4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
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|
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o pkg/ggl90: fix computation of control volumes for the case of |
o verification, ad-tests: |
8 |
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- reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, |
9 |
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global_ocean_ebm and offline_exf_seaice.thsice. |
10 |
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o verification/halfpipe_streamice: |
11 |
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- found a bug in s/r pkg/streamice/streamice_advect_thickness which caused |
12 |
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flux input boundary conditions to be ignored; a fix for this bug changed |
13 |
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verification results for forward test. |
14 |
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- add adjoint test. |
15 |
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o pkg/ptracers: |
16 |
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- allow to restart without SOM pickup (resetting SOM to zero). |
17 |
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o pkg/gmredi: |
18 |
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- New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added. |
19 |
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- It uses mixing length theory and suppression by steering level effects to |
20 |
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calculate a diffusivity used in the Redi tensor (see Bates et al., submitted |
21 |
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to JPO, for more details). |
22 |
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- It also uses the diffusivity to calculate an eddy induced streamfunction |
23 |
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based on a PV closure (rather than a buoyancy closure as in GM). |
24 |
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- New files added to pkg/gmredi: |
25 |
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gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy |
26 |
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induced overturning streamfunction (called from gmredi_calc_tensor) |
27 |
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gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required |
28 |
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for use in gmredi_k3d |
29 |
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gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate |
30 |
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the eddy diffusivity |
31 |
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|
32 |
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checkpoint64i (2013/06/18) |
33 |
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o pkg/cheapaml: |
34 |
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- take src files from MITgcm_contrib/verification_other/offline_cheapaml/code |
35 |
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that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics) |
36 |
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with pkg/cheapaml. |
37 |
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o utils/python: add subpackage for cubed sphere function, first example is |
38 |
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simple cs.pcol to plot 2D fields on a map |
39 |
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o pkg/streamice: |
40 |
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- This is a new package in MITgcm, which solves dynamic equations for ice |
41 |
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sheets and ice streams |
42 |
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- At the moment it is independent of atmosphere/ocean dynamics, or any |
43 |
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other physical packages in MITgcm, even ShelfIce (although it is anticipat- |
44 |
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ed that this will change) |
45 |
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- There is a new verification exercise that tests it, halfpipe_streamice, |
46 |
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evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a |
47 |
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rectangular embayment |
48 |
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- halfpipe_streamice is forward-only for now, will have TAF test soon |
49 |
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- for questions, email dgoldber@mit.edu |
50 |
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o pkg/thsice: |
51 |
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- fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing |
52 |
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of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40); |
53 |
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- remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new |
54 |
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call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect ); |
55 |
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- allow precip from pkg/cheapaml to make snow over seaice. |
56 |
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o pkg/cfc: |
57 |
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- move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC |
58 |
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- remove atmos CFC 2-D arrays from common bloc (now local variables) |
59 |
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- change some hard-coded constant to run time parameter for reading and |
60 |
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and interpolating atmospheric CFC ; keep same default as previously. |
61 |
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- more flexible reading of Atmos CFC (number of records no longer hard-coded) |
62 |
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- put arguments in standard order: myTime, myIter, myThid |
63 |
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- use standard S/R GET_PERIODIC_INTERVAL for time interpolation of |
64 |
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atmospheric CFC ; fix for the case myIter < PTRACERS_iter0. |
65 |
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- fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf |
66 |
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- new routine to print summary of CFC params and check for consistency. |
67 |
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o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff, |
68 |
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similar to thsice_advdiff. |
69 |
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Note that for the B-grid case the routine parameters uc/vc are overwritten. |
70 |
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o pkg/cfc: |
71 |
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- change time interpolation for atmospheric CFC-11 (now same as for CFC-12); |
72 |
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update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline. |
73 |
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- fix interpolation of atmphspheric CFC between Sorthern and Northern |
74 |
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hemisphere value. |
75 |
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o pkg/seaice: |
76 |
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- allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml) |
77 |
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o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics; |
78 |
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so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE. |
79 |
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- requires an additional time level that is stored in the pickup |
80 |
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- you can start with AB2 from a pickup without this time level with |
81 |
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pickupStrictlyMatch = .false. |
82 |
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|
83 |
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checkpoint64h (2013/05/26) |
84 |
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o pkg/cheapaml: |
85 |
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- replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux); |
86 |
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affect machine truncation (but exp cheapAML_box still pass with 13 digits). |
87 |
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- consistent treatment of uWind,vWind location: assume everywhere in |
88 |
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pkg/cheapaml that they are on C-grid (@ uVel,vVel location) |
89 |
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(Note: was already the case for Tair,Qair advection); |
90 |
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add option (INCONSISTENT_WIND_LOCATION) to recover old results. |
91 |
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- compute diabatic forcing only in the interior (excluding overlap regions) |
92 |
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- fill in array "Qsw" (for short-wave heating); |
93 |
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- add diagnostic for precip ; fill-in diagnostics for cheapAML state vars |
94 |
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before any update (consistent with MITgcm state var diagnostics); |
95 |
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- cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if |
96 |
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non periodic ; + adjusted for uWind,vWind (C-grid). |
97 |
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o pkg/seaice: |
98 |
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- remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and |
99 |
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add explicitly pkg/exf in experiments that currently use pkg/seaice. |
100 |
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- allows to compile pkg/seaice without pkg/exf. |
101 |
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o tools/OAD_support: |
102 |
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- use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds |
103 |
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of array "ourStepOf" in function rvNextAction (revolve.F90). |
104 |
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o pkg/aim_compon_interf renamed to pkg/atm_compon_interf |
105 |
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- change pkg name (to be used with other atmospheric physics pkg) |
106 |
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but by-pass CVS when making the new pkg so that we keep the CVS history. |
107 |
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o pkg/offline: |
108 |
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- call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F |
109 |
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(previously called from pkg/dic_surfforcing_init.F) |
110 |
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o model/src: |
111 |
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- re-order sequence of calls within packages_init_variables.F, using |
112 |
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standard order, except for: |
113 |
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DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top), |
114 |
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CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom) |
115 |
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o new pkg: atm_phys |
116 |
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- add entry point and source code (previously in contrib |
117 |
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verification_other/atm_gray/code_gray/) for new pkg "atm_phys" |
118 |
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(atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008). |
119 |
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- re-order sequence of calls within packages_readparms.F, |
120 |
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packages_init_fixed.F and packages_write_pickup.F |
121 |
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(but skip packages_init_variables.F because of TAF issues). |
122 |
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- update contrib/*/atm_gray/ experiment. |
123 |
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o pkg/seaice (ITD code): |
124 |
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- simplify and fix the writing of pickup-files for ITD case |
125 |
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o pkg/seaice (ITD code): |
126 |
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- introduce floe size dependent lateral melt for ITD case; |
127 |
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- cleaning (avoid division by zero, change to f77 syntax, remove tabs) |
128 |
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- update seaice_itd experiment main output. |
129 |
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o pkg/thsice: |
130 |
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- remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and |
131 |
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declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F; |
132 |
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changed accordingly pkg/atm2d. |
133 |
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|
134 |
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checkpoint64g (2013/05/01) |
135 |
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o pkg/exf ALLOW_RUNOFTEMP |
136 |
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- if defined, river and glacier runoff temperature can be read-in from |
137 |
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runoftempfile; runoftempfile needs to have same format as runofffile |
138 |
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o pkg/thsice (& pkg/bulk_force): |
139 |
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- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
140 |
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for energy content of Precip + RunOff & Evap (like with pkg/exf). |
141 |
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- change computation domain to always be the interior (without overlap). |
142 |
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- fix bug (wrong overlap) when using EXF and stressReduction > 0. |
143 |
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o verification/tutorial_global_oce_biogeo: |
144 |
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- add preliminary OpenAD setup (still has problems) |
145 |
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o pkg/seaice: |
146 |
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- turn some parameters for choosing the convergence criterion of |
147 |
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the inexact Newton method (JFNK) into runtime parameters for convenience |
148 |
|
- clean up seaice_calc_viscosities.F: remove/retire two options for |
149 |
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SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes |
150 |
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the results of lab_sea/input because a division has been replaced by |
151 |
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a multiplication with the reciprocal (sumNorm) |
152 |
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- modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve |
153 |
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convergence of solver (changes results, of course), and to test some |
154 |
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new features |
155 |
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o model/src: |
156 |
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- remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call. |
157 |
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- remove unused forcing field "dQdT" and associated parameter "dQdTFile". |
158 |
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- move forcing adjustment (balancing surface forcing) in specific S/R |
159 |
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where might also be applied exchanges (if needed) to forcing arrays. |
160 |
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o pkg/shelfice: |
161 |
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- allow to specify the Ice-Shelf mass per unit area (instead of |
162 |
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shelficeLoadAnomaly) and do the conversion from one to the other |
163 |
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- move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA |
164 |
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to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and |
165 |
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(b) will be loaded in time (before calling INI_PRESSURE) in case it is |
166 |
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needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc |
167 |
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- update isomip experiment forward output (get machine truncation error |
168 |
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from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly) |
169 |
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o verification/offline_exf_seaice: |
170 |
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revise data.seaice in input.thermo and input_ad and update results accordingly |
171 |
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HO = 0.2, SEAICE_areaLossFormula = 2, |
172 |
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SEAICE_growMeltByConv = .TRUE., |
173 |
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SEAICE_doOpenWaterMelt = .TRUE., |
174 |
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Improve consistency with input.thsice and fix the spurious 500m ice corners |
175 |
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o verification/global_ocean.cs32x15: |
176 |
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- set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0., |
177 |
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in icedyn (thsice+seaice-dyn) test and update output. |
178 |
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o verification/offline_exf_seaice: |
179 |
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- adjust list of tested variables (with testreport) and update |
180 |
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standard test output with better slection of monitored fields. |
181 |
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o pkg/cd_code: |
182 |
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- swtich off Adams-Bashforth on the 1rst iteration. Update output of |
183 |
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experiment lab_sea.hb87 |
184 |
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o tools/genmake2: |
185 |
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- change default makedepend from the system default to tools/xmakedepend: |
186 |
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When no makedepend is specified, select tools/xmakedepend it the test pass, |
187 |
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otherwise select the system default (if exist and pass the test) or |
188 |
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try to build cyrus-makedepend ; stop if none of the 3 works. |
189 |
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o pkg/exf & pkg/thsice: |
190 |
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- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
191 |
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for energy content of Precip + RunOff & Evap. Assumes: |
192 |
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1) Rain has same temp as Air. |
193 |
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2) Snow has no heat capacity (consistent with seaice & thsice pkgs) |
194 |
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3) Run-Off comes at the temp of surface water (with same Cp) |
195 |
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4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be |
196 |
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put directly into Latent Heat flux & should use water-vapor heat capacity. |
197 |
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5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent |
198 |
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with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL). |
199 |
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o pkg/seaice: simplify the use of CPP flags in JFNK-related files |
200 |
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(compile when SEAICE_ALLOW_JFNK is defined) |
201 |
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o pkg/thsice: |
202 |
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- fix oceanic flux diagnostics & timeave (left from new sequence of calls |
203 |
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implementation): move THSICE_AVE call after the advection (called directly |
204 |
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from thsice_do_advect.F). |
205 |
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o verification/global_ocean.90x40x15 and OpenAD: |
206 |
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New experiment for OpenAD is identical to the one in input_ad except that |
207 |
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multiDimAdvection=.FALSE., |
208 |
|
There is still an issue with this. |
209 |
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o pkg/thsice: |
210 |
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- account for ice velocity (ocean relative velocity) in turbulent heat flux |
211 |
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at the base of the ice; update output of global_ocean.cs32x15 (icedyn) |
212 |
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and offline_exf_seaice (main test). |
213 |
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|
214 |
|
checkpoint64f (2013/03/31) |
215 |
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o verification/OpenAD: |
216 |
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- new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran. |
217 |
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o verification/isomip, pkg/shelfice and OpenAD: |
218 |
|
- add OpenAD setup to this exp and make shelfice package work with OpenAD |
219 |
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o verification/tutorial_global_oce_biogeo: |
220 |
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- update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h) |
221 |
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o verification/offline_exf_seaice: |
222 |
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- replace adjoint experiment (now similar to fwd input.thermo/ setup). |
223 |
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o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD: |
224 |
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- add OpenAD setup to this exp and make ptracers package work with OpenAD |
225 |
|
o pkg/seaice/seaice_evp.F: |
226 |
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mask the asymmetric contribution of the ice-ocean stress (when |
227 |
|
the turningAngle is non-zero) over open water to avoid stripes |
228 |
|
in the EVP-solutions after many EVP-substeps. This does not change |
229 |
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the verification experiment (because turningAngle=0 in that experiment), |
230 |
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but will affect other EVP solutions with turningAngle.ne.0 |
231 |
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o verification, AD & TLM output: |
232 |
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- new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple |
233 |
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additions and multiplications which affect results at machine truncation |
234 |
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level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5, |
235 |
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lab_sea.noseaicedyn & offline_exf_seaice) and TLM output |
236 |
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(1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12 |
237 |
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digits of matching. |
238 |
|
o pkg/seaice: |
239 |
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modify lsr-algorithm so that it vectorizes AND converges by using a |
240 |
|
"zebra" method: split vector loop into two with step size 2; this |
241 |
|
solves a general convergence problem for the JFNK solver on a vector |
242 |
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computer. It has the potential to even improve convergence for |
243 |
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non-vector machines, but it does change the results so it is turned |
244 |
|
off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and |
245 |
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SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h |
246 |
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|
247 |
|
checkpoint64e (2013/03/05) |
248 |
|
o pkg/ecco and several verification experiments: |
249 |
|
Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F |
250 |
|
from ecco package, and revert to unified routine in model/src/ |
251 |
|
Adjust verification experiments accordingly, especially gloal_oce_llc90 |
252 |
|
Should conclude long-standing work by Gael to reconsile the_main_loop with |
253 |
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ECCO and will enable OpenAD's revolve loop in ECCO setup. |
254 |
|
o pkg/generic_advdiff: |
255 |
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- implement compressible flow method for multi-dim advection (similar to |
256 |
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gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since |
257 |
|
TAF generates many recomputations) to use it; no yet coded with implicit |
258 |
|
vertical advection. |
259 |
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- change experiment advect_cs (new output) and advect_xy (same output) |
260 |
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to test compressible flow multi-dim advection. |
261 |
|
o pkg/generic_advdiff: |
262 |
|
- fix SOM advection for unusual cases (linear Free-Surf in r*, other |
263 |
|
cases where linear Free-Surf is not @ k=1, e.g., useShelfIce) |
264 |
|
o pkg/seaice: |
265 |
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- fix bug in the no-slip implementation in seaice_calc_strainrates.F, this |
266 |
|
bug affects two verification experiments (lab_sea and lab_sea.hb87), |
267 |
|
recover old (wrong) results by setting noSlipFac = 2. in |
268 |
|
seaice_calc_strainrates.F; |
269 |
|
- add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0 |
270 |
|
- add runtime parameter SEAICE_JFNKepsilon for that finite difference |
271 |
|
gradient in the Jacobian times vector operation (s/r seaice_jacvec) |
272 |
|
- fix line search in seaice_jfnk.F (s/r seaice_jfnk_update) |
273 |
|
o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code: |
274 |
|
- new subroutines seaice_lsr_tridiagu/v |
275 |
|
- introduce loop bounds i/jmin/max to be able to use a restricted |
276 |
|
additive Schwarz method, but not used for now. |
277 |
|
- rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS |
278 |
|
- use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner |
279 |
|
o OpenAD support |
280 |
|
Reorganize S/R call for overall time-stepping loop to facilitate |
281 |
|
OpenAD revolve loop replacement |
282 |
|
(new S/R main_do_loop.F) |
283 |
|
o model/src: |
284 |
|
- add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3; |
285 |
|
- pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R |
286 |
|
ADAMS_BASHFORTH2. |
287 |
|
o pkg/cheapaml: |
288 |
|
- add new parameter (default=F, same as before) to disable full domain |
289 |
|
(including land) periodicity in X & Y dir. |
290 |
|
- new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of |
291 |
|
prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer |
292 |
|
into single S/R CHEAPAML_TIMESTEP. |
293 |
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|
294 |
|
checkpoint64d (2013/02/17) |
295 |
|
o pkg/monitor (angular momentum): |
296 |
|
- do not add Eta contribution to the total AM if using rigid-lid; |
297 |
|
- correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta). |
298 |
|
- horizontal discretisation: compute Zonal wind contribution separately for |
299 |
|
each component (instead of from cell centered averaged) and use the 4 |
300 |
|
grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part. |
301 |
|
- Check that AM is conserved with linear dynamics (momAdvection=F and linear |
302 |
|
FreeSurf) if using vectorInvariant momentum. |
303 |
|
o model/src (horizontal grid): |
304 |
|
- move initialisation of all horizontal grid arrays to null value |
305 |
|
from specific horizontal grid S/R to main S/R INI_GRID; |
306 |
|
- add 2 new arrays to project model C-grid velocity on to zonal direction |
307 |
|
(similar to AngleCosC & -AngleSinC but at U and V point location) and |
308 |
|
compute them in S/R CALC_GRID_ANGLES. |
309 |
|
o pkg/seaice: replace a hard coded parameter by a runtime parameter |
310 |
|
SEAICE_JFNK_tolIter |
311 |
|
o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in |
312 |
|
preconditioner for JFNK (run LSR into the overlaps as far as possible, |
313 |
|
i.e OLx/y-2, but overwrite the solution in the overlaps) |
314 |
|
- extend loop range in seaice_calc_viscosity |
315 |
|
- add new parameters SEAICE_OLx/y (default = OLx/y-2) |
316 |
|
- add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs |
317 |
|
- slightly modify loops in tridiagonal solver lsr-preconditioner |
318 |
|
- by default remove the extra exchange in seaice_preconditioner with a |
319 |
|
replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE |
320 |
|
- modify offline_exf_seaice so that old results without RAS are reproduced |
321 |
|
for output.dyn_jfnk.txt |
322 |
|
in seaice_fgmres.F (unrelated to RAS) |
323 |
|
- add a cpp-flag option for a re-ordered mapping (potentially more |
324 |
|
efficient), but because this changes the results, turn it off by |
325 |
|
default |
326 |
|
- replace the save statement by local common blocks |
327 |
|
o utils/matlab: |
328 |
|
- fix tile-offset in rdmnc.m when output was produced using EXCH2. |
329 |
|
- update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab) |
330 |
|
instead of local script "load_cs.m". |
331 |
|
o pkg/seaice: |
332 |
|
- fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected |
333 |
|
to the scalarProductMetric and the unrolling. By chance this does not |
334 |
|
change the verification experiment, because of the particular domain |
335 |
|
decomposition |
336 |
|
o pkg/diagnostics: |
337 |
|
- change default missing_value from UNSET_RL to -999. |
338 |
|
o pkg/layers: improve vectorization of layers_fluxcalc.F |
339 |
|
- step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu |
340 |
|
time spent in this routine by more than a factor of 3 on an NEC-SX8 |
341 |
|
- step 2: replace search algorithm by a bisection algorithm found in |
342 |
|
Press et al. Numerical Recipes in Fortran. This algorithm can be |
343 |
|
vectorized and finds the correct bin in approx. log2(Nlayers) steps. |
344 |
|
For now, use this algorithm only for TARGET_NEC_SX defined. |
345 |
|
- moved the search algorithm into a separate subroutine, that is kept |
346 |
|
within the same file for automatic inlining. |
347 |
|
- modified catching potential errors |
348 |
|
o pkg/ecco: |
349 |
|
- add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY. |
350 |
|
o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk : |
351 |
|
- modifications for ALLOW_GENTIM2D_CONTROL |
352 |
|
-- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes. |
353 |
|
-- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid ) |
354 |
|
-- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc |
355 |
|
-- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F |
356 |
|
o model/src: |
357 |
|
- account for moist thermodynamics in (dry) potential temperature equation; |
358 |
|
update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev) |
359 |
|
and cpl_aim+ocn. |
360 |
|
- also switch to standard compiler (gfortran, was using ifort previously) |
361 |
|
for fizhi-cs experiments reference output. |
362 |
|
o pkg/ctrl: |
363 |
|
- 1st step toward generic time-varying control variable (2D) via CPP option |
364 |
|
ALLOW_GENTIM2D_CONTROL |
365 |
|
- note new namelist ctrl_nml_genarr in data.ctrl |
366 |
|
o verification/global_ocean.cs32x15: |
367 |
|
- switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new |
368 |
|
thsice calling sequence and update "output.icedyn.txt" output file. |
369 |
|
o pkg/ptracers: |
370 |
|
- from Ryan A.: code to allow to restart a tracer at regular time interval |
371 |
|
specifying a reset frequency and a reset-phase (for each tracers). |
372 |
|
o pkg/thsice: |
373 |
|
- implement new sequence of calls for thsice+seaice: |
374 |
|
previously: ice-Dyn,ice-Advect,ice-Thermo(thsice) |
375 |
|
new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect |
376 |
|
- allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE" |
377 |
|
in CPP_OPTIONS.h) to recover old sequence; |
378 |
|
- update diagnostics for Intermediate State thsice diagnostics: now filled |
379 |
|
just before advection (instead of just after advection in old sequence); |
380 |
|
- update output of experiment offline_exf_seaice (standard test); |
381 |
|
- in global_ocean.cs32x15 exp., postpone output.icedyn.txt update |
382 |
|
by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h |
383 |
|
o pkg/aim_v23: |
384 |
|
- use tiled array for aim_CO2 and surface wind speed for export to coupler; |
385 |
|
- use standard pkg/mdsio routines to read & write CO2 pickup file; |
386 |
|
- in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F; |
387 |
|
- Implement new sequence of calls for seaice advection (with thsice and |
388 |
|
seaice diffusion): do ice advection after ice-Thermodynamic (previously |
389 |
|
was done before); change aim_do_physics.F (split the bi,bj loops block); |
390 |
|
- use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence; |
391 |
|
o pkg/thsice: |
392 |
|
- add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case |
393 |
|
where just seaice diffusion is used without seaice-dynamics. |
394 |
|
|
395 |
|
checkpoint64c (2013/01/18) |
396 |
|
o pkg/seaice: |
397 |
|
- add a parameter JFNKres_tFac that can replace JFNKres_t |
398 |
|
(= JFNKres_tFac*JFNKresidual before JFNK solver) |
399 |
|
- add a line search option to the JFNK solver |
400 |
|
- move update of u/vIce and computation of initial residual into a separate |
401 |
|
routine (same file); makes the code a little easier to read (?) |
402 |
|
- the line search requires computation of the residual and for some reason |
403 |
|
I cannot do the update of u/vIce at the beginning of the Newton loop |
404 |
|
without changing the results, so we move computation of the new residual |
405 |
|
also to the end of the Newton loop, even without the line search |
406 |
|
o pkg/mdsio: |
407 |
|
- write missing value (corresponding to undefined array value) to meta files; |
408 |
|
skip this if missing value is one (UNSET_RL would be a better value for the |
409 |
|
case of undefined missing value but it's current the default missing-value); |
410 |
|
Also update mdsio_read_meta.F (reading timeInterval & missing-value). |
411 |
|
o pkg/exf & thsice: |
412 |
|
- for diagnostics purpose, fill-up and update Qsw array (+ fill the |
413 |
|
diagnostics) even when SHORTWAVE_HEATING is #undef; |
414 |
|
o verification/cfc_example: |
415 |
|
- turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to |
416 |
|
illustrate how to use it). |
417 |
|
o verification/offline_exf_seaice: |
418 |
|
in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing |
419 |
|
files to only one time-record. |
420 |
|
in input.thermo: narrow the 2 bands of low initial ice-concentration near |
421 |
|
N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for |
422 |
|
snapshot output; same mcPheePiston value as in thsice with |
423 |
|
surf-current=0.2m/s. |
424 |
|
in input.thsice: similar set-up as in input.thermo (channel with same seaice |
425 |
|
initial conditions). |
426 |
|
o verification/cfc_example: |
427 |
|
- update file "data" with more standard choice (default rotationPeriod, |
428 |
|
exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F, |
429 |
|
set deltaTFreeSurf to deltaTtracer) and update the output. |
430 |
|
o pkg/layers: |
431 |
|
- fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC; |
432 |
|
- ensure that "layers_bolus" is switched to False when useGMRedi=False. |
433 |
|
o verification/offline_exf_seaice: |
434 |
|
- set all {field}period to zero for constant-in-time forcing (not tested |
435 |
|
anywhere else). |
436 |
|
o verification/offline_exf_seaice: |
437 |
|
- dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice; |
438 |
|
- dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice. |
439 |
|
o model/src: |
440 |
|
- implement Finite-Volume method for (hydrostatic) presure gradient |
441 |
|
from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate. |
442 |
|
o pkg/seaice: implement EVP* by Lemieux et al. (2012). |
443 |
|
- In order to be compatible with the default EVP code, this requires changing |
444 |
|
the EVP code around a little; and because any small change immediately |
445 |
|
breaks the lab_sea.hb87 verification experiment, the reference output is |
446 |
|
updated two times (each time the remaining aggrement was only 2 digits): |
447 |
|
- after replacing 1/dt by 1*recip_dt with a precomputed recip_dt |
448 |
|
- after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt |
449 |
|
The adjoint test lab_sea.evp also needed to be updated. |
450 |
|
- Turn on EVP* by setting SEAICE_deltaTevp as before, and setting |
451 |
|
SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be |
452 |
|
a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps |
453 |
|
explicitly with SEAICEnEVPstarSteps (thereby overriding the default of |
454 |
|
INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately |
455 |
|
kept obscure, because I need to test it a little more. |
456 |
|
o pkg/cheapaml: |
457 |
|
- fix few incorrect type (_RL/_RS) in subroutine calls. |
458 |
|
o pkg/seaice: |
459 |
|
- new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays |
460 |
|
to _RL vector; this fixes JFNK code when compiling with "-use_r4" option. |
461 |
|
o model/src: |
462 |
|
- add a warning if using select_rStar=2 with nonlinFreeSurf <> 4; |
463 |
|
change (in input_ad*/data) select_rStar from 2 to 1 for AD verification |
464 |
|
experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output) |
465 |
|
o pkg/cheapaml: |
466 |
|
- replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and |
467 |
|
update output of experiment cheapAML_box. |
468 |
|
- store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity, |
469 |
|
and set them only in one place (cheapaml_readparms.F). |
470 |
|
- replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI" |
471 |
|
- remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms) |
472 |
|
and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia). |
473 |
|
o model/src/the_main_loop.F: |
474 |
|
- fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION. |
475 |
|
o pkg/seaice: |
476 |
|
- remove legacy branch code. |
477 |
|
- retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly. |
478 |
|
o verification/*/code*/SEAICE_OPTIONS.h: |
479 |
|
- remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY, |
480 |
|
SEAICE_CAP_HEFF). |
481 |
|
o pkg/cheapaml: |
482 |
|
- use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time |
483 |
|
to load new forcing fields. |
484 |
|
- add missing "_d 0" where it's needed; + some editing (improve indentation). |
485 |
|
- remove switch to "-r8" compiler option (no longer needed) in verification |
486 |
|
cheapAML_box, keep same output (small trucation error differences). |
487 |
|
o verification/offline_exf_seaice: |
488 |
|
- add thermodynamics only test. |
489 |
|
o verification/cheapAML_box: |
490 |
|
- split the domain in 8 (2x4) tiles; add MPI and multi-threaded test; |
491 |
|
keep same output (same 14 digits for cg2d). |
492 |
|
- switch on "-r8" compiler option (some numerical values are missing |
493 |
|
the "_d 0") and update output (only 6 digits for cg2d were preserved). |
494 |
|
|
495 |
|
checkpoint64b (2012/12/24) |
496 |
|
o pkg/cheapaml: |
497 |
|
- remove un-used variables (Qnet,EmPmR) from pickup files. |
498 |
|
- store tendency of advected variables into cheapaml pickup file |
499 |
|
and fix the AB-2 restart. |
500 |
|
o verification/offline_exf_seaice and lab_sea adjoint: |
501 |
|
- switch to new code (#undef SEAICE_GROWTH_LEGACY). |
502 |
|
- switch to 4 time steps in offline, consistent with lab_sea. |
503 |
|
- match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice. |
504 |
|
- update results after change of experiment seaice. |
505 |
|
o pkg/seaice: |
506 |
|
- remove option SEAICE_MULTICATEGORY; has been replaced with run-time |
507 |
|
parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is |
508 |
|
still defined since SEAICE_multDim needs to be set to MULTDIM value (from |
509 |
|
SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default. |
510 |
|
o model/src: |
511 |
|
- add run-time parameter to select CG2D solver minimum-residual solution |
512 |
|
(in case of a poor convergence). |
513 |
|
o pkg/seaice/seaice_lsr.F |
514 |
|
- move calculation of matrix coefficients into new |
515 |
|
S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same |
516 |
|
file; the main purpose of this change is to be able to reuse the code |
517 |
|
in S/R SEAICE_PRECONDITIONER |
518 |
|
- modify the computation of the residual so that the mass of sea-ice |
519 |
|
is not used twice; this simplifies the calculations, but since |
520 |
|
the residual is never used except when LSR_mixIniGuess.ge.4---and this is |
521 |
|
not tested in testreport---this does not affect the testreport results. |
522 |
|
o verification/seaice_obcs: |
523 |
|
- disable SEAICE_GROWTH_LEGACY; reset input files to match those of |
524 |
|
verification/lab_sea/input.salt_plume; changes results/output.txt* |
525 |
|
o model/src: |
526 |
|
- adapt quasi-hydrostatic formulation to work with p or p* coordinate. |
527 |
|
o pkg/seaice: |
528 |
|
- improve description of parameters in seaice_fgmres.F and start |
529 |
|
cleaning up the code |
530 |
|
- change name of SCALPROD to SEAICE_SCALPROD and modify meaning of |
531 |
|
second argument |
532 |
|
- add a metric based on grid cell area to SEAICE_SCALPROD; update |
533 |
|
results of offline_exf_seaice.dyn_jfnk |
534 |
|
- compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD |
535 |
|
o pkg/aim_v23: |
536 |
|
- fix an other bug in dissipation heating (grid-cell area was missing). |
537 |
|
o model/src + pkg/seaice: |
538 |
|
- add global (multi-tile) linear solver for pair of tri-diagonal system |
539 |
|
along X and Y lines, respectively for U and V component. |
540 |
|
Note: 1) MPI and cube-exchange not yet coded. |
541 |
|
2) probably not accurate for poorly conditioned / large size problem. |
542 |
|
- add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver; |
543 |
|
default: not compiled and not used. |
544 |
|
o pkg/seaice: |
545 |
|
- first attempt at a multi-threaded fgmres solver for the JFNK solver: |
546 |
|
introduce bi/bj loops and use global_sum_tile_rl instead of |
547 |
|
mpi_allreduce in seaice_fgmres.F |
548 |
|
- improve diagnostics output for fgmres solver (seaice_fgmres.F) |
549 |
|
- replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F) |
550 |
|
- add a verification experiment for JFNK in offline_exf_seaice |
551 |
|
o verification: |
552 |
|
- change (for now, only fwd test) offline_exf_seaice experiment: |
553 |
|
use a re-entrant channel with idealized coastline (trapezoidal shape) |
554 |
|
at southern boundary to explore seaice dynamics and thermodynamics |
555 |
|
with simple forcing. Main set-up has dynamics+thermo and SST relaxation; |
556 |
|
secondary test (input.thsice) use thermodynamics only with SST relaxation. |
557 |
|
- add seaice-dynamics only secondary test using LSR and pkg/thsice advection. |
558 |
|
o pkg/exf: |
559 |
|
- disable "sstExtrapol" when Nr=1 |
560 |
|
o verification: |
561 |
|
- add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble) |
562 |
|
to test pkg/cheapaml. |
563 |
|
o pkg/aim_v23 & pkg/shap_filt: |
564 |
|
- fix dissipation heating (erroneous gravity multiplication factor). |
565 |
|
o pkg/seaice: |
566 |
|
- remove unused field pressPre from jfnk solver |
567 |
|
- rename two subroutines in seaice_preconditioner.F |
568 |
|
o eesupp/src: |
569 |
|
- S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...) |
570 |
|
o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again |
571 |
|
- remove wrong parts of the rhs and the lhs (were in there |
572 |
|
because I did not understand the concept of this preconditioner) |
573 |
|
- add an exchange between u- and v-sweep. This increases communication |
574 |
|
by a factor of two but improves the convergence of jfnk. Ideally, |
575 |
|
one would like the u- and v-sweep to be independent. So far within |
576 |
|
undocumented ifdefs |
577 |
|
- reorganize the extra computations for printing the residuals |
578 |
|
o tools/genmake2: |
579 |
|
- comment out the "mpif.h" include in NetCDF test programm (for MPI built) |
580 |
|
since it's not necessary (and was preventing to use MNC in some cases). |
581 |
|
|
582 |
|
checkpoint64a (2012/11/16) |
583 |
|
o pkg/autodiff: |
584 |
|
- improve pkg-internal logical parameter switch (inAd/inFwd mode) so that |
585 |
|
autodiff_readparms.F no longer depends on calling order (within |
586 |
|
packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h): |
587 |
|
rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd |
588 |
|
and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd. |
589 |
|
o pkg/obcs: |
590 |
|
- adding tidal velocity forcing capability to obcs |
591 |
|
for usage example, see verification/seaice_obcs/input.tides |
592 |
|
o pkg/seaice: |
593 |
|
- turn the LSR-relaxation parameters WFAU/V into runtime parameters |
594 |
|
SEAICE_LSRrelaxU/V |
595 |
|
- introduce runtime parameter SEAICEetaZmethod (=0 by default) |
596 |
|
o pkg/aim_v23: |
597 |
|
- implement heating from friction (bottom friction and stratospheric drag). |
598 |
|
o pkg/shap_filt: |
599 |
|
- fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from |
600 |
|
dissipation but only for Shap_funct=2, active when addFrictionHeating=T. |
601 |
|
o model/src: |
602 |
|
- move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in |
603 |
|
time-constant addMass field from file (addMassFile); |
604 |
|
- support for heating due to friction (and Kinetic Energy dissipation): |
605 |
|
add option, run-time switch and 3-D field array + support code ; each pkg |
606 |
|
or S/R can add heating contribution (if there is a sink of KE); the sum is |
607 |
|
accounted for as a Temperature tendency term (EXTERNAL_FORCING_T). |
608 |
|
o pkg/seaice: |
609 |
|
- complete merge of ITD code into seaice_growth.F |
610 |
|
from MITgcm_contrib/torge/itd/code/ |
611 |
|
no verification so far, but Torge Martin tested |
612 |
|
"1-D test case and Beaufort set up; |
613 |
|
deliver okay results after 1 model year." |
614 |
|
- complete merge of SEAICE_SIZE.h into all relevant routines |
615 |
|
- move computation of eta at Z-points into calc_viscosities |
616 |
|
+ introduce global field etaZ |
617 |
|
+ add different methods for computing etaZ, for now the old |
618 |
|
method (simple averages of eta to Z-points) is hardwired |
619 |
|
+ replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual, |
620 |
|
seaice_preconditioner |
621 |
|
- simplify computations for SEAICE_ZETA_SMOOTHREG |
622 |
|
- seaice_preconditioner: |
623 |
|
+ replace one remaining press by pressLoc (mistake) |
624 |
|
+ adjust printing of residuals |
625 |
|
- improve I/O of diagnostics of JFNK in seaice_jfnk.F: |
626 |
|
+ add (SEAICE.h) and rename some counters (initiliased in |
627 |
|
seaice_init_fixed.F) |
628 |
|
+ add _BEGIN/END_MASTER (myThid) around print statements |
629 |
|
+ print total number of iterations and failures over SEAICE_monFreq |
630 |
|
interval to STDOUT |
631 |
|
- move control over output-messages by fgmres to seaice_jfnk to save |
632 |
|
some operations |
633 |
|
- move resetting initial guess for fgmres outside of seaice_fgmres_driver |
634 |
|
in order to make restarts with sol .ne. zero (fgmres with restarts) |
635 |
|
(seaice_jfnk.F, seaice_fgmres.F) |
636 |
|
- seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes |
637 |
|
a serious convergence problem when open boundaries are involved |
638 |
|
o pkg/ggl90: fix computation of control volumes for the case of |
639 |
ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes |
ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes |
640 |
up half a grid cell from C-centered to W-centered (pointed out by C. Eden) |
up half a grid cell from C-centered to W-centered (pointed out by C. Eden) |
641 |
o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC |
o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC |
642 |
o pkg/autodiff |
o pkg/autodiff |
643 |
- Add inAdMode switch for SEAICEuseDYNAMICS: |
- Add inAdMode switch for SEAICEuseDYNAMICS: |
644 |
SEAICEuseDYNAMICSinAdMode |
SEAICEuseDYNAMICSinAdMode |
645 |
(extend logic in ADAUTODIFF_INADMODE_SET) |
(extend logic in ADAUTODIFF_INADMODE_SET) |
646 |
o pkg/seaice |
o pkg/seaice |
647 |
- Step 1 of merging ice-thickness distribution (ITD) code from |
- Step 1 of merging ice-thickness distribution (ITD) code from |