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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 |
5 |
============================== |
============================== |
6 |
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|
7 |
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o make mnc honor the writeBinaryPrec flag for most kinds of output |
8 |
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o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
9 |
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o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
10 |
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error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
11 |
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o add brackets in multi-terms sum to get same truncation, independent of |
12 |
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the face number (manage to get exactly same value of gU,gV at the cs-edge) |
13 |
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affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
14 |
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o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
15 |
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and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
16 |
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a maximum grid-scale Reynolds number. Also, changes all length calculations |
17 |
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in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
18 |
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Suggested values of viscosity parameters found in mom_calc_visc. |
19 |
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Many new viscosity diagnostics available. |
20 |
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|
21 |
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checkpoint57s_post |
22 |
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o Add clearing-house for viscosity calculations, mom_calc_visc and |
23 |
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correct numerous bugs in LeithD and Smagorinsky discretizations. |
24 |
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mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
25 |
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used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
26 |
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Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
27 |
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and with Strain-Tension viscous term calculation (mom_hdissip.F). |
28 |
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The Strain-Tension form is now called with useStrainTensonVisc=.true. |
29 |
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ViscAhStrain and viscAhTension are now retired. |
30 |
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o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
31 |
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o In response to JMC's bug report, genmake2 now ignores any soft-links |
32 |
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that it finds in the *current* directory when searching for files. |
33 |
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Soft-links found in any other source directories will still work as |
34 |
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they did before. |
35 |
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o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
36 |
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a C routine to unlimit the stack size |
37 |
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o mnc-ify pkg/aim snapshot vars |
38 |
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o mnc-ify pkg/land as requested by Daniel |
39 |
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o various changes to mnc including: |
40 |
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- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
41 |
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- output can now be grouped so that all files within a group |
42 |
|
change the ITER portion of their names in lock-step together |
43 |
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- can now read ("global") PER-FACE (in addition to PER-TILE) files |
44 |
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and works with both EXCH1 and EXCH2 (but needs more testing) |
45 |
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- writing works for all verification test cases w/ g77 on Linux |
46 |
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|
47 |
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checkpoint57r_post |
48 |
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o make MNC variable initialization happen earlier |
49 |
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o add diagnostics for (almost) each term of the momentum Eq. |
50 |
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o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
51 |
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o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
52 |
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o remove MINIMAL_TAVE_OUTPUT option ; |
53 |
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add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
54 |
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o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
55 |
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allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
56 |
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o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
57 |
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o add time-dependent SST, SSS control |
58 |
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o cost terms in ecco/ modularized (new cost_generic.F) |
59 |
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o cost_averages routines are modularized (new cost_averagesgeneric.F) |
60 |
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o new infrastructure for seaice model vs. obs misfits in seaice/ |
61 |
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* driver from the_main_loop.F is seaice_cost_driver.F |
62 |
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* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
63 |
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* gradient check in Exp. 6a of natl_box_adjoint/ |
64 |
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o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
65 |
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(see README file) |
66 |
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|
67 |
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checkpoint57q_post |
68 |
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o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
69 |
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o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
70 |
|
- bug was reported by Jean-Michel and Ian Fenty |
71 |
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o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
72 |
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update exp. cpl_aim+ocn output. |
73 |
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o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
74 |
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Needed for high-res. runs with large global files |
75 |
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to be able to limit tapelev size |
76 |
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o Changed some tests for adjoint: |
77 |
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* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
78 |
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* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
79 |
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* global_ocean.90x40x15/ back to default 3-level checkpointing |
80 |
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o Modifications to enable scripted COMMON to MODULE conversion |
81 |
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* verification/OpenAD/code/ has necessary scripts and description; |
82 |
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* converts, compiles and runs successfully; |
83 |
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|
84 |
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checkpoint57p_post |
85 |
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o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
86 |
|
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
87 |
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(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
88 |
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o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
89 |
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o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
90 |
|
(was already the case for dissipation with mom_vecinv, |
91 |
|
and also the case for grad.PhiHyd when staggered-timeStep) |
92 |
|
This will allow to put dissipation out-off the AB time-stepping. |
93 |
|
Unfortunately, affects truncation error. Update output of exp. that "fails" |
94 |
|
(cg2d matching number) and leave the others for later: front_relax(10), |
95 |
|
global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
96 |
|
matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
97 |
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|
98 |
|
checkpoint57o_post |
99 |
|
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
100 |
|
(2) its ready to be documented during the 20050801 DocFest |
101 |
|
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
102 |
|
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
103 |
|
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
104 |
|
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
105 |
|
(worth another tag) |
106 |
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|
107 |
|
checkpoint57n_post |
108 |
|
o adding precip control xx_precip 32 |
109 |
|
o adding swflux control xx_swflux 33 |
110 |
|
o Replacing 10 forcing penalty cost routines by 1 generic. |
111 |
|
o Implementing partitioning in time-mean and variable adjustment |
112 |
|
for atmos. state. |
113 |
|
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
114 |
|
o in natl_box_adjoint: |
115 |
|
* updated exp 1 to 10 |
116 |
|
(but does not have time-mean vs. variable split results yet) |
117 |
|
o updated global1x1/*_seaice_adj/ |
118 |
|
to incorporate latest changes |
119 |
|
o enable useSingleCpuIO for mdsio vector routines |
120 |
|
(applies in particular to tapelev I/O) |
121 |
|
o removed inefficient K-loop in all active_file*control*.F |
122 |
|
|
123 |
|
checkpoint57m_post |
124 |
|
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
125 |
|
and advect_cs (use EXCH-2 and standard cs-32 grid files). |
126 |
|
o pkg/exch2: filling of face-corner halo regions is optional |
127 |
|
(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
128 |
|
|
129 |
|
checkpoint57l_post |
130 |
|
tag before updating tutorials (pre-release-2) |
131 |
|
o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
132 |
|
for output and interpolation of input fields onto model grid) |
133 |
|
o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
134 |
|
Affects results of exp. rotating_tank ; update output.txt. |
135 |
|
o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
136 |
|
and taking the square quantity and/or using a fraction-weight field. |
137 |
|
o fix aim_diagnostics_init.F mate numbers. |
138 |
|
o add mnc output capability to diagnostics/diagstat and update |
139 |
|
our cvsignore files for the ACSII output generated |
140 |
|
|
141 |
|
checkpoint57k_post |
142 |
|
o lab_sea now uses diagnostics package and provides a suite of |
143 |
|
new EXF diagnostics output. |
144 |
|
|
145 |
|
checkpoint57j_post |
146 |
|
o exf |
147 |
|
* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
148 |
|
Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
149 |
|
terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
150 |
|
* extended diagnostics output |
151 |
|
- now includes all EXF variables |
152 |
|
- hs, hl moved to common block |
153 |
|
- separate S/R for diagnostics, called after ctrl vector is added |
154 |
|
- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
155 |
|
- EXFqnet contains true Qnet (i.e. includes qsw) |
156 |
|
* updated verif. lab_sea, global_with_exf |
157 |
|
* Rearranging hflux (exf_mapfields -> exf_getforcing) |
158 |
|
to ensure that diagnostics sees a true EXFqnet |
159 |
|
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
160 |
|
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
161 |
|
several times with different frequencies. |
162 |
|
o mnc-ify the thsice package as requested by Daniel Enderton |
163 |
|
- the monitor--MNC output needs work |
164 |
|
- many attributes need to be added (most are currently blank) |
165 |
|
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
166 |
|
- many attributes need to be added (most are currently blank) |
167 |
|
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
168 |
|
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
169 |
|
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
170 |
|
update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
171 |
|
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
172 |
|
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
173 |
|
(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
174 |
|
|
175 |
|
checkpoint57i_post |
176 |
|
o Diagnostics package was changed: diagnostic allocation is now deactivated |
177 |
|
by setting an empty file name in the namelist (used to be by setting 0 frequency) |
178 |
|
o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
179 |
|
add 1rst Order upwind vertical Shear. |
180 |
|
o add a quick fix for A/B checkpointing in OFFLINE mode |
181 |
|
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
182 |
|
end-run around the C/Fortran linking horror in eesup/src/timers.F |
183 |
|
o added pkg/runclock: allows user to terminate run based on wall clock |
184 |
|
o added non-hydrostatic scaling parameter: nh_am2 |
185 |
|
o pkg/my82: futile attempt to make results compiler-independent by adding |
186 |
|
some "_d 0", etc. no effect. |
187 |
|
o for mnc output, fill the 'T' coordinate var with myTime and create a |
188 |
|
separate 'iter' variable for iteration count |
189 |
|
o pkg/diagnostics: |
190 |
|
add new capability: output of Global/Regional & per-level statistics ; |
191 |
|
tested against monitor output (including land & thSIce) on various exp. |
192 |
|
o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
193 |
|
|
194 |
|
checkpoint57h_done |
195 |
|
tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
196 |
|
data.diagnostics, data.gchem, data.ptracers) is done. |
197 |
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|
198 |
|
o pkg/diagnostics: prepare for Global/Regional statistics. |
199 |
|
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
200 |
|
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
201 |
|
and rename it: DIFFERENT_MULTIPLE |
202 |
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|
203 |
|
checkpoint57h_post |
204 |
|
o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
205 |
|
o pkg/diagnostics: change output frequency, now in seconds (instead |
206 |
|
of Nb of iterations). This requires to change data.diagnostics. |
207 |
|
checkpoint57h_pre |
208 |
|
|
209 |
|
o in mnc, let the user create the output dir if both mnc_outdir_date |
210 |
|
and mnc_outdir_num are false |
211 |
|
o add fflags() to pkg/diagnostics which allows one to specify, on a |
212 |
|
per-file basis, the file precision [default behavior is unchanged] |
213 |
|
o added diagnostics to pkg/kpp, including computation of mixed layer |
214 |
|
depth based on a temperature/density criterion |
215 |
|
o updated verification/natl_box to test the new pkg/kpp diagnostics |
216 |
|
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
217 |
|
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
218 |
|
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
219 |
|
not mnc -- this mistake was found by JMC and is now corrected |
220 |
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|
221 |
|
checkpoint57g_post |
222 |
|
o add Adams-Bashforth 3rd Order time stepping: |
223 |
|
- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
224 |
|
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
225 |
|
checkpoint57g_pre |
226 |
|
|
227 |
|
o make lambda[Theta,Salt]ClimRelax spatially varying |
228 |
|
(default remains spatially uniform constant based on tau) |
229 |
|
o added new control variables |
230 |
|
* init. uVel, vVel, etanN |
231 |
|
* lambda[Theta,Salt]ClimRelax |
232 |
|
o separate masks used for ctrl_pack/unpack 'from write_grid' output |
233 |
|
(suggested by G. Forget) |
234 |
|
|
235 |
|
checkpoint57f_post |
236 |
|
o add parameter "baseTime" = model base time = time at iteration zero |
237 |
|
new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
238 |
|
account for baseTime shift |
239 |
|
o move Coriolis arrays from PARAMS.h to GRID.h |
240 |
|
checkpoint57f_pre |
241 |
|
|
242 |
|
o mnc-ifying the seaice package |
243 |
|
o introduced an alternative length scale calculation for use in the limiting |
244 |
|
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
245 |
|
o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
246 |
|
o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
247 |
|
as well as grad(vort3). Made it compatible with both approximate form |
248 |
|
for the cubed sphere and full form of these gradients. Added flag |
249 |
|
useFullLeith to select between approximate and full form. |
250 |
|
o add "d0" in getcon.F to reduce differences between compilers/platforms |
251 |
|
update output.txt of exp. fizhi-gridalt-hs |
252 |
|
o change port_rand funtion to allow to set the seed. |
253 |
|
o fix obscure MNC bug involving conversion between reals and integers |
254 |
|
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
255 |
|
new version is now more standards-compliant |
256 |
|
o adjoint-related modifications |
257 |
|
* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
258 |
|
* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
259 |
|
* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
260 |
|
|
261 |
|
checkpoint57e_post |
262 |
|
o Adding eddy stress controls a la Ferreira et al. |
263 |
|
checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
264 |
|
|
265 |
|
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
266 |
|
update output.txt of exp. fizhi-gridalt-hs |
267 |
|
o add more "Z" dimensions and associated coordinate vars to MNC |
268 |
|
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
269 |
|
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
270 |
|
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
271 |
|
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
272 |
|
months and years. Requires pkg/cal. |
273 |
|
o diagnostics: add pickup functionality |
274 |
|
- off by default for backwards compatibility |
275 |
|
- current version only uses MDSIO -- MNC will be added |
276 |
|
o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
277 |
|
o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
278 |
|
|
279 |
|
checkpoint57d_post |
280 |
|
o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
281 |
|
o modify verification/ideal_2D_oce so that it tests the creation of mnc |
282 |
|
output from the diagnostics package |
283 |
|
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
284 |
|
o make genmake2 more portable by using ".$FS" instead of ".f" for more |
285 |
|
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
286 |
|
o add coordinate variables to the MNC output from the diagnostics package |
287 |
|
o change MNC-flags default value: true when useMNC=TRUE |
288 |
|
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
289 |
|
the ability (off by default) to read the grid information using MNC |
290 |
|
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
291 |
|
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
292 |
|
o do snap-shot diagnostics at the middle of the time-interval (instead of |
293 |
|
at the end). |
294 |
|
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
295 |
|
new test for AIM with thSIce + slab-ocean |
296 |
|
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
297 |
|
o move state variable diagnostics to the beginning of the time step ; |
298 |
|
(note: still needs some work specially for snap-shot diagnostics) |
299 |
|
duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
300 |
|
|
301 |
|
checkpoint57c_post |
302 |
|
o Change testing option (-ieee) to get closer agreement between g77 & ifort |
303 |
|
o generate new output.txt files on faulks with g77 & the new -ieee option |
304 |
|
checkpoint57c_pre |
305 |
|
|
306 |
|
o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
307 |
|
update output.txt of exp. global_ocean.90x40x15 |
308 |
|
o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
309 |
|
results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
310 |
|
o add saltFlux(+File) forcing capability with periodicExternalForcing |
311 |
|
o allow to use pkg diagnostics for GM-Redi & ThSIce output |
312 |
|
o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
313 |
|
o improvements for the MNC output from DIAGNOSTICS: |
314 |
|
- correct handling of the unlimitied dimension |
315 |
|
- all dims now have associated coordinate variables |
316 |
|
- variables located at U, V, and Corner ("Z") points are now written |
317 |
|
with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
318 |
|
*all* data points are output |
319 |
|
o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
320 |
|
o added pkg/seaice/seaice_monitor.F |
321 |
|
o mdsio_readfield.F can now read files visible only to master MPI process. |
322 |
|
o pkg/seaice: some test code for ice-modified ocean stress |
323 |
|
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
324 |
|
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
325 |
|
spurious negative numbers for precipitation and humidity. Will cause |
326 |
|
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
327 |
|
o pkg/ctrl/ |
328 |
|
* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
329 |
|
May be enabled via doPackDiag |
330 |
|
* introduce z-scaling of |
331 |
|
+ gradient (doZscalePack) and |
332 |
|
+ control (doZscaleUnpack) |
333 |
|
o pkg/mdsio/ |
334 |
|
* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
335 |
|
* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
336 |
|
|
337 |
|
checkpoint57b_post |
338 |
|
o simplify options in diagnostics_fill arguments (remove weird combinations) |
339 |
|
o fix MNC coordinate variables so that they now contain per-face index |
340 |
|
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
341 |
|
general, EXCH2 grids are only aligned to a "local" coordinate system |
342 |
|
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
343 |
|
o Implement instantaneous output within pkg diagnostics: |
344 |
|
setting a negative frequency in data.diagnostics produces |
345 |
|
"snap-shot" output (as opposed to time-average if freq > 0) |
346 |
|
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
347 |
|
NOTE: change ptracer diagnostics name: use 2 characters to work with |
348 |
|
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
349 |
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
350 |
becomes the coordinate variable for the 'T' dimension |
becomes the coordinate variable for the 'T' dimension |
351 |
o add CF-style coordinate variables to MNC |
o add CF-style coordinate variables to MNC |