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3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
4 |
============================== |
============================== |
5 |
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6 |
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checkpoint55g_post |
7 |
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o Renaming carbon AD experiments to comply with testreport conventions |
8 |
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o Updating adjoint of Held-Suarez hs94.1x64x5 |
9 |
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o Fixing directives for non-ECCO forward_step, after ECCO directives |
10 |
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have been fixed to avoid recomp. of do_oceanic_phys |
11 |
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Works well for global_ocean.90x40x15, |
12 |
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but recomp. issue remains for carbon |
13 |
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o Updating adjoint output for natl_box_adjoint after |
14 |
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pkg/ecco has been modified (see taga c55d_post) |
15 |
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|
16 |
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checkpoint55f_post |
17 |
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o rename to timeave_init_fixed |
18 |
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|
19 |
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checkpoint55e_post |
20 |
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o some delicate re-shuffle of store directives to avoid one |
21 |
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extra call of do_oceanic_physics |
22 |
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affects ecco_the_main_loop.F, do_oceanic_physics.F |
23 |
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checkpoint_lev1_directives.h |
24 |
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o NB: this may break global_ocean adjoint temporarily, |
25 |
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but it is clear how to fix it. Will do later, need this now. |
26 |
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|
27 |
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checkpoint55d_post |
28 |
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o ECCO specific cost function terms (up-to-date with 1x1 runs) |
29 |
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o ecco_cost_weights is modified to 1x1 runs |
30 |
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o modifs to allow observations to be read in as |
31 |
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single file or yearly files |
32 |
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o enable to read exf forcing fields as either |
33 |
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single file or yearly files (flag useExfYearlyFields) |
34 |
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checkpoint55d_pre |
35 |
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|
36 |
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o switch between 2-level and 3-level checkpointing |
37 |
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o add ability of MNC to write local and "partial" (eg. 2D slices where |
38 |
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the full 3D field is never actually stored) arrays to NetCDF files |
39 |
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with the correct (that is, the complete multi-dimensional) set of |
40 |
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array indicies |
41 |
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- used in mom_vecinv() to write the diagFreq output |
42 |
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- tested (demonstrated) in verification/aim.5l_cs |
43 |
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o further mnc-ification |
44 |
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- add verification/lab_sea to the list with mnc setups |
45 |
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- fix undefined mnc v-names in cd_code |
46 |
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- add kpp to mnc output (both snapshot and timeave) |
47 |
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o non-hydrostatic code |
48 |
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- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
49 |
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in calc_gw.F |
50 |
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- defaults to viscAh |
51 |
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- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
52 |
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friction or Leith) in non-hydrostatic mode, as long as there is |
53 |
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no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
54 |
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o pkg/cost |
55 |
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extend simple cost functions to treat time mean quantities |
56 |
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(T,U,V) via cost_accumulate_state from cost_tile |
57 |
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o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
58 |
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be 2 times larger than the minimum size the advection scheme requires. |
59 |
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now get a perfect conservation of salt in advect_cs test-exp (updated) |
60 |
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o GGL90 (Gaspar's TKE mixed layer) |
61 |
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- add horizontal diffusion of TKE, requires exchanges in |
62 |
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do_fields_blocking_exchanges, horizontal diffusivity is zero by |
63 |
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default. In OPA there is no horizontal diffusion of TKE but the |
64 |
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mixing coefficients are computed from a horizontal average of TKE of |
65 |
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6 points or so. I think that diffusion has a little more physical |
66 |
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justification. |
67 |
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- clean up ggl90_calc in the hope of reducing memory usage (this hope |
68 |
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was in vain) |
69 |
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- mask tke-variable in ggl90_init |
70 |
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o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
71 |
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o fix biharmonic diffusion on CS-grid. |
72 |
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o more obcs stuff |
73 |
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- added obcs_external_fields_load as an alternative to the EXF-pkg option |
74 |
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for reading boundary values. This routine is called from |
75 |
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obcs_prescribe_read |
76 |
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- updated obcs_check |
77 |
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- changed sponge layer relaxation parameter units for days to seconds |
78 |
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- turned off sponge layer by default |
79 |
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- changed argument list of OBCS_CALC to myTime+deltaTclock |
80 |
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- fixed about 35 bugs in obcs_external_fields_load |
81 |
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|
82 |
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checkpoint55c_post |
83 |
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o obcs stuff |
84 |
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- new runtime flags useOBCSprescribe, useOBCSbalance |
85 |
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- re-arranged obcs_calc |
86 |
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- moved exf_getobcs to obcs_prescibe_read |
87 |
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obcs_prescibe_read is called after ORLANSKI stuff |
88 |
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and independent of it (executable can contain all). |
89 |
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- updated obcs_check |
90 |
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- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
91 |
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These may be necessary only if tangential velocities are |
92 |
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prescribed at OB, not sure, needs testing. |
93 |
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o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
94 |
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which simplifies the calls and passes the ifc check-bounds test |
95 |
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|
96 |
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checkpoint55b_post |
97 |
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o add a 2D scalar, Z location, exchange_2 routine. |
98 |
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o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
99 |
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to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
100 |
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affects advect_cs results (for the wrong reason): update output.txt |
101 |
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o use a more standard discretization for biharmonic viscosity ; |
102 |
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(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
103 |
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affects results of dome set-up: update output.txt |
104 |
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o fix gad_advection.F (CubedSphere part), back to version 1.23 |
105 |
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o fix bug in mom_vi_del2uv.F (CubedSphere part). |
106 |
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|
107 |
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checkpoint55a_post |
108 |
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o merged code to |
109 |
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* prescribe/read time-dependent open boundaries |
110 |
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(works in conjunction with exf, cal) |
111 |
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* sponge layer code for open boundaries |
112 |
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* each boundary N/S/E/W now has its own CPP option |
113 |
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(healthy for the adjoint) |
114 |
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|
115 |
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checkpoint55 |
116 |
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o up-to-date adjoint of previous breaks |
117 |
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- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
118 |
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- global_ocean_ebm: adjoint still needs fix (TLM ok) |
119 |
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- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
120 |
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- carbon: * remove tr1-related adjoint verification |
121 |
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* add ptracer as control variable |
122 |
|
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
123 |
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(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
124 |
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|
125 |
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checkpoint54f_post |
126 |
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o in verification/carbin/ remove experiment related to |
127 |
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ALLOW_PASSIVE_TRACER (array tr1 etc) |
128 |
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code_ad/ input_ad/ results_ad |
129 |
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|
130 |
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o add two new packages |
131 |
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- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
132 |
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+ subject to optimization (memory) |
133 |
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- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
134 |
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+ subject to reordering (many GOTOs in the original code) |
135 |
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+ so far opps is called for every (i,j) point, and then operates in |
136 |
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the vertical; one may want to reorder the scheme in order operate in |
137 |
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horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
138 |
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fields) |
139 |
|
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
140 |
|
- all verification tests compile and run with linux_ia32_g77 |
141 |
|
- defaults are compatible with current input files--nothing |
142 |
|
should change if you were not previously using MNC |
143 |
|
- MNC output has been added in numerous places (eg. timeave) |
144 |
|
but there are still a few writes not yet do-able with MNC |
145 |
|
(this is in progress) |
146 |
|
- flags now allow for either/or/both use of MDSIO and MNC and |
147 |
|
documentation will soon follow |
148 |
|
- numerous small formatting cleanups for ProTeX |
149 |
|
o add version info (via BUILD_INFO.h) to MNC and stdout |
150 |
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|
151 |
|
checkpoint54e_post |
152 |
|
o add two new packages |
153 |
|
- pp81 (Packanowski and Philander, 1981), Richardson number and |
154 |
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stratification dependent mixing |
155 |
|
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
156 |
|
- these scheme operate in a similar manner as KPP (without ghat, of |
157 |
|
course), however there is only one diffusivity that is used for both |
158 |
|
temperature and salinity (and passive tracers)ç |
159 |
|
o add offline package |
160 |
|
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
161 |
|
provided by Stephanie Dutkiewicz |
162 |
|
o genmake2: add ability to search for C compilers and cleanup test output |
163 |
|
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
164 |
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|
165 |
|
checkpoint54d_post |
166 |
|
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
167 |
|
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
168 |
|
leading to additional shift by 5 days each year of integration |
169 |
|
(i.e. leading to considerable offset over the years) |
170 |
|
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
171 |
|
o start with no AB and no initial filtering (staggerTimeStep): |
172 |
|
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
173 |
|
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
174 |
|
(external loading & cpl import/export stay in forward_step.F) |
175 |
|
o update coupling interface to work with new staggerTimeStep |
176 |
|
o change MDSIO ptracers_pickup. |
177 |
|
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
178 |
|
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
179 |
|
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
180 |
|
|
181 |
|
checkpoint54c_post |
182 |
|
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
183 |
|
this affects (truncation error) output.txt of test-exp: |
184 |
|
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
185 |
|
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
186 |
|
o change Qnet to always be the net heat flux, (+upward). |
187 |
|
affects (truncation error) output of natl_box exp.: updated |
188 |
|
o define the max number of passive tracers in PTRACERS_SIZE.h |
189 |
|
o start to test mnc routinely in exp0 |
190 |
|
o add sea-ice loading (sIceLoad) as a new forcing field. |
191 |
|
|
192 |
|
checkpoint54b_post |
193 |
|
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
194 |
|
impressive on Altix and Opteron systems) |
195 |
|
o diagnostics can now write NetCDF files through the mnc package |
196 |
|
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
197 |
|
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
198 |
|
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
199 |
|
affects (truncation error) output of lab_sea & natl_box exp.: updated |
200 |
|
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
201 |
|
|
202 |
|
checkpoint54a_post |
203 |
|
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
204 |
|
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
205 |
|
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
206 |
|
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
207 |
|
+ internal_wave (shift in writing cg2d_ini_res) |
208 |
|
checkpoint54a_pre |
209 |
|
|
210 |
|
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
211 |
|
- modified verification/lab_sea and natl_box_adjoint accordingly |
212 |
|
|
213 |
|
checkpoint54 |
214 |
|
checkpoint53g_post |
215 |
|
o prepare splitting of thermodynamics: store convect.counter in common block |
216 |
|
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
217 |
|
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
218 |
|
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
219 |
|
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
220 |
|
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
221 |
|
o restore adjointability |
222 |
|
|
223 |
|
checkpoint53f_post |
224 |
|
o modifications that affect AIM experiment results (update output.txt): |
225 |
|
- no advection of S at top interface Nr (pkg/generic_advdiff) |
226 |
|
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
227 |
|
o AIM pkg: |
228 |
|
- include stability function into surf.Flux derivative relative to Tsurf |
229 |
|
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
230 |
|
|
231 |
|
checkpoint53e_post |
232 |
|
o merged cylindrical coord configuration |
233 |
|
o added rotating_tank experiment |
234 |
|
checkpoint53e_pre |
235 |
|
|
236 |
|
checkpoint53d_post |
237 |
|
o faulks upgraded: re-generate output.txt that have changed: |
238 |
|
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
239 |
|
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
240 |
|
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
241 |
|
o added Sadourny discretization of Coriolis |
242 |
|
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
243 |
|
- re-enabled use of omega3 (useAbsVorticity) |
244 |
|
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
245 |
|
vector-invariant equations |
246 |
|
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
247 |
|
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
248 |
|
hopefully without new bugs |
249 |
|
- still to do: biharmonic friction for non-hydrostatic w |
250 |
|
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
251 |
|
o regenerated output for global_ocean_ebm (using -ieee) |
252 |
|
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
253 |
|
of mom_common/ |
254 |
|
- simple re-arrangement of instructions within computing loop |
255 |
|
checkpoint53d_pre |
256 |
|
|
257 |
|
checkpoint53c_post |
258 |
|
o new version of coupler for AIM+thSIce and Ocean models |
259 |
|
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
260 |
|
- land: change Evaporation of snow |
261 |
|
- aim with thSIce: fix bug in snow-precip. |
262 |
|
o changes to calc_gw.F |
263 |
|
- bug fix for w^2 term near the bottom boundary |
264 |
|
- (hopefully) improve the lateral slip boundary condtions for use with |
265 |
|
partial/looped cells |
266 |
|
- because the bug fix changes two verification experiments anyway (exp5 |
267 |
|
and plume on slope), change the lateral boundary condition from half slip |
268 |
|
to the value of no_slip_sides |
269 |
|
o ebm package wasnt quite up to the parallel task. Fixed that. |
270 |
|
o Adjoint of EBM package + verification |
271 |
|
* TLM OK |
272 |
|
* ADM not sufficient accuracy yet (needs further testing) |
273 |
|
|
274 |
|
checkpoint53b_post |
275 |
|
o Commiting new energy balance model to repository |
276 |
|
* package is pkg/ebm |
277 |
|
* verif. is verification/global_ocean_ebm |
278 |
|
* references are in ebm_driver.F |
279 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
280 |
|
C Global thermohaline circulation. Part I: |
281 |
|
C Sensitivity to atmospheric moisture transport. |
282 |
|
C J. Climate 12(1), 71-82 |
283 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
284 |
|
C Global thermohaline circulation. Part II: |
285 |
|
C Sensitivity with interactive transport. |
286 |
|
C J. Climate 12(1), 83-91 |
287 |
|
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
288 |
|
C Destabilization of the thermohaline circulation |
289 |
|
C by atmospheric eddy transports. |
290 |
|
C J. Climate 7(12), 1870-1882 |
291 |
|
o Will need long integration testing. |
292 |
|
checkpoint53b_pre |
293 |
|
|
294 |
|
o created pkg/mom_common in preparation for variable viscosity code |
295 |
|
o renamed and split ini_mnc_io |
296 |
|
o pkg/land: only liquid water can diffuse or run-off |
297 |
|
o AIM using land: soil wetness availability account for snow |
298 |
|
o added printMapIncludesZeros to EEPARMS namelist |
299 |
|
|
300 |
|
checkpoint53a_post |
301 |
|
o restore TAMC compatiility for exf_constants.h |
302 |
|
(no usage of _d in .h) |
303 |
|
o Additional storing in KPP in an attempt to fix |
304 |
|
TAMC problem with adjoint of KPP code. |
305 |
|
(no success...) |
306 |
|
Identical code works fine with TAF. |
307 |
|
o Fixed verification/natl_box_adjoint experiments. |
308 |
|
Initial conditions for Experiments 4 and 5 are now |
309 |
|
set to "SEAICE_initialHEFF=0", which is more reasonable, |
310 |
|
and hence gives results closer to that of Experiment 2. |
311 |
|
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
312 |
|
|
313 |
|
checkpoint53 |
314 |
|
o stable checkpoint with up to date adjoint |
315 |
|
TLM tests only run for 1st grdchk at the moment. Its unclear if |
316 |
|
this is a code problem or a problem with resetting code for g_ |
317 |
|
variables that is being autogenerated wrong. |
318 |
|
Otherwise: |
319 |
|
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
320 |
|
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
321 |
|
are both still in chaos following their security messes. |
322 |
|
|
323 |
|
checkpoint52n_post |
324 |
|
o various build (mostly genmake2) changes including: |
325 |
|
- ability to build/run more easily within Cygwin and MacOS X |
326 |
|
- more complicated Makefiles with a stronger dependence on Gnu Make |
327 |
|
o pkg/seaice modifications |
328 |
|
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
329 |
|
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
330 |
|
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
331 |
|
- changed proxy for geostrophic velocity and updated |
332 |
|
verification/lab_sea/results/* accordingly |
333 |
|
- removed ADI dynamic solver from pkg/seaice |
334 |
|
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
335 |
|
they caused a segmentation fault under certain circumstances |
336 |
|
- removed unused field WATR |
337 |
|
o bug fix in exf-package: |
338 |
|
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
339 |
|
now reflect that. |
340 |
|
o small fixes in the cal-package: |
341 |
|
- set reference date to first of January for the 'model'-calendar |
342 |
|
- failing of cal_CheckDate in cal_FullDate now actually results in a |
343 |
|
warning |
344 |
|
o small modifications in exf-package to increase flexibility: |
345 |
|
- change climtempfreeze from a constant to a runtime parameter that |
346 |
|
is specified in data.exf_clim (default = -1.9) |
347 |
|
- introduce runtime parameter windstressmax (default = 2.0) that is |
348 |
|
specified in data.exf |
349 |
|
o fix in pkg/thsice: |
350 |
|
- update Evap (Tsf changes) to be consistent with Latent heat flux |
351 |
|
- maintain snow precipitation unchanged (even if Tsf >=0). |
352 |
|
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
353 |
|
|
354 |
|
checkpoint52m_post |
355 |
|
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
356 |
|
this does not change any of the results, because myIter=0 in swfrac always |
357 |
|
lead to jwtype=2 (the default anyway), but the call makes little sense |
358 |
|
as a default |
359 |
|
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
360 |
|
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
361 |
|
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
362 |
|
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
363 |
|
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
364 |
|
o extending useSingleCpuIO option to work with new exch2 I/O format |
365 |
|
- old-style, missing-tile I/O is still accessible by defining CPP |
366 |
|
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
367 |
|
o monitor package can write to NetCDF files and/or STDOUT |
368 |
|
o fix re-definition bug in MNC_GRID_INIT_ALL() |
369 |
|
o doc/api_reference added |
370 |
|
- a framework for building an API Reference Manual using all |
371 |
|
the "protex" comments embedded in the code |
372 |
|
- see pkg/generic_advdiff, pkg/mnc for examples |
373 |
|
o MNC: |
374 |
|
- make myThid the last argument for all subroutines |
375 |
|
- new default for the grid files: NO halos |
376 |
|
- add useMNC and other run-time flags |
377 |
|
- separate per-file-group handling of the unlimited dimension |
378 |
|
- early initialization of MNC w/ flags read at the eeboot stage |
379 |
|
and lookup tables set in initialize_fixed |
380 |
|
- write all MNC output to a freshly-created directory |
381 |
o thermodynamics sea-ice (thsice) is now tested with testreport. |
o thermodynamics sea-ice (thsice) is now tested with testreport. |
382 |
o test exp. advect_cs: use the standard cs32 grid ; update output. |
o test exp. advect_cs: use the standard cs32 grid ; update output. |
383 |
|
o Added functionality to grdchk: |
384 |
|
pick global i,j,k position (or nearest wet) where to perform check. |
385 |
|
|
386 |
checkpoint52l_post |
checkpoint52l_post |
387 |
o new land formulation: |
o new land formulation: |