4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
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|
7 |
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o pkg/seaice: |
8 |
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- account for melting in seaice age evolution. |
9 |
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|
10 |
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checkpoint62h (2010/06/18) |
11 |
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o pkg/exch2: |
12 |
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- remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1). |
13 |
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o tools/genmake2 |
14 |
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- remove "-pdefault" option: redundant with the use of "packages.conf"; |
15 |
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- remove file pkg/pkg_default : set the default as a pkg group |
16 |
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("default_pkg_list") defined in pkg/pkg_groups; |
17 |
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- fix for case pkg/pkg_depend is missing (was hanging before); |
18 |
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- add option "-pgroups" to specify a different pkg_groups than the default. |
19 |
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o verification/adjustment.cs-32x32x1: |
20 |
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add a "minimal" set-up test (code_min & input_min) which only compiles |
21 |
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eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc. |
22 |
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o tools/genmake2 |
23 |
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- extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg])) |
24 |
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- fix details of checking for mnc & profile pkg when NetCDF is unavailable. |
25 |
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o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these |
26 |
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files are nearly the same anyway. |
27 |
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Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04: |
28 |
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- redefinition of tau(i,i) (by a factor of ustar) |
29 |
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- 1./exf(Const/T) -> exf(-Const/T) (big change in the results) |
30 |
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- replace rhonil by rhoConstFresh in computation of evap (bug fix) |
31 |
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- replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results) |
32 |
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- replace |
33 |
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rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh ) |
34 |
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shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j) |
35 |
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by |
36 |
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shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh ) |
37 |
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(changes results) |
38 |
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-> exf_bulkformulae v1.22, |
39 |
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update verification experiments lab_sea, offline_exf_seaice, seaice_obcs |
40 |
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(lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13, |
41 |
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output.txt 1.63 |
42 |
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offline_exf_seaice: output.seaicetd.txt 1.7 |
43 |
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seaice_obcs: output.txt 1.10) |
44 |
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Step 2: do the actual merge and remove exf_bulk_largeyeager04.F |
45 |
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-> exf_bulkformulae v1.23, |
46 |
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unfortunately requires updating lab_sea.salt_plume (6 matching digits), |
47 |
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and global_ocean.cs32x15.icedyn (only 11 matching digits) |
48 |
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Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice. |
49 |
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o adjoint of exch-1: |
50 |
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- pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list) |
51 |
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(note: was already like this when using EXCH-2) and remove flow dir |
52 |
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and hand-written AD version of high-level EXCH S/R (pkg/autodiff); |
53 |
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- provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow); |
54 |
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- update pkg/exch2 diff list. |
55 |
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|
56 |
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checkpoint62g (2010/05/19) |
57 |
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o eesupp/src (exch-1): |
58 |
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- split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F) |
59 |
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and remove argument "simulationMode"; same thing for all exch_*rx_cube.F |
60 |
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(renamed to exch1_*rx_cube.F). |
61 |
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- change accordingly exch_*_rx.template and AD version in pkg/autodiff |
62 |
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to call new exch1 S/R ; update Makefile and .cvsignore. |
63 |
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- replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove |
64 |
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exch2_xy_rx later) |
65 |
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Note: after updating your code, need to run "make clean" in eesupp/src |
66 |
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o test experiment bottom_ctrl_5x5: |
67 |
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new output_adm.txt with fewer grdchk & less monitor output. |
68 |
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o model/src: |
69 |
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remove the call to ini_cori in initialise_varia.F (just keep the usual one |
70 |
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in initialise_fixed.F). More consistent with coriolis & horizontal grid |
71 |
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beeing treated in the same way (ini_grid is not called a 2nd time). |
72 |
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o pkg/exf: |
73 |
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- rewrite exf_bulk_largeyeager04.F for better vectorization, changes |
74 |
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global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated |
75 |
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- fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now) |
76 |
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- cosmetic changes to exf_bulkformulae.F to make it look more like |
77 |
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exf_bulk_largeyeager04.F |
78 |
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o eesupp/src (exch-1): |
79 |
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- Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1). |
80 |
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- Separate buffer filling and MPI sending: allow EXCH-1 to work for local |
81 |
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array (non-shared) when using MPI+MTH. Also reduces number of BARRIER |
82 |
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(even without using MPI). |
83 |
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- Message mode: move RecvAck setting (indicator of buffer being ready) |
84 |
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from send_put to recv_get S/R (was useless before, but not sure if |
85 |
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it's much more useful now); |
86 |
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- Switch the order of sync: MPI-proc 1rst and then threads; |
87 |
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- take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead. |
88 |
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- fix AD code for communication mode ='get' (but not used). |
89 |
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o model/src: |
90 |
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initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does |
91 |
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not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp). |
92 |
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o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API |
93 |
|
o pkg/ctrl: require a specific set of control variables and exf-flags for |
94 |
|
adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied) |
95 |
|
o model/src: |
96 |
|
a) 1rst version of a new driver S/R to turn-off output freq and flags after the |
97 |
|
1rst forward sweep, to avoid over-writing output files during recomputations |
98 |
|
recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?) |
99 |
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b) 2nd version: |
100 |
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- add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO); |
101 |
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- switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast, |
102 |
|
writePickupAtEnd) + seaice & ptracers output; |
103 |
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- do not switch off MNC flags (otherwise, won't get admonitor netcdf file) |
104 |
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o model/src: |
105 |
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- new S/R rotate_uv2en_rl (..._rs) that rotates vector fields. |
106 |
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o pkg/exch2: |
107 |
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- remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ; |
108 |
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- add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch). |
109 |
|
o pkg/autodiff & exch2: |
110 |
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process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF |
111 |
|
(for now, only if ALLOW_EXCH2 is defined). |
112 |
|
o pkg/autodiff: |
113 |
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- include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F |
114 |
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(not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly. |
115 |
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+ clean-up comments (_RS is not always real*4) |
116 |
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- fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R) |
117 |
|
- add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2: |
118 |
|
was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs. |
119 |
|
o testreport (AD-tests): |
120 |
|
no longer link files from dir "../input" (1rst link files from |
121 |
|
"../input_ad.[xx]" if secondary test "xx" and then from "../input_ad") |
122 |
|
|
123 |
|
checkpoint62f (2010/04/29) |
124 |
|
o model/src/the_main_loop.F: |
125 |
|
adjust store directives for seaice evp and multicategory according to |
126 |
|
pkg/ecco/the_main_loop.F |
127 |
|
o adjoint: |
128 |
|
global_sum_ad was incomplete (noted many times by many people ;) |
129 |
|
nice description by Jean U. as follows: |
130 |
|
* allreduce(var) in global_sum.F can be interpreted as |
131 |
|
reduce(sum) followed by broadcast of sum. |
132 |
|
* The adjoint of that is |
133 |
|
sum(adjoint) followed by broadcast(summed adjoint value) |
134 |
|
or in other words, allreduce(sum, adjoint vars) |
135 |
|
We were missing the sum(adjoint)! |
136 |
|
Benign, except(!) for "global" scalars appearing in tile loops (bi,bj) |
137 |
|
(noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset). |
138 |
|
The fix should produce 16-digit accuracy between |
139 |
|
single-CPU multi-tile (e.g. nSx=2, nPx=1) and |
140 |
|
multi-CPU single-tile (e.g. nSx=1, nPx-2) |
141 |
|
We'll probably change this yet again shortly |
142 |
|
o eesupp/src: |
143 |
|
- fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?) |
144 |
|
o pkg/icefront |
145 |
|
- ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving |
146 |
|
specification of addmass array based on a 2D field, which is added |
147 |
|
at bottommost wet level at each horizontal location. |
148 |
|
o model/src: |
149 |
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horizontal grid initialisation (other than curvilinear): add code for Exch2 IO |
150 |
|
layout; (not always compatible with delX,delY setting; commented out for now). |
151 |
|
o pkg/exch2: |
152 |
|
change tile to processor setting (case nSy*nPy > 1): allows default model mapping |
153 |
|
(myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config. |
154 |
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|
155 |
|
checkpoint62e (2010/04/15) |
156 |
|
o pkg/obcs: |
157 |
|
- fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert). |
158 |
|
o pkg/dic: |
159 |
|
-fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up; |
160 |
|
(note: not presently tested in any forward verification exp.) |
161 |
|
update tutorial_global_oce_biogeo AD output file. |
162 |
|
o pkg/exf: |
163 |
|
- account for the variation of albedo as a function of zenith angle |
164 |
|
by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h |
165 |
|
o build_options: |
166 |
|
- rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas" |
167 |
|
o pkg/dic: |
168 |
|
change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart: |
169 |
|
- use binary pickup file for restart; |
170 |
|
- initialise atmos-CO2 box from dic_pCO2 parameter; |
171 |
|
- fix multi-threaded. |
172 |
|
o pkg/rbcs: |
173 |
|
- clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ; |
174 |
|
change (+ fix IO calls) type of array RBC_mask from _RL to _RS. |
175 |
|
- add RBCS to exp4 passive tracer 01 (rbcs was previously untested) |
176 |
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and update output.txt |
177 |
|
o pkg/kpp: |
178 |
|
- add diagnostics for KPP non-local flux of Temp, Salinity and pTracers; |
179 |
|
- change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS |
180 |
|
(= ratio of KPP non-local (salt) flux relative to surface-flux) when |
181 |
|
using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat '); |
182 |
|
- change pkg/offline to read-in average KPPghat*KPPdiffKzS from file |
183 |
|
KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile). |
184 |
|
o pkg/offline: |
185 |
|
fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor |
186 |
|
(bug was added in version 1.10 on 2007-08-23). |
187 |
|
o pkg/offline: |
188 |
|
- no need to specify periodicExternalForcing, etc ... to use offline pack |
189 |
|
- offline input files no longer just single prec --> parameter offlineLoadPrec |
190 |
|
o verification/lab_sea: |
191 |
|
change AD test to multi-tile setup and update all 4 AD output. |
192 |
|
NOTE: while cost function values remain very similar, |
193 |
|
gradients are very different, although gradient checks are self-consistent |
194 |
|
Should try to get to the bottom of this (cost function summation order?) |
195 |
|
o pkg/dic: |
196 |
|
in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid |
197 |
|
a weakness of TAF that drops part of double precision in log10 derivative. |
198 |
|
<= changes removed since problem has been fixed in current TAF version 1.9.71 |
199 |
|
update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo. |
200 |
|
o pkg/ecco: |
201 |
|
add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F |
202 |
|
update all 4 lab_sea AD output. |
203 |
|
|
204 |
|
checkpoint62d (2010/03/22) |
205 |
|
o build_options: |
206 |
|
remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles. |
207 |
|
o remove unbalanced quote (single or double) in commented line of source code |
208 |
|
(may cause some warning with some preprocessor/makedepend versions). |
209 |
|
o pkg/seaice: |
210 |
|
fix seaice_model.F for adjoint (gael) and update AD results of experiments |
211 |
|
lab_sea (std + evp + noseaicedyn) and offline_exf_seaice. |
212 |
|
o testreport: |
213 |
|
add option '-runonly' (short: '-ro') to just do the run part (without make). |
214 |
|
o eesupp: remove JAM communication code (obsolete). |
215 |
|
o add option to genmake2 & testreport to switch "_RS" type to "real*4" |
216 |
|
(if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return |
217 |
|
to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1 |
218 |
|
(update also the output). |
219 |
|
|
220 |
|
checkpoint62c (2010/03/02) |
221 |
|
o tools/build_options : |
222 |
|
move (some) old optfiles from build_options/ to build_options/unsupported/ |
223 |
|
o model/src and pkg/exf |
224 |
|
surface relaxation -- separating data and data.exf options |
225 |
|
The point is to ensure that we specify the surface relaxation |
226 |
|
either in data or in data.exf (but not half and half) and to |
227 |
|
avoid an accidental relaxation to 0 (which happened if a time |
228 |
|
scale was specified but the file name was left empty) |
229 |
|
o model/src model/inc and pkg/mom_common |
230 |
|
ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity |
231 |
|
=> addition to the viscosity field as computed by others schemes |
232 |
|
o tools/build_options: |
233 |
|
- rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile) |
234 |
|
but keep the former optfile for few weeks for smooth transition |
235 |
|
o pkg/ecco |
236 |
|
- allow user defined cost function contributions |
237 |
|
CPP: ALLOW_USERCOST_CONTRIBUTION |
238 |
|
USAGE: compute contributions in cost_usercost_all.F |
239 |
|
- note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. |
240 |
|
the two options are complementary. |
241 |
|
o pkg/smooth |
242 |
|
- migration from contrib to the main repository |
243 |
|
|
244 |
|
checkpoint62b (2010/01/26) |
245 |
|
o pkg/monitor: |
246 |
|
- change back mon_printstats_rl.F & mon_stats_rl.F and add a stop |
247 |
|
(in case someone forgot to update customized pieces of code) |
248 |
|
o nonHydrostatic: |
249 |
|
- add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested); |
250 |
|
- add a simple 2-D experiment (short_surf_wave) to test it. |
251 |
|
o pkg/icefront: |
252 |
|
adding the shell of, and the hooks to, a new package that |
253 |
|
will model melting and freezing of vertical glacier ice fronts |
254 |
|
o momentum: |
255 |
|
add diagnostics of momentum tendency from Hydrostatic pressure gradient |
256 |
|
(without surf.pressure term: would need a 2nd filling since implicit term). |
257 |
|
o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace |
258 |
|
two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR |
259 |
|
cannot deal with the former |
260 |
|
o cleaning: |
261 |
|
- remove all (except OpenAD) old TLM output from results_ad dirs. |
262 |
|
- remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R) |
263 |
|
- comment out maskH definition (replaced by maskInC) |
264 |
|
o pkg/monitor: |
265 |
|
- change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl |
266 |
|
& mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs. |
267 |
|
|
268 |
|
checkpoint62a (2010/01/15) |
269 |
|
o model/src: |
270 |
|
- bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4) |
271 |
|
o pkg/diagnostics: |
272 |
|
- add optional level number diagnostics (i.e., level number to be define |
273 |
|
explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X". |
274 |
|
- strictly check for valid parser-code(10) ; |
275 |
|
- check if adding diag to the list from the right place. |
276 |
|
o pkg/longstep: |
277 |
|
- change parameters and fix tracer conservation with rstar/nonlinear free surface |
278 |
|
o diagnostics: |
279 |
|
- in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer |
280 |
|
S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics. |
281 |
|
o pkg/diagnostics: |
282 |
|
- Add option for writing vertical integral (sum of selected levels) of an output |
283 |
|
field instead of writing output field levels. Activate this option on a per |
284 |
|
output-file basis, by setting the 2nd character of fileflag to 'I'. |
285 |
|
- Add field-specific information relative to level integral in 3rd postion |
286 |
|
of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate |
287 |
|
vertically (x level-thickness x hFac), "r"=same but without hFac. |
288 |
|
o do_the_model_io: |
289 |
|
- pass end-of-model-run flag as argument, from forward_step to diagnostics_write: |
290 |
|
in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before |
291 |
|
writing pickups and stopping. |
292 |
|
o pkg/diagnostics (for now, only with mdsio): |
293 |
|
- write time information to meta file (and modify accordingly rdmds.m) : |
294 |
|
time-averaged diagnostics output: write starting and ending time of the |
295 |
|
time-averaging interval ; snap-shot diagnostics output remains unchanged; |
296 |
|
o pkg/timeave: |
297 |
|
- S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously |
298 |
|
always Nr), now assumed to be equal to number of levels of averaged field; |
299 |
|
only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F |
300 |
|
o pkg/sbo: |
301 |
|
- fix ocean bottom pressure global-average & 2-D time-ave output (was |
302 |
|
neither initialised nor filled). |
303 |
|
- add starting iteration in suffix of global-average output file |
304 |
|
(to avoid over-writing the file after a restart) |
305 |
|
- use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb). |
306 |
|
o time-average: |
307 |
|
- use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj) |
308 |
|
(pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf, |
309 |
|
ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice) |
310 |
|
this fix DIC_COST cumulative-time array (previously: bi,bj,k) |
311 |
|
- fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice) |
312 |
|
- fix missing accumulation for pkg/opps. |
313 |
|
- cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0) |
314 |
|
(pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81); |
315 |
|
- fix initialisation of time-ave vars and do only full time-step increment |
316 |
|
(i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81); |
317 |
|
o pkg/layers: |
318 |
|
- use standard RW pkg S/R to write the output |
319 |
|
and remove local write_fld version (which had a problem). |
320 |
|
- use simple cumulative-time array (no level index) to fix time-ave S/R calls. |
321 |
|
- fix LAYERS_CALC argument list. |
322 |
|
o pkg/timeave: |
323 |
|
- store cumulative-time in a simple tiled array (drop the level index) |
324 |
|
- add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array. |
325 |
|
o pkg/ocn,aim_compon_interf |
326 |
|
- changes for multi-threaded coupled run. (tested with ifort-11 on danton) |
327 |
|
|
328 |
checkpoint62 (2009/12/23) |
checkpoint62 (2009/12/23) |
329 |
o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output. |
o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output. |
330 |
(was not previously tested in any other exp.) |
(was not previously tested in any other exp.) |