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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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============================== |
============================== |
| 6 |
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o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
| 7 |
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and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
| 8 |
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a maximum grid-scale Reynolds number. Also, changes all length calculations |
| 9 |
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in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
| 10 |
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Suggested values of viscosity parameters found in mom_calc_visc. |
| 11 |
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Many new viscosity diagnostics available. |
| 12 |
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| 13 |
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checkpoint57s_post |
| 14 |
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o Add clearing-house for viscosity calculations, mom_calc_visc and |
| 15 |
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correct numerous bugs in LeithD and Smagorinsky discretizations. |
| 16 |
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mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
| 17 |
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used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
| 18 |
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Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
| 19 |
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and with Strain-Tension viscous term calculation (mom_hdissip.F). |
| 20 |
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The Strain-Tension form is now called with useStrainTensonVisc=.true. |
| 21 |
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ViscAhStrain and viscAhTension are now retired. |
| 22 |
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o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
| 23 |
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o In response to JMC's bug report, genmake2 now ignores any soft-links |
| 24 |
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that it finds in the *current* directory when searching for files. |
| 25 |
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Soft-links found in any other source directories will still work as |
| 26 |
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they did before. |
| 27 |
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o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
| 28 |
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a C routine to unlimit the stack size |
| 29 |
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o mnc-ify pkg/aim snapshot vars |
| 30 |
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o mnc-ify pkg/land as requested by Daniel |
| 31 |
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o various changes to mnc including: |
| 32 |
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- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
| 33 |
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- output can now be grouped so that all files within a group |
| 34 |
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change the ITER portion of their names in lock-step together |
| 35 |
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- can now read ("global") PER-FACE (in addition to PER-TILE) files |
| 36 |
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and works with both EXCH1 and EXCH2 (but needs more testing) |
| 37 |
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- writing works for all verification test cases w/ g77 on Linux |
| 38 |
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|
| 39 |
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checkpoint57r_post |
| 40 |
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o make MNC variable initialization happen earlier |
| 41 |
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o add diagnostics for (almost) each term of the momentum Eq. |
| 42 |
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o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
| 43 |
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o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
| 44 |
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o remove MINIMAL_TAVE_OUTPUT option ; |
| 45 |
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add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
| 46 |
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o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
| 47 |
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allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
| 48 |
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o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
| 49 |
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o add time-dependent SST, SSS control |
| 50 |
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o cost terms in ecco/ modularized (new cost_generic.F) |
| 51 |
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o cost_averages routines are modularized (new cost_averagesgeneric.F) |
| 52 |
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o new infrastructure for seaice model vs. obs misfits in seaice/ |
| 53 |
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* driver from the_main_loop.F is seaice_cost_driver.F |
| 54 |
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* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
| 55 |
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* gradient check in Exp. 6a of natl_box_adjoint/ |
| 56 |
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o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
| 57 |
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(see README file) |
| 58 |
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|
| 59 |
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checkpoint57q_post |
| 60 |
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o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
| 61 |
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o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
| 62 |
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- bug was reported by Jean-Michel and Ian Fenty |
| 63 |
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o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
| 64 |
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update exp. cpl_aim+ocn output. |
| 65 |
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o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
| 66 |
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Needed for high-res. runs with large global files |
| 67 |
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to be able to limit tapelev size |
| 68 |
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o Changed some tests for adjoint: |
| 69 |
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* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
| 70 |
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* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
| 71 |
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* global_ocean.90x40x15/ back to default 3-level checkpointing |
| 72 |
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o Modifications to enable scripted COMMON to MODULE conversion |
| 73 |
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* verification/OpenAD/code/ has necessary scripts and description; |
| 74 |
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* converts, compiles and runs successfully; |
| 75 |
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|
| 76 |
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checkpoint57p_post |
| 77 |
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o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
| 78 |
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o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
| 79 |
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(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
| 80 |
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o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
| 81 |
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o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
| 82 |
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(was already the case for dissipation with mom_vecinv, |
| 83 |
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and also the case for grad.PhiHyd when staggered-timeStep) |
| 84 |
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This will allow to put dissipation out-off the AB time-stepping. |
| 85 |
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Unfortunately, affects truncation error. Update output of exp. that "fails" |
| 86 |
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(cg2d matching number) and leave the others for later: front_relax(10), |
| 87 |
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global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
| 88 |
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matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
| 89 |
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|
| 90 |
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checkpoint57o_post |
| 91 |
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o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
| 92 |
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(2) its ready to be documented during the 20050801 DocFest |
| 93 |
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o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
| 94 |
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for ideal_2D_oce and lab_sea on linux_ia32_g77 |
| 95 |
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o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
| 96 |
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in global1x1_tot/code_seaice_adj to access indices 32, 33 |
| 97 |
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(worth another tag) |
| 98 |
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|
| 99 |
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checkpoint57n_post |
| 100 |
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o adding precip control xx_precip 32 |
| 101 |
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o adding swflux control xx_swflux 33 |
| 102 |
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o Replacing 10 forcing penalty cost routines by 1 generic. |
| 103 |
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o Implementing partitioning in time-mean and variable adjustment |
| 104 |
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for atmos. state. |
| 105 |
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o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
| 106 |
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o in natl_box_adjoint: |
| 107 |
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* updated exp 1 to 10 |
| 108 |
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(but does not have time-mean vs. variable split results yet) |
| 109 |
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o updated global1x1/*_seaice_adj/ |
| 110 |
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to incorporate latest changes |
| 111 |
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o enable useSingleCpuIO for mdsio vector routines |
| 112 |
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(applies in particular to tapelev I/O) |
| 113 |
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o removed inefficient K-loop in all active_file*control*.F |
| 114 |
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|
| 115 |
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checkpoint57m_post |
| 116 |
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o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
| 117 |
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and advect_cs (use EXCH-2 and standard cs-32 grid files). |
| 118 |
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o pkg/exch2: filling of face-corner halo regions is optional |
| 119 |
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(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
| 120 |
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|
| 121 |
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checkpoint57l_post |
| 122 |
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tag before updating tutorials (pre-release-2) |
| 123 |
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o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
| 124 |
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for output and interpolation of input fields onto model grid) |
| 125 |
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o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
| 126 |
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Affects results of exp. rotating_tank ; update output.txt. |
| 127 |
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o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
| 128 |
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and taking the square quantity and/or using a fraction-weight field. |
| 129 |
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o fix aim_diagnostics_init.F mate numbers. |
| 130 |
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o add mnc output capability to diagnostics/diagstat and update |
| 131 |
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our cvsignore files for the ACSII output generated |
| 132 |
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|
| 133 |
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checkpoint57k_post |
| 134 |
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o lab_sea now uses diagnostics package and provides a suite of |
| 135 |
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new EXF diagnostics output. |
| 136 |
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|
| 137 |
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checkpoint57j_post |
| 138 |
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o exf |
| 139 |
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* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
| 140 |
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Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
| 141 |
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terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
| 142 |
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* extended diagnostics output |
| 143 |
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- now includes all EXF variables |
| 144 |
|
- hs, hl moved to common block |
| 145 |
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- separate S/R for diagnostics, called after ctrl vector is added |
| 146 |
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- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
| 147 |
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- EXFqnet contains true Qnet (i.e. includes qsw) |
| 148 |
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* updated verif. lab_sea, global_with_exf |
| 149 |
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* Rearranging hflux (exf_mapfields -> exf_getforcing) |
| 150 |
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to ensure that diagnostics sees a true EXFqnet |
| 151 |
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o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
| 152 |
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o diagnostics pkg: change pointers so that 1 diagnostic can be used |
| 153 |
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several times with different frequencies. |
| 154 |
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o mnc-ify the thsice package as requested by Daniel Enderton |
| 155 |
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- the monitor--MNC output needs work |
| 156 |
|
- many attributes need to be added (most are currently blank) |
| 157 |
|
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
| 158 |
|
- many attributes need to be added (most are currently blank) |
| 159 |
|
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
| 160 |
|
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
| 161 |
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o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
| 162 |
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update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
| 163 |
|
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
| 164 |
|
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
| 165 |
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(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
| 166 |
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|
| 167 |
|
checkpoint57i_post |
| 168 |
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o Diagnostics package was changed: diagnostic allocation is now deactivated |
| 169 |
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by setting an empty file name in the namelist (used to be by setting 0 frequency) |
| 170 |
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o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
| 171 |
|
add 1rst Order upwind vertical Shear. |
| 172 |
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o add a quick fix for A/B checkpointing in OFFLINE mode |
| 173 |
|
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
| 174 |
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end-run around the C/Fortran linking horror in eesup/src/timers.F |
| 175 |
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o added pkg/runclock: allows user to terminate run based on wall clock |
| 176 |
|
o added non-hydrostatic scaling parameter: nh_am2 |
| 177 |
|
o pkg/my82: futile attempt to make results compiler-independent by adding |
| 178 |
|
some "_d 0", etc. no effect. |
| 179 |
|
o for mnc output, fill the 'T' coordinate var with myTime and create a |
| 180 |
|
separate 'iter' variable for iteration count |
| 181 |
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o pkg/diagnostics: |
| 182 |
|
add new capability: output of Global/Regional & per-level statistics ; |
| 183 |
|
tested against monitor output (including land & thSIce) on various exp. |
| 184 |
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o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
| 185 |
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|
| 186 |
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checkpoint57h_done |
| 187 |
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tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
| 188 |
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data.diagnostics, data.gchem, data.ptracers) is done. |
| 189 |
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|
| 190 |
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o pkg/diagnostics: prepare for Global/Regional statistics. |
| 191 |
|
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
| 192 |
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o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
| 193 |
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and rename it: DIFFERENT_MULTIPLE |
| 194 |
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|
| 195 |
|
checkpoint57h_post |
| 196 |
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o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
| 197 |
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o pkg/diagnostics: change output frequency, now in seconds (instead |
| 198 |
|
of Nb of iterations). This requires to change data.diagnostics. |
| 199 |
|
checkpoint57h_pre |
| 200 |
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|
| 201 |
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o in mnc, let the user create the output dir if both mnc_outdir_date |
| 202 |
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and mnc_outdir_num are false |
| 203 |
|
o add fflags() to pkg/diagnostics which allows one to specify, on a |
| 204 |
|
per-file basis, the file precision [default behavior is unchanged] |
| 205 |
|
o added diagnostics to pkg/kpp, including computation of mixed layer |
| 206 |
|
depth based on a temperature/density criterion |
| 207 |
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o updated verification/natl_box to test the new pkg/kpp diagnostics |
| 208 |
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o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
| 209 |
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o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
| 210 |
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o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
| 211 |
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not mnc -- this mistake was found by JMC and is now corrected |
| 212 |
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|
| 213 |
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checkpoint57g_post |
| 214 |
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o add Adams-Bashforth 3rd Order time stepping: |
| 215 |
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- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
| 216 |
|
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
| 217 |
|
checkpoint57g_pre |
| 218 |
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|
| 219 |
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o make lambda[Theta,Salt]ClimRelax spatially varying |
| 220 |
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(default remains spatially uniform constant based on tau) |
| 221 |
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o added new control variables |
| 222 |
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* init. uVel, vVel, etanN |
| 223 |
|
* lambda[Theta,Salt]ClimRelax |
| 224 |
|
o separate masks used for ctrl_pack/unpack 'from write_grid' output |
| 225 |
|
(suggested by G. Forget) |
| 226 |
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|
| 227 |
|
checkpoint57f_post |
| 228 |
|
o add parameter "baseTime" = model base time = time at iteration zero |
| 229 |
|
new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
| 230 |
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account for baseTime shift |
| 231 |
|
o move Coriolis arrays from PARAMS.h to GRID.h |
| 232 |
|
checkpoint57f_pre |
| 233 |
|
|
| 234 |
|
o mnc-ifying the seaice package |
| 235 |
|
o introduced an alternative length scale calculation for use in the limiting |
| 236 |
|
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
| 237 |
|
o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
| 238 |
|
o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
| 239 |
|
as well as grad(vort3). Made it compatible with both approximate form |
| 240 |
|
for the cubed sphere and full form of these gradients. Added flag |
| 241 |
|
useFullLeith to select between approximate and full form. |
| 242 |
|
o add "d0" in getcon.F to reduce differences between compilers/platforms |
| 243 |
|
update output.txt of exp. fizhi-gridalt-hs |
| 244 |
|
o change port_rand funtion to allow to set the seed. |
| 245 |
|
o fix obscure MNC bug involving conversion between reals and integers |
| 246 |
|
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
| 247 |
|
new version is now more standards-compliant |
| 248 |
|
o adjoint-related modifications |
| 249 |
|
* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
| 250 |
|
* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
| 251 |
|
* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
| 252 |
|
|
| 253 |
|
checkpoint57e_post |
| 254 |
|
o Adding eddy stress controls a la Ferreira et al. |
| 255 |
|
checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
| 256 |
|
|
| 257 |
|
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
| 258 |
|
update output.txt of exp. fizhi-gridalt-hs |
| 259 |
|
o add more "Z" dimensions and associated coordinate vars to MNC |
| 260 |
|
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
| 261 |
|
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
| 262 |
|
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
| 263 |
|
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
| 264 |
|
months and years. Requires pkg/cal. |
| 265 |
|
o diagnostics: add pickup functionality |
| 266 |
|
- off by default for backwards compatibility |
| 267 |
|
- current version only uses MDSIO -- MNC will be added |
| 268 |
|
o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
| 269 |
|
o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
| 270 |
|
|
| 271 |
|
checkpoint57d_post |
| 272 |
|
o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
| 273 |
|
o modify verification/ideal_2D_oce so that it tests the creation of mnc |
| 274 |
|
output from the diagnostics package |
| 275 |
|
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
| 276 |
|
o make genmake2 more portable by using ".$FS" instead of ".f" for more |
| 277 |
|
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
| 278 |
|
o add coordinate variables to the MNC output from the diagnostics package |
| 279 |
|
o change MNC-flags default value: true when useMNC=TRUE |
| 280 |
|
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
| 281 |
|
the ability (off by default) to read the grid information using MNC |
| 282 |
|
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
| 283 |
|
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
| 284 |
|
o do snap-shot diagnostics at the middle of the time-interval (instead of |
| 285 |
|
at the end). |
| 286 |
|
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
| 287 |
|
new test for AIM with thSIce + slab-ocean |
| 288 |
|
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
| 289 |
|
o move state variable diagnostics to the beginning of the time step ; |
| 290 |
|
(note: still needs some work specially for snap-shot diagnostics) |
| 291 |
|
duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
| 292 |
|
|
| 293 |
|
checkpoint57c_post |
| 294 |
|
o Change testing option (-ieee) to get closer agreement between g77 & ifort |
| 295 |
|
o generate new output.txt files on faulks with g77 & the new -ieee option |
| 296 |
|
checkpoint57c_pre |
| 297 |
|
|
| 298 |
|
o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
| 299 |
|
update output.txt of exp. global_ocean.90x40x15 |
| 300 |
|
o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
| 301 |
|
results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
| 302 |
|
o add saltFlux(+File) forcing capability with periodicExternalForcing |
| 303 |
|
o allow to use pkg diagnostics for GM-Redi & ThSIce output |
| 304 |
|
o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
| 305 |
|
o improvements for the MNC output from DIAGNOSTICS: |
| 306 |
|
- correct handling of the unlimitied dimension |
| 307 |
|
- all dims now have associated coordinate variables |
| 308 |
|
- variables located at U, V, and Corner ("Z") points are now written |
| 309 |
|
with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
| 310 |
|
*all* data points are output |
| 311 |
|
o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
| 312 |
|
o added pkg/seaice/seaice_monitor.F |
| 313 |
o mdsio_readfield.F can now read files visible only to master MPI process. |
o mdsio_readfield.F can now read files visible only to master MPI process. |
| 314 |
o pkg/seaice: some test code for ice-modified ocean stress |
o pkg/seaice: some test code for ice-modified ocean stress |
| 315 |
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
| 316 |
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
| 317 |
spurious negative numbers for precipitation and humidity. Will cause |
spurious negative numbers for precipitation and humidity. Will cause |
| 318 |
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
| 319 |
|
o pkg/ctrl/ |
| 320 |
|
* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
| 321 |
|
May be enabled via doPackDiag |
| 322 |
|
* introduce z-scaling of |
| 323 |
|
+ gradient (doZscalePack) and |
| 324 |
|
+ control (doZscaleUnpack) |
| 325 |
|
o pkg/mdsio/ |
| 326 |
|
* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
| 327 |
|
* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
| 328 |
|
|
| 329 |
checkpoint57b_post |
checkpoint57b_post |
| 330 |
o simplify options in diagnostics_fill arguments (remove weird combinations) |
o simplify options in diagnostics_fill arguments (remove weird combinations) |
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