(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
| 10508 |
used unless genmake -disable=mdsio) |
used unless genmake -disable=mdsio) |
| 10519 |
o Non-Hydrostatic pickup file Pb fixed. |
o Non-Hydrostatic pickup file Pb fixed. |
| 10520 |
o bug with Rigid-lid version (since c35) fixed. |
o bug with Rigid-lid version (since c35) fixed. |
| 10521 |
|
|
| 10522 |
checkpoint36 |
checkpoint36 (2001/02/20) |
| 10523 |
o implement Crank-Nickelson barotropic time-stepping |
o implement Crank-Nickelson barotropic time-stepping |
| 10524 |
o recover Time-Average diagnostics |
o recover Time-Average diagnostics |
| 10525 |
o fix Pb in checkpoint (PR#19) |
o fix Pb in checkpoint (PR#19) |
| 10526 |
o AIM become a standard package ; clean unused CPP_kees |
o AIM become a standard package ; clean unused CPP_kees |
| 10527 |
|
|
| 10528 |
checkpoint35 |
checkpoint35 (2001/02/08) |
| 10529 |
o subtantial rewrite of dynamics.f |
o subtantial rewrite of dynamics.f |
| 10530 |
o allows staggered time-stepping |
o allows staggered time-stepping |
| 10531 |
o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
| 10532 |
o added bottom drag (linear + quadratic) |
o added bottom drag (linear + quadratic) |
| 10533 |
|
|
| 10534 |
checkpoint34 |
checkpoint34 (2001/01/30) |
| 10535 |
o Modified exchange routines for correct reverse simulation. |
o Modified exchange routines for correct reverse simulation. |
| 10536 |
o Added verification output to comply with bug fix in impldiff.F |
o Added verification output to comply with bug fix in impldiff.F |
| 10537 |
as of c33 (exp2, natl_box). |
as of c33 (exp2, natl_box). |
| 10542 |
o Added routine GLOBAL_SUM_INT to global_sum.F |
o Added routine GLOBAL_SUM_INT to global_sum.F |
| 10543 |
o Added mdsio_gl.F for ECCO purposes. |
o Added mdsio_gl.F for ECCO purposes. |
| 10544 |
|
|
| 10545 |
checkpoint33 |
checkpoint33 (2000/11/30) |
| 10546 |
o Fixed bug in lower BC in impldiff.F |
o Fixed bug in lower BC in impldiff.F |
| 10547 |
o Fixed confusion about units of forcing arrays in FFIELDS.h |
o Fixed confusion about units of forcing arrays in FFIELDS.h |
| 10548 |
namely Fu,Fv,Qnet,Qsw,EmPmR: |
namely Fu,Fv,Qnet,Qsw,EmPmR: |
| 10560 |
possibly use them. |
possibly use them. |
| 10561 |
o Corrected genmake to delete a temporary file during configuration |
o Corrected genmake to delete a temporary file during configuration |
| 10562 |
|
|
| 10563 |
checkpoint32 |
checkpoint32 (2000/11/13) |
| 10564 |
o Scaling of forcing fields moved from external_forcing.F to |
o Scaling of forcing fields moved from external_forcing.F to |
| 10565 |
external_fields_scale.F, called directly after loading fields. |
external_fields_scale.F, called directly after loading fields. |
| 10566 |
o Surface relaxation terms added to surface tendency fields in |
o Surface relaxation terms added to surface tendency fields in |
| 10571 |
o Modifications and bug fixes in KPP package. |
o Modifications and bug fixes in KPP package. |
| 10572 |
o Verification experiment for KPP added (verification/nat_box/) |
o Verification experiment for KPP added (verification/nat_box/) |
| 10573 |
|
|
| 10574 |
checkpoint31 |
checkpoint31 (2000/09/11) |
| 10575 |
o Packages interface brought in line with defined standard |
o Packages interface brought in line with defined standard |
| 10576 |
-> new routines packages_...F |
-> new routines packages_...F |
| 10577 |
-> changes in initialise_fixed.F, initialise_varia.F |
-> changes in initialise_fixed.F, initialise_varia.F |
| 10588 |
- not yet tested for GMRedi. |
- not yet tested for GMRedi. |
| 10589 |
- not yet tested for KPP. |
- not yet tested for KPP. |
| 10590 |
|
|
| 10591 |
checkpoint30 |
checkpoint30 (2000/07/13) |
| 10592 |
o Updates for OBCs |
o Updates for OBCs |
| 10593 |
o New experiment for test OBCs (internal_wave) |
o New experiment for test OBCs (internal_wave) |
| 10594 |
o New output.txt in verification/exp4/results/ |
o New output.txt in verification/exp4/results/ |
| 10597 |
o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) |
o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) |
| 10598 |
and entry for T90 in genmake |
and entry for T90 in genmake |
| 10599 |
|
|
| 10600 |
checkpoint29 |
checkpoint29 (2000/06/21) |
| 10601 |
o packaged KPP and GM/Redi |
o packaged KPP and GM/Redi |
| 10602 |
|
|
| 10603 |
checkpoint28 |
checkpoint28 (2000/06/09) |
| 10604 |
o Corrected initialization of hFacMin for difference vertical coordinates |
o Corrected initialization of hFacMin for difference vertical coordinates |
| 10605 |
o Modified calculation of partial cell thickness to more robust algorithm |
o Modified calculation of partial cell thickness to more robust algorithm |
| 10606 |
o config_summary.F: replaced write_1D_... by write_0D_... |
o config_summary.F: replaced write_1D_... by write_0D_... |
| 10613 |
included store directives and tape key computations required for TAMC. |
included store directives and tape key computations required for TAMC. |
| 10614 |
o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC |
o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC |
| 10615 |
|
|
| 10616 |
checkpoint27 |
checkpoint27 (2000/04/10) |
| 10617 |
o fixed calc_isoslopes() to so that cancellation of terms in tensor |
o fixed calc_isoslopes() to so that cancellation of terms in tensor |
| 10618 |
formulation works properly with variable resolution. |
formulation works properly with variable resolution. |
| 10619 |
o restructured the calling tree between the_model_main() and dynamics() |
o restructured the calling tree between the_model_main() and dynamics() |
| 10621 |
o introduced initialization file pSurfInitFile for free surface (cg2d_x) |
o introduced initialization file pSurfInitFile for free surface (cg2d_x) |
| 10622 |
in new routine ini_psurf() |
in new routine ini_psurf() |
| 10623 |
|
|
| 10624 |
checkpoint26 |
checkpoint26 (2000/04/05) |
| 10625 |
o moved some #ifdef in optional routines to encompass everything |
o moved some #ifdef in optional routines to encompass everything |
| 10626 |
except the argument declarations. This was using up some memory. |
except the argument declarations. This was using up some memory. |
| 10627 |
o fixed macros like _ADT to work with both versions of Linux cpp |
o fixed macros like _ADT to work with both versions of Linux cpp |
| 10631 |
(macros are now in eesupp/inc/CPP_EEMACROS.h) |
(macros are now in eesupp/inc/CPP_EEMACROS.h) |
| 10632 |
o patch for 2 processor JAM mode |
o patch for 2 processor JAM mode |
| 10633 |
|
|
| 10634 |
checkpoint25 |
checkpoint25 (2000/03/15) |
| 10635 |
o updates for OBCs and NH |
o updates for OBCs and NH |
| 10636 |
o dramatically reduced memory usage |
o dramatically reduced memory usage |
| 10637 |
o added "JAM" routines for use on Artic network |
o added "JAM" routines for use on Artic network |
| 10642 |
an explicit free-surface option) |
an explicit free-surface option) |
| 10643 |
o initial state input files for U and V |
o initial state input files for U and V |
| 10644 |
|
|
| 10645 |
checkpoint24 |
checkpoint24 (1999/08/02) |
| 10646 |
o Removed some spurious "REAL"s |
o Removed some spurious "REAL"s |
| 10647 |
o Updated KPP to latest version from JPL |
o Updated KPP to latest version from JPL |
| 10648 |
o Added a COS(latitude) in horizontal viscosity |
o Added a COS(latitude) in horizontal viscosity |
| 10649 |
|
|
| 10650 |
checkpoint23 |
checkpoint23 (1999/05/26) |
| 10651 |
o Added del^4 diffusion for salt and temperature |
o Added del^4 diffusion for salt and temperature |
| 10652 |
o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) |
o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) |
| 10653 |
|
|
| 10654 |
checkpoint22 |
checkpoint22 (1999/05/18) |
| 10655 |
o Made many small changes: implicit none, format(i5), etc... |
o Made many small changes: implicit none, format(i5), etc... |
| 10656 |
o Introduced KPP mixing scheme (compiles and runs but *not* tested) |
o Introduced KPP mixing scheme (compiles and runs but *not* tested) |
| 10657 |
|
|
| 10658 |
checkpoint21 |
checkpoint21 (1999/05/18) |
| 10659 |
o Introduced new I/O package that supports direct-access records (mdsio.F) |
o Introduced new I/O package that supports direct-access records (mdsio.F) |
| 10660 |
o Split-up mid-level I/O routines |
o Split-up mid-level I/O routines |
| 10661 |
o Updated input data for experiments 0,1,2,4 and 5 |
o Updated input data for experiments 0,1,2,4 and 5 |
| 10662 |
o Finally removed the genmake.* scripts (everyone seems happy with genmake) |
o Finally removed the genmake.* scripts (everyone seems happy with genmake) |
| 10663 |
|
|
| 10664 |
checkpoint20 |
checkpoint20 (1999/03/22) |
| 10665 |
o Tidied up open-boundaries some more |
o Tidied up open-boundaries some more |
| 10666 |
o Added non-hydrostatic code |
o Added non-hydrostatic code |
| 10667 |
o Fixed some input data |
o Fixed some input data |
| 10668 |
o Modified MPI start-up to work in "coupled" context. |
o Modified MPI start-up to work in "coupled" context. |
| 10669 |
|
|
| 10670 |
checkpoint19 |
checkpoint19 (1998/12/15) |
| 10671 |
o Tidied up directory structure for verification experiments. |
o Tidied up directory structure for verification experiments. |
| 10672 |
o Added new code for open boundaries. |
o Added new code for open boundaries. |
| 10673 |
o Corrected advective terms near boundaries. |
o Corrected advective terms near boundaries. |
| 10675 |
o Implemented free-slip/no-slip BCs and del^4 dissipation. |
o Implemented free-slip/no-slip BCs and del^4 dissipation. |
| 10676 |
o Split default parameters out of ini_parms.F into set_defaults.F. |
o Split default parameters out of ini_parms.F into set_defaults.F. |
| 10677 |
|
|
| 10678 |
checkpoint18 |
checkpoint18 (1998/11/30) |
| 10679 |
o Further changes for optional code generation with |
o Further changes for optional code generation with |
| 10680 |
CPP - ugh! |
CPP - ugh! |
| 10681 |
|
|
| 10682 |
checkpoint17 |
checkpoint17 (1998/11/03) |
| 10683 |
o Beginning to incorporating modularity |
o Beginning to incorporating modularity |
| 10684 |
for supporting atmos. and ocean configs. |
for supporting atmos. and ocean configs. |
| 10685 |
o Small changes for TAMC complinace |
o Small changes for TAMC complinace |
| 10686 |
o New ultra simple test case. Barotropic box |
o New ultra simple test case. Barotropic box |
| 10687 |
configuration "exp0". |
configuration "exp0". |
| 10688 |
|
|
| 10689 |
checkpoint16 |
checkpoint16 (1998/10/28) |
| 10690 |
o Minor changes to exchange routines to support |
o Minor changes to exchange routines to support |
| 10691 |
accumulation in reverse mode. Adjoint of an |
accumulation in reverse mode. Adjoint of an |
| 10692 |
assignment is an addition. |
assignment is an addition. |
| 10694 |
syntax) and by g77 under Linux ( 72 character |
syntax) and by g77 under Linux ( 72 character |
| 10695 |
limit ). |
limit ). |
| 10696 |
|
|
| 10697 |
checkpoint15 |
checkpoint15 (1998/09/29) |
| 10698 |
Rewrote exchange routines to allow |
Rewrote exchange routines to allow |
| 10699 |
o General tile <-> tile connectivity. |
o General tile <-> tile connectivity. |
| 10700 |
o TAMC reverse mode flag ( is this really needed? ) |
o TAMC reverse mode flag ( is this really needed? ) |
| 10703 |
shmput/shmget, VIA, SYSV shmem and every other cool |
shmput/shmget, VIA, SYSV shmem and every other cool |
| 10704 |
communication method. |
communication method. |
| 10705 |
|
|
| 10706 |
checkpoint14 |
checkpoint14 (1998/09/09) |
| 10707 |
Consistent isomorphism chages made. These allow dynamical core |
Consistent isomorphism chages made. These allow dynamical core |
| 10708 |
to support both pressure and meters as a vertical coordinate. |
to support both pressure and meters as a vertical coordinate. |
| 10709 |
|
|
| 10710 |
checkpoint13 |
checkpoint13 (1998/07/17) |
| 10711 |
Release which corrects global_max problem and a couple |
Release which corrects global_max problem and a couple |
| 10712 |
of KGM time-averaging diagnostic errors. Also contains |
of KGM time-averaging diagnostic errors. Also contains |
| 10713 |
a double-gyre experiment setup as well as the baseline |
a double-gyre experiment setup as well as the baseline |
| 10722 |
I don't want to commit the rDot to the main-trunk until |
I don't want to commit the rDot to the main-trunk until |
| 10723 |
we've actually tested it... |
we've actually tested it... |
| 10724 |
|
|
| 10725 |
checkpoint12 |
checkpoint12 (1998/07/08) |
| 10726 |
Tidy up and added generic genmake script (formerly |
Tidy up and added generic genmake script (formerly |
| 10727 |
configure script). |
configure script). |
| 10728 |
Released to testers. |
Released to testers. |
| 10729 |
|
|
| 10730 |
checkpoint11 |
checkpoint11 (1998/07/02) |
| 10731 |
Re-arranged initialise() and introduced ini_vertical_grid() |
Re-arranged initialise() and introduced ini_vertical_grid() |
| 10732 |
and ini_masks_etc(). |
and ini_masks_etc(). |
| 10733 |
|
|
| 10734 |
checkpoint10 |
checkpoint10 (1998/07/01) |
| 10735 |
Introduced the configure script. |
Introduced the configure script. |
| 10736 |
Separated out the diags package. |
Separated out the diags package. |
| 10737 |
Added template for writing time-averages of tile/intermediate quantities. |
Added template for writing time-averages of tile/intermediate quantities. |
| 10738 |
Updated SIZE.h in exp2 and made the data big-endian. |
Updated SIZE.h in exp2 and made the data big-endian. |
| 10739 |
|
|
| 10740 |
checkpoint9 |
checkpoint9 (1998/06/22) |
| 10741 |
MPI fix. Filename changes (meta/data). salbin*y stuff. |
MPI fix. Filename changes (meta/data). salbin*y stuff. |
| 10742 |
General tidy-up. |
General tidy-up. |
| 10743 |
SST.bin SSS.bin added to verification/exp2 |
SST.bin SSS.bin added to verification/exp2 |
| 10744 |
|
|
| 10745 |
checkpoint8 |
checkpoint8 (1998/06/22) |
| 10746 |
Inludes time-dependant forcing and time-averaging. |
Inludes time-dependant forcing and time-averaging. |
| 10747 |
Works at 4x4 and 2.8125x2.8125 global |
Works at 4x4 and 2.8125x2.8125 global |
| 10748 |
|
|
| 10752 |
model etc.. |
model etc.. |
| 10753 |
Configured for verification/exp2 - 4 degree global, two process. |
Configured for verification/exp2 - 4 degree global, two process. |
| 10754 |
|
|
| 10755 |
checkpoint7 |
checkpoint7 (1998/06/15) |
| 10756 |
Created by cnh |
Created by cnh |
| 10757 |
Simple 4 degree global simulation |
Simple 4 degree global simulation |
| 10758 |
configuration. |
configuration. |
| 10760 |
hydrography, bathymetry etc |
hydrography, bathymetry etc |
| 10761 |
Does not include Heat Flux and E-P |
Does not include Heat Flux and E-P |
| 10762 |
|
|
| 10763 |
checkpoint6 |
checkpoint6 (1998/06/08) |
| 10764 |
Created by cnh |
Created by cnh |
| 10765 |
merged checkpoint5 with CD and |
merged checkpoint5 with CD and |
| 10766 |
spherical polar code. |
spherical polar code. |
| 10767 |
Still some problems with GM Redi |
Still some problems with GM Redi |
| 10768 |
abd full topography. |
abd full topography. |
| 10769 |
|
|
| 10770 |
checkpoint5 |
checkpoint5 (1998/06/08) |
| 10771 |
Created by AJA |
Created by AJA |
| 10772 |
contains updates to GM Redi |
contains updates to GM Redi |
| 10773 |
and reordered timestepping loop |
and reordered timestepping loop |
| 10774 |
for Implicit Diffusion. |
for Implicit Diffusion. |
| 10775 |
|
|
| 10776 |
checkpoint4 |
checkpoint4 (1998/05/30) |
| 10777 |
Created by cnh |
Created by cnh |
| 10778 |
Contains memory saving macros ( _rdxc etc..) for when |
Contains memory saving macros ( _rdxc etc..) for when |
| 10779 |
grid variations are limited. |
grid variations are limited. |
| 10780 |
Contains polynomial coeffs for EOS and knudsen program |
Contains polynomial coeffs for EOS and knudsen program |
| 10781 |
for generation. |
for generation. |
| 10782 |
|
|
| 10783 |
checkpoint3 |
checkpoint3 (1998/05/26) |
| 10784 |
Created by cnh |
Created by cnh |
| 10785 |
Added extra flags for runtime options |
Added extra flags for runtime options |
| 10786 |
Added this file |
Added this file |
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