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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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|
7 |
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o pkg/bulk_force: |
8 |
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- add option and parameters to use AIM surface-flux formulae. |
9 |
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- Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ; |
10 |
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others forcing fields (defined in PARM05, parameter file "data") are loaded |
11 |
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from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F). |
12 |
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- initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F |
13 |
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- use the right EXCH call for uwind,vwind (to work on CS-grid). |
14 |
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- re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h) |
15 |
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and parameters (note: calcWindStress replaces .NOT.readwindstress). |
16 |
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- cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). |
17 |
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|
18 |
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checkpoint58 |
19 |
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o add "--embed-source" option to genmake2 which, when the supporting |
20 |
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tools can be compiled (as determined by genmake2) will turn on the |
21 |
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embed_files package which then embeds the entire MITgcm source code |
22 |
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(*.[fFhc] + Makefile) used for the build within the executable |
23 |
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- requested by CNH but off by default |
24 |
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- adds a paltry <9MB to the mitgcmuv executable in most cases |
25 |
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- only writes the output when useEMBEDSRC in eedata is true |
26 |
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o clean up 3-dim. relaxation codes: |
27 |
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* Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec |
28 |
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* Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) |
29 |
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* Thanks to Tom Haine for testing! |
30 |
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|
31 |
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checkpoint57z_post |
32 |
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o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): |
33 |
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affects output (@ truncation level) of exp. plume_on_slope ; updated. |
34 |
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o fix the pickup behavior for obcs in combination with ptracers |
35 |
|
o fix a bug in ptracers_external_fields_load |
36 |
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o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...) |
37 |
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affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) |
38 |
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o transfered surface NH pressure to eta field (if exactConserv). |
39 |
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o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign) |
40 |
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and update lab_sea output.txt file. |
41 |
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o completing 3-dim. relaxation code: additional term |
42 |
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1/tau*( theta(i,j,k) - thetaStar(i,j,k) ) |
43 |
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in S/R EXTERNAL_FORCING_T (file external_forcing.F) |
44 |
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* At compile time, in "EXF_OPTIONS.h" set |
45 |
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#define ALLOW_CLIMTEMP_RELAXATION |
46 |
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#define ALLOW_CLIMSALT_RELAXATION |
47 |
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* At runtime in "data", under &PARM03 set (e.g., units in seconds) |
48 |
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tauThetaClimRelax3Dim = 15552000.0, |
49 |
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tauSaltClimRelax3Dim = 15552000.0, |
50 |
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* 3 cases: |
51 |
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1) Use a constant-in-time 3-dim. field |
52 |
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2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec. |
53 |
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3) Real-time relax. to time-evolving prescribed field |
54 |
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o Adding Laplacian-type smoothness constraint on |
55 |
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initial and boundary (forcing) controls (ic, bc) |
56 |
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* enable at compile-time via |
57 |
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ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION |
58 |
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* enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1 |
59 |
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* Absolute scale somewhat unclear so far |
60 |
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* no area weighting was included since no other cost term does so far |
61 |
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|
62 |
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checkpoint57y_post |
63 |
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First step for a NLFS adjoint |
64 |
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o initially suppress rStar (new flag DISABLE_RSTAR_CODE) |
65 |
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o new init. routines for calc_r_star, calc_surf_dr |
66 |
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o still need to deal with ini_masks_etc |
67 |
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o testreport seemed happy |
68 |
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checkpoint57y_pre |
69 |
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|
70 |
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o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
71 |
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o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) |
72 |
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o add new offset feature to offline pkg (plus minor cleanup) |
73 |
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o cfc fixes for final year of integration |
74 |
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o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should |
75 |
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be in GCHEM_OPTIONS). |
76 |
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|
77 |
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checkpoint57x_post |
78 |
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o fix testreport Pb in multiple test experiment. |
79 |
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o cleanup our namelist syntax in verification: |
80 |
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- make it more F95 standards compliant (some work still needed) |
81 |
|
- allows the vast majority of our tests to work with gfortran |
82 |
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o Non-Hydrostatic: |
83 |
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- put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h |
84 |
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- fix exchange calls for CS-grid using the new EXCH_S3D_RL. |
85 |
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o Allow to apply AB on T,S rather than on AB(gT,gS): |
86 |
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- implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 |
87 |
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- use the same arrays (gtNm,gsNm) to hold tracer field at previous |
88 |
|
time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). |
89 |
|
- need a "clever" read_pickup to restart from the other AB formulation |
90 |
|
o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h |
91 |
|
o remove some unused variables (reduces number of compiler warnings) |
92 |
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o adjoint |
93 |
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* Disable useVariableViscosity for adjoint for time being |
94 |
|
(there are a number of extensive recomputations) |
95 |
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* Initialize certain variables needed for adjoint |
96 |
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|
97 |
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checkpoint57w_post |
98 |
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o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names |
99 |
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fix the singleCpuIO RS version of MDSWRITEFIELD |
100 |
|
and add a WARNING if using globalFiles=T with multi-processors. |
101 |
|
o write grid-file(s) in only one format (MDS or MNC): default=MNC (if |
102 |
|
using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc |
103 |
|
o tracer advection scheme: |
104 |
|
add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get |
105 |
|
those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, |
106 |
|
was not very convenient). |
107 |
|
add implicit version for DST-3 & DST3_Flux_Limit vertical advection; |
108 |
|
(further tests needed for the implicit DST & Flux-Limiter schemes). |
109 |
|
o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef |
110 |
|
and sRef for convenience, handy, when you want to initialize |
111 |
|
ptracers in a large domain with a constant non-zero value. Also, |
112 |
|
untangle ptracers_init.F a little. |
113 |
|
|
114 |
|
checkpoint57v_post |
115 |
|
o change dome exp. to use variable viscosity in side-drag terms. |
116 |
|
o remove all the files from the cfc_offline test since they are now |
117 |
|
incorporated into tutorial_cfc_offline which has been producing |
118 |
|
identical results for a few days of testing |
119 |
|
o add new parameter: sideDragFactor to enable half-slip-side BC |
120 |
|
and change side-drag S/R to use viscosity from mom_calc_visc |
121 |
|
(can switch back by setting sideDragFactor=0.); affects results at |
122 |
|
truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), |
123 |
|
global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). |
124 |
|
o vorticity & strain are now computed without masking, to account for |
125 |
|
no-slip-side BC in variable viscosity calculation ; mask is applied |
126 |
|
anyway later on, before computing advection/coriolis terms. |
127 |
|
o modify exp4 to test new obcs support for reading from external files |
128 |
|
and for passive tracers |
129 |
|
o fix behavior of ptracers_monitor when monitor output is written to a |
130 |
|
netcdf-file; still not independent of monitor.F (writes in the same |
131 |
|
file). |
132 |
|
o change default value of tRef (put a uniform, meaningful value for ocean |
133 |
|
& atmos) and initialize sRef (was missing, as Martin mentioned). |
134 |
|
o Redefine viscC?Leith*. Change the coefficients of Leith viscosity |
135 |
|
to be proportional to enstrophy dissipation length. Thus, |
136 |
|
viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) |
137 |
|
This is now consistent with Smagorinsky and with the manual. |
138 |
|
|
139 |
|
checkpoint57u_post |
140 |
|
o OBCS and PTRACERS: add open boundary support for passive tracers |
141 |
|
- either use homogenous (pseudo) v.Neumann conditions or prescribe |
142 |
|
OB-values from file; this is not different from the way theta and salinity |
143 |
|
are treated |
144 |
|
- however, Orlanski-radiation conditions are not supported, and the model |
145 |
|
will stop if you use pTracers and Orlanski at the same time. |
146 |
|
- beefed up the rountine obcs_external_fields_load: now only those open |
147 |
|
boundary values are overwritten with values from files for which there |
148 |
|
are really files, otherwise the OB-fields remain untouched. This makes |
149 |
|
it possible to use different OBs at different ends of the domain (as |
150 |
|
with EXF) |
151 |
|
o reduce number of exch calls in shap_filt (s2). |
152 |
|
o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ |
153 |
|
truncation level) 4/5 MLAdjust test results (11&12 digits match). |
154 |
|
|
155 |
|
checkpoint57t_post |
156 |
|
o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
157 |
|
o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
158 |
|
same truncation, independent of the face number: affects affects several |
159 |
|
test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). |
160 |
|
o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); |
161 |
|
note that biharmonic viscosity + no-slip was not tested in any experiment. |
162 |
|
o fix bug in non-linear free-surf side-drag ; generate new output for |
163 |
|
global_ocean.cs32x15(+.thsice) & global_ocean_pressure. |
164 |
|
o make mnc honor the writeBinaryPrec flag for most kinds of output |
165 |
|
o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
166 |
|
o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
167 |
|
error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
168 |
|
o add brackets in multi-terms sum to get same truncation, independent of |
169 |
|
the face number (manage to get exactly same value of gU,gV at the cs-edge) |
170 |
|
affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
171 |
|
o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
172 |
|
and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
173 |
|
a maximum grid-scale Reynolds number. Also, changes all length calculations |
174 |
|
in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
175 |
|
Suggested values of viscosity parameters found in mom_calc_visc. |
176 |
|
Many new viscosity diagnostics available. |
177 |
|
|
178 |
|
checkpoint57s_post |
179 |
|
o Add clearing-house for viscosity calculations, mom_calc_visc and |
180 |
|
correct numerous bugs in LeithD and Smagorinsky discretizations. |
181 |
|
mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
182 |
|
used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
183 |
|
Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
184 |
|
and with Strain-Tension viscous term calculation (mom_hdissip.F). |
185 |
|
The Strain-Tension form is now called with useStrainTensonVisc=.true. |
186 |
|
ViscAhStrain and viscAhTension are now retired. |
187 |
|
o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
188 |
|
o In response to JMC's bug report, genmake2 now ignores any soft-links |
189 |
|
that it finds in the *current* directory when searching for files. |
190 |
|
Soft-links found in any other source directories will still work as |
191 |
|
they did before. |
192 |
|
o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
193 |
|
a C routine to unlimit the stack size |
194 |
|
o mnc-ify pkg/aim snapshot vars |
195 |
|
o mnc-ify pkg/land as requested by Daniel |
196 |
|
o various changes to mnc including: |
197 |
|
- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
198 |
|
- output can now be grouped so that all files within a group |
199 |
|
change the ITER portion of their names in lock-step together |
200 |
|
- can now read ("global") PER-FACE (in addition to PER-TILE) files |
201 |
|
and works with both EXCH1 and EXCH2 (but needs more testing) |
202 |
|
- writing works for all verification test cases w/ g77 on Linux |
203 |
|
|
204 |
|
checkpoint57r_post |
205 |
|
o make MNC variable initialization happen earlier |
206 |
|
o add diagnostics for (almost) each term of the momentum Eq. |
207 |
|
o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
208 |
|
o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
209 |
|
o remove MINIMAL_TAVE_OUTPUT option ; |
210 |
|
add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
211 |
|
o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
212 |
|
allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
213 |
|
o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
214 |
|
o add time-dependent SST, SSS control |
215 |
|
o cost terms in ecco/ modularized (new cost_generic.F) |
216 |
|
o cost_averages routines are modularized (new cost_averagesgeneric.F) |
217 |
|
o new infrastructure for seaice model vs. obs misfits in seaice/ |
218 |
|
* driver from the_main_loop.F is seaice_cost_driver.F |
219 |
|
* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
220 |
|
* gradient check in Exp. 6a of natl_box_adjoint/ |
221 |
|
o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
222 |
|
(see README file) |
223 |
|
|
224 |
|
checkpoint57q_post |
225 |
|
o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
226 |
|
o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
227 |
|
- bug was reported by Jean-Michel and Ian Fenty |
228 |
|
o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
229 |
|
update exp. cpl_aim+ocn output. |
230 |
|
o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
231 |
|
Needed for high-res. runs with large global files |
232 |
|
to be able to limit tapelev size |
233 |
|
o Changed some tests for adjoint: |
234 |
|
* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
235 |
|
* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
236 |
|
* global_ocean.90x40x15/ back to default 3-level checkpointing |
237 |
|
o Modifications to enable scripted COMMON to MODULE conversion |
238 |
|
* verification/OpenAD/code/ has necessary scripts and description; |
239 |
|
* converts, compiles and runs successfully; |
240 |
|
|
241 |
|
checkpoint57p_post |
242 |
|
o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
243 |
|
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
244 |
|
(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
245 |
|
o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
246 |
|
o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
247 |
|
(was already the case for dissipation with mom_vecinv, |
248 |
|
and also the case for grad.PhiHyd when staggered-timeStep) |
249 |
|
This will allow to put dissipation out-off the AB time-stepping. |
250 |
|
Unfortunately, affects truncation error. Update output of exp. that "fails" |
251 |
|
(cg2d matching number) and leave the others for later: front_relax(10), |
252 |
|
global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
253 |
|
matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
254 |
|
|
255 |
|
checkpoint57o_post |
256 |
|
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
257 |
|
(2) its ready to be documented during the 20050801 DocFest |
258 |
|
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
259 |
|
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
260 |
|
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
261 |
|
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
262 |
|
(worth another tag) |
263 |
|
|
264 |
|
checkpoint57n_post |
265 |
|
o adding precip control xx_precip 32 |
266 |
|
o adding swflux control xx_swflux 33 |
267 |
|
o Replacing 10 forcing penalty cost routines by 1 generic. |
268 |
|
o Implementing partitioning in time-mean and variable adjustment |
269 |
|
for atmos. state. |
270 |
|
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
271 |
|
o in natl_box_adjoint: |
272 |
|
* updated exp 1 to 10 |
273 |
|
(but does not have time-mean vs. variable split results yet) |
274 |
|
o updated global1x1/*_seaice_adj/ |
275 |
|
to incorporate latest changes |
276 |
|
o enable useSingleCpuIO for mdsio vector routines |
277 |
|
(applies in particular to tapelev I/O) |
278 |
|
o removed inefficient K-loop in all active_file*control*.F |
279 |
|
|
280 |
|
checkpoint57m_post |
281 |
|
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
282 |
|
and advect_cs (use EXCH-2 and standard cs-32 grid files). |
283 |
|
o pkg/exch2: filling of face-corner halo regions is optional |
284 |
|
(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
285 |
|
|
286 |
|
checkpoint57l_post |
287 |
|
tag before updating tutorials (pre-release-2) |
288 |
|
o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
289 |
|
for output and interpolation of input fields onto model grid) |
290 |
|
o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
291 |
|
Affects results of exp. rotating_tank ; update output.txt. |
292 |
|
o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
293 |
|
and taking the square quantity and/or using a fraction-weight field. |
294 |
|
o fix aim_diagnostics_init.F mate numbers. |
295 |
|
o add mnc output capability to diagnostics/diagstat and update |
296 |
|
our cvsignore files for the ACSII output generated |
297 |
|
|
298 |
|
checkpoint57k_post |
299 |
|
o lab_sea now uses diagnostics package and provides a suite of |
300 |
|
new EXF diagnostics output. |
301 |
|
|
302 |
|
checkpoint57j_post |
303 |
|
o exf |
304 |
|
* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
305 |
|
Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
306 |
|
terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
307 |
|
* extended diagnostics output |
308 |
|
- now includes all EXF variables |
309 |
|
- hs, hl moved to common block |
310 |
|
- separate S/R for diagnostics, called after ctrl vector is added |
311 |
|
- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
312 |
|
- EXFqnet contains true Qnet (i.e. includes qsw) |
313 |
|
* updated verif. lab_sea, global_with_exf |
314 |
|
* Rearranging hflux (exf_mapfields -> exf_getforcing) |
315 |
|
to ensure that diagnostics sees a true EXFqnet |
316 |
|
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
317 |
|
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
318 |
|
several times with different frequencies. |
319 |
|
o mnc-ify the thsice package as requested by Daniel Enderton |
320 |
|
- the monitor--MNC output needs work |
321 |
|
- many attributes need to be added (most are currently blank) |
322 |
|
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
323 |
|
- many attributes need to be added (most are currently blank) |
324 |
|
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
325 |
|
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
326 |
|
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
327 |
|
update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
328 |
|
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
329 |
|
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
330 |
|
(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
331 |
|
|
332 |
|
checkpoint57i_post |
333 |
|
o Diagnostics package was changed: diagnostic allocation is now deactivated |
334 |
|
by setting an empty file name in the namelist (used to be by setting 0 frequency) |
335 |
|
o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
336 |
|
add 1rst Order upwind vertical Shear. |
337 |
|
o add a quick fix for A/B checkpointing in OFFLINE mode |
338 |
|
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
339 |
|
end-run around the C/Fortran linking horror in eesup/src/timers.F |
340 |
|
o added pkg/runclock: allows user to terminate run based on wall clock |
341 |
|
o added non-hydrostatic scaling parameter: nh_am2 |
342 |
|
o pkg/my82: futile attempt to make results compiler-independent by adding |
343 |
|
some "_d 0", etc. no effect. |
344 |
|
o for mnc output, fill the 'T' coordinate var with myTime and create a |
345 |
|
separate 'iter' variable for iteration count |
346 |
|
o pkg/diagnostics: |
347 |
|
add new capability: output of Global/Regional & per-level statistics ; |
348 |
|
tested against monitor output (including land & thSIce) on various exp. |
349 |
|
o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
350 |
|
|
351 |
|
checkpoint57h_done |
352 |
|
tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
353 |
|
data.diagnostics, data.gchem, data.ptracers) is done. |
354 |
|
|
355 |
|
o pkg/diagnostics: prepare for Global/Regional statistics. |
356 |
|
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
357 |
|
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
358 |
|
and rename it: DIFFERENT_MULTIPLE |
359 |
|
|
360 |
|
checkpoint57h_post |
361 |
|
o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
362 |
|
o pkg/diagnostics: change output frequency, now in seconds (instead |
363 |
|
of Nb of iterations). This requires to change data.diagnostics. |
364 |
|
checkpoint57h_pre |
365 |
|
|
366 |
|
o in mnc, let the user create the output dir if both mnc_outdir_date |
367 |
|
and mnc_outdir_num are false |
368 |
|
o add fflags() to pkg/diagnostics which allows one to specify, on a |
369 |
|
per-file basis, the file precision [default behavior is unchanged] |
370 |
|
o added diagnostics to pkg/kpp, including computation of mixed layer |
371 |
|
depth based on a temperature/density criterion |
372 |
|
o updated verification/natl_box to test the new pkg/kpp diagnostics |
373 |
|
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
374 |
|
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
375 |
|
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
376 |
|
not mnc -- this mistake was found by JMC and is now corrected |
377 |
|
|
378 |
|
checkpoint57g_post |
379 |
|
o add Adams-Bashforth 3rd Order time stepping: |
380 |
|
- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
381 |
|
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
382 |
|
checkpoint57g_pre |
383 |
|
|
384 |
|
o make lambda[Theta,Salt]ClimRelax spatially varying |
385 |
|
(default remains spatially uniform constant based on tau) |
386 |
|
o added new control variables |
387 |
|
* init. uVel, vVel, etanN |
388 |
|
* lambda[Theta,Salt]ClimRelax |
389 |
|
o separate masks used for ctrl_pack/unpack 'from write_grid' output |
390 |
|
(suggested by G. Forget) |
391 |
|
|
392 |
|
checkpoint57f_post |
393 |
|
o add parameter "baseTime" = model base time = time at iteration zero |
394 |
|
new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
395 |
|
account for baseTime shift |
396 |
|
o move Coriolis arrays from PARAMS.h to GRID.h |
397 |
|
checkpoint57f_pre |
398 |
|
|
399 |
|
o mnc-ifying the seaice package |
400 |
|
o introduced an alternative length scale calculation for use in the limiting |
401 |
|
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
402 |
|
o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
403 |
|
o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
404 |
|
as well as grad(vort3). Made it compatible with both approximate form |
405 |
|
for the cubed sphere and full form of these gradients. Added flag |
406 |
|
useFullLeith to select between approximate and full form. |
407 |
|
o add "d0" in getcon.F to reduce differences between compilers/platforms |
408 |
|
update output.txt of exp. fizhi-gridalt-hs |
409 |
|
o change port_rand funtion to allow to set the seed. |
410 |
|
o fix obscure MNC bug involving conversion between reals and integers |
411 |
|
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
412 |
|
new version is now more standards-compliant |
413 |
|
o adjoint-related modifications |
414 |
|
* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
415 |
|
* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
416 |
|
* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
417 |
|
|
418 |
|
checkpoint57e_post |
419 |
|
o Adding eddy stress controls a la Ferreira et al. |
420 |
|
checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
421 |
|
|
422 |
|
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
423 |
|
update output.txt of exp. fizhi-gridalt-hs |
424 |
|
o add more "Z" dimensions and associated coordinate vars to MNC |
425 |
|
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
426 |
|
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
427 |
|
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
428 |
|
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
429 |
|
months and years. Requires pkg/cal. |
430 |
|
o diagnostics: add pickup functionality |
431 |
|
- off by default for backwards compatibility |
432 |
|
- current version only uses MDSIO -- MNC will be added |
433 |
|
o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
434 |
|
o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
435 |
|
|
436 |
|
checkpoint57d_post |
437 |
|
o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
438 |
|
o modify verification/ideal_2D_oce so that it tests the creation of mnc |
439 |
|
output from the diagnostics package |
440 |
|
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
441 |
|
o make genmake2 more portable by using ".$FS" instead of ".f" for more |
442 |
|
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
443 |
|
o add coordinate variables to the MNC output from the diagnostics package |
444 |
|
o change MNC-flags default value: true when useMNC=TRUE |
445 |
|
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
446 |
|
the ability (off by default) to read the grid information using MNC |
447 |
|
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
448 |
|
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
449 |
|
o do snap-shot diagnostics at the middle of the time-interval (instead of |
450 |
|
at the end). |
451 |
|
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
452 |
|
new test for AIM with thSIce + slab-ocean |
453 |
|
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
454 |
|
o move state variable diagnostics to the beginning of the time step ; |
455 |
|
(note: still needs some work specially for snap-shot diagnostics) |
456 |
|
duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
457 |
|
|
458 |
|
checkpoint57c_post |
459 |
|
o Change testing option (-ieee) to get closer agreement between g77 & ifort |
460 |
|
o generate new output.txt files on faulks with g77 & the new -ieee option |
461 |
|
checkpoint57c_pre |
462 |
|
|
463 |
|
o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
464 |
|
update output.txt of exp. global_ocean.90x40x15 |
465 |
|
o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
466 |
|
results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
467 |
|
o add saltFlux(+File) forcing capability with periodicExternalForcing |
468 |
|
o allow to use pkg diagnostics for GM-Redi & ThSIce output |
469 |
|
o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
470 |
|
o improvements for the MNC output from DIAGNOSTICS: |
471 |
|
- correct handling of the unlimitied dimension |
472 |
|
- all dims now have associated coordinate variables |
473 |
|
- variables located at U, V, and Corner ("Z") points are now written |
474 |
|
with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
475 |
|
*all* data points are output |
476 |
|
o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
477 |
|
o added pkg/seaice/seaice_monitor.F |
478 |
|
o mdsio_readfield.F can now read files visible only to master MPI process. |
479 |
|
o pkg/seaice: some test code for ice-modified ocean stress |
480 |
|
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
481 |
|
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
482 |
|
spurious negative numbers for precipitation and humidity. Will cause |
483 |
|
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
484 |
|
o pkg/ctrl/ |
485 |
|
* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
486 |
|
May be enabled via doPackDiag |
487 |
|
* introduce z-scaling of |
488 |
|
+ gradient (doZscalePack) and |
489 |
|
+ control (doZscaleUnpack) |
490 |
|
o pkg/mdsio/ |
491 |
|
* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
492 |
|
* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
493 |
|
|
494 |
|
checkpoint57b_post |
495 |
|
o simplify options in diagnostics_fill arguments (remove weird combinations) |
496 |
|
o fix MNC coordinate variables so that they now contain per-face index |
497 |
|
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
498 |
|
general, EXCH2 grids are only aligned to a "local" coordinate system |
499 |
|
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
500 |
|
o Implement instantaneous output within pkg diagnostics: |
501 |
|
setting a negative frequency in data.diagnostics produces |
502 |
|
"snap-shot" output (as opposed to time-average if freq > 0) |
503 |
|
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
504 |
|
NOTE: change ptracer diagnostics name: use 2 characters to work with |
505 |
|
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
506 |
|
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
507 |
|
becomes the coordinate variable for the 'T' dimension |
508 |
|
o add CF-style coordinate variables to MNC |
509 |
|
- just a first cut: numbers are meaningless on the cubesphere and |
510 |
|
missing along the T axis but otherwise it works! |
511 |
|
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
512 |
|
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
513 |
|
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
514 |
|
this is based directly on what the model compute, so that the content of |
515 |
|
each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
516 |
|
o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
517 |
|
o clean up build options files for SunOS, in particular |
518 |
|
- remove -traditional from xmakedepend |
519 |
|
- change -xarch=v9 to -xarch=native for f77 |
520 |
|
- restore use of make (not gmake) |
521 |
|
- add CC=gcc if using g77 |
522 |
|
o changes per discussion of AM, JMC, & EH3 today: |
523 |
|
- move redundant "grid" variables out of "state" -- in preparation of |
524 |
|
creating proper CF-style coordinate variables and in recognition |
525 |
|
that any/all grid variables can be easily copied (eg. w/NCO) from |
526 |
|
the grid files into any of the other NetCDF files |
527 |
|
- *always* output grid variables with MDSIO (this will eventually be |
528 |
|
changed) |
529 |
|
- output MNC grid file if useMNC is true |
530 |
|
o every instance of _END_MASTER() has been found and replaced with |
531 |
|
_END_MASTER( myThid ) in order to satisfy certain picky Sun |
532 |
|
preprocessors |
533 |
|
o re-arrange diagnostics pkg initialisation: |
534 |
|
- allow each package to extend the available diagnostics list |
535 |
|
- add some checking and fix small problems (multi-threaded, ...) |
536 |
|
- new S/R diagnostics_fill (replace fill_diagnostics): |
537 |
|
look through the short list of active diag. (instead of the long list) |
538 |
|
create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
539 |
|
|
540 |
|
checkpoint57a_post |
541 |
|
o this set of changes restores TAMC compatibility |
542 |
|
tested for global_ocean.90x40x15 adjoint on trough |
543 |
|
(what a pain) |
544 |
|
|
545 |
|
checkpoint57a_pre |
546 |
|
o some modifs in tools/build_options for sunos |
547 |
|
o call ctrl_pack for ctrl at end for optimcycle=0 |
548 |
|
|
549 |
|
checkpoint57 |
550 |
|
o add horizontal bi-harmonic viscosity for vertical velocity |
551 |
|
- new parameter viscA4W (defaults to viscA4) |
552 |
|
- affects only non-hydrostatic code |
553 |
|
- to be done: no-slip lateral boundary conditions |
554 |
|
o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
555 |
|
o implement Implicit Vertical advection for pTracers |
556 |
|
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
557 |
|
(implemented also for implicit vertical diffusion & advection) |
558 |
|
o OBCS: extend application of tracer open boundary conditions |
559 |
|
to a strip beyond the boundary of width Olx/Oly |
560 |
|
o add call monitor to TAF set of required calls (flow directives) |
561 |
|
and include in natl_box_adjoint |
562 |
|
o untangle a few ifdefs related to cost, ctrl, autodiff |
563 |
|
untangel a few ALLOW_ECCO_OPTIMIZATION |
564 |
|
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
565 |
|
(theta2, salt2 in ecco_cost_weights) |
566 |
|
|
567 |
|
checkpoint56c_post |
568 |
|
o OBCS as control variables |
569 |
|
- update ctrl_ad_diff.list, obcs_ad_diff.list |
570 |
|
- remove balance of obcs controls from default |
571 |
|
- fix index bug nobcs in ctrl_init |
572 |
|
- fix dummy fields filen in ctrl_pack |
573 |
|
- add dummy weights for obcs |
574 |
|
o lsopt: comment out fort.94 output |
575 |
|
o optim: |
576 |
|
- remove unnecessary header files |
577 |
|
- adjusted namelists |
578 |
|
- add xerbla.F to Makefile |
579 |
|
o exf: |
580 |
|
- multiple modifications of exf_check_range |
581 |
|
- unit change in exf_init_runoff from [m/year] to [m/s] |
582 |
|
o mdsio: |
583 |
|
- i/o-vector change debugLevel from debLevA to debLevB |
584 |
|
|
585 |
|
checkpoint56b_post |
586 |
|
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
587 |
|
is called from DO_THE_MODEL_IO |
588 |
|
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
589 |
|
- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
590 |
|
- clean up PTRACERS_WRITE_TIMEAVE a little |
591 |
|
o add another verification experiment that tests both the cfc-pkg and |
592 |
|
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
593 |
|
reactive tendencies treated inline with regular timestepping |
594 |
|
o testreport previously did a lousy job of comparing small numbers, so |
595 |
|
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
596 |
|
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
597 |
|
testreport. |
598 |
|
o ptracers_monitor: bug fix for MPI |
599 |
|
|
600 |
|
checkpoint56a_post |
601 |
|
o GCHEM: finish reorganizating the package |
602 |
|
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
603 |
|
(introduces another 3D-array for each passive tracer, but only if |
604 |
|
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
605 |
|
gchemTendency is not needed because the timestep is done separately) |
606 |
|
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
607 |
|
- GCHEM is now---more or less cleanly---separate from PTRACERS |
608 |
|
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
609 |
|
so clear to me how that should be done in a general way. |
610 |
|
o CFC: improve formatting of output in CFC_ATMOS |
611 |
|
o PTRACERS: |
612 |
|
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
613 |
|
that ALL experiments with ptracers enable can be checked. This makes |
614 |
|
GCHEM_MONITOR obsolete. |
615 |
|
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
616 |
|
monitorFreq |
617 |
|
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
618 |
|
o add PTRACERS (PTR0[1-5]) to testreport output |
619 |
|
o exf_check_range: |
620 |
|
* default changed to .TRUE. |
621 |
|
* will check values for niter0 if debLevA, every timestep if debLevB |
622 |
|
* STOP in exf_check_range if 'out of range' |
623 |
|
* range chosen generous to allow for potential extema |
624 |
|
TBD: a version with stricter range |
625 |
|
permitted range would be runtime parameters |
626 |
|
o GMredi: |
627 |
|
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
628 |
|
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
629 |
|
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
630 |
|
o GCHEM: |
631 |
|
- move call to GCHEM_FORCING_SEP, so that it is now called before |
632 |
|
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
633 |
|
- introduced a useGCHEM runtime flag and applied it everywhere. |
634 |
|
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
635 |
|
this flag is now only visible within GCHEM-pkg routines. |
636 |
|
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
637 |
|
be replaced by a 3D array that is computed before thermodynamics; for |
638 |
|
this, the tracer ID iTracer had to be included into the parameter list |
639 |
|
of ptracers_forcing |
640 |
|
- set up forward_step to call gchem_forcing, that will replace |
641 |
|
gchem_forcing_int in ptracers_forcing |
642 |
|
- cleaning up |
643 |
|
o small cleaning of exch2: remove files that are also in eesupp/src |
644 |
|
|
645 |
|
checkpoint56 |
646 |
|
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
647 |
|
o mnc: cleanup "full" files--fixes out-of-memory problem |
648 |
|
o ECCO-GODAE |
649 |
|
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
650 |
|
* fully merged and updated from SIO code |
651 |
|
windstress sign change affects |
652 |
|
- exf_inscal_[u/v]stress |
653 |
|
- sign of xx_tau[u/v] adjustments |
654 |
|
- signs in cost_scat |
655 |
|
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
656 |
|
* natl_box_adjoint updated and compressed |
657 |
|
* 2-level checkpoint switch added |
658 |
|
(tested in EXP. 1 of natl_box_adjoint) |
659 |
|
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
660 |
|
o SVD |
661 |
|
* first complete, non-hacked version for SVD calculations |
662 |
|
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
663 |
|
performed via direct access files admtlm_vector.it???? |
664 |
|
(via ctrl_[un]pack) |
665 |
|
* optimcycle is used for ARPACK iteration counter |
666 |
|
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
667 |
|
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
668 |
|
and add linear transforms where necessary |
669 |
|
* controls are initial/final SST, SSS (can be extended; need to check |
670 |
|
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
671 |
|
o mdsio: filename info to both stderr, stdout |
672 |
|
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
673 |
|
from sign change |
674 |
|
|
675 |
|
checkpoint55j_post |
676 |
|
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
677 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
678 |
|
o add consistent build directories and .cvsignore files to verification |
679 |
|
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
680 |
|
o make all subroutines 30 or less characters in length for certain older |
681 |
|
compilers to work (a thorough search only turns up two routines in |
682 |
|
pkg/ptracers) |
683 |
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
684 |
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
685 |
|
|