4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
|
|
7 |
|
checkpoint57u_post |
8 |
|
o OBCS and PTRACERS: add open boundary support for passive tracers |
9 |
|
- either use homogenous (pseudo) v.Neumann conditions or prescribe |
10 |
|
OB-values from file; this is not different from the way theta and salinity |
11 |
|
are treated |
12 |
|
- however, Orlanski-radiation conditions are not supported, and the model |
13 |
|
will stop if you use pTracers and Orlanski at the same time. |
14 |
|
- beefed up the rountine obcs_external_fields_load: now only those open |
15 |
|
boundary values are overwritten with values from files for which there |
16 |
|
are really files, otherwise the OB-fields remain untouched. This makes |
17 |
|
it possible to use different OBs at different ends of the domain (as |
18 |
|
with EXF) |
19 |
|
o reduce number of exch calls in shap_filt (s2). |
20 |
|
o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ |
21 |
|
truncation level) 4/5 MLAdjust test results (11&12 digits match). |
22 |
|
|
23 |
|
checkpoint57t_post |
24 |
|
o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
25 |
|
o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
26 |
|
same truncation, independent of the face number: affects affects several |
27 |
|
test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). |
28 |
|
o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); |
29 |
|
note that biharmonic viscosity + no-slip was not tested in any experiment. |
30 |
|
o fix bug in non-linear free-surf side-drag ; generate new output for |
31 |
|
global_ocean.cs32x15(+.thsice) & global_ocean_pressure. |
32 |
|
o make mnc honor the writeBinaryPrec flag for most kinds of output |
33 |
|
o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
34 |
|
o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
35 |
|
error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
36 |
|
o add brackets in multi-terms sum to get same truncation, independent of |
37 |
|
the face number (manage to get exactly same value of gU,gV at the cs-edge) |
38 |
|
affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
39 |
|
o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
40 |
|
and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
41 |
|
a maximum grid-scale Reynolds number. Also, changes all length calculations |
42 |
|
in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
43 |
|
Suggested values of viscosity parameters found in mom_calc_visc. |
44 |
|
Many new viscosity diagnostics available. |
45 |
|
|
46 |
|
checkpoint57s_post |
47 |
|
o Add clearing-house for viscosity calculations, mom_calc_visc and |
48 |
|
correct numerous bugs in LeithD and Smagorinsky discretizations. |
49 |
|
mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
50 |
|
used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
51 |
|
Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
52 |
|
and with Strain-Tension viscous term calculation (mom_hdissip.F). |
53 |
|
The Strain-Tension form is now called with useStrainTensonVisc=.true. |
54 |
|
ViscAhStrain and viscAhTension are now retired. |
55 |
|
o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
56 |
|
o In response to JMC's bug report, genmake2 now ignores any soft-links |
57 |
|
that it finds in the *current* directory when searching for files. |
58 |
|
Soft-links found in any other source directories will still work as |
59 |
|
they did before. |
60 |
|
o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
61 |
|
a C routine to unlimit the stack size |
62 |
|
o mnc-ify pkg/aim snapshot vars |
63 |
|
o mnc-ify pkg/land as requested by Daniel |
64 |
|
o various changes to mnc including: |
65 |
|
- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
66 |
|
- output can now be grouped so that all files within a group |
67 |
|
change the ITER portion of their names in lock-step together |
68 |
|
- can now read ("global") PER-FACE (in addition to PER-TILE) files |
69 |
|
and works with both EXCH1 and EXCH2 (but needs more testing) |
70 |
|
- writing works for all verification test cases w/ g77 on Linux |
71 |
|
|
72 |
|
checkpoint57r_post |
73 |
|
o make MNC variable initialization happen earlier |
74 |
|
o add diagnostics for (almost) each term of the momentum Eq. |
75 |
|
o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
76 |
|
o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
77 |
|
o remove MINIMAL_TAVE_OUTPUT option ; |
78 |
|
add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
79 |
|
o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
80 |
|
allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
81 |
|
o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
82 |
|
o add time-dependent SST, SSS control |
83 |
|
o cost terms in ecco/ modularized (new cost_generic.F) |
84 |
|
o cost_averages routines are modularized (new cost_averagesgeneric.F) |
85 |
|
o new infrastructure for seaice model vs. obs misfits in seaice/ |
86 |
|
* driver from the_main_loop.F is seaice_cost_driver.F |
87 |
|
* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
88 |
|
* gradient check in Exp. 6a of natl_box_adjoint/ |
89 |
|
o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
90 |
|
(see README file) |
91 |
|
|
92 |
|
checkpoint57q_post |
93 |
|
o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
94 |
|
o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
95 |
|
- bug was reported by Jean-Michel and Ian Fenty |
96 |
|
o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
97 |
|
update exp. cpl_aim+ocn output. |
98 |
|
o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
99 |
|
Needed for high-res. runs with large global files |
100 |
|
to be able to limit tapelev size |
101 |
|
o Changed some tests for adjoint: |
102 |
|
* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
103 |
|
* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
104 |
|
* global_ocean.90x40x15/ back to default 3-level checkpointing |
105 |
|
o Modifications to enable scripted COMMON to MODULE conversion |
106 |
|
* verification/OpenAD/code/ has necessary scripts and description; |
107 |
|
* converts, compiles and runs successfully; |
108 |
|
|
109 |
|
checkpoint57p_post |
110 |
|
o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
111 |
|
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
112 |
|
(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
113 |
|
o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
114 |
|
o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
115 |
|
(was already the case for dissipation with mom_vecinv, |
116 |
|
and also the case for grad.PhiHyd when staggered-timeStep) |
117 |
|
This will allow to put dissipation out-off the AB time-stepping. |
118 |
|
Unfortunately, affects truncation error. Update output of exp. that "fails" |
119 |
|
(cg2d matching number) and leave the others for later: front_relax(10), |
120 |
|
global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
121 |
|
matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
122 |
|
|
123 |
|
checkpoint57o_post |
124 |
|
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
125 |
|
(2) its ready to be documented during the 20050801 DocFest |
126 |
|
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
127 |
|
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
128 |
|
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
129 |
|
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
130 |
|
(worth another tag) |
131 |
|
|
132 |
|
checkpoint57n_post |
133 |
|
o adding precip control xx_precip 32 |
134 |
|
o adding swflux control xx_swflux 33 |
135 |
|
o Replacing 10 forcing penalty cost routines by 1 generic. |
136 |
|
o Implementing partitioning in time-mean and variable adjustment |
137 |
|
for atmos. state. |
138 |
|
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
139 |
|
o in natl_box_adjoint: |
140 |
|
* updated exp 1 to 10 |
141 |
|
(but does not have time-mean vs. variable split results yet) |
142 |
|
o updated global1x1/*_seaice_adj/ |
143 |
|
to incorporate latest changes |
144 |
|
o enable useSingleCpuIO for mdsio vector routines |
145 |
|
(applies in particular to tapelev I/O) |
146 |
|
o removed inefficient K-loop in all active_file*control*.F |
147 |
|
|
148 |
|
checkpoint57m_post |
149 |
|
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
150 |
|
and advect_cs (use EXCH-2 and standard cs-32 grid files). |
151 |
|
o pkg/exch2: filling of face-corner halo regions is optional |
152 |
|
(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
153 |
|
|
154 |
|
checkpoint57l_post |
155 |
|
tag before updating tutorials (pre-release-2) |
156 |
|
o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
157 |
|
for output and interpolation of input fields onto model grid) |
158 |
|
o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
159 |
|
Affects results of exp. rotating_tank ; update output.txt. |
160 |
|
o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
161 |
|
and taking the square quantity and/or using a fraction-weight field. |
162 |
|
o fix aim_diagnostics_init.F mate numbers. |
163 |
|
o add mnc output capability to diagnostics/diagstat and update |
164 |
|
our cvsignore files for the ACSII output generated |
165 |
|
|
166 |
|
checkpoint57k_post |
167 |
|
o lab_sea now uses diagnostics package and provides a suite of |
168 |
|
new EXF diagnostics output. |
169 |
|
|
170 |
|
checkpoint57j_post |
171 |
|
o exf |
172 |
|
* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
173 |
|
Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
174 |
|
terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
175 |
|
* extended diagnostics output |
176 |
|
- now includes all EXF variables |
177 |
|
- hs, hl moved to common block |
178 |
|
- separate S/R for diagnostics, called after ctrl vector is added |
179 |
|
- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
180 |
|
- EXFqnet contains true Qnet (i.e. includes qsw) |
181 |
|
* updated verif. lab_sea, global_with_exf |
182 |
|
* Rearranging hflux (exf_mapfields -> exf_getforcing) |
183 |
|
to ensure that diagnostics sees a true EXFqnet |
184 |
|
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
185 |
|
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
186 |
|
several times with different frequencies. |
187 |
|
o mnc-ify the thsice package as requested by Daniel Enderton |
188 |
|
- the monitor--MNC output needs work |
189 |
|
- many attributes need to be added (most are currently blank) |
190 |
|
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
191 |
|
- many attributes need to be added (most are currently blank) |
192 |
|
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
193 |
|
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
194 |
|
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
195 |
|
update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
196 |
|
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
197 |
|
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
198 |
|
(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
199 |
|
|
200 |
|
checkpoint57i_post |
201 |
|
o Diagnostics package was changed: diagnostic allocation is now deactivated |
202 |
|
by setting an empty file name in the namelist (used to be by setting 0 frequency) |
203 |
|
o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
204 |
|
add 1rst Order upwind vertical Shear. |
205 |
|
o add a quick fix for A/B checkpointing in OFFLINE mode |
206 |
|
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
207 |
|
end-run around the C/Fortran linking horror in eesup/src/timers.F |
208 |
|
o added pkg/runclock: allows user to terminate run based on wall clock |
209 |
|
o added non-hydrostatic scaling parameter: nh_am2 |
210 |
|
o pkg/my82: futile attempt to make results compiler-independent by adding |
211 |
|
some "_d 0", etc. no effect. |
212 |
|
o for mnc output, fill the 'T' coordinate var with myTime and create a |
213 |
|
separate 'iter' variable for iteration count |
214 |
|
o pkg/diagnostics: |
215 |
|
add new capability: output of Global/Regional & per-level statistics ; |
216 |
|
tested against monitor output (including land & thSIce) on various exp. |
217 |
|
o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
218 |
|
|
219 |
|
checkpoint57h_done |
220 |
|
tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
221 |
|
data.diagnostics, data.gchem, data.ptracers) is done. |
222 |
|
|
223 |
|
o pkg/diagnostics: prepare for Global/Regional statistics. |
224 |
|
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
225 |
|
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
226 |
|
and rename it: DIFFERENT_MULTIPLE |
227 |
|
|
228 |
|
checkpoint57h_post |
229 |
|
o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
230 |
|
o pkg/diagnostics: change output frequency, now in seconds (instead |
231 |
|
of Nb of iterations). This requires to change data.diagnostics. |
232 |
|
checkpoint57h_pre |
233 |
|
|
234 |
|
o in mnc, let the user create the output dir if both mnc_outdir_date |
235 |
|
and mnc_outdir_num are false |
236 |
|
o add fflags() to pkg/diagnostics which allows one to specify, on a |
237 |
|
per-file basis, the file precision [default behavior is unchanged] |
238 |
|
o added diagnostics to pkg/kpp, including computation of mixed layer |
239 |
|
depth based on a temperature/density criterion |
240 |
|
o updated verification/natl_box to test the new pkg/kpp diagnostics |
241 |
|
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
242 |
|
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
243 |
|
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
244 |
|
not mnc -- this mistake was found by JMC and is now corrected |
245 |
|
|
246 |
|
checkpoint57g_post |
247 |
|
o add Adams-Bashforth 3rd Order time stepping: |
248 |
|
- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
249 |
|
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
250 |
checkpoint57g_pre |
checkpoint57g_pre |
251 |
|
|
252 |
o make lambda[Theta,Salt]ClimRelax spatially varying |
o make lambda[Theta,Salt]ClimRelax spatially varying |