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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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checkpoint57t_post |
8 |
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o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
9 |
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o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
10 |
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same truncation, independent of the face number: affects affects several |
11 |
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test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). |
12 |
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o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); |
13 |
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note that biharmonic viscosity + no-slip was not tested in any experiment. |
14 |
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o fix bug in non-linear free-surf side-drag ; generate new output for |
15 |
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global_ocean.cs32x15(+.thsice) & global_ocean_pressure. |
16 |
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o make mnc honor the writeBinaryPrec flag for most kinds of output |
17 |
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o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
18 |
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o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
19 |
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error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
20 |
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o add brackets in multi-terms sum to get same truncation, independent of |
21 |
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the face number (manage to get exactly same value of gU,gV at the cs-edge) |
22 |
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affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
23 |
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o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
24 |
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and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
25 |
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a maximum grid-scale Reynolds number. Also, changes all length calculations |
26 |
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in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
27 |
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Suggested values of viscosity parameters found in mom_calc_visc. |
28 |
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Many new viscosity diagnostics available. |
29 |
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30 |
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checkpoint57s_post |
31 |
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o Add clearing-house for viscosity calculations, mom_calc_visc and |
32 |
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correct numerous bugs in LeithD and Smagorinsky discretizations. |
33 |
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mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
34 |
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used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
35 |
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Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
36 |
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and with Strain-Tension viscous term calculation (mom_hdissip.F). |
37 |
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The Strain-Tension form is now called with useStrainTensonVisc=.true. |
38 |
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ViscAhStrain and viscAhTension are now retired. |
39 |
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o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
40 |
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o In response to JMC's bug report, genmake2 now ignores any soft-links |
41 |
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that it finds in the *current* directory when searching for files. |
42 |
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Soft-links found in any other source directories will still work as |
43 |
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they did before. |
44 |
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o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
45 |
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a C routine to unlimit the stack size |
46 |
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o mnc-ify pkg/aim snapshot vars |
47 |
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o mnc-ify pkg/land as requested by Daniel |
48 |
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o various changes to mnc including: |
49 |
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- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
50 |
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- output can now be grouped so that all files within a group |
51 |
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change the ITER portion of their names in lock-step together |
52 |
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- can now read ("global") PER-FACE (in addition to PER-TILE) files |
53 |
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and works with both EXCH1 and EXCH2 (but needs more testing) |
54 |
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- writing works for all verification test cases w/ g77 on Linux |
55 |
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56 |
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checkpoint57r_post |
57 |
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o make MNC variable initialization happen earlier |
58 |
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o add diagnostics for (almost) each term of the momentum Eq. |
59 |
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o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
60 |
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o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
61 |
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o remove MINIMAL_TAVE_OUTPUT option ; |
62 |
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add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
63 |
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o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
64 |
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allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
65 |
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o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
66 |
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o add time-dependent SST, SSS control |
67 |
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o cost terms in ecco/ modularized (new cost_generic.F) |
68 |
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o cost_averages routines are modularized (new cost_averagesgeneric.F) |
69 |
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o new infrastructure for seaice model vs. obs misfits in seaice/ |
70 |
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* driver from the_main_loop.F is seaice_cost_driver.F |
71 |
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* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
72 |
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* gradient check in Exp. 6a of natl_box_adjoint/ |
73 |
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o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
74 |
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(see README file) |
75 |
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76 |
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checkpoint57q_post |
77 |
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o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
78 |
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o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
79 |
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- bug was reported by Jean-Michel and Ian Fenty |
80 |
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o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
81 |
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update exp. cpl_aim+ocn output. |
82 |
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o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
83 |
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Needed for high-res. runs with large global files |
84 |
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to be able to limit tapelev size |
85 |
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o Changed some tests for adjoint: |
86 |
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* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
87 |
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* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
88 |
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* global_ocean.90x40x15/ back to default 3-level checkpointing |
89 |
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o Modifications to enable scripted COMMON to MODULE conversion |
90 |
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* verification/OpenAD/code/ has necessary scripts and description; |
91 |
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* converts, compiles and runs successfully; |
92 |
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93 |
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checkpoint57p_post |
94 |
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o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
95 |
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o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
96 |
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(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
97 |
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o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
98 |
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o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
99 |
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(was already the case for dissipation with mom_vecinv, |
100 |
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and also the case for grad.PhiHyd when staggered-timeStep) |
101 |
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This will allow to put dissipation out-off the AB time-stepping. |
102 |
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Unfortunately, affects truncation error. Update output of exp. that "fails" |
103 |
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(cg2d matching number) and leave the others for later: front_relax(10), |
104 |
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global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
105 |
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matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
106 |
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107 |
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checkpoint57o_post |
108 |
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o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
109 |
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(2) its ready to be documented during the 20050801 DocFest |
110 |
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o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
111 |
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for ideal_2D_oce and lab_sea on linux_ia32_g77 |
112 |
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o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
113 |
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in global1x1_tot/code_seaice_adj to access indices 32, 33 |
114 |
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(worth another tag) |
115 |
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116 |
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checkpoint57n_post |
117 |
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o adding precip control xx_precip 32 |
118 |
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o adding swflux control xx_swflux 33 |
119 |
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o Replacing 10 forcing penalty cost routines by 1 generic. |
120 |
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o Implementing partitioning in time-mean and variable adjustment |
121 |
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for atmos. state. |
122 |
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o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
123 |
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o in natl_box_adjoint: |
124 |
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* updated exp 1 to 10 |
125 |
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(but does not have time-mean vs. variable split results yet) |
126 |
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o updated global1x1/*_seaice_adj/ |
127 |
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to incorporate latest changes |
128 |
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o enable useSingleCpuIO for mdsio vector routines |
129 |
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(applies in particular to tapelev I/O) |
130 |
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o removed inefficient K-loop in all active_file*control*.F |
131 |
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|
132 |
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checkpoint57m_post |
133 |
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o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
134 |
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and advect_cs (use EXCH-2 and standard cs-32 grid files). |
135 |
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o pkg/exch2: filling of face-corner halo regions is optional |
136 |
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(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
137 |
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|
138 |
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checkpoint57l_post |
139 |
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tag before updating tutorials (pre-release-2) |
140 |
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o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
141 |
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for output and interpolation of input fields onto model grid) |
142 |
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o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
143 |
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Affects results of exp. rotating_tank ; update output.txt. |
144 |
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o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
145 |
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and taking the square quantity and/or using a fraction-weight field. |
146 |
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o fix aim_diagnostics_init.F mate numbers. |
147 |
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o add mnc output capability to diagnostics/diagstat and update |
148 |
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our cvsignore files for the ACSII output generated |
149 |
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|
150 |
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checkpoint57k_post |
151 |
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o lab_sea now uses diagnostics package and provides a suite of |
152 |
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new EXF diagnostics output. |
153 |
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|
154 |
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checkpoint57j_post |
155 |
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o exf |
156 |
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* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
157 |
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Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
158 |
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terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
159 |
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* extended diagnostics output |
160 |
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- now includes all EXF variables |
161 |
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- hs, hl moved to common block |
162 |
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- separate S/R for diagnostics, called after ctrl vector is added |
163 |
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- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
164 |
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- EXFqnet contains true Qnet (i.e. includes qsw) |
165 |
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* updated verif. lab_sea, global_with_exf |
166 |
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* Rearranging hflux (exf_mapfields -> exf_getforcing) |
167 |
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to ensure that diagnostics sees a true EXFqnet |
168 |
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o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
169 |
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o diagnostics pkg: change pointers so that 1 diagnostic can be used |
170 |
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several times with different frequencies. |
171 |
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o mnc-ify the thsice package as requested by Daniel Enderton |
172 |
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- the monitor--MNC output needs work |
173 |
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- many attributes need to be added (most are currently blank) |
174 |
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o mnc-ify theaim_v23 package as requested by Daniel Enderton |
175 |
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- many attributes need to be added (most are currently blank) |
176 |
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o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
177 |
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o add Sadourny like discretization to the 4th.O vorticity advection scheme |
178 |
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o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
179 |
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update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
180 |
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fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
181 |
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o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
182 |
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(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
183 |
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|
184 |
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checkpoint57i_post |
185 |
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o Diagnostics package was changed: diagnostic allocation is now deactivated |
186 |
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by setting an empty file name in the namelist (used to be by setting 0 frequency) |
187 |
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o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
188 |
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add 1rst Order upwind vertical Shear. |
189 |
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o add a quick fix for A/B checkpointing in OFFLINE mode |
190 |
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o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
191 |
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end-run around the C/Fortran linking horror in eesup/src/timers.F |
192 |
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o added pkg/runclock: allows user to terminate run based on wall clock |
193 |
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o added non-hydrostatic scaling parameter: nh_am2 |
194 |
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o pkg/my82: futile attempt to make results compiler-independent by adding |
195 |
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some "_d 0", etc. no effect. |
196 |
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o for mnc output, fill the 'T' coordinate var with myTime and create a |
197 |
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separate 'iter' variable for iteration count |
198 |
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o pkg/diagnostics: |
199 |
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add new capability: output of Global/Regional & per-level statistics ; |
200 |
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tested against monitor output (including land & thSIce) on various exp. |
201 |
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o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
202 |
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203 |
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checkpoint57h_done |
204 |
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tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
205 |
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data.diagnostics, data.gchem, data.ptracers) is done. |
206 |
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|
207 |
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o pkg/diagnostics: prepare for Global/Regional statistics. |
208 |
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add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
209 |
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o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
210 |
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and rename it: DIFFERENT_MULTIPLE |
211 |
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|
212 |
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checkpoint57h_post |
213 |
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o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
214 |
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o pkg/diagnostics: change output frequency, now in seconds (instead |
215 |
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of Nb of iterations). This requires to change data.diagnostics. |
216 |
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checkpoint57h_pre |
217 |
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|
218 |
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o in mnc, let the user create the output dir if both mnc_outdir_date |
219 |
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and mnc_outdir_num are false |
220 |
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o add fflags() to pkg/diagnostics which allows one to specify, on a |
221 |
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per-file basis, the file precision [default behavior is unchanged] |
222 |
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o added diagnostics to pkg/kpp, including computation of mixed layer |
223 |
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depth based on a temperature/density criterion |
224 |
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o updated verification/natl_box to test the new pkg/kpp diagnostics |
225 |
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o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
226 |
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o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
227 |
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o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
228 |
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not mnc -- this mistake was found by JMC and is now corrected |
229 |
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|
230 |
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checkpoint57g_post |
231 |
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o add Adams-Bashforth 3rd Order time stepping: |
232 |
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- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
233 |
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- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
234 |
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checkpoint57g_pre |
235 |
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|
236 |
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o make lambda[Theta,Salt]ClimRelax spatially varying |
237 |
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(default remains spatially uniform constant based on tau) |
238 |
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o added new control variables |
239 |
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* init. uVel, vVel, etanN |
240 |
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* lambda[Theta,Salt]ClimRelax |
241 |
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o separate masks used for ctrl_pack/unpack 'from write_grid' output |
242 |
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(suggested by G. Forget) |
243 |
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|
244 |
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checkpoint57f_post |
245 |
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o add parameter "baseTime" = model base time = time at iteration zero |
246 |
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new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
247 |
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account for baseTime shift |
248 |
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o move Coriolis arrays from PARAMS.h to GRID.h |
249 |
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checkpoint57f_pre |
250 |
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|
251 |
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o mnc-ifying the seaice package |
252 |
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o introduced an alternative length scale calculation for use in the limiting |
253 |
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maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
254 |
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o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
255 |
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o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
256 |
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as well as grad(vort3). Made it compatible with both approximate form |
257 |
|
for the cubed sphere and full form of these gradients. Added flag |
258 |
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useFullLeith to select between approximate and full form. |
259 |
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o add "d0" in getcon.F to reduce differences between compilers/platforms |
260 |
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update output.txt of exp. fizhi-gridalt-hs |
261 |
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o change port_rand funtion to allow to set the seed. |
262 |
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o fix obscure MNC bug involving conversion between reals and integers |
263 |
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- it caused no problems with certain (eg. gcc, ifc) compilers but the |
264 |
|
new version is now more standards-compliant |
265 |
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o adjoint-related modifications |
266 |
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* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
267 |
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* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
268 |
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* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
269 |
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|
270 |
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checkpoint57e_post |
271 |
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o Adding eddy stress controls a la Ferreira et al. |
272 |
|
checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
273 |
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|
274 |
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o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
275 |
|
update output.txt of exp. fizhi-gridalt-hs |
276 |
|
o add more "Z" dimensions and associated coordinate vars to MNC |
277 |
|
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
278 |
|
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
279 |
|
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
280 |
|
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
281 |
|
months and years. Requires pkg/cal. |
282 |
|
o diagnostics: add pickup functionality |
283 |
|
- off by default for backwards compatibility |
284 |
|
- current version only uses MDSIO -- MNC will be added |
285 |
|
o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
286 |
|
o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
287 |
|
|
288 |
|
checkpoint57d_post |
289 |
|
o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
290 |
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o modify verification/ideal_2D_oce so that it tests the creation of mnc |
291 |
|
output from the diagnostics package |
292 |
|
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
293 |
|
o make genmake2 more portable by using ".$FS" instead of ".f" for more |
294 |
|
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
295 |
|
o add coordinate variables to the MNC output from the diagnostics package |
296 |
|
o change MNC-flags default value: true when useMNC=TRUE |
297 |
|
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
298 |
|
the ability (off by default) to read the grid information using MNC |
299 |
|
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
300 |
|
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
301 |
|
o do snap-shot diagnostics at the middle of the time-interval (instead of |
302 |
|
at the end). |
303 |
|
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
304 |
|
new test for AIM with thSIce + slab-ocean |
305 |
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
306 |
o move state variable diagnostics to the beginning of the time step ; |
o move state variable diagnostics to the beginning of the time step ; |
307 |
(note: still needs some work specially for snap-shot diagnostics) |
(note: still needs some work specially for snap-shot diagnostics) |