3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
4 |
============================== |
============================== |
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checkpoint46h_post |
8 |
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o cleaned up the use of rhoNil and rhoConst. |
9 |
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- rhoNil should only appear in the LINEAR equation of state, everywhere |
10 |
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else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
11 |
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and the dynamical equations are all divided by rhoConst |
12 |
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o introduced new parameter rhoConstFresh, a reference density of fresh |
13 |
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water, to remove the fresh water flux's dependence on rhoNil. The default |
14 |
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value is 999.8 kg/m^3 |
15 |
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o cleanup up external_forcing.F and external_forcing_surf.F |
16 |
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- can now be used by both OCEANIC and OCEANICP |
17 |
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checkpoint46h_pre |
18 |
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|
19 |
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Added code to convert surface volume flux (fresh water) into |
20 |
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a mass flux when using P coordinates in the ocean (OCEANICP). |
21 |
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Note: It assumes you have set rho0=rhoConst=density of fresh water. |
22 |
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|
23 |
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checkpoint46g_post |
24 |
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o Include a new diagnostic variable phiHydLow for the ocean model |
25 |
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- in z-coordinates, it is the bottom pressure anomaly |
26 |
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- in p-coordinates, it is the sea surface elevation |
27 |
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- in both cases, these variable have global drift, reflecting the mass |
28 |
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drift in z-coordinates and the volume drift in p-coordinates |
29 |
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- included time averaging for phiHydLow, be aware of the drift! |
30 |
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o depth-dependent computation of Bo_surf for pressure coordinates |
31 |
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in the ocean (buoyancyRelation='OCEANICP') |
32 |
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- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
33 |
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Theta, Salinity, and Pressure in the parameter list. This routine is |
34 |
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presently contained in find_rho.F. This routine does not give the |
35 |
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correct density for 'POLY3', which would be a z-dependent reference |
36 |
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density. |
37 |
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o cleaned up find_rho |
38 |
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- removed obsolete 'eqn' from the parameter list. |
39 |
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o added two new verification experiments: gop and goz |
40 |
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(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
41 |
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checkpoint46g_pre |
42 |
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|
43 |
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checkpoint46f_post |
44 |
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o Enable tangent linear (forward mode) gradient checks: |
45 |
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- extended active file handling to g_... files |
46 |
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- added TANGENT_SIMULATION to theSimulationMode |
47 |
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- extended grdchk package accordingly |
48 |
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o added tangent linear setup in verification/carbon/code_ftl |
49 |
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o added adjoint setup in verification/front_relax/code_ad |
50 |
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|
51 |
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checkpoint46e_post |
52 |
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o Added new equation of state -> MDJWF |
53 |
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- EOS of McDougall et al., 2002, JAOT, submitted |
54 |
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- caveat: the equation of state is only valid for a smaller (more |
55 |
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realistic?) range of values than JMD95P/Z and UNESCO |
56 |
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- added masks to the calculation of pressure in store_pressure |
57 |
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- added more check values for density in check_eos (ini_eos.F), some of |
58 |
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the old check values are out of the range of the MDJWF-eos, so don't |
59 |
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expect perfect matches for those |
60 |
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checkpoint46e_pre |
61 |
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|
62 |
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checkpoint46d_post |
63 |
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o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
64 |
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'OCEANICP', also initialised field pressure correctly in ini_eos in the |
65 |
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case of pressure coordinates. eosType='JMD95Z' in |
66 |
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combination with buoyancyRelation='OCEANICP' now causes an error. |
67 |
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o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
68 |
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in find_alpha/beta. |
69 |
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checkpoint46d_pre |
70 |
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|
71 |
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o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
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so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
73 |
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|
74 |
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checkpoint46c_post |
75 |
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o Changes necessary for ocean in p-coordinates |
76 |
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- Added new buoyancy relation = 'OCEANICP' |
77 |
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- Added new parameters = gravitySign (this used to be contained inside |
78 |
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the factor dRdZ which I added when we first switched to R coordinates). |
79 |
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X GM/Redi is not compatible (yet) |
80 |
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X bottom drag and no-slip need to be debugged. |
81 |
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checkpoint46c_pre |
82 |
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83 |
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checkpoint46b_post |
84 |
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o Added new equation of state -> JMD95Z and JMD95P |
85 |
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- EOS of Jackett and McDougall, 1995, JAOT |
86 |
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- moved all EOS parameters into EOS.h |
87 |
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- new routines ini_eos.F, store_pressure.F |
88 |
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o Added UNESCO EOS, but not recommended because it requires |
89 |
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in-situ temperature (see JMD95) |
90 |
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o Modified formatting for knudsen2.f in utils/knudsen2 and added |
91 |
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unesco.f to be used with POLY3 |
92 |
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checkpoint46b_pre |
93 |
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|
94 |
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checkpoint46a_post |
95 |
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o Added (atmospheric) pressure loading |
96 |
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- new field in FFIELDS.h, etc... |
97 |
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- new cpp flag ATMOSPHERIC_LOADING |
98 |
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o Changed hFacC to _hFacC in calc_phi_hyd.F |
99 |
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o Added SHORTWAVE_HEATING to some files for consistency |
100 |
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checkpoint46a_pre |
101 |
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|
102 |
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checkpoint46 |
103 |
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further merges from release1_p5 |
104 |
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o new ctrl package |
105 |
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- adopted from ECCO environment to enable optimization |
106 |
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- added Eliassen Palm fluxes to controls |
107 |
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o added Eliassen Palm flux controls to gradient check package |
108 |
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o cost package |
109 |
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- Compatible with new ctrl package |
110 |
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- added Eliassen Palm cost hooks |
111 |
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- modif's of existing cost functions |
112 |
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o Adjoint-related bug fixes in kpp: |
113 |
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- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
114 |
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- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
115 |
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o autodiff package |
116 |
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- flow directives: |
117 |
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+ new for S/R do_the_model_io |
118 |
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+ enhanced for S/R checkpoint |
119 |
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+ new gmredi.flow |
120 |
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- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
121 |
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disable adcommon.h/g_common.h by default. |
122 |
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- fixed problem for adjoint of global_max |
123 |
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o modified verification/carbon/ |
124 |
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o New setup for adjoint of global_ocean |
125 |
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o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
126 |
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o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
127 |
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o incorporated hooks for sponge layer code (external_forcing.F) |
128 |
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|
129 |
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checkpoint45d_post |
130 |
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o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
131 |
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o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
132 |
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(affects plume_on_slope "cg2d" output) |
133 |
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o add new parameter deltaTfreesurf for free-surface time stepping |
134 |
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o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
135 |
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o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
136 |
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o change phiMin in exp1 (to agree with documentation) |
137 |
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o add new flags: |
138 |
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- T,S forcing inside/outside Adams-Bashforth |
139 |
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- turn off temp,salt advection and/or forcing |
140 |
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- for each tracer, define internal flag for multiDimAdvection & A-B |
141 |
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o monitor: change definition of KE to check conservation of Energy |
142 |
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|
143 |
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checkpoint45c_post |
144 |
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o Removed f90 comments ("!") |
145 |
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o Modified initialisations to enable exf package for MITgcm |
146 |
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(without invoking ECCO_PACKAGE). |
147 |
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o modifications to gradient check package (Martin Losch) |
148 |
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- enable centered differences |
149 |
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- modified format of standard output |
150 |
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|
151 |
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checkpoint45b_post |
152 |
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o cleaned exchange calls in cg2d |
153 |
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o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
154 |
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o included CPP option SINGLE_LAYER_MODE in thermodynamics |
155 |
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to configure barotropic setup (Martin Losch) |
156 |
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o moved some initialisations within bi,bj loop in dynamics |
157 |
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(TAF flow dependency) |
158 |
|
o in initialise_varia, moved call packages_init_variables |
159 |
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before convective_adjustment_init |
160 |
|
(corresponding adjustment of TAF tape initialisation). |
161 |
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o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
162 |
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|
163 |
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checkpoint45a_post |
164 |
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o compute Rho over the whole domain (extend iMin,jMin indices) |
165 |
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o specific exchange for X-slice domain (case Ny=1) |
166 |
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o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
167 |
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o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
168 |
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|
169 |
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checkpoint44h_post = checkpoint45 |
170 |
|
o Fix to restore differentiability: |
171 |
|
place at which packages_init_variables is called in |
172 |
|
initialise_varia is crucial for reverse control flow. |
173 |
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o modifications in GMRedi to enable stable adjoint |
174 |
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(corresponding modif's in thermodynamics, dynamics) |
175 |
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o added missing hook for sponge layer code in external_forcing |
176 |
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o modified test cost functions |
177 |
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o storing in gad_advection (plus removal of write(0,*)! |
178 |
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o missing headers TR1.h added in convective_adjustment routines |
179 |
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o errorMessageUnit set non-equal zero in eeboot |
180 |
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(conflict on some platforms, e.g. IBM SP3) |
181 |
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o modified carbon verif. |
182 |
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|
183 |
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checkpoint44h_pre |
184 |
|
o vertical grid option: allow to put the Interface at the middle between |
185 |
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2 cell-centers ; replace delZ in pkg/kpp by drF. |
186 |
|
o GM Advective form: Tracers are advected using the residual transport (= |
187 |
|
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
188 |
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|
189 |
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checkpoint44g_post |
190 |
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o fix surface correction term in multiDimAdvection (affects plume_on_slope |
191 |
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results) ; ifdef missing in thermodynamics.F |
192 |
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|
193 |
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checkpoint44f_pre,checkpoint44f_post |
194 |
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o added PTRACERS package |
195 |
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This allows an arbitrary number of passive tracers to be integrated |
196 |
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forward simultaneously with the dynamicaly model. |
197 |
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+ Implemented so far: |
198 |
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- basic forward algorithm (time-stepping, advection, diffusion, convection) |
199 |
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- I/O and checkpointing |
200 |
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- GM/Redi *but* using the GM/Redi coefficient of Salt |
201 |
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+ Not implemented so far: |
202 |
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- KPP |
203 |
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- OBCS |
204 |
|
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
205 |
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necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
206 |
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line in data.pkg. |
207 |
|
+ This package is disabled by default since it increases storage. |
208 |
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|
209 |
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|
210 |
|
o testscript: added -cleanup option |
211 |
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o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
212 |
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b) enable to filter 2D fields. |
213 |
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|
214 |
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checkpoint44e_pre,post |
215 |
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o re-wrote convective adjustment to use pre-calculated weights |
216 |
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Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
217 |
|
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
218 |
|
Original calls to convect() still in place. |
219 |
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|
220 |
|
chkpt44d_pre,post |
221 |
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o added missing EXCLUDE_MONITOR flags |
222 |
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o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
223 |
|
(incompatible typ in MIN/MAX expressions caused problems |
224 |
|
on IBM SP3) |
225 |
|
o in genmake added variable MAKEDEPEND |
226 |
|
plus resetting for case SunOS |
227 |
|
o added timer_stats.c routine for IBM SP3 |
228 |
|
o removed variables in dynamics |
229 |
|
!!! I forgot to create tag chkpt44d_pre !!! |
230 |
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!!! But chkpt44d_pre = chkpt44c_post !!! |
231 |
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|
232 |
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o real fresh water flux implemented with non-linear free-surface. |
233 |
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|
234 |
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chkpt44c_pre,post |
235 |
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o few fix (mask in shap_s2, EmPmR in external_field_load, |
236 |
|
USE_NATURAL_BCS in solve_for_P); |
237 |
|
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
238 |
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|
239 |
|
checkpoint44b_pre/_post |
240 |
|
o merge of relevant stuff from the ecco-branch: |
241 |
|
- genmake: removed $S64 overwrite for case SunOS |
242 |
|
- pkg/exf: update and corrections for field swapping and obcs |
243 |
|
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
244 |
|
harmonized between ECCO and MITgcm |
245 |
|
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
246 |
|
updated checkpointing_lev... lists for obcs |
247 |
|
- model/src: minor changes in forward_step, plot_field |
248 |
|
added directive for divided adjoint in the_main_loop |
249 |
|
- pkg/mdsio: added mdsio_gl_slice |
250 |
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|
251 |
|
o check parameters & config (chkpt44a_pre,post) |
252 |
|
o OBC and NonLin_FrSurf. |
253 |
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|
254 |
|
checkpoint44 |
255 |
|
o fix bug in mom_vi_del2uv |
256 |
|
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
257 |
|
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
258 |
|
o update AIM experiments (NCEP input files) |
259 |
|
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
260 |
|
o added some stuff for AD |
261 |
|
|
262 |
|
checkpoint43 |
263 |
|
o added two new advection tests |
264 |
|
o added global 4x4 degree ocean test |
265 |
|
o added test of H&S94 with free surface on cube |
266 |
|
o some final mods for gradient check, adjoint,... |
267 |
|
|
268 |
|
checkpoint42 |
269 |
|
Fixed AD-related problems: |
270 |
|
o Store directives up-to-date with re-arranged Adams-Bashforth |
271 |
|
(mainly thermodynamics.F) |
272 |
|
o New store directives for multi-dim. advection schemes |
273 |
|
* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
274 |
|
* new common block and key passkey |
275 |
|
(mainly gad_advection.F) |
276 |
|
o Modified store directives for split of dynamics/thermodynamics |
277 |
|
for the case ALLOW_KPP |
278 |
|
o Cleaned argument list for timestep_tracer.F |
279 |
|
|
280 |
|
checkpoint41 |
281 |
|
o re-formatted/added comments in prologues of key subroutines |
282 |
|
to work with protex |
283 |
|
|
284 |
|
checkpoint40 |
285 |
|
o moved calc_gs, calc_gt and calc_tr1 back to model/src |
286 |
|
o added FLT (floats) package from Arne along with demo. experiment |
287 |
|
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
288 |
|
implementation of forward-in-time forcing terms |
289 |
|
o more mods for non-linear free-surface including new variable |
290 |
|
o modified multi-dim method to work on cube |
291 |
|
o bug fix in KPP (from DM) |
292 |
|
|
293 |
|
checkpoint40pre9 |
294 |
|
o added DST advection schemes |
295 |
|
o fix MPI bug on SGI's |
296 |
|
o modifications for non-linear free-surface |
297 |
|
o fixed conditionals for fixed flow/passive tracer only mode |
298 |
|
o added tension/strain form of stress tensor |
299 |
|
o changes to commenting of arguments for TAF/TAMC |
300 |
|
o added/updated many matlab scripts |
301 |
|
o added multi-dimensional advection method for tracers |
302 |
|
|
303 |
|
checkpoint40pre8 |
304 |
|
o new package rw/ |
305 |
|
Added method for dumping intermediate local arrays: |
306 |
|
mdsio_writetile - same as mdsio_writefield except works from inside |
307 |
|
bi,bj loop |
308 |
|
mdsio_writelocal - same as mdsio_writetile except works for local |
309 |
|
arrays |
310 |
|
write_local_r? - higher-level wrapper for mdsio_writelocal |
311 |
|
Controlled by diagFreq. Defaults to zero (ie. no dumps) |
312 |
|
Example given at end of mom_vecinv.F that dumps some local arrays. |
313 |
|
o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
314 |
|
control flux-form versus vector invariant code. |
315 |
|
Switch is runtime flag vectorInvariantMomentum (defaults to false) |
316 |
|
or genmake -DISABLE ... |
317 |
|
o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
318 |
|
(additional storing is now needed for case vecinv; |
319 |
|
currently nothing implemented to switch this storing off |
320 |
|
in case fluxform is used since no CPP flag available). |
321 |
|
|
322 |
|
checkpoint40pre7 |
323 |
|
o bug fix in dynamics.F |
324 |
|
calc_viscosity called before k=1,Nr loop. |
325 |
|
o added some #ifdef's ALLOW_PASSIVE_TRACER |
326 |
|
o cleaned initialisations in ctrl_map_ini |
327 |
|
related to TAF |
328 |
|
|
329 |
|
checkpoint40pre6 |
330 |
|
o split dynamics into thermodynamics & dynamics |
331 |
|
o corresponding split of calc_diffusivity into |
332 |
|
calc_diffusivity, calc_viscosity |
333 |
|
(kpp_calc_diff, kpp_calc_visc). |
334 |
|
o Added diffkr, kapgm to control variables |
335 |
|
o bug fix in gmredi_slope_limit for ldd97 |
336 |
|
|
337 |
|
checkpoint40pre5 |
338 |
|
o proper initialization of Adams-Bashforth time stepping |
339 |
|
+ uses forward step for very first step of model (iter=0) |
340 |
|
o re-generated *all* output since almost all output is modified by this |
341 |
|
change (sorry but we've been putting this one off for about 2 years) |
342 |
|
+ natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were |
343 |
|
*not* regenerated since they are already out of date and I don't |
344 |
|
want to create the impression that they are suddenly working. |
345 |
|
o removed KAP stuff for DEC's |
346 |
|
o modified/added many .cvsignore files in */code and */input |
347 |
|
o added new expt "solid-body.cs-32x32x1" |
348 |
|
+ this uses an alternative form of ini_curvilinear_grid.F which |
349 |
|
is not necessarily any better than the current one... |
350 |
|
|
351 |
|
checkpoint40pre4 |
352 |
|
o added re-initialisations of utrans,vtrans,rtrans in |
353 |
|
calc_common_factors which are crucial for TAF. |
354 |
|
o extended iMin,jMin range for calc_common_factors, |
355 |
|
calc_diffusivity |
356 |
|
o added option ALLOW_PASSIVE_TRACER |
357 |
|
o a few minor updates and fixes |
358 |
|
|
359 |
|
checkpoint40pre3 |
360 |
|
o created calc_gtr1.F for gad package |
361 |
|
o split the_main_loop and re-introduced forward_step |
362 |
|
o some recomputations of nIter0 for TAMC |
363 |
|
|
364 |
|
checkpoint40pre2 |
365 |
|
o Updated to latest branch of AJA, JMC |
366 |
|
o Added gradient check package |
367 |
|
o Added routines for passive tracer handling |
368 |
|
o Added carbon sequestration sensitivity experiment |
369 |
|
|
370 |
|
checkpoint39 |
371 |
|
o Modifications and fixes to support TAMC |
372 |
|
(mainly missing or wrong directives) |
373 |
|
o Corrected common blocks when fooling TAMC to produce adjoint I/O |
374 |
|
in addummy_in_stepping |
375 |
|
o Updated verification/vero/ (bug fixes in code/, correct pickups in input/) |
376 |
|
o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs. |
377 |
|
o Included following packages: |
378 |
|
cal: calendar |
379 |
|
exf: external forcing |
380 |
|
ecco: essential routines to control use of cal, exf |
381 |
|
(NB: this is not the full ECCO environment) |
382 |
|
o disabled some packages by default in genmake |
383 |
|
|
384 |
|
checkpoint38 |
385 |
|
o see notes_c37_adj.txt |
386 |
|
o corrected wrong layer index in external_forcing_t |
387 |
|
o replaced the_main_loop/forward_step by the_main_loop |
388 |
|
o removed forceoutput from write_state |
389 |
|
(replaced criteria for initial/final state) |
390 |
|
o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
391 |
|
|
392 |
|
checkpoint37 |
393 |
|
o mdsio.F routine split and packaged in pkg/mdsio |
394 |
|
(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
395 |
|
used unless genmake -disable=mdsio) |
396 |
|
o allow a more precise surface-geopotential gradient for the atmosphere |
397 |
|
taking into account the change in space of Alpha (=1/rho) at the surface. |
398 |
|
o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit] |
399 |
|
(ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa]) |
400 |
|
o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and |
401 |
|
Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential |
402 |
|
[m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere). |
403 |
|
o Time-Average diagnostics defined as a pseudo package "timeave". |
404 |
|
o pickup files : old pickup (before c35) did not work with new code (c35 |
405 |
|
and after) unless activating 2 commented lines in initialise-varia. |
406 |
|
o Non-Hydrostatic pickup file Pb fixed. |
407 |
|
o bug with Rigid-lid version (since c35) fixed. |
408 |
|
|
409 |
|
checkpoint36 |
410 |
|
o implement Crank-Nickelson barotropic time-stepping |
411 |
|
o recover Time-Average diagnostics |
412 |
|
o fix Pb in checkpoint (PR#19) |
413 |
|
o AIM become a standard package ; clean unused CPP_kees |
414 |
|
|
415 |
|
checkpoint35 |
416 |
|
o subtantial rewrite of dynamics.f |
417 |
|
o allows staggered time-stepping |
418 |
|
o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
419 |
|
o added bottom drag (linear + quadratic) |
420 |
|
|
421 |
checkpoint34 |
checkpoint34 |
422 |
o Modified exchange routines for correct reverse simulation. |
o Modified exchange routines for correct reverse simulation. |
423 |
o Added verification output to comply with bug fix in impldiff.F |
o Added verification output to comply with bug fix in impldiff.F |
426 |
o Corrected array boundaries in impldiff.F |
o Corrected array boundaries in impldiff.F |
427 |
o Corrected array dimensions in gmredi. |
o Corrected array dimensions in gmredi. |
428 |
Added temporary scalars to avoid storage by TAMC (gmredi, kpp). |
Added temporary scalars to avoid storage by TAMC (gmredi, kpp). |
429 |
|
o Added routine GLOBAL_SUM_INT to global_sum.F |
430 |
o Added mdsio_gl.F for ECCO purposes. |
o Added mdsio_gl.F for ECCO purposes. |
431 |
|
|
432 |
checkpoint33 |
checkpoint33 |