| 1 |
$Header$ |
$Header$ |
| 2 |
|
$Name$ |
| 3 |
|
|
| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
|
|
| 7 |
|
o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
| 8 |
|
o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
| 9 |
|
error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
| 10 |
|
o add brackets in multi-terms sum to get same truncation, independent of |
| 11 |
|
the face number (manage to get exactly same value of gU,gV at the cs-edge) |
| 12 |
|
affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
| 13 |
|
o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
| 14 |
|
and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
| 15 |
|
a maximum grid-scale Reynolds number. Also, changes all length calculations |
| 16 |
|
in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
| 17 |
|
Suggested values of viscosity parameters found in mom_calc_visc. |
| 18 |
|
Many new viscosity diagnostics available. |
| 19 |
|
|
| 20 |
|
checkpoint57s_post |
| 21 |
|
o Add clearing-house for viscosity calculations, mom_calc_visc and |
| 22 |
|
correct numerous bugs in LeithD and Smagorinsky discretizations. |
| 23 |
|
mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
| 24 |
|
used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
| 25 |
|
Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
| 26 |
|
and with Strain-Tension viscous term calculation (mom_hdissip.F). |
| 27 |
|
The Strain-Tension form is now called with useStrainTensonVisc=.true. |
| 28 |
|
ViscAhStrain and viscAhTension are now retired. |
| 29 |
|
o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
| 30 |
|
o In response to JMC's bug report, genmake2 now ignores any soft-links |
| 31 |
|
that it finds in the *current* directory when searching for files. |
| 32 |
|
Soft-links found in any other source directories will still work as |
| 33 |
|
they did before. |
| 34 |
|
o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
| 35 |
|
a C routine to unlimit the stack size |
| 36 |
|
o mnc-ify pkg/aim snapshot vars |
| 37 |
|
o mnc-ify pkg/land as requested by Daniel |
| 38 |
|
o various changes to mnc including: |
| 39 |
|
- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
| 40 |
|
- output can now be grouped so that all files within a group |
| 41 |
|
change the ITER portion of their names in lock-step together |
| 42 |
|
- can now read ("global") PER-FACE (in addition to PER-TILE) files |
| 43 |
|
and works with both EXCH1 and EXCH2 (but needs more testing) |
| 44 |
|
- writing works for all verification test cases w/ g77 on Linux |
| 45 |
|
|
| 46 |
|
checkpoint57r_post |
| 47 |
|
o make MNC variable initialization happen earlier |
| 48 |
|
o add diagnostics for (almost) each term of the momentum Eq. |
| 49 |
|
o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
| 50 |
|
o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
| 51 |
|
o remove MINIMAL_TAVE_OUTPUT option ; |
| 52 |
|
add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
| 53 |
|
o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
| 54 |
|
allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
| 55 |
|
o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
| 56 |
|
o add time-dependent SST, SSS control |
| 57 |
|
o cost terms in ecco/ modularized (new cost_generic.F) |
| 58 |
|
o cost_averages routines are modularized (new cost_averagesgeneric.F) |
| 59 |
|
o new infrastructure for seaice model vs. obs misfits in seaice/ |
| 60 |
|
* driver from the_main_loop.F is seaice_cost_driver.F |
| 61 |
|
* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
| 62 |
|
* gradient check in Exp. 6a of natl_box_adjoint/ |
| 63 |
|
o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
| 64 |
|
(see README file) |
| 65 |
|
|
| 66 |
|
checkpoint57q_post |
| 67 |
|
o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
| 68 |
|
o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
| 69 |
|
- bug was reported by Jean-Michel and Ian Fenty |
| 70 |
|
o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
| 71 |
|
update exp. cpl_aim+ocn output. |
| 72 |
|
o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
| 73 |
|
Needed for high-res. runs with large global files |
| 74 |
|
to be able to limit tapelev size |
| 75 |
|
o Changed some tests for adjoint: |
| 76 |
|
* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
| 77 |
|
* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
| 78 |
|
* global_ocean.90x40x15/ back to default 3-level checkpointing |
| 79 |
|
o Modifications to enable scripted COMMON to MODULE conversion |
| 80 |
|
* verification/OpenAD/code/ has necessary scripts and description; |
| 81 |
|
* converts, compiles and runs successfully; |
| 82 |
|
|
| 83 |
|
checkpoint57p_post |
| 84 |
|
o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
| 85 |
|
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
| 86 |
|
(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
| 87 |
|
o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
| 88 |
|
o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
| 89 |
|
(was already the case for dissipation with mom_vecinv, |
| 90 |
|
and also the case for grad.PhiHyd when staggered-timeStep) |
| 91 |
|
This will allow to put dissipation out-off the AB time-stepping. |
| 92 |
|
Unfortunately, affects truncation error. Update output of exp. that "fails" |
| 93 |
|
(cg2d matching number) and leave the others for later: front_relax(10), |
| 94 |
|
global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
| 95 |
|
matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
| 96 |
|
|
| 97 |
|
checkpoint57o_post |
| 98 |
|
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
| 99 |
|
(2) its ready to be documented during the 20050801 DocFest |
| 100 |
|
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
| 101 |
|
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
| 102 |
|
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
| 103 |
|
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
| 104 |
|
(worth another tag) |
| 105 |
|
|
| 106 |
|
checkpoint57n_post |
| 107 |
|
o adding precip control xx_precip 32 |
| 108 |
|
o adding swflux control xx_swflux 33 |
| 109 |
|
o Replacing 10 forcing penalty cost routines by 1 generic. |
| 110 |
|
o Implementing partitioning in time-mean and variable adjustment |
| 111 |
|
for atmos. state. |
| 112 |
|
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
| 113 |
|
o in natl_box_adjoint: |
| 114 |
|
* updated exp 1 to 10 |
| 115 |
|
(but does not have time-mean vs. variable split results yet) |
| 116 |
|
o updated global1x1/*_seaice_adj/ |
| 117 |
|
to incorporate latest changes |
| 118 |
|
o enable useSingleCpuIO for mdsio vector routines |
| 119 |
|
(applies in particular to tapelev I/O) |
| 120 |
|
o removed inefficient K-loop in all active_file*control*.F |
| 121 |
|
|
| 122 |
|
checkpoint57m_post |
| 123 |
|
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
| 124 |
|
and advect_cs (use EXCH-2 and standard cs-32 grid files). |
| 125 |
|
o pkg/exch2: filling of face-corner halo regions is optional |
| 126 |
|
(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
| 127 |
|
|
| 128 |
|
checkpoint57l_post |
| 129 |
|
tag before updating tutorials (pre-release-2) |
| 130 |
|
o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
| 131 |
|
for output and interpolation of input fields onto model grid) |
| 132 |
|
o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
| 133 |
|
Affects results of exp. rotating_tank ; update output.txt. |
| 134 |
|
o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
| 135 |
|
and taking the square quantity and/or using a fraction-weight field. |
| 136 |
|
o fix aim_diagnostics_init.F mate numbers. |
| 137 |
|
o add mnc output capability to diagnostics/diagstat and update |
| 138 |
|
our cvsignore files for the ACSII output generated |
| 139 |
|
|
| 140 |
|
checkpoint57k_post |
| 141 |
|
o lab_sea now uses diagnostics package and provides a suite of |
| 142 |
|
new EXF diagnostics output. |
| 143 |
|
|
| 144 |
|
checkpoint57j_post |
| 145 |
|
o exf |
| 146 |
|
* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
| 147 |
|
Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
| 148 |
|
terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
| 149 |
|
* extended diagnostics output |
| 150 |
|
- now includes all EXF variables |
| 151 |
|
- hs, hl moved to common block |
| 152 |
|
- separate S/R for diagnostics, called after ctrl vector is added |
| 153 |
|
- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
| 154 |
|
- EXFqnet contains true Qnet (i.e. includes qsw) |
| 155 |
|
* updated verif. lab_sea, global_with_exf |
| 156 |
|
* Rearranging hflux (exf_mapfields -> exf_getforcing) |
| 157 |
|
to ensure that diagnostics sees a true EXFqnet |
| 158 |
|
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
| 159 |
|
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
| 160 |
|
several times with different frequencies. |
| 161 |
|
o mnc-ify the thsice package as requested by Daniel Enderton |
| 162 |
|
- the monitor--MNC output needs work |
| 163 |
|
- many attributes need to be added (most are currently blank) |
| 164 |
|
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
| 165 |
|
- many attributes need to be added (most are currently blank) |
| 166 |
|
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
| 167 |
|
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
| 168 |
|
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
| 169 |
|
update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
| 170 |
|
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
| 171 |
|
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
| 172 |
|
(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
| 173 |
|
|
| 174 |
|
checkpoint57i_post |
| 175 |
|
o Diagnostics package was changed: diagnostic allocation is now deactivated |
| 176 |
|
by setting an empty file name in the namelist (used to be by setting 0 frequency) |
| 177 |
|
o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
| 178 |
|
add 1rst Order upwind vertical Shear. |
| 179 |
|
o add a quick fix for A/B checkpointing in OFFLINE mode |
| 180 |
|
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
| 181 |
|
end-run around the C/Fortran linking horror in eesup/src/timers.F |
| 182 |
|
o added pkg/runclock: allows user to terminate run based on wall clock |
| 183 |
|
o added non-hydrostatic scaling parameter: nh_am2 |
| 184 |
|
o pkg/my82: futile attempt to make results compiler-independent by adding |
| 185 |
|
some "_d 0", etc. no effect. |
| 186 |
|
o for mnc output, fill the 'T' coordinate var with myTime and create a |
| 187 |
|
separate 'iter' variable for iteration count |
| 188 |
|
o pkg/diagnostics: |
| 189 |
|
add new capability: output of Global/Regional & per-level statistics ; |
| 190 |
|
tested against monitor output (including land & thSIce) on various exp. |
| 191 |
|
o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
| 192 |
|
|
| 193 |
|
checkpoint57h_done |
| 194 |
|
tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
| 195 |
|
data.diagnostics, data.gchem, data.ptracers) is done. |
| 196 |
|
|
| 197 |
|
o pkg/diagnostics: prepare for Global/Regional statistics. |
| 198 |
|
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
| 199 |
|
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
| 200 |
|
and rename it: DIFFERENT_MULTIPLE |
| 201 |
|
|
| 202 |
|
checkpoint57h_post |
| 203 |
|
o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
| 204 |
|
o pkg/diagnostics: change output frequency, now in seconds (instead |
| 205 |
|
of Nb of iterations). This requires to change data.diagnostics. |
| 206 |
|
checkpoint57h_pre |
| 207 |
|
|
| 208 |
|
o in mnc, let the user create the output dir if both mnc_outdir_date |
| 209 |
|
and mnc_outdir_num are false |
| 210 |
|
o add fflags() to pkg/diagnostics which allows one to specify, on a |
| 211 |
|
per-file basis, the file precision [default behavior is unchanged] |
| 212 |
|
o added diagnostics to pkg/kpp, including computation of mixed layer |
| 213 |
|
depth based on a temperature/density criterion |
| 214 |
|
o updated verification/natl_box to test the new pkg/kpp diagnostics |
| 215 |
|
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
| 216 |
|
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
| 217 |
|
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
| 218 |
|
not mnc -- this mistake was found by JMC and is now corrected |
| 219 |
|
|
| 220 |
|
checkpoint57g_post |
| 221 |
|
o add Adams-Bashforth 3rd Order time stepping: |
| 222 |
|
- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
| 223 |
|
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
| 224 |
|
checkpoint57g_pre |
| 225 |
|
|
| 226 |
o make lambda[Theta,Salt]ClimRelax spatially varying |
o make lambda[Theta,Salt]ClimRelax spatially varying |
| 227 |
(default remains spatially uniform constant based on tau) |
(default remains spatially uniform constant based on tau) |
| 228 |
o added new control variables |
o added new control variables |
Parent Directory
| 
Revision Log
| 
Revision Graph
| 
Patch