3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
4 |
============================== |
============================== |
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checkpoint47c_post |
7 |
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o Added a verification experiment for a global cubed-sphere ocean run |
8 |
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- verification/global_ocean.cubed32x32x30 |
9 |
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- uses pkg/therm_seaice and pkg/bulk_forcing |
10 |
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|
11 |
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|
12 |
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o allow to run AIM physics with SPEEDY input files (from Franco Molteni) |
13 |
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o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) |
14 |
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when using P-coordinate; only implemented for atmospheric config. |
15 |
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o OCEANICP & realFreshWater: include P-E direct effect on wVel ; |
16 |
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NOTES: requires option NONLIN_FRSURF to be "#define". |
17 |
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o update advect_xz/results/output.txt (left from checkpoint44g_post) |
18 |
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|
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checkpoint47b_post |
20 |
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Merging from release1_p9: |
21 |
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o pkg/seaice |
22 |
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- removed GOTO's and added taf directives |
23 |
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- double precision constants to reduce the g77 (Linux) |
24 |
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to F77 (SGI) differences reported in release1_p8 |
25 |
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o tools/genmake |
26 |
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- added SGI options |
27 |
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o verification/testscript |
28 |
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- updated to that of checkpoint47a_post |
29 |
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o verification/global_ocean.90x40x15/input/eedata |
30 |
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- modified for SGI f77 compatibility |
31 |
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o verification/lab_sea |
32 |
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- added description of sea-ice model |
33 |
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- added missing matlab routines |
34 |
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- added test of thermodynamics parallelization |
35 |
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|
36 |
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checkpoint47a_post |
37 |
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o new pkg: aim_v23 |
38 |
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= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
39 |
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for now, keep the same surface forcing as before. |
40 |
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- Part-Cell implemented into AIM; check that Heat & Water are conserved |
41 |
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- aim.5l_cs: use new aim pkg (run 10yr & get better results than before) |
42 |
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- aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg |
43 |
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o add diagnostic of surface correction term in monitor output |
44 |
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|
45 |
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o bulk_force and therm_seaice |
46 |
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- Two packages: bulk_force (Bulk forcing) |
47 |
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and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 |
48 |
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- Earlier integration from Stephaine Dutkiewicz |
49 |
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and Patrick Heimbach. |
50 |
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- Two ifdef statements for compile time, |
51 |
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ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE |
52 |
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|
53 |
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checkpoint47 |
54 |
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differentiable version of checkpoint46n_post |
55 |
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o bug fix in quasihydrostaticterms |
56 |
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o * "clean" adjoint code (in terms of extensive recomputations) |
57 |
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can now be obtained for all GMREDI options (i.e. for |
58 |
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- GM_VISBECK_VARIABLE_K |
59 |
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- GM_NON_UNITY_DIAGONAL |
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- GM_EXTRA_DIAGONAL |
61 |
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- GM_BOLUS_ADVEC ) |
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* However, wrong gradient check problem remains unsolved. |
63 |
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* New CPP options have been introduced for different |
64 |
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tapering schemes |
65 |
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o external_fields_load now part of differentiation list |
66 |
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o pressure needs multiple storing; |
67 |
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would be nice to have store_pressure at beginning or |
68 |
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end of forward_step, e.g. by having phiHyd global (5-dim.) |
69 |
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(NB: pressure is needed for certain cases in find_rho, |
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which is also invoked through convective_adjustment). |
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o recomputations in find_rho for cases |
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'JMD95'/'UNESCO' or 'MDJWF' are OK. |
73 |
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o #define ATMOSPHERIC_LOADING should be differentiable |
74 |
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o ini_forcing shifted to begining of initialise_varia |
75 |
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o Incorporating QNVS line search routines into MITgcm |
76 |
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(this is separate code, and therefore not under pkg) |
77 |
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lsopt/, optim/ |
78 |
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o Updated verification/carbon/ |
79 |
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- #define GM_VISBECK_VARIABLE_K |
80 |
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- GM_taper_scheme = 'ldd97' |
81 |
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|
82 |
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checkpoint46n_post |
83 |
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Merging from release1_p8: |
84 |
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o verification/natl_box: |
85 |
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updating new external_fields_load routine |
86 |
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o New package: pkg/seaice |
87 |
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Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). |
88 |
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The sea-ice code is based on Hibler (1979-1980). |
89 |
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Two sea-ice dynamic solvers, ADI and LSR, are included. |
90 |
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In addition to computing prognostic sea-ice variables and diagnosing |
91 |
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the forcing/external data fields that drive the ocean model, |
92 |
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SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
93 |
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The implied surface heat flux is then stored in variable |
94 |
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surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and |
95 |
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kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the |
96 |
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non-local transport term. Because this call precedes model |
97 |
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thermodynamics, temperature under sea-ice may not be "exactly" at |
98 |
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the freezing point by the time theta is dumped or time-averaged. |
99 |
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N.B.: fairly large differences in accuracy occur across |
100 |
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different platforms/compilers; comparison between |
101 |
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g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) |
102 |
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generated output gives: |
103 |
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T S U V |
104 |
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C D M c m s m s m s m s |
105 |
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n p a R g m m e . m m e . m m e . m m e . |
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f n k u 2 i a a d i a a d i a a d i a a d |
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g d e n d n x n . n x n . n x n . n x n . |
108 |
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|
109 |
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Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea |
110 |
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o GAD: |
111 |
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- generated new common blocks to account for call of |
112 |
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same gad routines with differing traceridentities |
113 |
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(needed to modify tracerIdentity indices in GAD.h) |
114 |
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- generated separate common blocks for case useCubedSphereExchange |
115 |
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(Department of Futurology) |
116 |
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- parameter lists to gmredi_?transport: added tracerIdentity |
117 |
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- added new key indices to tamc.h |
118 |
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o external_fields_load: |
119 |
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- added this routine to TAF list |
120 |
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- needed to make some common blocks global and additional storing |
121 |
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along the same lines as exf package (checkpoint_lev?_directives.h) |
122 |
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o exf: |
123 |
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updated external forcing package |
124 |
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- bug fixes carried over from ecco-branch |
125 |
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(missing OBCS_OPTIONS.h in two routines) |
126 |
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- enable easy to use "no forcing". |
127 |
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- added exf I/O for atmospheric loading |
128 |
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- added exf I/O for runoff data |
129 |
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- transfered scaling between exf <-> MITgcm to exf namelist |
130 |
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o Adding new verification experiment global_with_exf. |
131 |
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This verification experiment is almost identical to the |
132 |
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global_ocean.90x40x15 experiment, except that it uses |
133 |
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the exf (and cal) package instead of the |
134 |
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external_fields_load routine (cf README file). |
135 |
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|
136 |
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checkpoint46m_post |
137 |
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o modified testscript to return -- when there are no lines of "%MON" output |
138 |
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o added new flag "quasiHydrostatic" for QH mode |
139 |
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and new routine quasihydrostaticterms() |
140 |
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o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
141 |
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New routine: mom_u_coriolis_nh() |
142 |
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o fixed sign of non-hydrostatic metric terms in u and v equations. |
143 |
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Depend on correct sign of gravitySign. |
144 |
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o added work.pc* to .cvsignore in aim directories using ifc |
145 |
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o introduced flag for controllin non-hydrostatic metric terms |
146 |
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o removed gravitySign from PARM04 |
147 |
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o switched to g77/ifc from pgf77 in aim experiments |
148 |
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|
149 |
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checkpoint46l_post |
150 |
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o made convective adjustment work with pressure coordinates: |
151 |
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- changed the direction of k-loop in convective_adjustment.F for the |
152 |
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case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
153 |
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- adjusted the reference pressure k-index in convective_adjustment.F |
154 |
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- adjusted the convection condition in convect.F (in analogy to |
155 |
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calc_ivdc.F) |
156 |
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- convective_adjustment no longer computes anything on the halos |
157 |
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- removed the warnings about negative salinity from find_rho.F and |
158 |
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find_alpha.F; instead the new routine look_for_neg_salinity, called |
159 |
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at the beginning of find_rho, find_alpha, and find_beta, does a |
160 |
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check of the entire slice, if CPP-option |
161 |
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CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined |
162 |
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checkpoint46l_pre |
163 |
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|
164 |
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checkpoint46k_post |
165 |
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o fixed the verification/global_ocean.90x40x15 experiment: |
166 |
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- new bathymetry (the world according to A., JMC, and M.) |
167 |
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- new initial fields and forcing fields (*.bin files) |
168 |
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- new POLY3.COEFFS (for the next release one should switch to a full |
169 |
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equation of state: JMD95P or MDJWF) |
170 |
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- fixed several errors and redundancies in the data file |
171 |
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- experiment uses looped cells |
172 |
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- added matlab directory with diagnostic scripts for plotting of output |
173 |
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|
174 |
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o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
175 |
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- read AIM physics parameters from a file (data.aimphys) |
176 |
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- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
177 |
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|
178 |
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checkpoint46j_post |
179 |
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o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
180 |
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o move wVel computation at the end of the time step, in S/R integr_continuity |
181 |
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o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
182 |
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o update timeave pkg for wVel diagnostic. |
183 |
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checkpoint46j_pre |
184 |
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|
185 |
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checkpoint46i_post |
186 |
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o Clean up AIM package (and keep the results unchanged): |
187 |
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include CPP_OPTION and use IMPLICT NONE in all routines ; |
188 |
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declare all the variables _RL ; use _d 0 for all numerical constants. |
189 |
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use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
190 |
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|
191 |
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checkpoint46h_post |
192 |
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o cleaned up the use of rhoNil and rhoConst. |
193 |
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- rhoNil should only appear in the LINEAR equation of state, everywhere |
194 |
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else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
195 |
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and the dynamical equations are all divided by rhoConst |
196 |
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o introduced new parameter rhoConstFresh, a reference density of fresh |
197 |
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water, to remove the fresh water flux's dependence on rhoNil. The default |
198 |
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value is 999.8 kg/m^3 |
199 |
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o cleanup up external_forcing.F and external_forcing_surf.F |
200 |
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- can now be used by both OCEANIC and OCEANICP |
201 |
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checkpoint46h_pre |
202 |
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|
203 |
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Added code to convert surface volume flux (fresh water) into |
204 |
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a mass flux when using P coordinates in the ocean (OCEANICP). |
205 |
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Note: It assumes you have set rho0=rhoConst=density of fresh water. |
206 |
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|
207 |
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checkpoint46g_post |
208 |
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o Include a new diagnostic variable phiHydLow for the ocean model |
209 |
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- in z-coordinates, it is the bottom pressure anomaly |
210 |
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- in p-coordinates, it is the sea surface elevation |
211 |
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- in both cases, these variable have global drift, reflecting the mass |
212 |
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drift in z-coordinates and the volume drift in p-coordinates |
213 |
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- included time averaging for phiHydLow, be aware of the drift! |
214 |
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o depth-dependent computation of Bo_surf for pressure coordinates |
215 |
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in the ocean (buoyancyRelation='OCEANICP') |
216 |
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- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
217 |
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Theta, Salinity, and Pressure in the parameter list. This routine is |
218 |
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presently contained in find_rho.F. This routine does not give the |
219 |
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correct density for 'POLY3', which would be a z-dependent reference |
220 |
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density. |
221 |
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o cleaned up find_rho |
222 |
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- removed obsolete 'eqn' from the parameter list. |
223 |
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o added two new verification experiments: gop and goz |
224 |
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(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
225 |
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checkpoint46g_pre |
226 |
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|
227 |
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checkpoint46f_post |
228 |
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o Enable tangent linear (forward mode) gradient checks: |
229 |
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- extended active file handling to g_... files |
230 |
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- added TANGENT_SIMULATION to theSimulationMode |
231 |
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- extended grdchk package accordingly |
232 |
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o added tangent linear setup in verification/carbon/code_ftl |
233 |
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o added adjoint setup in verification/front_relax/code_ad |
234 |
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|
235 |
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checkpoint46e_post |
236 |
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o Added new equation of state -> MDJWF |
237 |
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- EOS of McDougall et al., 2002, JAOT, submitted |
238 |
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- caveat: the equation of state is only valid for a smaller (more |
239 |
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realistic?) range of values than JMD95P/Z and UNESCO |
240 |
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- added masks to the calculation of pressure in store_pressure |
241 |
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- added more check values for density in check_eos (ini_eos.F), some of |
242 |
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the old check values are out of the range of the MDJWF-eos, so don't |
243 |
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expect perfect matches for those |
244 |
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checkpoint46e_pre |
245 |
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|
246 |
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checkpoint46d_post |
247 |
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o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
248 |
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'OCEANICP', also initialised field pressure correctly in ini_eos in the |
249 |
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case of pressure coordinates. eosType='JMD95Z' in |
250 |
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combination with buoyancyRelation='OCEANICP' now causes an error. |
251 |
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o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
252 |
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in find_alpha/beta. |
253 |
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checkpoint46d_pre |
254 |
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|
255 |
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o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
256 |
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so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
257 |
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|
258 |
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checkpoint46c_post |
259 |
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o Changes necessary for ocean in p-coordinates |
260 |
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- Added new buoyancy relation = 'OCEANICP' |
261 |
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- Added new parameters = gravitySign (this used to be contained inside |
262 |
|
the factor dRdZ which I added when we first switched to R coordinates). |
263 |
|
X GM/Redi is not compatible (yet) |
264 |
|
X bottom drag and no-slip need to be debugged. |
265 |
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checkpoint46c_pre |
266 |
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|
267 |
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checkpoint46b_post |
268 |
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o Added new equation of state -> JMD95Z and JMD95P |
269 |
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- EOS of Jackett and McDougall, 1995, JAOT |
270 |
|
- moved all EOS parameters into EOS.h |
271 |
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- new routines ini_eos.F, store_pressure.F |
272 |
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o Added UNESCO EOS, but not recommended because it requires |
273 |
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in-situ temperature (see JMD95) |
274 |
|
o Modified formatting for knudsen2.f in utils/knudsen2 and added |
275 |
|
unesco.f to be used with POLY3 |
276 |
|
checkpoint46b_pre |
277 |
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|
278 |
|
checkpoint46a_post |
279 |
|
o Added (atmospheric) pressure loading |
280 |
|
- new field in FFIELDS.h, etc... |
281 |
|
- new cpp flag ATMOSPHERIC_LOADING |
282 |
|
o Changed hFacC to _hFacC in calc_phi_hyd.F |
283 |
|
o Added SHORTWAVE_HEATING to some files for consistency |
284 |
|
checkpoint46a_pre |
285 |
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|
286 |
|
checkpoint46 |
287 |
|
further merges from release1_p5 |
288 |
|
o new ctrl package |
289 |
|
- adopted from ECCO environment to enable optimization |
290 |
|
- added Eliassen Palm fluxes to controls |
291 |
|
o added Eliassen Palm flux controls to gradient check package |
292 |
|
o cost package |
293 |
|
- Compatible with new ctrl package |
294 |
|
- added Eliassen Palm cost hooks |
295 |
|
- modif's of existing cost functions |
296 |
|
o Adjoint-related bug fixes in kpp: |
297 |
|
- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
298 |
|
- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
299 |
|
o autodiff package |
300 |
|
- flow directives: |
301 |
|
+ new for S/R do_the_model_io |
302 |
|
+ enhanced for S/R checkpoint |
303 |
|
+ new gmredi.flow |
304 |
|
- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
305 |
|
disable adcommon.h/g_common.h by default. |
306 |
|
- fixed problem for adjoint of global_max |
307 |
|
o modified verification/carbon/ |
308 |
|
o New setup for adjoint of global_ocean |
309 |
|
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
310 |
|
o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
311 |
|
o incorporated hooks for sponge layer code (external_forcing.F) |
312 |
|
|
313 |
|
checkpoint45d_post |
314 |
|
o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
315 |
|
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
316 |
|
(affects plume_on_slope "cg2d" output) |
317 |
|
o add new parameter deltaTfreesurf for free-surface time stepping |
318 |
|
o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
319 |
|
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
320 |
|
o change phiMin in exp1 (to agree with documentation) |
321 |
|
o add new flags: |
322 |
|
- T,S forcing inside/outside Adams-Bashforth |
323 |
|
- turn off temp,salt advection and/or forcing |
324 |
|
- for each tracer, define internal flag for multiDimAdvection & A-B |
325 |
|
o monitor: change definition of KE to check conservation of Energy |
326 |
|
|
327 |
|
checkpoint45c_post |
328 |
|
o Removed f90 comments ("!") |
329 |
|
o Modified initialisations to enable exf package for MITgcm |
330 |
|
(without invoking ECCO_PACKAGE). |
331 |
|
o modifications to gradient check package (Martin Losch) |
332 |
|
- enable centered differences |
333 |
|
- modified format of standard output |
334 |
|
|
335 |
|
checkpoint45b_post |
336 |
|
o cleaned exchange calls in cg2d |
337 |
|
o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
338 |
|
o included CPP option SINGLE_LAYER_MODE in thermodynamics |
339 |
|
to configure barotropic setup (Martin Losch) |
340 |
|
o moved some initialisations within bi,bj loop in dynamics |
341 |
|
(TAF flow dependency) |
342 |
|
o in initialise_varia, moved call packages_init_variables |
343 |
|
before convective_adjustment_init |
344 |
|
(corresponding adjustment of TAF tape initialisation). |
345 |
|
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
346 |
|
|
347 |
|
checkpoint45a_post |
348 |
|
o compute Rho over the whole domain (extend iMin,jMin indices) |
349 |
|
o specific exchange for X-slice domain (case Ny=1) |
350 |
|
o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
351 |
|
o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
352 |
|
|
353 |
|
checkpoint44h_post = checkpoint45 |
354 |
|
o Fix to restore differentiability: |
355 |
|
place at which packages_init_variables is called in |
356 |
|
initialise_varia is crucial for reverse control flow. |
357 |
|
o modifications in GMRedi to enable stable adjoint |
358 |
|
(corresponding modif's in thermodynamics, dynamics) |
359 |
|
o added missing hook for sponge layer code in external_forcing |
360 |
|
o modified test cost functions |
361 |
|
o storing in gad_advection (plus removal of write(0,*)! |
362 |
|
o missing headers TR1.h added in convective_adjustment routines |
363 |
|
o errorMessageUnit set non-equal zero in eeboot |
364 |
|
(conflict on some platforms, e.g. IBM SP3) |
365 |
|
o modified carbon verif. |
366 |
|
|
367 |
|
checkpoint44h_pre |
368 |
|
o vertical grid option: allow to put the Interface at the middle between |
369 |
|
2 cell-centers ; replace delZ in pkg/kpp by drF. |
370 |
|
o GM Advective form: Tracers are advected using the residual transport (= |
371 |
|
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
372 |
|
|
373 |
|
checkpoint44g_post |
374 |
|
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
375 |
|
results) ; ifdef missing in thermodynamics.F |
376 |
|
|
377 |
|
checkpoint44f_pre,checkpoint44f_post |
378 |
|
o added PTRACERS package |
379 |
|
This allows an arbitrary number of passive tracers to be integrated |
380 |
|
forward simultaneously with the dynamicaly model. |
381 |
|
+ Implemented so far: |
382 |
|
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
383 |
|
- I/O and checkpointing |
384 |
|
- GM/Redi *but* using the GM/Redi coefficient of Salt |
385 |
|
+ Not implemented so far: |
386 |
|
- KPP |
387 |
|
- OBCS |
388 |
|
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
389 |
|
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
390 |
|
line in data.pkg. |
391 |
|
+ This package is disabled by default since it increases storage. |
392 |
|
|
393 |
|
|
394 |
|
o testscript: added -cleanup option |
395 |
|
o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
396 |
|
b) enable to filter 2D fields. |
397 |
|
|
398 |
|
checkpoint44e_pre,post |
399 |
|
o re-wrote convective adjustment to use pre-calculated weights |
400 |
|
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
401 |
|
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
402 |
|
Original calls to convect() still in place. |
403 |
|
|
404 |
|
chkpt44d_pre,post |
405 |
|
o added missing EXCLUDE_MONITOR flags |
406 |
|
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
407 |
|
(incompatible typ in MIN/MAX expressions caused problems |
408 |
|
on IBM SP3) |
409 |
|
o in genmake added variable MAKEDEPEND |
410 |
|
plus resetting for case SunOS |
411 |
|
o added timer_stats.c routine for IBM SP3 |
412 |
|
o removed variables in dynamics |
413 |
|
!!! I forgot to create tag chkpt44d_pre !!! |
414 |
|
!!! But chkpt44d_pre = chkpt44c_post !!! |
415 |
|
|
416 |
|
o real fresh water flux implemented with non-linear free-surface. |
417 |
|
|
418 |
|
chkpt44c_pre,post |
419 |
|
o few fix (mask in shap_s2, EmPmR in external_field_load, |
420 |
|
USE_NATURAL_BCS in solve_for_P); |
421 |
|
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
422 |
|
|
423 |
|
checkpoint44b_pre/_post |
424 |
|
o merge of relevant stuff from the ecco-branch: |
425 |
|
- genmake: removed $S64 overwrite for case SunOS |
426 |
|
- pkg/exf: update and corrections for field swapping and obcs |
427 |
|
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
428 |
|
harmonized between ECCO and MITgcm |
429 |
|
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
430 |
|
updated checkpointing_lev... lists for obcs |
431 |
|
- model/src: minor changes in forward_step, plot_field |
432 |
|
added directive for divided adjoint in the_main_loop |
433 |
|
- pkg/mdsio: added mdsio_gl_slice |
434 |
|
|
435 |
|
o check parameters & config (chkpt44a_pre,post) |
436 |
|
o OBC and NonLin_FrSurf. |
437 |
|
|
438 |
|
checkpoint44 |
439 |
|
o fix bug in mom_vi_del2uv |
440 |
|
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
441 |
|
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
442 |
|
o update AIM experiments (NCEP input files) |
443 |
|
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
444 |
|
o added some stuff for AD |
445 |
|
|
446 |
|
checkpoint43 |
447 |
|
o added two new advection tests |
448 |
|
o added global 4x4 degree ocean test |
449 |
|
o added test of H&S94 with free surface on cube |
450 |
|
o some final mods for gradient check, adjoint,... |
451 |
|
|
452 |
|
checkpoint42 |
453 |
|
Fixed AD-related problems: |
454 |
|
o Store directives up-to-date with re-arranged Adams-Bashforth |
455 |
|
(mainly thermodynamics.F) |
456 |
|
o New store directives for multi-dim. advection schemes |
457 |
|
* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
458 |
|
* new common block and key passkey |
459 |
|
(mainly gad_advection.F) |
460 |
|
o Modified store directives for split of dynamics/thermodynamics |
461 |
|
for the case ALLOW_KPP |
462 |
|
o Cleaned argument list for timestep_tracer.F |
463 |
|
|
464 |
|
checkpoint41 |
465 |
|
o re-formatted/added comments in prologues of key subroutines |
466 |
|
to work with protex |
467 |
|
|
468 |
|
checkpoint40 |
469 |
|
o moved calc_gs, calc_gt and calc_tr1 back to model/src |
470 |
|
o added FLT (floats) package from Arne along with demo. experiment |
471 |
|
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
472 |
|
implementation of forward-in-time forcing terms |
473 |
|
o more mods for non-linear free-surface including new variable |
474 |
|
o modified multi-dim method to work on cube |
475 |
|
o bug fix in KPP (from DM) |
476 |
|
|
477 |
|
checkpoint40pre9 |
478 |
|
o added DST advection schemes |
479 |
|
o fix MPI bug on SGI's |
480 |
|
o modifications for non-linear free-surface |
481 |
|
o fixed conditionals for fixed flow/passive tracer only mode |
482 |
|
o added tension/strain form of stress tensor |
483 |
|
o changes to commenting of arguments for TAF/TAMC |
484 |
|
o added/updated many matlab scripts |
485 |
|
o added multi-dimensional advection method for tracers |
486 |
|
|
487 |
|
checkpoint40pre8 |
488 |
|
o new package rw/ |
489 |
|
Added method for dumping intermediate local arrays: |
490 |
|
mdsio_writetile - same as mdsio_writefield except works from inside |
491 |
|
bi,bj loop |
492 |
|
mdsio_writelocal - same as mdsio_writetile except works for local |
493 |
|
arrays |
494 |
|
write_local_r? - higher-level wrapper for mdsio_writelocal |
495 |
|
Controlled by diagFreq. Defaults to zero (ie. no dumps) |
496 |
|
Example given at end of mom_vecinv.F that dumps some local arrays. |
497 |
|
o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
498 |
|
control flux-form versus vector invariant code. |
499 |
|
Switch is runtime flag vectorInvariantMomentum (defaults to false) |
500 |
|
or genmake -DISABLE ... |
501 |
|
o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
502 |
|
(additional storing is now needed for case vecinv; |
503 |
|
currently nothing implemented to switch this storing off |
504 |
|
in case fluxform is used since no CPP flag available). |
505 |
|
|
506 |
|
checkpoint40pre7 |
507 |
|
o bug fix in dynamics.F |
508 |
|
calc_viscosity called before k=1,Nr loop. |
509 |
|
o added some #ifdef's ALLOW_PASSIVE_TRACER |
510 |
|
o cleaned initialisations in ctrl_map_ini |
511 |
|
related to TAF |
512 |
|
|
513 |
|
checkpoint40pre6 |
514 |
|
o split dynamics into thermodynamics & dynamics |
515 |
|
o corresponding split of calc_diffusivity into |
516 |
|
calc_diffusivity, calc_viscosity |
517 |
|
(kpp_calc_diff, kpp_calc_visc). |
518 |
|
o Added diffkr, kapgm to control variables |
519 |
|
o bug fix in gmredi_slope_limit for ldd97 |
520 |
|
|
521 |
|
checkpoint40pre5 |
522 |
|
o proper initialization of Adams-Bashforth time stepping |
523 |
|
+ uses forward step for very first step of model (iter=0) |
524 |
|
o re-generated *all* output since almost all output is modified by this |
525 |
|
change (sorry but we've been putting this one off for about 2 years) |
526 |
|
+ natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were |
527 |
|
*not* regenerated since they are already out of date and I don't |
528 |
|
want to create the impression that they are suddenly working. |
529 |
|
o removed KAP stuff for DEC's |
530 |
|
o modified/added many .cvsignore files in */code and */input |
531 |
|
o added new expt "solid-body.cs-32x32x1" |
532 |
|
+ this uses an alternative form of ini_curvilinear_grid.F which |
533 |
|
is not necessarily any better than the current one... |
534 |
|
|
535 |
|
checkpoint40pre4 |
536 |
|
o added re-initialisations of utrans,vtrans,rtrans in |
537 |
|
calc_common_factors which are crucial for TAF. |
538 |
|
o extended iMin,jMin range for calc_common_factors, |
539 |
|
calc_diffusivity |
540 |
|
o added option ALLOW_PASSIVE_TRACER |
541 |
|
o a few minor updates and fixes |
542 |
|
|
543 |
|
checkpoint40pre3 |
544 |
|
o created calc_gtr1.F for gad package |
545 |
|
o split the_main_loop and re-introduced forward_step |
546 |
|
o some recomputations of nIter0 for TAMC |
547 |
|
|
548 |
|
checkpoint40pre2 |
549 |
|
o Updated to latest branch of AJA, JMC |
550 |
|
o Added gradient check package |
551 |
|
o Added routines for passive tracer handling |
552 |
|
o Added carbon sequestration sensitivity experiment |
553 |
|
|
554 |
|
checkpoint39 |
555 |
|
o Modifications and fixes to support TAMC |
556 |
|
(mainly missing or wrong directives) |
557 |
|
o Corrected common blocks when fooling TAMC to produce adjoint I/O |
558 |
|
in addummy_in_stepping |
559 |
|
o Updated verification/vero/ (bug fixes in code/, correct pickups in input/) |
560 |
|
o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs. |
561 |
|
o Included following packages: |
562 |
|
cal: calendar |
563 |
|
exf: external forcing |
564 |
|
ecco: essential routines to control use of cal, exf |
565 |
|
(NB: this is not the full ECCO environment) |
566 |
|
o disabled some packages by default in genmake |
567 |
|
|
568 |
|
checkpoint38 |
569 |
|
o see notes_c37_adj.txt |
570 |
|
o corrected wrong layer index in external_forcing_t |
571 |
|
o replaced the_main_loop/forward_step by the_main_loop |
572 |
|
o removed forceoutput from write_state |
573 |
|
(replaced criteria for initial/final state) |
574 |
|
o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
575 |
|
|
576 |
|
checkpoint37 |
577 |
|
o mdsio.F routine split and packaged in pkg/mdsio |
578 |
|
(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
579 |
|
used unless genmake -disable=mdsio) |
580 |
|
o allow a more precise surface-geopotential gradient for the atmosphere |
581 |
|
taking into account the change in space of Alpha (=1/rho) at the surface. |
582 |
|
o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit] |
583 |
|
(ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa]) |
584 |
|
o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and |
585 |
|
Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential |
586 |
|
[m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere). |
587 |
|
o Time-Average diagnostics defined as a pseudo package "timeave". |
588 |
|
o pickup files : old pickup (before c35) did not work with new code (c35 |
589 |
|
and after) unless activating 2 commented lines in initialise-varia. |
590 |
|
o Non-Hydrostatic pickup file Pb fixed. |
591 |
|
o bug with Rigid-lid version (since c35) fixed. |
592 |
|
|
593 |
|
checkpoint36 |
594 |
|
o implement Crank-Nickelson barotropic time-stepping |
595 |
|
o recover Time-Average diagnostics |
596 |
|
o fix Pb in checkpoint (PR#19) |
597 |
|
o AIM become a standard package ; clean unused CPP_kees |
598 |
|
|
599 |
|
checkpoint35 |
600 |
|
o subtantial rewrite of dynamics.f |
601 |
|
o allows staggered time-stepping |
602 |
|
o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
603 |
|
o added bottom drag (linear + quadratic) |
604 |
|
|
605 |
|
checkpoint34 |
606 |
|
o Modified exchange routines for correct reverse simulation. |
607 |
|
o Added verification output to comply with bug fix in impldiff.F |
608 |
|
as of c33 (exp2, natl_box). |
609 |
|
o Corrected store directives in dynamics.F |
610 |
|
o Corrected array boundaries in impldiff.F |
611 |
|
o Corrected array dimensions in gmredi. |
612 |
|
Added temporary scalars to avoid storage by TAMC (gmredi, kpp). |
613 |
|
o Added routine GLOBAL_SUM_INT to global_sum.F |
614 |
|
o Added mdsio_gl.F for ECCO purposes. |
615 |
|
|
616 |
|
checkpoint33 |
617 |
|
o Fixed bug in lower BC in impldiff.F |
618 |
|
o Fixed confusion about units of forcing arrays in FFIELDS.h |
619 |
|
namely Fu,Fv,Qnet,Qsw,EmPmR: |
620 |
|
- Removed verification/natl_box/code/external_fields_scale.F |
621 |
|
(did not differ from that in model/src) |
622 |
|
- Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units |
623 |
|
(see FFIELDS.h for description) |
624 |
|
- Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F, |
625 |
|
kpp_calc.F and kpp_transport_t.F |
626 |
|
- Removed model/src/external_fields_scale.F and calls to it |
627 |
|
- verification/natl_box uses flux data with "atmospheric" sign so |
628 |
|
a special version of external_fields_load.F is used to |
629 |
|
change the data as it's read in. This way, the arrays |
630 |
|
have the right units and signs at all times tha a user could |
631 |
|
possibly use them. |
632 |
|
o Corrected genmake to delete a temporary file during configuration |
633 |
|
|
634 |
|
checkpoint32 |
635 |
|
o Scaling of forcing fields moved from external_forcing.F to |
636 |
|
external_fields_scale.F, called directly after loading fields. |
637 |
|
o Surface relaxation terms added to surface tendency fields in |
638 |
|
extra subroutine. |
639 |
|
o impldiff.F changed to avoid storing by TAMC of huge intermediate |
640 |
|
fields. |
641 |
|
o Changes in GMRedi to comply with packaging structure. |
642 |
|
o Modifications and bug fixes in KPP package. |
643 |
|
o Verification experiment for KPP added (verification/nat_box/) |
644 |
|
|
645 |
|
checkpoint31 |
646 |
|
o Packages interface brought in line with defined standard |
647 |
|
-> new routines packages_...F |
648 |
|
-> changes in initialise_fixed.F, initialise_varia.F |
649 |
|
-> enables initialisation interface for ECCO package |
650 |
|
o Rescaling of external forcing fields immediately after read |
651 |
|
(removed from external_forcing.F) |
652 |
|
-> new: surface_fields_scale.F |
653 |
|
-> affects ini_foorcing.F, external_fields_load.F |
654 |
|
o Computation of surface tendencies before tendency updates. |
655 |
|
-> new: external_forcing_surf.F |
656 |
|
o Change of variable names useGMRedi, useKPP, useECCO |
657 |
|
o Further changes in dynamics.F, impldiff.F for TAMC |
658 |
|
o Tested for experiments 0, 2, 4. |
659 |
|
- not yet tested for GMRedi. |
660 |
|
- not yet tested for KPP. |
661 |
|
|
662 |
|
checkpoint30 |
663 |
|
o Updates for OBCs |
664 |
|
o New experiment for test OBCs (internal_wave) |
665 |
|
o New output.txt in verification/exp4/results/ |
666 |
|
o Updates for KPP: calculation of viscosity corrected, new variables |
667 |
|
kpp_dumpFreq and kpp_taveFreq |
668 |
|
o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) |
669 |
|
and entry for T90 in genmake |
670 |
|
|
671 |
|
checkpoint29 |
672 |
|
o packaged KPP and GM/Redi |
673 |
|
|
674 |
|
checkpoint28 |
675 |
|
o Corrected initialization of hFacMin for difference vertical coordinates |
676 |
|
o Modified calculation of partial cell thickness to more robust algorithm |
677 |
|
o config_summary.F: replaced write_1D_... by write_0D_... |
678 |
|
read_write.F: added subroutines write_0D_... |
679 |
|
o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho: |
680 |
|
included some initialisations required for TAMC. |
681 |
|
o routine calc_isoslopes: modified sqrt computation to make it |
682 |
|
differentiable for zero argument. |
683 |
|
o routines dynamics, impldiff: |
684 |
|
included store directives and tape key computations required for TAMC. |
685 |
|
o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC |
686 |
|
|
687 |
|
checkpoint27 |
688 |
|
o fixed calc_isoslopes() to so that cancellation of terms in tensor |
689 |
|
formulation works properly with variable resolution. |
690 |
|
o restructured the calling tree between the_model_main() and dynamics() |
691 |
|
o split initialise() into initialise_fixed() and initialise_varia() |
692 |
|
o introduced initialization file pSurfInitFile for free surface (cg2d_x) |
693 |
|
in new routine ini_psurf() |
694 |
|
|
695 |
|
checkpoint26 |
696 |
|
o moved some #ifdef in optional routines to encompass everything |
697 |
|
except the argument declarations. This was using up some memory. |
698 |
|
o fixed macros like _ADT to work with both versions of Linux cpp |
699 |
|
o cleaned up some unused and uninitialized variables |
700 |
|
(helps when debugging with strict compile options) |
701 |
|
o split up CPP_EEOPTIONS.h into options and macros |
702 |
|
(macros are now in eesupp/inc/CPP_EEMACROS.h) |
703 |
|
o patch for 2 processor JAM mode |
704 |
|
|
705 |
|
checkpoint25 |
706 |
|
o updates for OBCs and NH |
707 |
|
o dramatically reduced memory usage |
708 |
|
o added "JAM" routines for use on Artic network |
709 |
|
o parameterization of convection by implicit vertical diffusion |
710 |
|
o added a diagnostic of convective index |
711 |
|
o moved call to calc_divg_hat() from dynamics() to solve_for_pressure() |
712 |
|
(this is was partly for OBCs and NH but also in anticipation of |
713 |
|
an explicit free-surface option) |
714 |
|
o initial state input files for U and V |
715 |
|
|
716 |
|
checkpoint24 |
717 |
|
o Removed some spurious "REAL"s |
718 |
|
o Updated KPP to latest version from JPL |
719 |
|
o Added a COS(latitude) in horizontal viscosity |
720 |
|
|
721 |
|
checkpoint23 |
722 |
|
o Added del^4 diffusion for salt and temperature |
723 |
|
o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) |
724 |
|
|
725 |
|
checkpoint22 |
726 |
|
o Made many small changes: implicit none, format(i5), etc... |
727 |
|
o Introduced KPP mixing scheme (compiles and runs but *not* tested) |
728 |
|
|
729 |
|
checkpoint21 |
730 |
|
o Introduced new I/O package that supports direct-access records (mdsio.F) |
731 |
|
o Split-up mid-level I/O routines |
732 |
|
o Updated input data for experiments 0,1,2,4 and 5 |
733 |
|
o Finally removed the genmake.* scripts (everyone seems happy with genmake) |
734 |
|
|
735 |
|
checkpoint20 |
736 |
|
o Tidied up open-boundaries some more |
737 |
|
o Added non-hydrostatic code |
738 |
|
o Fixed some input data |
739 |
|
o Modified MPI start-up to work in "coupled" context. |
740 |
|
|
741 |
|
checkpoint19 |
742 |
|
o Tidied up directory structure for verification experiments. |
743 |
|
o Added new code for open boundaries. |
744 |
|
o Corrected advective terms near boundaries. |
745 |
|
o Added CPP flag for "old UV" geometry and corrected spherical geometry. |
746 |
|
o Implemented free-slip/no-slip BCs and del^4 dissipation. |
747 |
|
o Split default parameters out of ini_parms.F into set_defaults.F. |
748 |
|
|
749 |
|
checkpoint18 |
750 |
|
o Further changes for optional code generation with |
751 |
|
CPP - ugh! |
752 |
|
|
753 |
|
checkpoint17 |
754 |
|
o Beginning to incorporating modularity |
755 |
|
for supporting atmos. and ocean configs. |
756 |
|
o Small changes for TAMC complinace |
757 |
|
o New ultra simple test case. Barotropic box |
758 |
|
configuration "exp0". |
759 |
|
|
760 |
|
checkpoint16 |
761 |
|
o Minor changes to exchange routines to support |
762 |
|
accumulation in reverse mode. Adjoint of an |
763 |
|
assignment is an addition. |
764 |
|
o Changes to support compilation by TAMC (LR(1) |
765 |
|
syntax) and by g77 under Linux ( 72 character |
766 |
|
limit ). |
767 |
|
|
768 |
|
checkpoint15 |
769 |
|
Rewrote exchange routines to allow |
770 |
|
o General tile <-> tile connectivity. |
771 |
|
o TAMC reverse mode flag ( is this really needed? ) |
772 |
|
o Variable width overlap and exchange region widths. |
773 |
|
o Hooks for sharing data via DMA, Arctic, Memory Channel, |
774 |
|
shmput/shmget, VIA, SYSV shmem and every other cool |
775 |
|
communication method. |
776 |
|
|
777 |
|
checkpoint14 |
778 |
|
Consistent isomorphism chages made. These allow dynamical core |
779 |
|
to support both pressure and meters as a vertical coordinate. |
780 |
|
|
781 |
|
checkpoint13 |
782 |
|
Release which corrects global_max problem and a couple |
783 |
|
of KGM time-averaging diagnostic errors. Also contains |
784 |
|
a double-gyre experiment setup as well as the baseline |
785 |
|
4 degree global template. The double gyre template is |
786 |
|
organised to allow it to be applied automatically to |
787 |
|
the baseline configuration. |
788 |
|
|
789 |
|
branch-point-rdot |
790 |
|
A few tidy-ups have been made bt the real point of this |
791 |
|
check-point (excuse the pun) is to allow a branch to be |
792 |
|
made for the purposes of adding the rDot alterations. |
793 |
|
I don't want to commit the rDot to the main-trunk until |
794 |
|
we've actually tested it... |
795 |
|
|
796 |
|
checkpoint12 |
797 |
|
Tidy up and added generic genmake script (formerly |
798 |
|
configure script). |
799 |
|
Released to testers. |
800 |
|
|
801 |
|
checkpoint11 |
802 |
|
Re-arranged initialise() and introduced ini_vertical_grid() |
803 |
|
and ini_masks_etc(). |
804 |
|
|
805 |
|
checkpoint10 |
806 |
|
Introduced the configure script. |
807 |
|
Separated out the diags package. |
808 |
|
Added template for writing time-averages of tile/intermediate quantities. |
809 |
|
Updated SIZE.h in exp2 and made the data big-endian. |
810 |
|
|
811 |
|
checkpoint9 |
812 |
|
MPI fix. Filename changes (meta/data). salbin*y stuff. |
813 |
|
General tidy-up. |
814 |
|
SST.bin SSS.bin added to verification/exp2 |
815 |
|
|
816 |
|
checkpoint8 |
817 |
|
Inludes time-dependant forcing and time-averaging. |
818 |
|
Works at 4x4 and 2.8125x2.8125 global |
819 |
|
|
820 |
|
checkpoint7-4degree-ref |
821 |
|
Branch from checkpoint7. Released for application to |
822 |
|
global modeling and general modeling - process studies, regional |
823 |
|
model etc.. |
824 |
|
Configured for verification/exp2 - 4 degree global, two process. |
825 |
|
|
826 |
checkpoint7 |
checkpoint7 |
827 |
Created by cnh |
Created by cnh |
828 |
Simple 4 degree global simulation |
Simple 4 degree global simulation |