3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
4 |
============================== |
============================== |
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o pkg/cost |
7 |
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extend simple cost functions to treat time mean quantities |
8 |
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(T,U,V) via cost_accumulate_state from cost_tile |
9 |
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o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
10 |
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be 2 times larger than the minimum size the advection scheme requires. |
11 |
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now get a perfect conservation of salt in advect_cs test-exp (updated) |
12 |
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o GGL90 (Gaspar's TKE mixed layer) |
13 |
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- add horizontal diffusion of TKE, requires exchanges in |
14 |
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do_fields_blocking_exchanges, horizontal diffusivity is zero by |
15 |
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default. In OPA there is no horizontal diffusion of TKE but the |
16 |
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mixing coefficients are computed from a horizontal average of TKE of |
17 |
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6 points or so. I think that diffusion has a little more physical |
18 |
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justification. |
19 |
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- clean up ggl90_calc in the hope of reducing memory usage (this hope |
20 |
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was in vain) |
21 |
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- mask tke-variable in ggl90_init |
22 |
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o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
23 |
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o fix biharmonic diffusion on CS-grid. |
24 |
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o more obcs stuff |
25 |
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- added obcs_external_fields_load as an alternative to the EXF-pkg option |
26 |
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for reading boundary values. This routine is called from |
27 |
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obcs_prescribe_read |
28 |
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- updated obcs_check |
29 |
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- changed sponge layer relaxation parameter units for days to seconds |
30 |
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- turned off sponge layer by default |
31 |
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- changed argument list of OBCS_CALC to myTime+deltaTclock |
32 |
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|
33 |
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checkpoint55c_post |
34 |
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o obcs stuff |
35 |
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- new runtime flags useOBCSprescribe, useOBCSbalance |
36 |
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- re-arranged obcs_calc |
37 |
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- moved exf_getobcs to obcs_prescibe_read |
38 |
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obcs_prescibe_read is called after ORLANSKI stuff |
39 |
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and independent of it (executable can contain all). |
40 |
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- updated obcs_check |
41 |
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- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
42 |
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These may be necessary only if tangential velocities are |
43 |
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prescribed at OB, not sure, needs testing. |
44 |
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o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
45 |
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which simplifies the calls and passes the ifc check-bounds test |
46 |
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|
47 |
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checkpoint55b_post |
48 |
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o add a 2D scalar, Z location, exchange_2 routine. |
49 |
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o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
50 |
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to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
51 |
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affects advect_cs results (for the wrong reason): update output.txt |
52 |
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o use a more standard discretization for biharmonic viscosity ; |
53 |
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(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
54 |
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affects results of dome set-up: update output.txt |
55 |
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o fix gad_advection.F (CubedSphere part), back to version 1.23 |
56 |
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o fix bug in mom_vi_del2uv.F (CubedSphere part). |
57 |
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|
58 |
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checkpoint55a_post |
59 |
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o merged code to |
60 |
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* prescribe/read time-dependent open boundaries |
61 |
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(works in conjunction with exf, cal) |
62 |
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* sponge layer code for open boundaries |
63 |
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* each boundary N/S/E/W now has its own CPP option |
64 |
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(healthy for the adjoint) |
65 |
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|
66 |
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checkpoint55 |
67 |
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o up-to-date adjoint of previous breaks |
68 |
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- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
69 |
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- global_ocean_ebm: adjoint still needs fix (TLM ok) |
70 |
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- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
71 |
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- carbon: * remove tr1-related adjoint verification |
72 |
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* add ptracer as control variable |
73 |
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o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
74 |
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(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
75 |
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|
76 |
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checkpoint54f_post |
77 |
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o in verification/carbin/ remove experiment related to |
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ALLOW_PASSIVE_TRACER (array tr1 etc) |
79 |
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code_ad/ input_ad/ results_ad |
80 |
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|
81 |
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o add two new packages |
82 |
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- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
83 |
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+ subject to optimization (memory) |
84 |
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- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
85 |
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+ subject to reordering (many GOTOs in the original code) |
86 |
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+ so far opps is called for every (i,j) point, and then operates in |
87 |
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the vertical; one may want to reorder the scheme in order operate in |
88 |
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horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
89 |
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fields) |
90 |
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o overhaul of IO so that we now have flags for MDSIO and/or MNC |
91 |
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- all verification tests compile and run with linux_ia32_g77 |
92 |
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- defaults are compatible with current input files--nothing |
93 |
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should change if you were not previously using MNC |
94 |
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- MNC output has been added in numerous places (eg. timeave) |
95 |
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but there are still a few writes not yet do-able with MNC |
96 |
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(this is in progress) |
97 |
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- flags now allow for either/or/both use of MDSIO and MNC and |
98 |
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documentation will soon follow |
99 |
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- numerous small formatting cleanups for ProTeX |
100 |
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o add version info (via BUILD_INFO.h) to MNC and stdout |
101 |
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|
102 |
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checkpoint54e_post |
103 |
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o add two new packages |
104 |
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- pp81 (Packanowski and Philander, 1981), Richardson number and |
105 |
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stratification dependent mixing |
106 |
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- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
107 |
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- these scheme operate in a similar manner as KPP (without ghat, of |
108 |
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course), however there is only one diffusivity that is used for both |
109 |
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temperature and salinity (and passive tracers)ç |
110 |
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o add offline package |
111 |
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o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
112 |
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provided by Stephanie Dutkiewicz |
113 |
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o genmake2: add ability to search for C compilers and cleanup test output |
114 |
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- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
115 |
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|
116 |
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checkpoint54d_post |
117 |
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o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
118 |
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o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
119 |
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leading to additional shift by 5 days each year of integration |
120 |
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(i.e. leading to considerable offset over the years) |
121 |
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o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
122 |
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o start with no AB and no initial filtering (staggerTimeStep): |
123 |
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change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
124 |
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o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
125 |
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(external loading & cpl import/export stay in forward_step.F) |
126 |
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o update coupling interface to work with new staggerTimeStep |
127 |
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o change MDSIO ptracers_pickup. |
128 |
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o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
129 |
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o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
130 |
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o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
131 |
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|
132 |
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checkpoint54c_post |
133 |
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o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
134 |
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this affects (truncation error) output.txt of test-exp: |
135 |
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global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
136 |
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o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
137 |
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o change Qnet to always be the net heat flux, (+upward). |
138 |
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affects (truncation error) output of natl_box exp.: updated |
139 |
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o define the max number of passive tracers in PTRACERS_SIZE.h |
140 |
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o start to test mnc routinely in exp0 |
141 |
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o add sea-ice loading (sIceLoad) as a new forcing field. |
142 |
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|
143 |
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checkpoint54b_post |
144 |
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o add testreport "-j JOBS" option for parallel builds (tested and pretty |
145 |
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impressive on Altix and Opteron systems) |
146 |
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o diagnostics can now write NetCDF files through the mnc package |
147 |
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o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
148 |
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o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
149 |
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o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
150 |
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affects (truncation error) output of lab_sea & natl_box exp.: updated |
151 |
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o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
152 |
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|
153 |
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checkpoint54a_post |
154 |
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o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
155 |
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o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
156 |
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o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
157 |
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o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
158 |
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+ internal_wave (shift in writing cg2d_ini_res) |
159 |
|
checkpoint54a_pre |
160 |
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|
161 |
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o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
162 |
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- modified verification/lab_sea and natl_box_adjoint accordingly |
163 |
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|
164 |
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checkpoint54 |
165 |
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checkpoint53g_post |
166 |
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o prepare splitting of thermodynamics: store convect.counter in common block |
167 |
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o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
168 |
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output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
169 |
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o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
170 |
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o new parameter "nShapS": allow to treat differently S from T (nShapT) |
171 |
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o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
172 |
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o restore adjointability |
173 |
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|
174 |
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checkpoint53f_post |
175 |
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o modifications that affect AIM experiment results (update output.txt): |
176 |
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- no advection of S at top interface Nr (pkg/generic_advdiff) |
177 |
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- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
178 |
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o AIM pkg: |
179 |
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- include stability function into surf.Flux derivative relative to Tsurf |
180 |
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- calculate clear-sky radiation & surface temp. change (for diagnostics) |
181 |
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|
182 |
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checkpoint53e_post |
183 |
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o merged cylindrical coord configuration |
184 |
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o added rotating_tank experiment |
185 |
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checkpoint53e_pre |
186 |
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|
187 |
|
checkpoint53d_post |
188 |
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o faulks upgraded: re-generate output.txt that have changed: |
189 |
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global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
190 |
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o Added Bryan and Lewis, 1979, vertical diffusivity profile |
191 |
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o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
192 |
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o added Sadourny discretization of Coriolis |
193 |
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- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
194 |
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- re-enabled use of omega3 (useAbsVorticity) |
195 |
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o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
196 |
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vector-invariant equations |
197 |
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- note: does *NOT* yet use same variable visc. for no-slip BC's. |
198 |
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o recoded the lateral boundary conditions for non-hydrostatic w, this time |
199 |
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hopefully without new bugs |
200 |
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- still to do: biharmonic friction for non-hydrostatic w |
201 |
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o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
202 |
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o regenerated output for global_ocean_ebm (using -ieee) |
203 |
|
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
204 |
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of mom_common/ |
205 |
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- simple re-arrangement of instructions within computing loop |
206 |
|
checkpoint53d_pre |
207 |
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|
208 |
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checkpoint53c_post |
209 |
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o new version of coupler for AIM+thSIce and Ocean models |
210 |
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- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
211 |
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- land: change Evaporation of snow |
212 |
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- aim with thSIce: fix bug in snow-precip. |
213 |
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o changes to calc_gw.F |
214 |
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- bug fix for w^2 term near the bottom boundary |
215 |
|
- (hopefully) improve the lateral slip boundary condtions for use with |
216 |
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partial/looped cells |
217 |
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- because the bug fix changes two verification experiments anyway (exp5 |
218 |
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and plume on slope), change the lateral boundary condition from half slip |
219 |
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to the value of no_slip_sides |
220 |
|
o ebm package wasnt quite up to the parallel task. Fixed that. |
221 |
|
o Adjoint of EBM package + verification |
222 |
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* TLM OK |
223 |
|
* ADM not sufficient accuracy yet (needs further testing) |
224 |
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|
225 |
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checkpoint53b_post |
226 |
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o Commiting new energy balance model to repository |
227 |
|
* package is pkg/ebm |
228 |
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* verif. is verification/global_ocean_ebm |
229 |
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* references are in ebm_driver.F |
230 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
231 |
|
C Global thermohaline circulation. Part I: |
232 |
|
C Sensitivity to atmospheric moisture transport. |
233 |
|
C J. Climate 12(1), 71-82 |
234 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
235 |
|
C Global thermohaline circulation. Part II: |
236 |
|
C Sensitivity with interactive transport. |
237 |
|
C J. Climate 12(1), 83-91 |
238 |
|
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
239 |
|
C Destabilization of the thermohaline circulation |
240 |
|
C by atmospheric eddy transports. |
241 |
|
C J. Climate 7(12), 1870-1882 |
242 |
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o Will need long integration testing. |
243 |
|
checkpoint53b_pre |
244 |
|
|
245 |
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o created pkg/mom_common in preparation for variable viscosity code |
246 |
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o renamed and split ini_mnc_io |
247 |
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o pkg/land: only liquid water can diffuse or run-off |
248 |
|
o AIM using land: soil wetness availability account for snow |
249 |
|
o added printMapIncludesZeros to EEPARMS namelist |
250 |
|
|
251 |
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checkpoint53a_post |
252 |
|
o restore TAMC compatiility for exf_constants.h |
253 |
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(no usage of _d in .h) |
254 |
|
o Additional storing in KPP in an attempt to fix |
255 |
|
TAMC problem with adjoint of KPP code. |
256 |
|
(no success...) |
257 |
|
Identical code works fine with TAF. |
258 |
|
o Fixed verification/natl_box_adjoint experiments. |
259 |
|
Initial conditions for Experiments 4 and 5 are now |
260 |
|
set to "SEAICE_initialHEFF=0", which is more reasonable, |
261 |
|
and hence gives results closer to that of Experiment 2. |
262 |
|
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
263 |
|
|
264 |
|
checkpoint53 |
265 |
|
o stable checkpoint with up to date adjoint |
266 |
|
TLM tests only run for 1st grdchk at the moment. Its unclear if |
267 |
|
this is a code problem or a problem with resetting code for g_ |
268 |
|
variables that is being autogenerated wrong. |
269 |
|
Otherwise: |
270 |
|
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
271 |
|
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
272 |
|
are both still in chaos following their security messes. |
273 |
|
|
274 |
|
checkpoint52n_post |
275 |
|
o various build (mostly genmake2) changes including: |
276 |
|
- ability to build/run more easily within Cygwin and MacOS X |
277 |
|
- more complicated Makefiles with a stronger dependence on Gnu Make |
278 |
|
o pkg/seaice modifications |
279 |
|
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
280 |
|
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
281 |
|
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
282 |
|
- changed proxy for geostrophic velocity and updated |
283 |
|
verification/lab_sea/results/* accordingly |
284 |
|
- removed ADI dynamic solver from pkg/seaice |
285 |
|
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
286 |
|
they caused a segmentation fault under certain circumstances |
287 |
|
- removed unused field WATR |
288 |
|
o bug fix in exf-package: |
289 |
|
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
290 |
|
now reflect that. |
291 |
|
o small fixes in the cal-package: |
292 |
|
- set reference date to first of January for the 'model'-calendar |
293 |
|
- failing of cal_CheckDate in cal_FullDate now actually results in a |
294 |
|
warning |
295 |
|
o small modifications in exf-package to increase flexibility: |
296 |
|
- change climtempfreeze from a constant to a runtime parameter that |
297 |
|
is specified in data.exf_clim (default = -1.9) |
298 |
|
- introduce runtime parameter windstressmax (default = 2.0) that is |
299 |
|
specified in data.exf |
300 |
|
o fix in pkg/thsice: |
301 |
|
- update Evap (Tsf changes) to be consistent with Latent heat flux |
302 |
|
- maintain snow precipitation unchanged (even if Tsf >=0). |
303 |
|
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
304 |
|
|
305 |
|
checkpoint52m_post |
306 |
|
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
307 |
|
this does not change any of the results, because myIter=0 in swfrac always |
308 |
|
lead to jwtype=2 (the default anyway), but the call makes little sense |
309 |
|
as a default |
310 |
|
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
311 |
|
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
312 |
|
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
313 |
|
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
314 |
|
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
315 |
|
o extending useSingleCpuIO option to work with new exch2 I/O format |
316 |
|
- old-style, missing-tile I/O is still accessible by defining CPP |
317 |
|
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
318 |
|
o monitor package can write to NetCDF files and/or STDOUT |
319 |
|
o fix re-definition bug in MNC_GRID_INIT_ALL() |
320 |
|
o doc/api_reference added |
321 |
|
- a framework for building an API Reference Manual using all |
322 |
|
the "protex" comments embedded in the code |
323 |
|
- see pkg/generic_advdiff, pkg/mnc for examples |
324 |
|
o MNC: |
325 |
|
- make myThid the last argument for all subroutines |
326 |
|
- new default for the grid files: NO halos |
327 |
|
- add useMNC and other run-time flags |
328 |
|
- separate per-file-group handling of the unlimited dimension |
329 |
|
- early initialization of MNC w/ flags read at the eeboot stage |
330 |
|
and lookup tables set in initialize_fixed |
331 |
|
- write all MNC output to a freshly-created directory |
332 |
|
o thermodynamics sea-ice (thsice) is now tested with testreport. |
333 |
|
o test exp. advect_cs: use the standard cs32 grid ; update output. |
334 |
|
o Added functionality to grdchk: |
335 |
|
pick global i,j,k position (or nearest wet) where to perform check. |
336 |
|
|
337 |
|
checkpoint52l_post |
338 |
|
o new land formulation: |
339 |
|
a) use ground enthalpy as prognostic variable to ensure exact |
340 |
|
energy conservation. |
341 |
|
b) account for water temperature and for latent heat of freezing |
342 |
|
in all processes (rain, run-off, ground storage) |
343 |
|
c) compute surface and ground temperature implicitly. |
344 |
|
o aim_v23 modification for new land model: |
345 |
|
a) Treat separately land / ocean / sea-ice surface fluxes |
346 |
|
to allow implicit computation of land & sea-ice surface temp. |
347 |
|
b) add snow precipitation. |
348 |
|
checkpoint52l_pre |
349 |
|
|
350 |
|
o fix problem (when 1 tile is empty) in min/max monitor. |
351 |
|
o fix bug in timeAve (u,vZetatave in common block) |
352 |
|
o no restoring terms under ice for pkg/seaice |
353 |
|
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
354 |
|
o bug fix for pkg/seaice pickups |
355 |
|
o change MNC call locations and add coordinate attributes |
356 |
|
o mask vorticity at the corner ; affects global_ocean.cs output |
357 |
|
o fix ini_curvilinear_grid ; test CS experiments with mpi |
358 |
|
o aim.5l_cs: modify sea-ice fraction input file ; update output |
359 |
|
o exf: Adding simple range check routine for exf fields after read |
360 |
|
|
361 |
|
checkpoint52k_post |
362 |
|
o removed top-level directory "diags" |
363 |
|
- we migrated these functions to pkg/timeave a long time ago |
364 |
|
o fixed bug introduced in pkg/monitor |
365 |
|
o accuracy ctrlprec = 32 insuffient for gradient checks using |
366 |
|
averaged fields (I/O via cost_averages) |
367 |
|
-> use ctrl.h in active_file*.F to control I/O precision. |
368 |
|
o paramter list of CALL ADTHE_MAIN_LOOP |
369 |
|
o added initial do_the_model_io to ecco |
370 |
|
o set all ...Freq to zero after cost_final |
371 |
|
taveFreq, dumpFreq, pChkptFreq |
372 |
|
o MAIN and ECCO differentiability restored |
373 |
|
|
374 |
|
checkpoint52j_post |
375 |
|
o fix nchklev in tamc.h for global_ocean... |
376 |
|
o Bringing flow and store directives up-to-date |
377 |
|
o Really weird thing! |
378 |
|
call do_the_model_io from the_main_loop with parameters |
379 |
|
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
380 |
|
TAF places a faulty re-call of initialise_varia |
381 |
|
after cost_final call which should not be there! |
382 |
|
checkpoint52j_pre |
383 |
|
|
384 |
|
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
385 |
|
error messages |
386 |
|
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
387 |
|
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
388 |
|
debug output |
389 |
|
o modfied mdsio_writefield.F to handle non-global files under exch2 |
390 |
|
o update AIM Cubed-Sphere exp (aim.5l_cs): |
391 |
|
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
392 |
|
o update AIM Equatorial Channel exp: |
393 |
|
use standard aim_v23 pkg and change the SST fields to be more realistic. |
394 |
|
o globalFile now works with exch2 |
395 |
|
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
396 |
|
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
397 |
|
o limit timeave output for hi-res integrations |
398 |
|
|
399 |
|
checkpoint52i_post |
400 |
|
o removed CPP_EEOPTIONS.h from verification/*/code |
401 |
|
o updated the tiling for global_ocean_pressure |
402 |
|
checkpoint52i_pre |
403 |
|
|
404 |
|
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
405 |
|
the old pkg/aim). |
406 |
|
|
407 |
|
checkpoint52h_pre |
408 |
|
o shortened offending lines in exch2_send_rx?.template |
409 |
|
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
410 |
|
o genmake2: add build & execute test for NetCDF code |
411 |
|
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
412 |
|
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
413 |
|
o added useSingleCPUIO flag to monitor.F and mon_out.F |
414 |
|
o added temporary hack for sea-ice dynamics on the cube: |
415 |
|
metric terms are ignored and it is assumed that |
416 |
|
there is no sea-ice on cube faces 1, 2, 4, and 5. |
417 |
|
|
418 |
|
checkpoint52f_post |
419 |
|
o added exch2 cube routines to pkg/exch2 |
420 |
|
o modified hs94.cs-32x32x5 to use it |
421 |
|
o added new grid files to hs94.cs-32x32x5 |
422 |
|
checkpoint52f_pre |
423 |
|
|
424 |
|
checkpoint52e_post |
425 |
|
o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
426 |
|
for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
427 |
|
o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
428 |
|
to work with implicit vertical advection and AB ; |
429 |
|
o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
430 |
|
o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
431 |
|
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
432 |
|
checkpoint52e_pre |
433 |
|
|
434 |
|
o fix bug in impldiff when Nr=1 or Nr=2. |
435 |
|
o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
436 |
|
o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
437 |
|
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
438 |
|
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
439 |
|
o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
440 |
|
o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
441 |
|
o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
442 |
|
|
443 |
|
checkpoint52d_post |
444 |
|
o re-tiled many expts to allow comparison in multi-processor mode |
445 |
|
- updated output accordingly |
446 |
|
- changed hs94.128x64x5 to use intial T from file rather than use the |
447 |
|
random number generator |
448 |
|
o add infrastructure in model routines for fizhi and gridalt packages |
449 |
|
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
450 |
|
o changes to permit hi-res, cubed-sphere, configuration |
451 |
|
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
452 |
|
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
453 |
|
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
454 |
|
of surface winds for the cube |
455 |
|
(A verification experiment, based on global_ocean.cs32x15, but with |
456 |
|
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
457 |
|
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
458 |
|
complete with example surface forcing files and matlab scripts to look |
459 |
|
at the output and compare it with that of global_ocean.cs32x15.) |
460 |
|
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
461 |
|
but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
462 |
|
to conform to the common rule. |
463 |
|
o check-in the first version of the coupler + interfaces for multi-components |
464 |
|
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
465 |
|
- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
466 |
|
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
467 |
|
- ocean and atmos. share the same horizontal grid (no interpolation). |
468 |
|
- exchanges between component and coupler is done in forward_step |
469 |
|
o new verification experiment, cpl_aim+ocn: |
470 |
|
coupled ocean - AIM atmosphere on cs32 grid. |
471 |
|
|
472 |
|
checkpoint52d_pre |
473 |
|
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
474 |
|
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
475 |
|
|
476 |
|
checkpoint52c_post |
477 |
|
o Fixing OPTIONS files for use of exf: |
478 |
|
- ALLOW_ECCO not needed |
479 |
|
- ECCO_CPPOPTIONS.h should not be included from |
480 |
|
EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
481 |
|
as has been the case in the past |
482 |
|
- All cal/exf related options are currently set in |
483 |
|
single header file. Should remain so until we |
484 |
|
agree on a consistent new policy. |
485 |
|
o Removed all CPP options for cal package. |
486 |
|
cal has no more CPP options. |
487 |
|
o modified STOREs in GAD_ADVECTION |
488 |
|
o corrected key comp. for passkey |
489 |
|
|
490 |
|
checkpoint52b_post |
491 |
|
o new version: "thsice" of thermodynamic sea-ice pkg: |
492 |
|
- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
493 |
|
- modify fluxes but do not change theta directly; |
494 |
|
- light cleaning of bulk_force pkg (still needed with thsice). |
495 |
|
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
496 |
|
+ output_thsice.txt to test thsice & bulk_force pkgs. |
497 |
|
o put back grid & coriolis monitor output. |
498 |
|
checkpoint52b_pre |
499 |
|
|
500 |
|
o call "do_the_model_io" at the beginning (=> dump initial state) |
501 |
|
o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
502 |
|
o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
503 |
|
(need info on NUMBER_OF_PTRACERS) |
504 |
|
o missing PTRACERS headers in some routines |
505 |
|
o default tamc.h in pkg/autodiff supposed to crash |
506 |
|
to ensure proper customization |
507 |
|
|
508 |
|
checkpoint52a_post |
509 |
|
o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
510 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
511 |
|
- subroutine FREEZE_SURFACE now limits only surface temperature |
512 |
|
and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
513 |
|
=> new output.txt for global_ocean.cs32x15 & global_with_exf |
514 |
|
- keep the old version of FREEZE for backward compatibility; |
515 |
|
global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
516 |
|
- corresponding modifs for TAF directives |
517 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
518 |
|
o time-averaged output for pkg/ptracers |
519 |
|
o fix problem with ECCO-related divided adjoint |
520 |
|
snapshot file was missing some ad-variables, |
521 |
|
but no warning issued by TAF |
522 |
|
|
523 |
|
checkpoint52a_pre |
524 |
|
o some bug fixes for #undef REAL4_IS_SLOW |
525 |
|
|
526 |
|
checkpoint52 = ecco_c52_e35 |
527 |
|
o after testing adjoints of checkpoint51u_post |
528 |
|
|
529 |
|
checkpoint51u_post |
530 |
|
o this is the post-merge tag of the ecco-branch |
531 |
|
(needs another clean checkout and re-testing) |
532 |
|
o various natl_box_adjoint configs and results |
533 |
|
but no input fields |
534 |
|
o obcs adjoint not yet merged! |
535 |
|
o adding ECCO global 1x1 and 2x2 degree configs |
536 |
|
o updated/extended some store directives for seaice |
537 |
|
o pkg/ecco now containes ecco-specific part of cost function |
538 |
|
o top level routines the_main_loop, forward_step |
539 |
|
supersede those in model/src/ |
540 |
|
previous input data.cost now in data.ecco |
541 |
|
(new namelist ecco_cost_nml) |
542 |
|
o in ctrl/ cleaned some cross-dependencies and updated CPP options |
543 |
|
|
544 |
|
checkpoint51t_post |
545 |
|
o this is the pre-merge tag of the ecco-branch |
546 |
|
|
547 |
|
checkpoint51s_post |
548 |
|
o cleanup: removed various obsolete #define-s |
549 |
|
o pkg/grdchk |
550 |
|
- renamed 'ph-grd 3' to 'grad-res' |
551 |
|
- merged from ecco-branch |
552 |
|
(remaining bug fixes for obcs gradient checks) |
553 |
|
- additional high-precision output for testreport |
554 |
|
(grep for 'precision_grdchk_result') |
555 |
|
|
556 |
|
checkpoint51r_post |
557 |
|
o cleaned up or removed CPP_OPTIONS.h files |
558 |
|
o updated results for some of the tests to reflect the new |
559 |
|
optfiles (-ieee: -O0 instead of -O3) |
560 |
|
|
561 |
|
checkpoint51q_post |
562 |
|
o cd_code: |
563 |
|
- moved cd_scheme.F -> cd_code_scheme.F |
564 |
|
- separate read_checkpoint from cd_code_ini_vars.F |
565 |
|
- separated cd_code part from write_checkpoint |
566 |
|
- updated AD_SOURCE, generated .flow |
567 |
|
- added CD_CODE_VARS.h to the_main_loop |
568 |
|
- Moving cd_code specific store dir.s to pkg/cd_code |
569 |
|
o ctrl package totally restructured |
570 |
|
- pack/unpack now optional and decoupled from |
571 |
|
xx_/adxx_ I/O |
572 |
|
- ctrl_pack/unpack cleaned |
573 |
|
(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
574 |
|
- confined inclusion of AD_CONFIG.h to where necessary. |
575 |
|
o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
576 |
|
|
577 |
|
checkpoint51p_post |
578 |
|
o create initial cd_code package |
579 |
|
- WARNING: the initialization of fields within packages |
580 |
|
is broken because INI_FIELDS (where READ_CHECKPOINT is |
581 |
|
called) is called *before* PACKAGES_INIT_VARIABLES. |
582 |
|
This seems to be backwards since |
583 |
|
1) its important to initially zero the entire field including |
584 |
|
the "halo" region |
585 |
|
2) zeroing needs to be done *before* reading pickup info |
586 |
|
and the pickup call might or might not happen in any |
587 |
|
particular run |
588 |
|
- this needs an overhaul for R2 |
589 |
|
o cleanup verification/*/code/GMREDI_OPTIONS.h |
590 |
|
o cleanup testreport |
591 |
|
|
592 |
|
checkpoint51o_post |
593 |
|
o bringing AD-related verif's up to date with genmake2 |
594 |
|
- carbon/ |
595 |
|
- global_ocean.90x40x15/ |
596 |
|
- hs.94.1x64x5/ |
597 |
|
- (front_relax/ ) |
598 |
|
o (more) consistent directory structure for AD-related verif.'s |
599 |
|
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
600 |
|
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
601 |
|
o bug fix in find_alpha.F for MDJWF: |
602 |
|
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
603 |
|
change rho -> rho-rhoConst |
604 |
|
- replace call find_rho to find_rhonum |
605 |
|
o initialisation of rFlx extended to full array (required by TAF) |
606 |
|
and shifted to thermodynamics |
607 |
|
o removed PTRACERS.h in ptracers routine |
608 |
|
o added surfacetendencyPtr to S/R parameter list pracers_forcing |
609 |
|
o Correcting initialisations for fVerU, fVerV. |
610 |
|
o helping TAF to recognize dependency on kUp for |
611 |
|
fVerU, fVerV |
612 |
|
o Replacing delZ by delR in pkg/ctrl/ |
613 |
|
checkpoint51o_pre |
614 |
|
|
615 |
|
o undid all of cp51 pending some cleanups and discussion |
616 |
|
o added the [#include "AD_CONFIG.h"] statement to all files that need |
617 |
|
it for adjoint/tl #defines |
618 |
|
o re-worked the build logic in genmake2 to support AD_CONFIG.h |
619 |
|
o removed tools/genmake since it no longer works |
620 |
|
|
621 |
|
checkpoint51n_post |
622 |
|
o modifications to make FREEZE flux visible to pkg/kpp |
623 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
624 |
|
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
625 |
|
- subroutine FREEZE now limits only surface temperature |
626 |
|
(this means new output.txt for global_ocean.90x40x15, |
627 |
|
global_ocean.cs32x15, and global_with_exf) |
628 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
629 |
|
|
630 |
|
checkpoint51n_pre |
631 |
|
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
632 |
|
o added [#include "AD_CONFIG.h"] to all files that use the following |
633 |
|
defines: |
634 |
|
- ALLOW_ADJOINT_RUN |
635 |
|
- ALLOW_TANGENTLINEAR_RUN |
636 |
|
- ALLOW_ECCO_OPTIMIZATION |
637 |
|
|
638 |
|
checkpoint51m_post |
639 |
|
o incorporating changes to get TAMC/TAF working in genmake2 |
640 |
|
- added new TAMC/TAF targets to the Makefile |
641 |
|
- various cleanups related to package handling |
642 |
|
- these changes should have no impact on the forward model |
643 |
|
|
644 |
|
checkpoint51l_post |
645 |
|
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
646 |
|
- faster algorithm for cal_addtime.F |
647 |
|
- higher precision arithmetic, where needed |
648 |
|
- pkg/exf *startdate variables changed from calendar date to |
649 |
|
model integration time |
650 |
|
|
651 |
|
checkpoint51l_pre |
652 |
|
o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
653 |
|
o enable to apply restoring on S & T only in a latitude band. |
654 |
|
o update output (external_forcing_surf modif. change truncation errors) |
655 |
|
global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
656 |
|
|
657 |
|
checkpoint51k_post |
658 |
|
o change default to: useNHMTerms=.FALSE. |
659 |
|
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
660 |
|
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
661 |
|
- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
662 |
|
exp1, ideal_2D_oce |
663 |
|
- change data file of oceanic exp (leave the results unchanged for now) |
664 |
|
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
665 |
|
o set gravitySign automatically according to the vertical coordinate used |
666 |
|
(and change sign: back to "logical" value: +1 when R increases downward) |
667 |
|
o added an include barrier to the default CPP_OPTIONS.h and |
668 |
|
removed the #include "PACKAGES_CONFIG.h" from it |
669 |
|
o fix a bug in mom_fluxform (from chk51j_post) |
670 |
|
|
671 |
|
checkpoint51j_post |
672 |
|
o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
673 |
|
o adjusted some flow directives (dynamics, thermodynamics) |
674 |
|
o added cubed-sphere case to test cost function |
675 |
|
o heckpoint_lev?_directives.h now include |
676 |
|
pkg-specific directives, whenever those are enabled. |
677 |
|
o Moving pkg-specific flow directives to corresponding pkg |
678 |
|
Moving pkg-specific differentiation list to corresponding pkg |
679 |
|
Moving pkg-specific checkpoint-lev storing to corresponding pkg |
680 |
|
---> conventions are |
681 |
|
- pkg_ad.flow |
682 |
|
- pkg_ad_diff.list |
683 |
|
- pkg_ad_check_lev?_dir.h |
684 |
|
|
685 |
|
checkpoint51i_post |
686 |
|
o merge of the branch-genmake2 |
687 |
|
- knowingly breaks the older genmake |
688 |
|
- automatic generation of all ALLOW_${PKG_NAME} defines |
689 |
|
- new testreport supersedes older testscript |
690 |
|
o large number of package inclusion and header cleanups |
691 |
|
checkpoint51i_pre |
692 |
|
|
693 |
|
o new output for adjoin of global ocean vector invariant |
694 |
|
o fix for checkpoint of thermodynamic seaice and bulk_force |
695 |
|
o Steph gchem various cleanups |
696 |
|
|
697 |
|
checkpoint 51h_pre |
698 |
|
o fixed some single quotes |
699 |
|
o modify gchem pkg to be more versatile |
700 |
|
o modifications to clean up dic pkg |
701 |
|
o add pkg/cfc |
702 |
|
|
703 |
|
checkpoint51g_post |
704 |
|
o provide links for ARPACK and ADM*TLM |
705 |
|
o start removing verification/vero/ |
706 |
|
o update AD-related stuff |
707 |
|
(in particular some IF-statements in model/src/ routines) |
708 |
|
o adding to verification/global_ocean.90x40x15/ adjoint of |
709 |
|
vector invariant setup |
710 |
|
|
711 |
|
checkpoint51f_post |
712 |
|
o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
713 |
|
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
714 |
|
of tracer Green's fucntions for ocean inversion project. |
715 |
|
|
716 |
|
checkpoint51f_pre |
717 |
|
o Added on-the-fly spatial interpolation capability |
718 |
|
"USE_EXF_INTERPOLATION" to pkg/exf. |
719 |
|
- This is a temporary Cartesian-grid hack until |
720 |
|
the super-duper ESMF coupler becomes available. |
721 |
|
- See verification/global_with_exf/README for usage example. |
722 |
|
- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
723 |
|
flags and modified pkg/seaice accordingly. |
724 |
|
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
725 |
|
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
726 |
|
non-local transport term. |
727 |
|
|
728 |
checkpoint51e_post |
checkpoint51e_post |
729 |
o pkg/mom_vecinv: |
o pkg/mom_vecinv: |
730 |
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |