4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
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|
7 |
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o testreport: |
8 |
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- changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, |
9 |
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perform additional runs (number of additional runs is "add_DIVA_runs" taken |
10 |
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from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h"). |
11 |
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o verification/lab_sea (AD test): |
12 |
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- change to test Divided Adjoint Run in this set-up (both standard AD test |
13 |
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and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test. |
14 |
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o pkg atm_ & ocn_compon_interf: |
15 |
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- remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old |
16 |
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staggerTimeStep implementation) and disable (retired) corresponding |
17 |
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parameter. |
18 |
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o pkg/offline: |
19 |
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- comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01]; |
20 |
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- add S/R OFFLINE_CHECK to print offline parameter summary |
21 |
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and stop if loading a file that is not used; |
22 |
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- enable to calculate GMRedi tensor, KPP mixing and convective index |
23 |
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when the corresponding file(s) is/are not specified (but pkg is used). |
24 |
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- comment out resetting of monitorFreq (to endTime) since it still useful |
25 |
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for monitoring CFL numbers and checking offline fields. |
26 |
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o OpenAD: |
27 |
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- do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get |
28 |
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smaller standard output) and generate new (smaller) output (on baudelaire |
29 |
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using gfortran with -ieee) for exp. tutorial_tracer_adjsens |
30 |
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o model/src: |
31 |
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- call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F), |
32 |
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(where external_forcing_adjust was called) and change list of arguments; |
33 |
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- merge external_forcing_adjust.F into external_forcing_surf.F |
34 |
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- put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F) |
35 |
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which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX, |
36 |
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previously in file "balance_relax.F", now removed); remove corresponding |
37 |
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arrays in FFIELDS.h. |
38 |
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- EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement |
39 |
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a hack for getting back surfaceForcingS (loaded from file) when using |
40 |
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ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up. |
41 |
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- update output of AD test experiment global_ocean.cs32x15.seaice_dynmix |
42 |
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(was getting only 11 digits for AD-grad, due to different truncation |
43 |
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error in AD code). |
44 |
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|
45 |
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checkpoint64j (2013/07/04) |
46 |
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o pkg/offline: |
47 |
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- to enable the use of other features with pkg offline (e.g., obcs), |
48 |
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also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come. |
49 |
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- comment out "allowFreezing" (now active) in 2 offline testing exp. |
50 |
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o pkg/exf ALLOW_RUNOFTEMP |
51 |
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- fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL |
52 |
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- ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice |
53 |
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- changes verification/global_ocean.cs32x15/results/output.seaice.txt |
54 |
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o pkg/atm_phys: |
55 |
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- allows to add some damping on uVel,vVel (strength only function of k). |
56 |
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o verification, ad-tests: |
57 |
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- reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, |
58 |
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global_ocean_ebm and offline_exf_seaice.thsice. |
59 |
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o verification/halfpipe_streamice: |
60 |
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- found a bug in s/r pkg/streamice/streamice_advect_thickness which caused |
61 |
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flux input boundary conditions to be ignored; a fix for this bug changed |
62 |
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verification results for forward test. |
63 |
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- add adjoint test. |
64 |
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o pkg/ptracers: |
65 |
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- allow to restart without SOM pickup (resetting SOM to zero). |
66 |
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o pkg/gmredi: |
67 |
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- New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added. |
68 |
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- It uses mixing length theory and suppression by steering level effects to |
69 |
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calculate a diffusivity used in the Redi tensor (see Bates et al., submitted |
70 |
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to JPO, for more details). |
71 |
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- It also uses the diffusivity to calculate an eddy induced streamfunction |
72 |
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based on a PV closure (rather than a buoyancy closure as in GM). |
73 |
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- New files added to pkg/gmredi: |
74 |
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gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy |
75 |
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induced overturning streamfunction (called from gmredi_calc_tensor) |
76 |
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gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required |
77 |
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for use in gmredi_k3d |
78 |
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gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate |
79 |
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the eddy diffusivity |
80 |
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|
81 |
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checkpoint64i (2013/06/18) |
82 |
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o pkg/cheapaml: |
83 |
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- take src files from MITgcm_contrib/verification_other/offline_cheapaml/code |
84 |
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that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics) |
85 |
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with pkg/cheapaml. |
86 |
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o utils/python: add subpackage for cubed sphere function, first example is |
87 |
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simple cs.pcol to plot 2D fields on a map |
88 |
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o pkg/streamice: |
89 |
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- This is a new package in MITgcm, which solves dynamic equations for ice |
90 |
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sheets and ice streams |
91 |
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- At the moment it is independent of atmosphere/ocean dynamics, or any |
92 |
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other physical packages in MITgcm, even ShelfIce (although it is anticipat- |
93 |
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ed that this will change) |
94 |
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- There is a new verification exercise that tests it, halfpipe_streamice, |
95 |
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evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a |
96 |
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rectangular embayment |
97 |
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- halfpipe_streamice is forward-only for now, will have TAF test soon |
98 |
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- for questions, email dgoldber@mit.edu |
99 |
|
o pkg/thsice: |
100 |
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- fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing |
101 |
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of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40); |
102 |
|
- remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new |
103 |
|
call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect ); |
104 |
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- allow precip from pkg/cheapaml to make snow over seaice. |
105 |
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o pkg/cfc: |
106 |
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- move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC |
107 |
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- remove atmos CFC 2-D arrays from common bloc (now local variables) |
108 |
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- change some hard-coded constant to run time parameter for reading and |
109 |
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and interpolating atmospheric CFC ; keep same default as previously. |
110 |
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- more flexible reading of Atmos CFC (number of records no longer hard-coded) |
111 |
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- put arguments in standard order: myTime, myIter, myThid |
112 |
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- use standard S/R GET_PERIODIC_INTERVAL for time interpolation of |
113 |
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atmospheric CFC ; fix for the case myIter < PTRACERS_iter0. |
114 |
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- fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf |
115 |
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- new routine to print summary of CFC params and check for consistency. |
116 |
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o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff, |
117 |
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similar to thsice_advdiff. |
118 |
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Note that for the B-grid case the routine parameters uc/vc are overwritten. |
119 |
|
o pkg/cfc: |
120 |
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- change time interpolation for atmospheric CFC-11 (now same as for CFC-12); |
121 |
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update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline. |
122 |
|
- fix interpolation of atmphspheric CFC between Sorthern and Northern |
123 |
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hemisphere value. |
124 |
|
o pkg/seaice: |
125 |
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- allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml) |
126 |
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o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics; |
127 |
|
so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE. |
128 |
|
- requires an additional time level that is stored in the pickup |
129 |
|
- you can start with AB2 from a pickup without this time level with |
130 |
|
pickupStrictlyMatch = .false. |
131 |
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|
132 |
|
checkpoint64h (2013/05/26) |
133 |
|
o pkg/cheapaml: |
134 |
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- replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux); |
135 |
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affect machine truncation (but exp cheapAML_box still pass with 13 digits). |
136 |
|
- consistent treatment of uWind,vWind location: assume everywhere in |
137 |
|
pkg/cheapaml that they are on C-grid (@ uVel,vVel location) |
138 |
|
(Note: was already the case for Tair,Qair advection); |
139 |
|
add option (INCONSISTENT_WIND_LOCATION) to recover old results. |
140 |
|
- compute diabatic forcing only in the interior (excluding overlap regions) |
141 |
|
- fill in array "Qsw" (for short-wave heating); |
142 |
|
- add diagnostic for precip ; fill-in diagnostics for cheapAML state vars |
143 |
|
before any update (consistent with MITgcm state var diagnostics); |
144 |
|
- cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if |
145 |
|
non periodic ; + adjusted for uWind,vWind (C-grid). |
146 |
|
o pkg/seaice: |
147 |
|
- remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and |
148 |
|
add explicitly pkg/exf in experiments that currently use pkg/seaice. |
149 |
|
- allows to compile pkg/seaice without pkg/exf. |
150 |
|
o tools/OAD_support: |
151 |
|
- use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds |
152 |
|
of array "ourStepOf" in function rvNextAction (revolve.F90). |
153 |
|
o pkg/aim_compon_interf renamed to pkg/atm_compon_interf |
154 |
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- change pkg name (to be used with other atmospheric physics pkg) |
155 |
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but by-pass CVS when making the new pkg so that we keep the CVS history. |
156 |
|
o pkg/offline: |
157 |
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- call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F |
158 |
|
(previously called from pkg/dic_surfforcing_init.F) |
159 |
|
o model/src: |
160 |
|
- re-order sequence of calls within packages_init_variables.F, using |
161 |
|
standard order, except for: |
162 |
|
DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top), |
163 |
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CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom) |
164 |
|
o new pkg: atm_phys |
165 |
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- add entry point and source code (previously in contrib |
166 |
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verification_other/atm_gray/code_gray/) for new pkg "atm_phys" |
167 |
|
(atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008). |
168 |
|
- re-order sequence of calls within packages_readparms.F, |
169 |
|
packages_init_fixed.F and packages_write_pickup.F |
170 |
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(but skip packages_init_variables.F because of TAF issues). |
171 |
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- update contrib/*/atm_gray/ experiment. |
172 |
|
o pkg/seaice (ITD code): |
173 |
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- simplify and fix the writing of pickup-files for ITD case |
174 |
|
o pkg/seaice (ITD code): |
175 |
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- introduce floe size dependent lateral melt for ITD case; |
176 |
|
- cleaning (avoid division by zero, change to f77 syntax, remove tabs) |
177 |
|
- update seaice_itd experiment main output. |
178 |
|
o pkg/thsice: |
179 |
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- remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and |
180 |
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declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F; |
181 |
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changed accordingly pkg/atm2d. |
182 |
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|
183 |
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checkpoint64g (2013/05/01) |
184 |
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o pkg/exf ALLOW_RUNOFTEMP |
185 |
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- if defined, river and glacier runoff temperature can be read-in from |
186 |
|
runoftempfile; runoftempfile needs to have same format as runofffile |
187 |
|
o pkg/thsice (& pkg/bulk_force): |
188 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
189 |
|
for energy content of Precip + RunOff & Evap (like with pkg/exf). |
190 |
|
- change computation domain to always be the interior (without overlap). |
191 |
|
- fix bug (wrong overlap) when using EXF and stressReduction > 0. |
192 |
|
o verification/tutorial_global_oce_biogeo: |
193 |
|
- add preliminary OpenAD setup (still has problems) |
194 |
|
o pkg/seaice: |
195 |
|
- turn some parameters for choosing the convergence criterion of |
196 |
|
the inexact Newton method (JFNK) into runtime parameters for convenience |
197 |
|
- clean up seaice_calc_viscosities.F: remove/retire two options for |
198 |
|
SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes |
199 |
|
the results of lab_sea/input because a division has been replaced by |
200 |
|
a multiplication with the reciprocal (sumNorm) |
201 |
|
- modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve |
202 |
|
convergence of solver (changes results, of course), and to test some |
203 |
|
new features |
204 |
|
o model/src: |
205 |
|
- remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call. |
206 |
|
- remove unused forcing field "dQdT" and associated parameter "dQdTFile". |
207 |
|
- move forcing adjustment (balancing surface forcing) in specific S/R |
208 |
|
where might also be applied exchanges (if needed) to forcing arrays. |
209 |
|
o pkg/shelfice: |
210 |
|
- allow to specify the Ice-Shelf mass per unit area (instead of |
211 |
|
shelficeLoadAnomaly) and do the conversion from one to the other |
212 |
|
- move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA |
213 |
|
to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and |
214 |
|
(b) will be loaded in time (before calling INI_PRESSURE) in case it is |
215 |
|
needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc |
216 |
|
- update isomip experiment forward output (get machine truncation error |
217 |
|
from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly) |
218 |
|
o verification/offline_exf_seaice: |
219 |
|
revise data.seaice in input.thermo and input_ad and update results accordingly |
220 |
|
HO = 0.2, SEAICE_areaLossFormula = 2, |
221 |
|
SEAICE_growMeltByConv = .TRUE., |
222 |
|
SEAICE_doOpenWaterMelt = .TRUE., |
223 |
|
Improve consistency with input.thsice and fix the spurious 500m ice corners |
224 |
|
o verification/global_ocean.cs32x15: |
225 |
|
- set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0., |
226 |
|
in icedyn (thsice+seaice-dyn) test and update output. |
227 |
|
o verification/offline_exf_seaice: |
228 |
|
- adjust list of tested variables (with testreport) and update |
229 |
|
standard test output with better slection of monitored fields. |
230 |
|
o pkg/cd_code: |
231 |
|
- swtich off Adams-Bashforth on the 1rst iteration. Update output of |
232 |
|
experiment lab_sea.hb87 |
233 |
|
o tools/genmake2: |
234 |
|
- change default makedepend from the system default to tools/xmakedepend: |
235 |
|
When no makedepend is specified, select tools/xmakedepend it the test pass, |
236 |
|
otherwise select the system default (if exist and pass the test) or |
237 |
|
try to build cyrus-makedepend ; stop if none of the 3 works. |
238 |
|
o pkg/exf & pkg/thsice: |
239 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
240 |
|
for energy content of Precip + RunOff & Evap. Assumes: |
241 |
|
1) Rain has same temp as Air. |
242 |
|
2) Snow has no heat capacity (consistent with seaice & thsice pkgs) |
243 |
|
3) Run-Off comes at the temp of surface water (with same Cp) |
244 |
|
4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be |
245 |
|
put directly into Latent Heat flux & should use water-vapor heat capacity. |
246 |
|
5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent |
247 |
|
with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL). |
248 |
|
o pkg/seaice: simplify the use of CPP flags in JFNK-related files |
249 |
|
(compile when SEAICE_ALLOW_JFNK is defined) |
250 |
|
o pkg/thsice: |
251 |
|
- fix oceanic flux diagnostics & timeave (left from new sequence of calls |
252 |
|
implementation): move THSICE_AVE call after the advection (called directly |
253 |
|
from thsice_do_advect.F). |
254 |
|
o verification/global_ocean.90x40x15 and OpenAD: |
255 |
|
New experiment for OpenAD is identical to the one in input_ad except that |
256 |
|
multiDimAdvection=.FALSE., |
257 |
|
There is still an issue with this. |
258 |
|
o pkg/thsice: |
259 |
|
- account for ice velocity (ocean relative velocity) in turbulent heat flux |
260 |
|
at the base of the ice; update output of global_ocean.cs32x15 (icedyn) |
261 |
|
and offline_exf_seaice (main test). |
262 |
|
|
263 |
|
checkpoint64f (2013/03/31) |
264 |
|
o verification/OpenAD: |
265 |
|
- new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran. |
266 |
|
o verification/isomip, pkg/shelfice and OpenAD: |
267 |
|
- add OpenAD setup to this exp and make shelfice package work with OpenAD |
268 |
|
o verification/tutorial_global_oce_biogeo: |
269 |
|
- update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h) |
270 |
|
o verification/offline_exf_seaice: |
271 |
|
- replace adjoint experiment (now similar to fwd input.thermo/ setup). |
272 |
|
o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD: |
273 |
|
- add OpenAD setup to this exp and make ptracers package work with OpenAD |
274 |
|
o pkg/seaice/seaice_evp.F: |
275 |
|
mask the asymmetric contribution of the ice-ocean stress (when |
276 |
|
the turningAngle is non-zero) over open water to avoid stripes |
277 |
|
in the EVP-solutions after many EVP-substeps. This does not change |
278 |
|
the verification experiment (because turningAngle=0 in that experiment), |
279 |
|
but will affect other EVP solutions with turningAngle.ne.0 |
280 |
|
o verification, AD & TLM output: |
281 |
|
- new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple |
282 |
|
additions and multiplications which affect results at machine truncation |
283 |
|
level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5, |
284 |
|
lab_sea.noseaicedyn & offline_exf_seaice) and TLM output |
285 |
|
(1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12 |
286 |
|
digits of matching. |
287 |
|
o pkg/seaice: |
288 |
|
modify lsr-algorithm so that it vectorizes AND converges by using a |
289 |
|
"zebra" method: split vector loop into two with step size 2; this |
290 |
|
solves a general convergence problem for the JFNK solver on a vector |
291 |
|
computer. It has the potential to even improve convergence for |
292 |
|
non-vector machines, but it does change the results so it is turned |
293 |
|
off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and |
294 |
|
SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h |
295 |
|
|
296 |
|
checkpoint64e (2013/03/05) |
297 |
|
o pkg/ecco and several verification experiments: |
298 |
|
Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F |
299 |
|
from ecco package, and revert to unified routine in model/src/ |
300 |
|
Adjust verification experiments accordingly, especially gloal_oce_llc90 |
301 |
|
Should conclude long-standing work by Gael to reconsile the_main_loop with |
302 |
|
ECCO and will enable OpenAD's revolve loop in ECCO setup. |
303 |
|
o pkg/generic_advdiff: |
304 |
|
- implement compressible flow method for multi-dim advection (similar to |
305 |
|
gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since |
306 |
|
TAF generates many recomputations) to use it; no yet coded with implicit |
307 |
|
vertical advection. |
308 |
|
- change experiment advect_cs (new output) and advect_xy (same output) |
309 |
|
to test compressible flow multi-dim advection. |
310 |
|
o pkg/generic_advdiff: |
311 |
|
- fix SOM advection for unusual cases (linear Free-Surf in r*, other |
312 |
|
cases where linear Free-Surf is not @ k=1, e.g., useShelfIce) |
313 |
|
o pkg/seaice: |
314 |
|
- fix bug in the no-slip implementation in seaice_calc_strainrates.F, this |
315 |
|
bug affects two verification experiments (lab_sea and lab_sea.hb87), |
316 |
|
recover old (wrong) results by setting noSlipFac = 2. in |
317 |
|
seaice_calc_strainrates.F; |
318 |
|
- add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0 |
319 |
|
- add runtime parameter SEAICE_JFNKepsilon for that finite difference |
320 |
|
gradient in the Jacobian times vector operation (s/r seaice_jacvec) |
321 |
|
- fix line search in seaice_jfnk.F (s/r seaice_jfnk_update) |
322 |
|
o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code: |
323 |
|
- new subroutines seaice_lsr_tridiagu/v |
324 |
|
- introduce loop bounds i/jmin/max to be able to use a restricted |
325 |
|
additive Schwarz method, but not used for now. |
326 |
|
- rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS |
327 |
|
- use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner |
328 |
|
o OpenAD support |
329 |
|
Reorganize S/R call for overall time-stepping loop to facilitate |
330 |
|
OpenAD revolve loop replacement |
331 |
|
(new S/R main_do_loop.F) |
332 |
|
o model/src: |
333 |
|
- add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3; |
334 |
|
- pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R |
335 |
|
ADAMS_BASHFORTH2. |
336 |
|
o pkg/cheapaml: |
337 |
|
- add new parameter (default=F, same as before) to disable full domain |
338 |
|
(including land) periodicity in X & Y dir. |
339 |
|
- new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of |
340 |
|
prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer |
341 |
|
into single S/R CHEAPAML_TIMESTEP. |
342 |
|
|
343 |
|
checkpoint64d (2013/02/17) |
344 |
|
o pkg/monitor (angular momentum): |
345 |
|
- do not add Eta contribution to the total AM if using rigid-lid; |
346 |
|
- correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta). |
347 |
|
- horizontal discretisation: compute Zonal wind contribution separately for |
348 |
|
each component (instead of from cell centered averaged) and use the 4 |
349 |
|
grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part. |
350 |
|
- Check that AM is conserved with linear dynamics (momAdvection=F and linear |
351 |
|
FreeSurf) if using vectorInvariant momentum. |
352 |
|
o model/src (horizontal grid): |
353 |
|
- move initialisation of all horizontal grid arrays to null value |
354 |
|
from specific horizontal grid S/R to main S/R INI_GRID; |
355 |
|
- add 2 new arrays to project model C-grid velocity on to zonal direction |
356 |
|
(similar to AngleCosC & -AngleSinC but at U and V point location) and |
357 |
|
compute them in S/R CALC_GRID_ANGLES. |
358 |
|
o pkg/seaice: replace a hard coded parameter by a runtime parameter |
359 |
|
SEAICE_JFNK_tolIter |
360 |
|
o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in |
361 |
|
preconditioner for JFNK (run LSR into the overlaps as far as possible, |
362 |
|
i.e OLx/y-2, but overwrite the solution in the overlaps) |
363 |
|
- extend loop range in seaice_calc_viscosity |
364 |
|
- add new parameters SEAICE_OLx/y (default = OLx/y-2) |
365 |
|
- add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs |
366 |
|
- slightly modify loops in tridiagonal solver lsr-preconditioner |
367 |
|
- by default remove the extra exchange in seaice_preconditioner with a |
368 |
|
replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE |
369 |
|
- modify offline_exf_seaice so that old results without RAS are reproduced |
370 |
|
for output.dyn_jfnk.txt |
371 |
|
in seaice_fgmres.F (unrelated to RAS) |
372 |
|
- add a cpp-flag option for a re-ordered mapping (potentially more |
373 |
|
efficient), but because this changes the results, turn it off by |
374 |
|
default |
375 |
|
- replace the save statement by local common blocks |
376 |
|
o utils/matlab: |
377 |
|
- fix tile-offset in rdmnc.m when output was produced using EXCH2. |
378 |
|
- update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab) |
379 |
|
instead of local script "load_cs.m". |
380 |
|
o pkg/seaice: |
381 |
|
- fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected |
382 |
|
to the scalarProductMetric and the unrolling. By chance this does not |
383 |
|
change the verification experiment, because of the particular domain |
384 |
|
decomposition |
385 |
|
o pkg/diagnostics: |
386 |
|
- change default missing_value from UNSET_RL to -999. |
387 |
|
o pkg/layers: improve vectorization of layers_fluxcalc.F |
388 |
|
- step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu |
389 |
|
time spent in this routine by more than a factor of 3 on an NEC-SX8 |
390 |
|
- step 2: replace search algorithm by a bisection algorithm found in |
391 |
|
Press et al. Numerical Recipes in Fortran. This algorithm can be |
392 |
|
vectorized and finds the correct bin in approx. log2(Nlayers) steps. |
393 |
|
For now, use this algorithm only for TARGET_NEC_SX defined. |
394 |
|
- moved the search algorithm into a separate subroutine, that is kept |
395 |
|
within the same file for automatic inlining. |
396 |
|
- modified catching potential errors |
397 |
|
o pkg/ecco: |
398 |
|
- add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY. |
399 |
|
o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk : |
400 |
|
- modifications for ALLOW_GENTIM2D_CONTROL |
401 |
|
-- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes. |
402 |
|
-- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid ) |
403 |
|
-- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc |
404 |
|
-- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F |
405 |
|
o model/src: |
406 |
|
- account for moist thermodynamics in (dry) potential temperature equation; |
407 |
|
update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev) |
408 |
|
and cpl_aim+ocn. |
409 |
|
- also switch to standard compiler (gfortran, was using ifort previously) |
410 |
|
for fizhi-cs experiments reference output. |
411 |
|
o pkg/ctrl: |
412 |
|
- 1st step toward generic time-varying control variable (2D) via CPP option |
413 |
|
ALLOW_GENTIM2D_CONTROL |
414 |
|
- note new namelist ctrl_nml_genarr in data.ctrl |
415 |
|
o verification/global_ocean.cs32x15: |
416 |
|
- switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new |
417 |
|
thsice calling sequence and update "output.icedyn.txt" output file. |
418 |
|
o pkg/ptracers: |
419 |
|
- from Ryan A.: code to allow to restart a tracer at regular time interval |
420 |
|
specifying a reset frequency and a reset-phase (for each tracers). |
421 |
|
o pkg/thsice: |
422 |
|
- implement new sequence of calls for thsice+seaice: |
423 |
|
previously: ice-Dyn,ice-Advect,ice-Thermo(thsice) |
424 |
|
new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect |
425 |
|
- allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE" |
426 |
|
in CPP_OPTIONS.h) to recover old sequence; |
427 |
|
- update diagnostics for Intermediate State thsice diagnostics: now filled |
428 |
|
just before advection (instead of just after advection in old sequence); |
429 |
|
- update output of experiment offline_exf_seaice (standard test); |
430 |
|
- in global_ocean.cs32x15 exp., postpone output.icedyn.txt update |
431 |
|
by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h |
432 |
|
o pkg/aim_v23: |
433 |
|
- use tiled array for aim_CO2 and surface wind speed for export to coupler; |
434 |
|
- use standard pkg/mdsio routines to read & write CO2 pickup file; |
435 |
|
- in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F; |
436 |
|
- Implement new sequence of calls for seaice advection (with thsice and |
437 |
|
seaice diffusion): do ice advection after ice-Thermodynamic (previously |
438 |
|
was done before); change aim_do_physics.F (split the bi,bj loops block); |
439 |
|
- use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence; |
440 |
|
o pkg/thsice: |
441 |
|
- add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case |
442 |
|
where just seaice diffusion is used without seaice-dynamics. |
443 |
|
|
444 |
|
checkpoint64c (2013/01/18) |
445 |
|
o pkg/seaice: |
446 |
|
- add a parameter JFNKres_tFac that can replace JFNKres_t |
447 |
|
(= JFNKres_tFac*JFNKresidual before JFNK solver) |
448 |
|
- add a line search option to the JFNK solver |
449 |
|
- move update of u/vIce and computation of initial residual into a separate |
450 |
|
routine (same file); makes the code a little easier to read (?) |
451 |
|
- the line search requires computation of the residual and for some reason |
452 |
|
I cannot do the update of u/vIce at the beginning of the Newton loop |
453 |
|
without changing the results, so we move computation of the new residual |
454 |
|
also to the end of the Newton loop, even without the line search |
455 |
|
o pkg/mdsio: |
456 |
|
- write missing value (corresponding to undefined array value) to meta files; |
457 |
|
skip this if missing value is one (UNSET_RL would be a better value for the |
458 |
|
case of undefined missing value but it's current the default missing-value); |
459 |
|
Also update mdsio_read_meta.F (reading timeInterval & missing-value). |
460 |
|
o pkg/exf & thsice: |
461 |
|
- for diagnostics purpose, fill-up and update Qsw array (+ fill the |
462 |
|
diagnostics) even when SHORTWAVE_HEATING is #undef; |
463 |
|
o verification/cfc_example: |
464 |
|
- turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to |
465 |
|
illustrate how to use it). |
466 |
|
o verification/offline_exf_seaice: |
467 |
|
in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing |
468 |
|
files to only one time-record. |
469 |
|
in input.thermo: narrow the 2 bands of low initial ice-concentration near |
470 |
|
N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for |
471 |
|
snapshot output; same mcPheePiston value as in thsice with |
472 |
|
surf-current=0.2m/s. |
473 |
|
in input.thsice: similar set-up as in input.thermo (channel with same seaice |
474 |
|
initial conditions). |
475 |
|
o verification/cfc_example: |
476 |
|
- update file "data" with more standard choice (default rotationPeriod, |
477 |
|
exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F, |
478 |
|
set deltaTFreeSurf to deltaTtracer) and update the output. |
479 |
|
o pkg/layers: |
480 |
|
- fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC; |
481 |
|
- ensure that "layers_bolus" is switched to False when useGMRedi=False. |
482 |
|
o verification/offline_exf_seaice: |
483 |
|
- set all {field}period to zero for constant-in-time forcing (not tested |
484 |
|
anywhere else). |
485 |
|
o verification/offline_exf_seaice: |
486 |
|
- dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice; |
487 |
|
- dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice. |
488 |
|
o model/src: |
489 |
|
- implement Finite-Volume method for (hydrostatic) presure gradient |
490 |
|
from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate. |
491 |
|
o pkg/seaice: implement EVP* by Lemieux et al. (2012). |
492 |
|
- In order to be compatible with the default EVP code, this requires changing |
493 |
|
the EVP code around a little; and because any small change immediately |
494 |
|
breaks the lab_sea.hb87 verification experiment, the reference output is |
495 |
|
updated two times (each time the remaining aggrement was only 2 digits): |
496 |
|
- after replacing 1/dt by 1*recip_dt with a precomputed recip_dt |
497 |
|
- after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt |
498 |
|
The adjoint test lab_sea.evp also needed to be updated. |
499 |
|
- Turn on EVP* by setting SEAICE_deltaTevp as before, and setting |
500 |
|
SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be |
501 |
|
a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps |
502 |
|
explicitly with SEAICEnEVPstarSteps (thereby overriding the default of |
503 |
|
INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately |
504 |
|
kept obscure, because I need to test it a little more. |
505 |
|
o pkg/cheapaml: |
506 |
|
- fix few incorrect type (_RL/_RS) in subroutine calls. |
507 |
|
o pkg/seaice: |
508 |
|
- new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays |
509 |
|
to _RL vector; this fixes JFNK code when compiling with "-use_r4" option. |
510 |
|
o model/src: |
511 |
|
- add a warning if using select_rStar=2 with nonlinFreeSurf <> 4; |
512 |
|
change (in input_ad*/data) select_rStar from 2 to 1 for AD verification |
513 |
|
experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output) |
514 |
|
o pkg/cheapaml: |
515 |
|
- replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and |
516 |
|
update output of experiment cheapAML_box. |
517 |
|
- store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity, |
518 |
|
and set them only in one place (cheapaml_readparms.F). |
519 |
|
- replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI" |
520 |
|
- remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms) |
521 |
|
and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia). |
522 |
|
o model/src/the_main_loop.F: |
523 |
|
- fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION. |
524 |
|
o pkg/seaice: |
525 |
|
- remove legacy branch code. |
526 |
|
- retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly. |
527 |
|
o verification/*/code*/SEAICE_OPTIONS.h: |
528 |
|
- remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY, |
529 |
|
SEAICE_CAP_HEFF). |
530 |
|
o pkg/cheapaml: |
531 |
|
- use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time |
532 |
|
to load new forcing fields. |
533 |
|
- add missing "_d 0" where it's needed; + some editing (improve indentation). |
534 |
|
- remove switch to "-r8" compiler option (no longer needed) in verification |
535 |
|
cheapAML_box, keep same output (small trucation error differences). |
536 |
|
o verification/offline_exf_seaice: |
537 |
|
- add thermodynamics only test. |
538 |
|
o verification/cheapAML_box: |
539 |
|
- split the domain in 8 (2x4) tiles; add MPI and multi-threaded test; |
540 |
|
keep same output (same 14 digits for cg2d). |
541 |
|
- switch on "-r8" compiler option (some numerical values are missing |
542 |
|
the "_d 0") and update output (only 6 digits for cg2d were preserved). |
543 |
|
|
544 |
|
checkpoint64b (2012/12/24) |
545 |
|
o pkg/cheapaml: |
546 |
|
- remove un-used variables (Qnet,EmPmR) from pickup files. |
547 |
|
- store tendency of advected variables into cheapaml pickup file |
548 |
|
and fix the AB-2 restart. |
549 |
|
o verification/offline_exf_seaice and lab_sea adjoint: |
550 |
|
- switch to new code (#undef SEAICE_GROWTH_LEGACY). |
551 |
|
- switch to 4 time steps in offline, consistent with lab_sea. |
552 |
|
- match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice. |
553 |
|
- update results after change of experiment seaice. |
554 |
|
o pkg/seaice: |
555 |
|
- remove option SEAICE_MULTICATEGORY; has been replaced with run-time |
556 |
|
parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is |
557 |
|
still defined since SEAICE_multDim needs to be set to MULTDIM value (from |
558 |
|
SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default. |
559 |
|
o model/src: |
560 |
|
- add run-time parameter to select CG2D solver minimum-residual solution |
561 |
|
(in case of a poor convergence). |
562 |
|
o pkg/seaice/seaice_lsr.F |
563 |
|
- move calculation of matrix coefficients into new |
564 |
|
S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same |
565 |
|
file; the main purpose of this change is to be able to reuse the code |
566 |
|
in S/R SEAICE_PRECONDITIONER |
567 |
|
- modify the computation of the residual so that the mass of sea-ice |
568 |
|
is not used twice; this simplifies the calculations, but since |
569 |
|
the residual is never used except when LSR_mixIniGuess.ge.4---and this is |
570 |
|
not tested in testreport---this does not affect the testreport results. |
571 |
|
o verification/seaice_obcs: |
572 |
|
- disable SEAICE_GROWTH_LEGACY; reset input files to match those of |
573 |
|
verification/lab_sea/input.salt_plume; changes results/output.txt* |
574 |
|
o model/src: |
575 |
|
- adapt quasi-hydrostatic formulation to work with p or p* coordinate. |
576 |
|
o pkg/seaice: |
577 |
|
- improve description of parameters in seaice_fgmres.F and start |
578 |
|
cleaning up the code |
579 |
|
- change name of SCALPROD to SEAICE_SCALPROD and modify meaning of |
580 |
|
second argument |
581 |
|
- add a metric based on grid cell area to SEAICE_SCALPROD; update |
582 |
|
results of offline_exf_seaice.dyn_jfnk |
583 |
|
- compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD |
584 |
|
o pkg/aim_v23: |
585 |
|
- fix an other bug in dissipation heating (grid-cell area was missing). |
586 |
|
o model/src + pkg/seaice: |
587 |
|
- add global (multi-tile) linear solver for pair of tri-diagonal system |
588 |
|
along X and Y lines, respectively for U and V component. |
589 |
|
Note: 1) MPI and cube-exchange not yet coded. |
590 |
|
2) probably not accurate for poorly conditioned / large size problem. |
591 |
|
- add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver; |
592 |
|
default: not compiled and not used. |
593 |
|
o pkg/seaice: |
594 |
|
- first attempt at a multi-threaded fgmres solver for the JFNK solver: |
595 |
|
introduce bi/bj loops and use global_sum_tile_rl instead of |
596 |
|
mpi_allreduce in seaice_fgmres.F |
597 |
|
- improve diagnostics output for fgmres solver (seaice_fgmres.F) |
598 |
|
- replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F) |
599 |
|
- add a verification experiment for JFNK in offline_exf_seaice |
600 |
|
o verification: |
601 |
|
- change (for now, only fwd test) offline_exf_seaice experiment: |
602 |
|
use a re-entrant channel with idealized coastline (trapezoidal shape) |
603 |
|
at southern boundary to explore seaice dynamics and thermodynamics |
604 |
|
with simple forcing. Main set-up has dynamics+thermo and SST relaxation; |
605 |
|
secondary test (input.thsice) use thermodynamics only with SST relaxation. |
606 |
|
- add seaice-dynamics only secondary test using LSR and pkg/thsice advection. |
607 |
|
o pkg/exf: |
608 |
|
- disable "sstExtrapol" when Nr=1 |
609 |
|
o verification: |
610 |
|
- add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble) |
611 |
|
to test pkg/cheapaml. |
612 |
|
o pkg/aim_v23 & pkg/shap_filt: |
613 |
|
- fix dissipation heating (erroneous gravity multiplication factor). |
614 |
|
o pkg/seaice: |
615 |
|
- remove unused field pressPre from jfnk solver |
616 |
|
- rename two subroutines in seaice_preconditioner.F |
617 |
|
o eesupp/src: |
618 |
|
- S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...) |
619 |
|
o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again |
620 |
|
- remove wrong parts of the rhs and the lhs (were in there |
621 |
|
because I did not understand the concept of this preconditioner) |
622 |
|
- add an exchange between u- and v-sweep. This increases communication |
623 |
|
by a factor of two but improves the convergence of jfnk. Ideally, |
624 |
|
one would like the u- and v-sweep to be independent. So far within |
625 |
|
undocumented ifdefs |
626 |
|
- reorganize the extra computations for printing the residuals |
627 |
|
o tools/genmake2: |
628 |
|
- comment out the "mpif.h" include in NetCDF test programm (for MPI built) |
629 |
|
since it's not necessary (and was preventing to use MNC in some cases). |
630 |
|
|
631 |
|
checkpoint64a (2012/11/16) |
632 |
|
o pkg/autodiff: |
633 |
|
- improve pkg-internal logical parameter switch (inAd/inFwd mode) so that |
634 |
|
autodiff_readparms.F no longer depends on calling order (within |
635 |
|
packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h): |
636 |
|
rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd |
637 |
|
and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd. |
638 |
|
o pkg/obcs: |
639 |
|
- adding tidal velocity forcing capability to obcs |
640 |
|
for usage example, see verification/seaice_obcs/input.tides |
641 |
|
o pkg/seaice: |
642 |
|
- turn the LSR-relaxation parameters WFAU/V into runtime parameters |
643 |
|
SEAICE_LSRrelaxU/V |
644 |
|
- introduce runtime parameter SEAICEetaZmethod (=0 by default) |
645 |
|
o pkg/aim_v23: |
646 |
|
- implement heating from friction (bottom friction and stratospheric drag). |
647 |
|
o pkg/shap_filt: |
648 |
|
- fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from |
649 |
|
dissipation but only for Shap_funct=2, active when addFrictionHeating=T. |
650 |
|
o model/src: |
651 |
|
- move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in |
652 |
|
time-constant addMass field from file (addMassFile); |
653 |
|
- support for heating due to friction (and Kinetic Energy dissipation): |
654 |
|
add option, run-time switch and 3-D field array + support code ; each pkg |
655 |
|
or S/R can add heating contribution (if there is a sink of KE); the sum is |
656 |
|
accounted for as a Temperature tendency term (EXTERNAL_FORCING_T). |
657 |
|
o pkg/seaice: |
658 |
|
- complete merge of ITD code into seaice_growth.F |
659 |
|
from MITgcm_contrib/torge/itd/code/ |
660 |
|
no verification so far, but Torge Martin tested |
661 |
|
"1-D test case and Beaufort set up; |
662 |
|
deliver okay results after 1 model year." |
663 |
|
- complete merge of SEAICE_SIZE.h into all relevant routines |
664 |
|
- move computation of eta at Z-points into calc_viscosities |
665 |
|
+ introduce global field etaZ |
666 |
|
+ add different methods for computing etaZ, for now the old |
667 |
|
method (simple averages of eta to Z-points) is hardwired |
668 |
|
+ replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual, |
669 |
|
seaice_preconditioner |
670 |
|
- simplify computations for SEAICE_ZETA_SMOOTHREG |
671 |
|
- seaice_preconditioner: |
672 |
|
+ replace one remaining press by pressLoc (mistake) |
673 |
|
+ adjust printing of residuals |
674 |
|
- improve I/O of diagnostics of JFNK in seaice_jfnk.F: |
675 |
|
+ add (SEAICE.h) and rename some counters (initiliased in |
676 |
|
seaice_init_fixed.F) |
677 |
|
+ add _BEGIN/END_MASTER (myThid) around print statements |
678 |
|
+ print total number of iterations and failures over SEAICE_monFreq |
679 |
|
interval to STDOUT |
680 |
|
- move control over output-messages by fgmres to seaice_jfnk to save |
681 |
|
some operations |
682 |
|
- move resetting initial guess for fgmres outside of seaice_fgmres_driver |
683 |
|
in order to make restarts with sol .ne. zero (fgmres with restarts) |
684 |
|
(seaice_jfnk.F, seaice_fgmres.F) |
685 |
|
- seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes |
686 |
|
a serious convergence problem when open boundaries are involved |
687 |
|
o pkg/ggl90: fix computation of control volumes for the case of |
688 |
|
ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes |
689 |
|
up half a grid cell from C-centered to W-centered (pointed out by C. Eden) |
690 |
|
o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC |
691 |
|
o pkg/autodiff |
692 |
|
- Add inAdMode switch for SEAICEuseDYNAMICS: |
693 |
|
SEAICEuseDYNAMICSinAdMode |
694 |
|
(extend logic in ADAUTODIFF_INADMODE_SET) |
695 |
|
o pkg/seaice |
696 |
|
- Step 1 of merging ice-thickness distribution (ITD) code from |
697 |
|
MITgcm_contrib/torge/itd/ (author: Torge Martin) |
698 |
|
The code implements concept laid out in Thorndike et al. (1975); |
699 |
|
code is enabled via CPP flag SEAICE_ITD |
700 |
|
nITD (in SEAICE_SIZE.h) defines number of ice thickness categories; |
701 |
|
code is not complete yet!! |
702 |
|
- SEAICE_SIZE.h now included in almost all seaice routines |
703 |
|
o verification (using seaice): |
704 |
|
- switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp. |
705 |
|
global_ocean.cs32x15.seaice ; update results. |
706 |
|
- compile B-grid dynamics in FW test exp 1D_ocean_ice_column ; |
707 |
|
- compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp |
708 |
|
offline_exf_seaice (previously compiling B-grid). |
709 |
|
o pkg/exf: |
710 |
|
- fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow |
711 |
|
to specify neither just 1 comp of wind or wind-stress, nor no surface momentum |
712 |
|
forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind. |
713 |
|
o pkg/layers (adjust changes from Sept 19): |
714 |
|
- do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F) |
715 |
|
this allows to remove "layers_maxNum" dimension from all layers arrays. |
716 |
|
o pkg/layers (adjust changes from Sept 19): |
717 |
|
- remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ; |
718 |
|
- snap-shot extended to all type of layers (not just the 1rst type); |
719 |
|
- remove layers variables when corresponding CPP option is undef. |
720 |
|
o pkg/layers: |
721 |
|
- rename pkg/layers variable and add new output (layer exist & un-weighted |
722 |
|
velocity in layer) |
723 |
|
o pkg/seaice: |
724 |
|
- simplify (?) ocean-drag coefficent computations by using |
725 |
|
the same routine in all three solvers (saves some code lines) |
726 |
|
- remove global fields DRAGA and DRAGS from C-grid code and |
727 |
|
declare them locally in lsr.F (the only place where they are |
728 |
|
still used) |
729 |
|
- update AD output of lab_sea.evp (very sensitive anyway). |
730 |
|
o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics |
731 |
|
(Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK |
732 |
|
and SEAICEuseJFNK=.true. A few things to note: |
733 |
|
- involves a FGMRES, that is parallel but very inefficient, |
734 |
|
because of many scalar products (global sums) in the Gram-Schmidt |
735 |
|
orthogonalization method. Needs to be replaced. Original code |
736 |
|
from J.-F. Lemieux |
737 |
|
- preconditioner for FGMRES is a stripped down version of LSOR |
738 |
|
- SOLV_MAX_ITERS is now used for LSOR as a solver and as a |
739 |
|
preconditioner. For the preconditioner, the default is set to 10. |
740 |
|
- Jacobian times vector is computed with finite differences |
741 |
|
- marginally related to JFNK-solver: add a smooth regularization for |
742 |
|
zeta with tanh that will improve convergence (Lemieux and Tremblay, |
743 |
|
2009) for any implicit solver (not implemented for EVP because EVP |
744 |
|
does not need this regularization in the first place). Define |
745 |
|
SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use. |
746 |
|
o eesupp/src: |
747 |
|
- check in genmake2 that intrinsic S/R flush is available. |
748 |
|
- add S/R to flush IO unit (if intrinsic S/R flush is available) |
749 |
|
- flush standard & error msg unit before MPI termination |
750 |
|
- if debugMode, flush IO unit after printing msg |
751 |
|
o pkg/ctrl: |
752 |
|
- ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call |
753 |
|
to ctrl_set_unpack_xyz. |
754 |
|
|
755 |
|
checkpoint64 (2012/10/09) |
756 |
|
o pkg/shelfice |
757 |
|
- in mom_fluxform.F, mom_vecinv.F: |
758 |
|
CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid) |
759 |
|
Bug fix KappaRU -> KappaRV |
760 |
|
does not change verification/isomip but may change other setups |
761 |
|
(presumably constant KappaRU=KappaRV) |
762 |
|
- fix diagnostics SHIU/Vdrag (thanks to Tom Millgate) |
763 |
|
o pkg/obcs: |
764 |
|
- fixed some indexing bugs in obcs_seaice_sponge.F |
765 |
|
- added obcs relaxation subroutines for HSALT and HSNOW |
766 |
|
- changes verification/seaice_obcs/results/obcs_seaice_sponge.F |
767 |
|
o pkg/seaice: |
768 |
|
- add "multicategory" parameterization for snow in analogy to ice, |
769 |
|
default is off for now. |
770 |
|
o pkg/obcs: |
771 |
|
- added obcs_seaice_sponge.F for obcs relaxation of seaice variables; |
772 |
|
see verification/seaice_obcs/input.seaiceSponge for example application. |
773 |
|
- remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB |
774 |
|
index setting by master-thread. This fix multi-threads Pb in previous modifs. |
775 |
|
o pkg/layers : |
776 |
|
- add diagnostics to pkg/layers |
777 |
|
- move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F |
778 |
|
(from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly. |
779 |
|
o pkg/generic_advdiff/gad_implicit_r.F : |
780 |
|
- fix ADVr diagnostics in case of both implicit vertical advection and diffusion. |
781 |
|
o pkg/seaice/seaice_growth.F: |
782 |
|
- fix SItflux diagnostics in virtual salt flux + balanceEmpmr case. |
783 |
|
o pkg/obcs: |
784 |
|
- change default setting of OBCS_UVICE_OLD from defined to undef; |
785 |
|
- use new parameter OB_indexNone for null index value (instead of hard-coded 0) |
786 |
|
in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F; |
787 |
|
- pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z; |
788 |
|
- change OB null index value (OB_indexNone) to -99 ; this fix the problem |
789 |
|
with Southern & Western OB at a tile edge (at least in a simple set-up). |
790 |
|
o pkg/obcs: |
791 |
|
- change settings of OB index in case OB coincides with tile edge (shared by |
792 |
|
2 tiles), so that common OB location is registered by both tiles (instead of |
793 |
|
only 1). However, for Southern and Western OB, index value = 0 is not |
794 |
|
recognized as valid OB index (=default null value) and needs to be fixed. |
795 |
|
- modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting) |
796 |
|
- new parameter "OB_indexNone" for null index value (for now, still zero) |
797 |
|
to replace hard-coded null index value of zero. |
798 |
|
o pkg/exch2: |
799 |
|
- improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON: |
800 |
|
always check buffer-size (but outside the loop); move checking for valid |
801 |
|
index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON, |
802 |
|
print each tile and point connection only if |W2_printMsg|>= 2 and 3. |
803 |
|
o pkg/ctrl (pack & unpack): |
804 |
|
- in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable |
805 |
|
(locally defined) for different variables (+ remove the variable-specific |
806 |
|
file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL |
807 |
|
(to be extended to other local file names in ctrl.h). |
808 |
|
o pkg/flt: |
809 |
|
- add a FLT_Iter0 option (similar to PTRACERS_Iter0). |
810 |
|
o pkg/mdsio: |
811 |
|
- fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing |
812 |
|
o tools/genmake2: |
813 |
|
- add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE |
814 |
|
(added by Alistair in version 1.51 for building without make depend); |
815 |
|
- remove Header files list (H_SRC_FILES) from the dependence of targets |
816 |
|
ad_input_code.f & ftl_input_code.f (not clear why it was added in the first |
817 |
|
place in version 1.23): this save going through staf when unrelated header |
818 |
|
file has been modified. |
819 |
|
Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without |
820 |
|
"make depend" step, still need to do "make links" before "make adtaf". |
821 |
|
o eesupp/src (+ few pkg src files) & genmake2: |
822 |
|
- finish to remove ALWAYS_USE_MPI in source code that TAF does not see; |
823 |
|
- no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2). |
824 |
|
- improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish |
825 |
|
upper/lower case ; account for space between "#" and undef/define) |
826 |
|
o pkg/flt (with exch2): |
827 |
|
- cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F; |
828 |
|
- simplify threads synchronisation; fix (many issues) multi-threaded with MPI. |
829 |
|
|
830 |
|
checkpoint63s (2012/09/05) |
831 |
|
o pkg/ecco: |
832 |
|
- remove #ifdef ALLOW_SMOOTH_CORREL3D brackets. |
833 |
|
- add more relevant #ifdef ALLOW_SMOOTH ones. |
834 |
|
- sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D. |
835 |
|
o pkg/ctrl: |
836 |
|
- CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D, |
837 |
|
ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D. |
838 |
|
- ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag, |
839 |
|
doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and |
840 |
|
ctrlSmoothCorrel3D (new). |
841 |
|
The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP. |
842 |
|
- ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist. |
843 |
|
- ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress |
844 |
|
controls when useAtmWind, and vice versa. |
845 |
|
- ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers. |
846 |
|
- ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with |
847 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH. |
848 |
|
- ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with |
849 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH. |
850 |
|
- ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F: |
851 |
|
replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D. |
852 |
|
o pkg/smooth: |
853 |
|
- remove un-necessary includes. |
854 |
|
- remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets. |
855 |
|
Those CPP options were never defined, and not necessary. |
856 |
|
o model/src: |
857 |
|
- fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi). |
858 |
|
- standard treatment of useSMOOTH. |
859 |
|
o pkg/autodiff: |
860 |
|
- add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode, |
861 |
|
useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint. |
862 |
|
o pkg/exch2: |
863 |
|
- add "if usingMPI" where it was missing (in exch2_rx?_cube*.template) |
864 |
|
+ start to remove ALWAYS_USE_MPI in source code that TAF does not see. |
865 |
|
- make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag |
866 |
|
and tiles to process mapping. |
867 |
|
- re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h) |
868 |
|
moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h; |
869 |
|
rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX |
870 |
|
from w2_eeboot.F to w2_readparms.F. |
871 |
|
o eesupp/src: |
872 |
|
- set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of |
873 |
|
ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F; |
874 |
|
also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F |
875 |
|
- in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI |
876 |
|
is defined (remove condition on usingMPI) to match cases where MPI_INIT |
877 |
|
has been called. |
878 |
|
- fix bug I put in previous modif of exch_sm_3d_rx.template (not much used); |
879 |
|
- change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings |
880 |
|
(so that on 1 proc, get same myPid independently of usingMPI) |
881 |
|
- add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and |
882 |
|
useCubedSphereExchange with EXCH-1 (safer). |
883 |
|
- add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI). |
884 |
|
o pkg/ggl90: |
885 |
|
- fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call) |
886 |
|
used in ALLOW_GGL90_SMOOTH code. |
887 |
|
o pkg/flt: |
888 |
|
- fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping |
889 |
|
floats at the Southern end of the domain). |
890 |
|
o eesupp/inc: |
891 |
|
- add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h); |
892 |
|
but not used (and not to be used) anywhere, just for documentation. |
893 |
|
o pkg/autodiff, exf, ptracers & seaice (AD & TL output): |
894 |
|
- comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since: |
895 |
|
a) can damage previously written records in any other multi-record files. |
896 |
|
b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S. |
897 |
|
o tools/genmake2: |
898 |
|
- define variable MAKE within Makefile and use it in place of 'make'; |
899 |
|
- update AD_CONFIG.h (if needed) before building any of the executable |
900 |
|
(forward, adjoint or tangent-lin); this involves a 2nd invocation of make; |
901 |
|
and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h; |
902 |
|
- always print usual warning comment 'this file is automatically generated' |
903 |
|
from script convert_cpp_cmd2defines (+ remove this warning from genmake2). |
904 |
|
o pkg/cheapaml: |
905 |
|
- updated to correspond to the code used in accepted paper (Nico Wienders). |
906 |
|
o pkg/exf: |
907 |
|
added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch. |
908 |
|
ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F) |
909 |
|
and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h). |
910 |
|
o pkg/exf, autodiff, ctrl, ecco and seaice: |
911 |
|
remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones. |
912 |
|
o pkg/ctrl, ecco: |
913 |
|
allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL. |
914 |
|
Depending on useAtmWind, one is inactive, and the other is active (see |
915 |
|
exf_getffields.F/exf_getsurfacefluxes.F). |
916 |
|
o tools/genmake2: |
917 |
|
- improve error msg when failing in 2nd test of check_for_broken_Ff |
918 |
|
- fix option '-makefile' short-name (-mf according to genmake2 -help) |
919 |
|
- source local config file "genmake_local" just after processing the genmake2 |
920 |
|
command arguments (previously done before processing arg). |
921 |
|
o pkg/grdchk: |
922 |
|
- add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call |
923 |
|
to this routine from cost_final has been dropped in g_cost_final) |
924 |
|
- improve printed information (more explicit msg, no longer using "print *," |
925 |
|
fix fcpertminus printed value). |
926 |
|
o model/src: |
927 |
|
- move call to COST_INIT_VARIA out of packages_init_variables.F directly |
928 |
|
into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES): |
929 |
|
this prevents getting cost-funct reset in adinitialise_varia recomputations. |
930 |
|
o pkg/dic: |
931 |
|
- move initialisation of "freefe" array from from dic_biotic_forcing.F to |
932 |
|
fe_chem.F: this prevents TAF from dropping this initialisation in TLM code. |
933 |
|
o pkg/grdchk: |
934 |
|
- grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid ) |
935 |
|
- grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0 |
936 |
|
o pkg/autodiff/ctrl/grdchk : |
937 |
|
- attempt to sort out what works and what does not, |
938 |
|
with regard to I/O, and to warn/stop accordingly. |
939 |
|
o pkg/grdchk: |
940 |
|
- attempt to fix grdchk in the case of useSingleCpuIO. |
941 |
|
- "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )" |
942 |
|
statements were moved from grdchk_main.F and into |
943 |
|
grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F. |
944 |
|
- a global sum is applied to record numbers icvrec/layer |
945 |
|
out of grdchk_loc so that they be passed to I/O routines. |
946 |
|
o pkg/smooth: |
947 |
|
- fix recomputation that appeared with nlfs : use smooth_recip_hFacC, |
948 |
|
smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case. |
949 |
|
o verification/testreport: |
950 |
|
- add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive); |
951 |
|
- can also use compressed (gzip) reference output file; |
952 |
|
- change format (in pkg/grdchk) of TLM output (+ add forward gradient) |
953 |
|
to be easier to collect by testreport. |
954 |
|
- update existing TLM output (half out-of-date by more than 3 yrs). |
955 |
|
- report NETCDF & LAPACK settings (from genmake2) in output dir. |
956 |
|
- report run-time in each individual summary (previously only for AD test); |
957 |
|
for TLM test, add also TAF version. |
958 |
|
- add daily TLM test on (old) aces cluster + weekly test on baudelaire. |
959 |
|
|
960 |
|
checkpoint63r (2012/08/15) |
961 |
|
o tools/genmake2: |
962 |
|
- fix Makefile for target ftlall (+ update files to clean after make ftlall) |
963 |
|
o pkg/ecco/ecco_cost_final.F : |
964 |
|
- fix fc print statements (to stdout and costfunction0000) so |
965 |
|
that the printed value is always after the global sum. |
966 |
|
o pkg/seaice/seaice_dynsolver.F : |
967 |
|
- fix ice strength assymptote at SEAICE_area_max<1 |
968 |
|
(no change for the standard case of SEAICE_area_max=1) |
969 |
|
o some cleaning: |
970 |
|
- pkg source files: ensure that all *.F files from each pkg included the |
971 |
|
corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which |
972 |
|
only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment |
973 |
|
code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding |
974 |
|
includes; |
975 |
|
- model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used. |
976 |
|
- ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR |
977 |
|
is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when |
978 |
|
ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop. |
979 |
|
- update option-file CPP_OPTIONS.h of all AD experiments: |
980 |
|
* no longer include PACKAGES_CONFIG.h ; |
981 |
|
* includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ; |
982 |
|
* def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before |
983 |
|
including ECCO_CPPOPTIONS.h). |
984 |
|
o pkg/cost, pkg/ctrl, pkg/ecco option-file: |
985 |
|
- clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into |
986 |
|
separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h, |
987 |
|
not necessary accurate). |
988 |
|
- add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in |
989 |
|
pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to |
990 |
|
deliberately break compilation (a remainder that it needs to be customized) |
991 |
|
- in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h |
992 |
|
- rename COST_CPPOPTIONS.h to COST_OPTIONS.h |
993 |
|
- rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h |
994 |
|
o tools/genamke2: |
995 |
|
- check for lapack. |
996 |
|
o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies. |
997 |
|
- pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions |
998 |
|
jointly. The exclusive ifdefs were removed, to add costs terms (when defined) |
999 |
|
from both packages. |
1000 |
|
- the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly. |
1001 |
|
- for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs. |
1002 |
|
- pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes |
1003 |
|
of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly. |
1004 |
|
o pkg/cost : add comments to explain special and/or untested setups. |
1005 |
|
o pkg/exf: |
1006 |
|
- use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h |
1007 |
|
(previously, ALLOW_AUTODIFF_TAMC was controling this switch). |
1008 |
|
o verification/*/code_ad: |
1009 |
|
mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file: |
1010 |
|
- reccord when this file is included (define ECCO_CPPOPTIONS_H) |
1011 |
|
- remove the most obvious obsolete features (e.g., #define ALLOW_COST not |
1012 |
|
allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h) |
1013 |
|
o pkg/seaice : |
1014 |
|
- added possibility to change ice strength/PRESS0 relationship to |
1015 |
|
HEFF, according to the following run time parameters |
1016 |
|
SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0) |
1017 |
|
SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0) |
1018 |
|
SEAICEpresH0 :: HEFF threshold for ice strength (m) |
1019 |
|
o pkg/ggl90 : |
1020 |
|
- added run time flag mxlSurfFlag to include the code that ensure |
1021 |
|
mixing between first and second level (previously included as a comment) |
1022 |
|
o verification/1D_ocean_ice_column/input_ad/data.autodiff : |
1023 |
|
- add test of newly added dumpAdByRec=T option where |
1024 |
|
we write all records to one file per variable. |
1025 |
|
o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h : |
1026 |
|
- switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES |
1027 |
|
to check that this code is ok with taf and compiles in adjoint. |
1028 |
|
o pkg/autodiff : |
1029 |
|
- added run time param dumpAdByRec : ad dump format switch. |
1030 |
|
If true then write all records to one file per variable. |
1031 |
|
Else write one file per record (remains the default). |
1032 |
|
- revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly. |
1033 |
|
o pkg/seaice: |
1034 |
|
- Added SEAICEuseTILT run time switch : if set to |
1035 |
|
false then omit the tilt term in seaice dynamics. |
1036 |
|
- Fix free drift calculation. |
1037 |
|
o pkg/shelfice: |
1038 |
|
When initializing SHELFICEDragQuadratic, set default to be |
1039 |
|
consistent with shiCdrag in case SHELFICEuseGammaFrict is used, |
1040 |
|
but retain option to set it independently |
1041 |
|
(inconsistenty spotted by Veronique Dansereau) |
1042 |
|
o eesupp/inc: |
1043 |
|
- in EEPARAMS.h, add real-type constant for some frequently used simple number |
1044 |
|
(0,1,2,1/2), with name explicitly referring to RS/RL type. |
1045 |
|
o model/src: |
1046 |
|
- move balancing of relaxation terms to new S/R balance_relax.F. |
1047 |
|
o pkg/autodiff: |
1048 |
|
re-write active I/O high-level (control) S/R: |
1049 |
|
- rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL |
1050 |
|
- add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R. |
1051 |
|
- use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and |
1052 |
|
MDS_READ/WRITE_FIELD); change loops to multi-threads. |
1053 |
|
- update and merge active_file_control_slice.flow into active_file_control.flow |
1054 |
|
- update the calls in lower level S/R (active_file.F, active_file_g.F and |
1055 |
|
active_file_ad.F) keeping the argument list and function unchanged. |
1056 |
|
- also update lower-level "_LOC" version (call same S/R with "useCurrentDir |
1057 |
|
=.TRUE.") and remove high-level (control) _loc version (not called anymore). |
1058 |
|
- new low-level active I/O routines, one for each type (RL/RS), for active var |
1059 |
|
of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr); |
1060 |
|
fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the |
1061 |
|
right type. |
1062 |
|
o autodiff and RS=real*4: |
1063 |
|
- call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf |
1064 |
|
ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ; |
1065 |
|
- change argument type of 3-D mask argument to _RS to match type in the call |
1066 |
|
(in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued. |
1067 |
|
o pkg/thsice: |
1068 |
|
- re-anable balanceEmPmR when useSEAICE=T with useThSIce=T. |
1069 |
|
- option to correct ocean fresh-water flux for imbalance of Atmos+Land |
1070 |
|
fresh-water flux: uniform correction or proportional to local precip. |
1071 |
|
o pkg/ctrl: |
1072 |
|
- new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D |
1073 |
|
- redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to |
1074 |
|
ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC |
1075 |
|
- verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL |
1076 |
|
|
1077 |
|
checkpoint63q (2012/07/30) |
1078 |
|
o pkg/autodiff: |
1079 |
|
note about monitor and snap-shot of ad-variables: |
1080 |
|
a) need to apply ADEXCH before monitor or output of ad-vars to include |
1081 |
|
overlap contributions (was done for adjDump but missing for monitor). |
1082 |
|
b) since ADEXCH implies adding overlap values to interior array, machine |
1083 |
|
truncation error is expected when adding an ADEXCH call in the middle of |
1084 |
|
the time-stepping (although mathematically identical). |
1085 |
|
modifs: |
1086 |
|
- fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars |
1087 |
|
declaration (adEddyPsiX,adEddyPsiY in adcommon.h). |
1088 |
|
- add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to |
1089 |
|
apply ADEXCH before monitor or snap-shot of ad-variables: |
1090 |
|
=0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy. |
1091 |
|
- implement new method (copy+adexch) for snap-shot and monitor of main model |
1092 |
|
ad-vars (initially not used by default -> output unchanged). |
1093 |
|
- change default (set to 2) to use new method and update few output_adm.txt |
1094 |
|
with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo |
1095 |
|
and both tutorial_tracer_adjsens tests). |
1096 |
|
- switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice) |
1097 |
|
and turn off momDissip_In_AB in the 2 other (needed for stable AB-3). |
1098 |
|
o pkg/ctrl: |
1099 |
|
enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of |
1100 |
|
generic control variables via |
1101 |
|
#define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL |
1102 |
|
Only required customization should be S/R ctrl_map_ini_genarr.F |
1103 |
|
(routine in repository contains example) |
1104 |
|
o pkg/exf: |
1105 |
|
- fix and refine checking of surface-relaxation setting when using EXF |
1106 |
|
o verification (adjoint exp): |
1107 |
|
- reduce length of simulation by half for experiment global_ocean.cs32x15 |
1108 |
|
(std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output. |
1109 |
|
o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag) |
1110 |
|
- replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers |
1111 |
|
of KE that can occur with aggressive optimization |
1112 |
|
+ put quadratic bottom drag calculation in separated loops (only done if |
1113 |
|
using bottomDragQuadratic) |
1114 |
|
o model/src: CG2D_NSA |
1115 |
|
- clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF |
1116 |
|
and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE. |
1117 |
|
- in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens), |
1118 |
|
change cg2d residual target to be expressed in Wunits (=> do not normalise |
1119 |
|
RHS ; this fix global_max Pb with TAF); update output. |
1120 |
|
o verification/tutorial_tracer_adjsens: |
1121 |
|
improve parameter consistency (and get rid of warnings): |
1122 |
|
- use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf); |
1123 |
|
- switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical) |
1124 |
|
- use staggerTimeStep (for stability) in som81; use default rotation period. |
1125 |
|
o pkg/exch2: |
1126 |
|
- with empty facet: fix compact-format (W2_mapIO=1) definition (was previously |
1127 |
|
reset to 0 = 1 long line in X) |
1128 |
|
o pkg/mdsio: |
1129 |
|
- fix reading of dimensions from meta file for large-size domain |
1130 |
|
o model/src: |
1131 |
|
- fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long); |
1132 |
|
- to refine CS-grid check, add logical flag "hasWetCSCorners": true if using |
1133 |
|
Cubed-Sphere Exch with CS-corners inside the domain; |
1134 |
|
make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate |
1135 |
|
globalArea and to set hasWetCSCorners. |
1136 |
|
- add warning if usingCurvilinearGrid and momAdvection in flux-form (missing |
1137 |
|
metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form. |
1138 |
|
- re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if |
1139 |
|
useCDscheme and useCubedSphereExchange). |
1140 |
|
o pkg/seaice/seaice_growth.F : |
1141 |
|
- compute the SEAICE_DISABLE_HEATCONSFIX term accordingly |
1142 |
|
for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0) |
1143 |
|
when the previous code was not correct. |
1144 |
|
- in all cases diagnoze the boundary condition mismatch to SIaaflux |
1145 |
|
- in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add |
1146 |
|
that term to QNET (essentially to set the melt/freeze water to 0degC). |
1147 |
|
when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed. |
1148 |
|
o verification/global_ocean.cs32x15/input.seaice : |
1149 |
|
- add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget. |
1150 |
|
- add diagnostics (commented out) for budget test using my matlab codes (gcmfaces). |
1151 |
|
- update results (output.seaice.txt) accordingly. |
1152 |
|
o verification/lab_sea/input/data.seaice : |
1153 |
|
- remove SEAICEheatConsFix, which is now be tested |
1154 |
|
in global_ocean.cs32x15. The presently coded fix |
1155 |
|
is only consistent with real fresh water + nlfs. |
1156 |
|
- update results (output.txt) accordingly. |
1157 |
|
o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd). |
1158 |
|
o AD_CONFIG.h file: |
1159 |
|
- in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h; |
1160 |
|
- remove #include "AD_CONFIG.h" from all included OPTIONS files and |
1161 |
|
add it explicitly in each fortran src file where it is needed. |
1162 |
|
motivation: header file AD_CONFIG.h is generated/modified after "make depend" |
1163 |
|
thus introducing potentially wrong dependency; therefore, better to include |
1164 |
|
it only where it's really needed, and after any other included OPTIONS file |
1165 |
|
(less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN |
1166 |
|
or ALLOW_TANGENTLINEAR_RUN). |
1167 |
|
|
1168 |
|
checkpoint63p (2012/07/06) |
1169 |
|
o pkg/autodiff: |
1170 |
|
- rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ; |
1171 |
|
- create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters |
1172 |
|
which are now read from new parameter file "data.autodiff" (inAdExact |
1173 |
|
previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg) |
1174 |
|
- add file "data.autodiff" in all verification/*/input_ad/ directories. |
1175 |
|
- add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward |
1176 |
|
mode (used in global_ocean.cs32x15.seaice_dynmix test exp.) |
1177 |
|
o verification/tutorial_tracer_adjsens/ |
1178 |
|
- add extra sub-verification which uses "SOM" advection scheme |
1179 |
|
(2nd Order-Moment Advection Scheme, Prather Limiter) with |
1180 |
|
#define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h |
1181 |
|
and in data: |
1182 |
|
multiDimAdvection=.TRUE., |
1183 |
|
tempAdvScheme=81, |
1184 |
|
saltAdvScheme=81, |
1185 |
|
o model/src: |
1186 |
|
- introduce ALLOW_BALANCE_RELAX which allow the removal |
1187 |
|
of the global mean of relaxation terms by setting |
1188 |
|
balanceThetaClimRelax and balanceSaltClimRelax |
1189 |
|
- disable balanceEmPmR and balanceQnet in the case when useSeaice. |
1190 |
|
This case is now treated appropriately in seaice_growth.F |
1191 |
|
o pkg/seaice: |
1192 |
|
- do balanceEmPmR and balanceQnet based on the net fluxes |
1193 |
|
(SItflux) that enter the ocean+ice system rather than QNET |
1194 |
|
and EMPMR. Works best in real fresh water. |
1195 |
|
- SIatmFW, SIatmQnet, and SItflux computations had to be moved |
1196 |
|
out of the diagnotics bloc, and stored in global arrays. |
1197 |
|
|
1198 |
|
checkpoint63o (2012/06/29) |
1199 |
|
o vertical mixing schemes: |
1200 |
|
- remove unused S/R CALC_BUOYANCY (left from branch-atmos merging) |
1201 |
|
- replace computation of density (in Function STATE1, opps_calc.F) by a call |
1202 |
|
to S/R FIND_RHO_SCALAR |
1203 |
|
- pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC |
1204 |
|
and use it for N^2 calculation in ggl90_calc.F (save 2 density computations); |
1205 |
|
affects output (vermix.ggl90) at truncation level. |
1206 |
|
o testreport: |
1207 |
|
- change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles |
1208 |
|
(nSx,nSy) for the number of threads (from eedata.mth) |
1209 |
|
o model/src: |
1210 |
|
- remove 2nd set of calls at the top of initialise_varia.F (Adjoint part) |
1211 |
|
related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary). |
1212 |
|
o verification/tutorial_tracer_adjsens/ |
1213 |
|
- compile with ALLOW_CG2D_NSA |
1214 |
|
- run with nonlinFreeSurf=3 |
1215 |
|
- update reference output_adm.txt |
1216 |
|
o tools/genmake2: |
1217 |
|
- add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ; |
1218 |
|
refine usePROFILES switching off (only when NetCDF is not available). |
1219 |
|
o verification (atmospheric set-up): |
1220 |
|
- change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration |
1221 |
|
o pkg/profiles : refine profiles and files handling. |
1222 |
|
o model/src and pkg/ecco : introduce run-time switch usePROFILES. |
1223 |
|
o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h : |
1224 |
|
- changes to use model/src/the_main_loop.F rather than the ecco version |
1225 |
|
in ecco type adjoint runs. |
1226 |
|
o model/src: |
1227 |
|
- move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID |
1228 |
|
- move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC |
1229 |
|
- update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL) |
1230 |
|
o model/src: |
1231 |
|
- fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before); |
1232 |
|
update output of test experiment bottom_ctrl_5x5. |
1233 |
|
o pkg/generic_advdiff: |
1234 |
|
- implement vertical bi-harmonic diffusion (for now, only for T & S and |
1235 |
|
only explicitly). |
1236 |
|
o verification/bottom_ctrl_5x5/ |
1237 |
|
update reference output (results changed quite some time ago, |
1238 |
|
not sure when; but new reference results look ok in terms of grdchk) |
1239 |
|
o verification/1D_ocean_ice_column/ |
1240 |
|
For verification purposes, the exact adjoint rather than an approx. |
1241 |
|
should be used (e.g., to comare against F.D. or TLM). |
1242 |
|
removed autodiff_inadmode*_ad.F routines in code_ad/ |
1243 |
|
Update results/ accordingly. |
1244 |
|
o pkg/cal: |
1245 |
|
- change cal_getdate.F so that output date is function of input time only |
1246 |
|
(less ambiguous, not mixed up with input iteration number). |
1247 |
|
- fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP). |
1248 |
|
o pkg/diagnostics: |
1249 |
|
- implement calendarDumps also for stats-diags |
1250 |
|
- implement calendarDumps also for snap-shot output (negative freq) |
1251 |
|
- for now, ignores calendarDumps if non-zero phase-lag. |
1252 |
|
|
1253 |
|
checkpoint63n (2012/06/04) |
1254 |
|
o model/src: |
1255 |
|
- recompute rSurfW & S to ensure consistent column thickness (needed for rStar) |
1256 |
|
between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice; |
1257 |
|
- use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more |
1258 |
|
similar to calc_r_star.F); update results of experiment internal_wave and |
1259 |
|
tutorial_global_oce_in_p (affected @ truncation level). |
1260 |
|
o pkg/shelfice: |
1261 |
|
- add parameterisation of advective-diffusive flux into the ice shelf |
1262 |
|
according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd |
1263 |
|
- simply eps3/3a computation |
1264 |
|
o eesupp: |
1265 |
|
- add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange |
1266 |
|
between tiles, just fill-in edges assuming locally periodic subdomain) and |
1267 |
|
add corresponding exchange subroutines (EXCH0); |
1268 |
|
- new CG-solver version (_EX0) for disconnected-tiles special case. |
1269 |
|
o model/src (CG-solvers): |
1270 |
|
- modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached |
1271 |
|
(similar final residual output and max-Iter number as with standard version); |
1272 |
|
- allows to store and use lowest-residual solution (standard & _SR versions); |
1273 |
|
- cleaning up (remove old, commented out code, LETS_MAKE_JAM ...). |
1274 |
|
- by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h) |
1275 |
|
o eesup/src: |
1276 |
|
- global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef |
1277 |
|
ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012) |
1278 |
|
o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn |
1279 |
|
|
1280 |
|
checkpoint63m (2012/04/27) |
1281 |
|
o pkg/shelfice: |
1282 |
|
- account for partical cells in surface level below ice-shelf for hydrostatic |
1283 |
|
pressure calculion (set uniformFreeSurfLev to F); update isomip experiments. |
1284 |
|
o ad test experiments: |
1285 |
|
- update and rename to "ad_optfile.local" local AD-optfile specific to a |
1286 |
|
particular adjoint verification experiment (in verification/*/code_ad/) |
1287 |
|
o pkg/seaice & pkg/exf: |
1288 |
|
- Part two of ECCO-CLIVAR code merges. |
1289 |
|
Completes merge of seaice area relax. code. |
1290 |
|
Requires unified CPP option EXF_ALLOW_SEAICE_RELAX |
1291 |
|
to be set in EXF_OPTIONS.h since this pkg controls its I/O |
1292 |
|
(and avoids second CPP option in SEAICE_OPTIONS.h) |
1293 |
|
- change default value of costIceStart & costIceEnd to a valid date. |
1294 |
|
- add snowPrecip to HSNOW in seaice_growth |
1295 |
|
o pkg/ptracers: |
1296 |
|
- move ptracers summary and setup check into separated S/R ; add a check for |
1297 |
|
valid PTRACERS_Iter0 value (error+stop or just warning). |
1298 |
|
o pkg/cal (+ pkg/ecco): |
1299 |
|
- avoid calling a S/R with 2 times the same arg (FWD: unless both are only used |
1300 |
|
as input; and for AD, unless both are not differentiable (e.g., k index)). |
1301 |
|
o model/src: |
1302 |
|
- define internal flag "uniformFreeSurfLev" (=T when free-surface level-index |
1303 |
|
is everywhere k=1) to speed-up some calculations (by pass kSurf reference); |
1304 |
|
temporary set to usingZCoords value (to be changed to F when using shelfice). |
1305 |
|
- hydrostatic pressure: implement partial cell near the surface also for |
1306 |
|
Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on |
1307 |
|
usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code). |
1308 |
|
o pkg/ctrl/ctrl_init.F: |
1309 |
|
- add a formal parameter to s/r ctrl_init_rec to print |
1310 |
|
xx_$(ctrl_valiable)_file for easier debugging |
1311 |
|
- move call of cal_* routines into the if-block where they are really |
1312 |
|
needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having |
1313 |
|
to specify a startdate |
1314 |
|
o pkg/seaice: |
1315 |
|
- update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and |
1316 |
|
global_ocean.cs32x15/code versions). |
1317 |
|
- turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for |
1318 |
|
verification experiment global_ocean.cs32x15.seaice and update results. |
1319 |
|
o pkg/exf: |
1320 |
|
- new S/R EXF_GETFIELD_START to return starting-time of a forcing field |
1321 |
|
(according to useExfYearlyFields). |
1322 |
|
o pkg/cal: |
1323 |
|
- move calendar setting & summary (previously in cal_readparams.F) into new |
1324 |
|
S/R CAL_INIT_FIXED to be called later in the initialisation process, once |
1325 |
|
length of the simulation is set (after SET_PARMS call); This is an attempt |
1326 |
|
to fix Pb when, e.g.: pkg/longstep, modifies the length of the run. |
1327 |
|
- For safety: keep a record of pkg/cal parameter settings status |
1328 |
|
to allow to STOP if one pkg/cal S/R is called too early. |
1329 |
|
- add a stop in all basic pkg/cal subroutines if called before setting is done. |
1330 |
|
- modify cal_getdate.F: stop when nothing was returned; |
1331 |
|
if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2); |
1332 |
|
this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F. |
1333 |
|
|
1334 |
|
checkpoint63l (2012/04/04) |
1335 |
|
o pkg/bbl: |
1336 |
|
- fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc); |
1337 |
|
update global_with_exf output.yearly.txt file. |
1338 |
|
o pkg/cal: |
1339 |
|
- start to clean-up cal_set.F ; fix for the case where baseTime is non-zero. |
1340 |
|
- remove 2 unsused and very short (1 line only) functions ; |
1341 |
|
- remove unsused subroutines from AD-Diff list. |
1342 |
|
o model/src: |
1343 |
|
- start to implement clean wait to stop in initialization S/R (config_check.F, |
1344 |
|
packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage) |
1345 |
|
o folowing PRINT_MESSAGE changes: |
1346 |
|
- remove reminder multiple print to the same file (STDOUT) when multi-threads. |
1347 |
|
o pkg/bbl: |
1348 |
|
- modification so it can work with z* |
1349 |
|
- replace deltaT with dTtracerLev(k) for asynchronous time stepping |
1350 |
|
- global_with_exf/input.yearly verification; changes output.yearly.txt |
1351 |
|
o eesupp/src: |
1352 |
|
- PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR); |
1353 |
|
writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1 |
1354 |
|
- CHECK_THREADS: specific code if using OpenMP threading: improve checking of |
1355 |
|
# of threads across processors (e.g., different env OMP_NUM_THREADS setting) |
1356 |
|
- improve special preliminary call to EESET_PARMS (if eedata is read 2 times). |
1357 |
|
- when using MPI, always set usingMPI=T ; set default accordingly and stop |
1358 |
|
if not consistent. |
1359 |
|
- ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread |
1360 |
|
argument is zero (in case called within single-thread section). |
1361 |
|
o pkg/fizhi: |
1362 |
|
clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored |
1363 |
|
in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO. |
1364 |
|
o pkg/exch2: |
1365 |
|
- add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to |
1366 |
|
activate EXCH_IGNORE_CORNERS in vector EXCH S/R). |
1367 |
|
- switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS) |
1368 |
|
but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data |
1369 |
|
with bad ones coming from a not-yet-updated halo. |
1370 |
|
This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx. |
1371 |
|
o pkg/frazil: |
1372 |
|
move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F |
1373 |
|
http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html |
1374 |
|
o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy |
1375 |
|
o verification/lab_sea |
1376 |
|
* #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING |
1377 |
|
* #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL |
1378 |
|
* nTimeSteps 3 -> 4 |
1379 |
|
* changed reference output accordingly |
1380 |
|
o pkg/ctrl: |
1381 |
|
* fix ctrl_get_gen for xx_sst, xx_sss |
1382 |
|
o pkg/fizhi: |
1383 |
|
- fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F |
1384 |
|
update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d) |
1385 |
|
- by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE); |
1386 |
|
fix few out-of-bounds indices in referencing vars (initialise igrd to 1); |
1387 |
|
clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array). |
1388 |
|
o pkg/gmredi: |
1389 |
|
- add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp |
1390 |
|
o pkg/fizhi: |
1391 |
|
- fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the |
1392 |
|
(old)aces open64 tuv test. |
1393 |
|
o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F |
1394 |
|
o pkg/mom_vecinv: |
1395 |
|
- fix 1 loop range in mom_vecinv.F to be like all the other loops which |
1396 |
|
set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv |
1397 |
|
with non-lin free-surf). |
1398 |
|
o model/src: move k-loop outside of i/j-loops when (re-)computing R_low |
1399 |
|
in ini/update_masks_etc.F in order to avoid -O3 optimization problems with |
1400 |
|
some compilers (gfortran 4.6.0 on MacOS) |
1401 |
|
o momentum: |
1402 |
|
- separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM |
1403 |
|
& MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised |
1404 |
|
fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control. |
1405 |
|
|
1406 |
|
checkpoint63k (2012/03/17) |
1407 |
|
o model/src: |
1408 |
|
- selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum |
1409 |
|
flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations. |
1410 |
|
- SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version |
1411 |
|
(#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp. |
1412 |
|
o model/src: solve_*diagonal.F |
1413 |
|
- replace division with multiplication by inverse (similar to original version) |
1414 |
|
update output of AD exp. global_ocean.90x40x15. |
1415 |
|
- fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F |
1416 |
|
to enable the use of the vectorized & differentiable solve_tridiagonal.F |
1417 |
|
- test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for |
1418 |
|
vertical advection (to get solve_tridiagonal tested in AD mode). |
1419 |
|
o pkg/seaice: ECCO-CLIVAR merge: |
1420 |
|
1. seaice AREA relaxation |
1421 |
|
* CPP option: SEAICE_ALLOW_AREA_RELAXATION |
1422 |
|
* runtime flag: SEAICE_tauAreaObsRelax |
1423 |
|
2. modified global mean cost imbalance code: CPP option |
1424 |
|
ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION |
1425 |
|
o another iteration on solve_*diagonal.F |
1426 |
|
Make choices independent of AUTODIFF |
1427 |
|
Default will be the adjoinable vectorized version. |
1428 |
|
Alternative choices are: |
1429 |
|
* non-adjoinable original version with low memory footprint: |
1430 |
|
#define SOLVE_DIAGONAL_LOWMEMORY |
1431 |
|
* still adjoinable but does not vectorize (k as inner-most loop): |
1432 |
|
#define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef) |
1433 |
|
o testreport |
1434 |
|
- add option to use a home made wrapper around "make" |
1435 |
|
- remove MITGCM_IEEE env. variable (no longer active) |
1436 |
|
o pkg/shelfice |
1437 |
|
- improve computation of friction velocity for velocity dependent |
1438 |
|
exchange coefficients: include velocities into SHELFICEBoundaryLayer |
1439 |
|
block to average velocities vertically |
1440 |
|
- add TAF store directives for SHI_ALLOW_GAMMAFRICT |
1441 |
|
o Modify diagonal solvers, now three versions (upon request): |
1442 |
|
#ifndef SOLVE_DIAGONAL_AUTODIFF |
1443 |
|
1. default version (dating back a while ago) |
1444 |
|
#else /* def SOLVE_DIAGONAL_AUTODIFF */ |
1445 |
|
# ifdef SOLVE_DIAGONAL_KINNER |
1446 |
|
2. adjoinable version with k-innermost loop (G. Forget) |
1447 |
|
# else |
1448 |
|
3. adjoinable vectorized version of 2. |
1449 |
|
# endif |
1450 |
|
#endif /* SOLVE_DIAGONAL_AUTODIFF */ |
1451 |
|
All flags are currently set within routines, but could/should be moved to CPP-options. |
1452 |
|
Array bounds for 1. are as before, for 2.,3. cover the entire domain |
1453 |
|
(could be changed for 1. too). |
1454 |
|
o verification/lab_sea (fwd): |
1455 |
|
- update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY, |
1456 |
|
use 7 categories (except hb87), new solve4temp params (except salt_plume), |
1457 |
|
constant salinity (=4) or variable salinity (salt_plume) done through |
1458 |
|
SItracer. |
1459 |
|
o pkg/seaice: |
1460 |
|
- rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0; |
1461 |
|
- remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t, |
1462 |
|
SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz) |
1463 |
|
from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when |
1464 |
|
SEAICE_freeze got retired) but already better than previously with |
1465 |
|
SEAICE_freeze=123456.7 deg.C; |
1466 |
|
- move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS |
1467 |
|
(safer multi-threaded setting); always set SEAICEuseEVP; |
1468 |
|
- setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to |
1469 |
|
SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report); |
1470 |
|
stop if multiple specifications for the same coeff; make sure default |
1471 |
|
SEAICE_mcPheePiston is compatible with drF(1) & deltaT. |
1472 |
|
o pkg/obcs: |
1473 |
|
- allow to switch to upwind 1rst order advection scheme for the advective |
1474 |
|
flux computation at the open-boundary; disabled for adjoint built. |
1475 |
|
o pkg/ptracers: |
1476 |
|
- rename PTRACERS_RESTART.h -> PTRACERS_START.h |
1477 |
|
- rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F |
1478 |
|
- add parameter to decide when to start a tracer; use internal flag to |
1479 |
|
know which tracer to step-forward; switch this internal flag at the top |
1480 |
|
of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled |
1481 |
|
for adjoint built. |
1482 |
|
o pkg/seaice: |
1483 |
|
- add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ; |
1484 |
|
- move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ; |
1485 |
|
- keep experiment offline_exf_seaice truly single category (set MULTDIM=1). |
1486 |
|
o pkg/ecco: |
1487 |
|
- fix writing of output file DiagnosCost_ClimSalt/Theta |
1488 |
|
and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc). |
1489 |
|
o pkg/seaice: |
1490 |
|
- add missing initialisation of COR_ICE array in dynsolver.F |
1491 |
|
- merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is |
1492 |
|
compiled either way, and is tested in all exps (multidim was only tested |
1493 |
|
in lab_sea ad before). |
1494 |
|
- cosmetic change to prepare for future addition of ITD. no change to results. |
1495 |
|
no defaults change. |
1496 |
|
- added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise). |
1497 |
|
- by lack of adequate verification experiments, I further used custom versions |
1498 |
|
of global_ocean.cs32x15 to test multicat or not, with pickup or not. All |
1499 |
|
should be correct. |
1500 |
|
- avoid recomputations in ad. |
1501 |
|
o array initialisation in adjoint mode: |
1502 |
|
1) pkg/mom_common/mom_calc_ke.F: |
1503 |
|
add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC): |
1504 |
|
The S/R which calls MOM_CALC_KE initialises KE but in some recomputation |
1505 |
|
part this initialisation is gone, resulting in Floating Point Exception |
1506 |
|
(caught by open64 compiler with debug option). |
1507 |
|
2) model/src/convective_weights.F |
1508 |
|
set output convectCount over the full array range (instead of doing |
1509 |
|
an update): this fix a similar issue when called within recomputation (adjoint) |
1510 |
|
which could by-pass the initialisation (normally done in the caller S/R). |
1511 |
|
o pkg/seaice: |
1512 |
|
- final version of turbulent flux params, as agreed at MIT ice meet: |
1513 |
|
SEAICE_mcPheePiston (default is ~ 0.000875) |
1514 |
|
SEAICE_mcPheeTaper (default is 0.) |
1515 |
|
SEAICE_frazilFrac (defualt is 1.) |
1516 |
|
SEAICE_mcPheeStepFunc (default is false) |
1517 |
|
- changes results at trunction error level |
1518 |
|
- ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo |
1519 |
|
o added pkg/frazil: |
1520 |
|
- see frazil_description.tex for details |
1521 |
|
- verification experiment is global_with_exf/input.yearly; changes output.yearly.txt |
1522 |
|
o pkg/shelfice/shelfice_thermodynamics.F |
1523 |
|
- fix exponents for velocity dependent exchange coefficients: change |
1524 |
|
from 2/3(=0) to 0.66666666666666667 |
1525 |
|
- move computation of velocity dependent exchange coefficients into |
1526 |
|
separate loop, so that it applies to both thermodynamics |
1527 |
|
- move some divisions by constants out of loops |
1528 |
|
|
1529 |
|
checkpoint63j (2012/02/16) |
1530 |
|
o pkg/seaice: |
1531 |
|
- overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc. |
1532 |
|
- SItracer: added run time params, and allow coupling to ocn salinity. |
1533 |
|
o pkg/seaice: remove (almost) all divisions by constants within loops |
1534 |
|
in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d |
1535 |
|
results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only |
1536 |
|
those, caused by 1/QI -> recip_QI) -> update output.seaice.txt, |
1537 |
|
output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt |
1538 |
|
o pkg/seaice : |
1539 |
|
- simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula |
1540 |
|
= 1 or 2, using newly added run time parameter SEAICE_availHeatTaper. |
1541 |
|
- fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148. |
1542 |
|
- add permanent SItflux diag that corresponds to TFLUX but includes |
1543 |
|
ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget. |
1544 |
|
- allow activation/testing of a fix for suspected missing term in |
1545 |
|
ocn-ice heat budget (to be confirmed). To test this, you want to |
1546 |
|
undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param |
1547 |
|
SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic. |
1548 |
|
- no change in results, fwd or ad. |
1549 |
|
o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below: |
1550 |
|
- switch to variable freezing point. |
1551 |
|
Results change : cg2d -> 1 digits; ad -> 3-6-6 digits. |
1552 |
|
- bug fix : the sublimation term that was missing is now activated. |
1553 |
|
Results change : cg2d -> 2 digits; ad -> 8-6-6 digits. |
1554 |
|
- bug fix : flooding sign term for SIsal0.NE.0. |
1555 |
|
Result change : cg2d -> 8 digits; ad -> 11-12-9 digits. |
1556 |
|
o pkg/seaice: |
1557 |
|
- unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT |
1558 |
|
is now the default, and the old default constant freezing point is recovered |
1559 |
|
with SEAICE_tempFrz0 = -1.96, |
1560 |
|
SEAICE_dTempFrz_dS = 0., |
1561 |
|
- retire SEAICE_freeze (= the old way of specifycing the constant freezing point) |
1562 |
|
- remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there. |
1563 |
|
- bug fix (thanks to M. Losch) : the sublimation term that was missing is now |
1564 |
|
activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM. |
1565 |
|
- bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211) |
1566 |
|
was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail). |
1567 |
|
- bug fix (thanks to O. Jahn) : area loss for melting got messed up in |
1568 |
|
seaice_growth r149 for legacy branch (no results change). |
1569 |
|
- introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code |
1570 |
|
from I. Fenty). |
1571 |
|
- results did not change except for global_ocean.cs32x15, mostly due to the |
1572 |
|
switch to variable freezing point (see above item for detail). |
1573 |
|
o pkg/thsice: |
1574 |
|
- fix and simplify interface to salt_plume pkg ; diagnose directly amount of |
1575 |
|
seawater freezing in thsice_calc_thickn (not used). |
1576 |
|
o pkg/seaice: turbulent flux term specification via run time params. |
1577 |
|
- replace CPP switches with run time switches to facilitate testing |
1578 |
|
- retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, |
1579 |
|
GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR |
1580 |
|
- added runtime parameter : SEAICEturbFluxFormula |
1581 |
|
- move Mcphee constants to SEAICE_PARAMS.h |
1582 |
|
- seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula; |
1583 |
|
SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); |
1584 |
|
remove seaice_summary call (moved to seaice_init_fixed) |
1585 |
|
- seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on |
1586 |
|
SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms) |
1587 |
|
- seaice_summary.F : add missing report of read turbulent flux term set up |
1588 |
|
and SITRACER. |
1589 |
|
- seaice_check.F : check range; inform and stop if retired CPPs are used |
1590 |
|
(incl. SEAICE_AGE). |
1591 |
|
- seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without |
1592 |
|
CPP switch, same computation as before for the different options. |
1593 |
|
- change results at the truncation level. |
1594 |
|
o pkg/seaice: |
1595 |
|
- remove un-used parameters LAD & MAX_TICE ; add new run-time parameters: |
1596 |
|
useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and |
1597 |
|
SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY. |
1598 |
|
- update verification/*/input*/data.seaice: |
1599 |
|
to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY |
1600 |
|
code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ; |
1601 |
|
and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code, |
1602 |
|
set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0. |
1603 |
|
o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY): |
1604 |
|
- remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same |
1605 |
|
algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0); |
1606 |
|
difference in results only due to machine truncation. |
1607 |
|
- remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using |
1608 |
|
MaykutPolySatVap; keep MIN_LWDOWN. |
1609 |
|
- adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation. |
1610 |
|
- update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87, |
1611 |
|
+ 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits). |
1612 |
|
o pkg/salt_plume: |
1613 |
|
- isolate saltPlumeFlux array exch into a specific S/R called from |
1614 |
|
do_oceanic_phys.F |
1615 |
|
- add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice. |
1616 |
|
o verification: |
1617 |
|
- move untested set-up to MITgcm_contrib/verification_other. |
1618 |
|
o pkg/seaice: |
1619 |
|
- retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER. |
1620 |
|
o pkg/seaice: |
1621 |
|
- seaice_solve4temp.F (keeping results unchanged): |
1622 |
|
* add 2 future run-time params to select which saturation vapor pressure |
1623 |
|
formula is used and how post-iteration fluxes are set. |
1624 |
|
Temporary set these 2 params according to option SOLVE4TEMP_LEGACY; |
1625 |
|
* New piece of code (not used) to update surf. atmos. heat flux F_ia using |
1626 |
|
the linearized expression to stay consistent with tsurf finding. |
1627 |
|
- seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x |
1628 |
|
can be < 0. |
1629 |
|
o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef): |
1630 |
|
- remove from F_ia (and from it's derivative dFiDTs1) the contribution of |
1631 |
|
conductive heat flux F_c , and add it explicitly when updating tsurf as |
1632 |
|
solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf |
1633 |
|
so that now F_ia has a consistent meaning through the entire routine. |
1634 |
|
This causes differences at truncation level: update output of fwd exp. |
1635 |
|
global_ocean.cs32x15.seaice. |
1636 |
|
o pkg/seaice: |
1637 |
|
- lots of editing/cleaning in seaice_solve4temp.F + better documentation |
1638 |
|
of arrays, sign/direction of fluxes; no effect on results. |
1639 |
|
- replace hard coded 273.16 (=previous value of celsius2K) by celsius2K |
1640 |
|
in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part); |
1641 |
|
note: this should have been done before changing celsius2K default. |
1642 |
|
- to keep results unchanged, add back old value of celsius2K in verification |
1643 |
|
exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs |
1644 |
|
- replace hard coded seawater freezing temp in seaice_solve4temp.F (part |
1645 |
|
SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default |
1646 |
|
value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater |
1647 |
|
freezing temp is consistent with value in seaice_growth.F ; this causes |
1648 |
|
differences at machine truncation level: update lab_sea AD output (3/4). |
1649 |
|
o pkg/seaice: |
1650 |
|
- mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask |
1651 |
|
and climsst/sss even when using seaice (to prevent calculation that might |
1652 |
|
use SST on land); does not affect any verification exp. |
1653 |
|
- apply mask to taux,tauy (in seaice_get_dynforcing.F); update output |
1654 |
|
of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix. |
1655 |
|
o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness |
1656 |
|
over land (non-legacy code) |
1657 |
|
o vectorize salt_plume package: |
1658 |
|
- add extra code to salt_plume_frac and salt_plume_tendency_apply_s |
1659 |
|
- this code computes plumebk everywhere (also over land), thus requires |
1660 |
|
code to avoid divisions by zero and catch the case of kLev=Nr. |
1661 |
|
- efficiency of salt_plume_frac is still sub-optimal |
1662 |
|
o tools (genmake2): |
1663 |
|
- fix makefile NAME specification (option: -makefile NAME) by adding |
1664 |
|
"-f $MAKEFILE" in few places where it was missing including makedepend |
1665 |
|
command (contribution from Paul). |
1666 |
|
|
1667 |
|
checkpoint63i (2012/01/24) |
1668 |
|
o model/src: |
1669 |
|
- add factorized versions of some EOS code to find_rho.F, |
1670 |
|
define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX) |
1671 |
|
o model/src: |
1672 |
|
- add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h; |
1673 |
|
- change default celsius2K from 273.16 to 273.15 |
1674 |
|
- to keep results unchanged, add back old value of celsius2K in verification |
1675 |
|
exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd), |
1676 |
|
global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm). |
1677 |
|
o model/src: add a little initialisation trick to find_rho.F and find_alpha.F |
1678 |
|
to make TAF generate vectorizable code |
1679 |
|
o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows. |
1680 |
|
Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers |
1681 |
|
have flags that do this more efficiently. |
1682 |
|
o pkg/diagnostics/diagstats_calc.F |
1683 |
|
- for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact |
1684 |
|
o pkg/obcs (with exch2): |
1685 |
|
- derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F) |
1686 |
|
and remove code (in obcs_readparms.F) which was based on EXCH of indices |
1687 |
|
(through buffer) and did not account for exch2 (e.g., CS-grid) topology. |
1688 |
|
o pkg/exf and seaice exp: |
1689 |
|
- change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0) |
1690 |
|
so that switching off area & heff advection flags does not affect results. |
1691 |
|
- change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h |
1692 |
|
- keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef |
1693 |
|
EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update |
1694 |
|
results of verification experiments: 1D_ocean_ice_column(fwd), |
1695 |
|
global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8) |
1696 |
|
and offline_exf_seaice (all 4). |
1697 |
|
o pkg/seaice: |
1698 |
|
- remove array YNEG, RIVER, TMIX (replaced by local var) from common block; |
1699 |
|
remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef. |
1700 |
|
- fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY) |
1701 |
|
but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and |
1702 |
|
not multi-dim advection; |
1703 |
|
- fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and |
1704 |
|
SHORTWAVE_HEATING #undef. |
1705 |
|
o optim: make Makefile more robust (?) |
1706 |
|
o pkg/obcs: |
1707 |
|
* fix treatment of obcs_read_pickup for TAF |
1708 |
|
o pkg/shelfice: |
1709 |
|
* add missing initialisation of num_shifwflx |
1710 |
|
* new adjoint verification exp. for isomip |
1711 |
|
* change Prandtl and Schmidt numbers from generic formulations |
1712 |
|
(in terms of model diffus. and visc.) to separate runtime |
1713 |
|
parameters, with Holland and Jenkins (1999) default values. |
1714 |
|
o pkg/exf (interpolation): |
1715 |
|
- extended input field (2 rows) near the N & S poles: |
1716 |
|
* fill in with the symetric value (when even Nb of data in longitude) |
1717 |
|
* add average value at the poles only for scalar quantities ; for vector |
1718 |
|
component interpolation, skip the averaging and keep duplicated values, |
1719 |
|
unless the 2 components have same location (uvInterp=T) in which case |
1720 |
|
interpolate the 2 components together using S/R EXF_INTERP_UV. |
1721 |
|
- new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field |
1722 |
|
together: this allows to account properly for local orientation when |
1723 |
|
averaging at N & S pole. |
1724 |
|
- add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding |
1725 |
|
exf-interpolation near N & S poles. Undef by default. |
1726 |
|
- add debug check/print on 1rst iter if debugLevel >=2. |
1727 |
|
o pkg/exf: |
1728 |
|
- change masking flags definition (no longer "parameter"), put them in |
1729 |
|
common block and set them in S/R EXF_INIT_FIXED. |
1730 |
|
- change recognized masking flag from s,u,v to c,w,s since the mask |
1731 |
|
to use (maskC,W,S) depends on position on model grid and has little to |
1732 |
|
do with scalar/vector difference; fix masking if using P-coordinates. |
1733 |
|
- fix masking of wind-stress (was wrong if interpolated or read on A-grid) |
1734 |
|
and update results of exp. global_with_exf (x2). |
1735 |
|
- fix setting of zenith-angle table when SHORTWAVE_HEATING is undef. |
1736 |
|
o pkg/obcs |
1737 |
|
- S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate) |
1738 |
|
o pkg/exf (interpolation): |
1739 |
|
- assume periodicity in X only if input field cover full longitude range. |
1740 |
|
- improve search for lat. index (supposed to be faster, in ~log2(ny) steps, |
1741 |
|
and should vectorise). |
1742 |
|
- fix input lat of the 2 added row (in case we provide N.pole data). |
1743 |
|
|
1744 |
|
checkpoint63h (2011/12/30) |
1745 |
|
o pkg/seaice: |
1746 |
|
- change declaration of UVM from _RL to _RS in order to get B-grid |
1747 |
|
uIce,vIce monitor when _RS = real*4 |
1748 |
|
o pkg/offline: |
1749 |
|
- new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags); |
1750 |
|
- compute vertical velocity if not read from file (switch on exactConserv |
1751 |
|
& staggerTimeStep); |
1752 |
|
- fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq. |
1753 |
|
o verification: |
1754 |
|
- update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input) |
1755 |
|
with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m": |
1756 |
|
fix Pb in yG definition @ 2 missing corners (previously yG was averaged); |
1757 |
|
- update output of exp. global_ocean.cs32x15.viscA4 after changing |
1758 |
|
grid-file angles (used here for coriolis-3d); |
1759 |
|
- remove (or gzip) few files not needed to run fizhi-cs experiments. |
1760 |
|
o pkg/exf (vector interpolation): |
1761 |
|
- rotate vector component toward local grid-axis orientation using grid-angles |
1762 |
|
(stored in GRID.h) instead of locally computed rotation angle; keep old code |
1763 |
|
available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default). |
1764 |
|
o pkg/seaice: |
1765 |
|
- allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION |
1766 |
|
undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined. |
1767 |
|
o pkg/PKG_OPTIONS.h files: |
1768 |
|
- move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h", |
1769 |
|
outside of the #ifdef ALLOW_THISPKG / #endif block. |
1770 |
|
- update verification/*/code/PKG_OPTIONS.h files. |
1771 |
|
o add a verification experiment (offline_exf_seaice/input.seaice) that test |
1772 |
|
the B-grid LSOR solver |
1773 |
|
o pkg/seaice: sort out emissivity and long wave radiation step 2: |
1774 |
|
- add emissivity for snow and ice as new run-time parameters |
1775 |
|
(unfortunately) that default to the corresponding exf values; this |
1776 |
|
changes results in most verification experiments so that for backward |
1777 |
|
compatibility these parameter have to be set explicitly to inconsistent |
1778 |
|
values (ugly); |
1779 |
|
- the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired |
1780 |
|
emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp |
1781 |
|
until we agree how to handle this bug properly |
1782 |
|
o pkg/exf (interpolation): |
1783 |
|
- add a set of run-time param ({inputfield}_interpMethod), one for |
1784 |
|
each interpolated input field, to select the interpolation method |
1785 |
|
with a value of zero switching off the interpolation; |
1786 |
|
- print interpolation parameters to standard output; |
1787 |
|
- refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined |
1788 |
|
(to use instead runoff_interpMethod=0 in data.exf). |
1789 |
|
- simplify default setting of interpolation parameters (for all fields, |
1790 |
|
set position to match model grid cell-center position, leading to trivial |
1791 |
|
interpolation in case of regular Lat-Lon grid) and fix for the case of |
1792 |
|
non-uniform delY. |
1793 |
|
o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for |
1794 |
|
within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1. |
1795 |
|
this factor is absolutely required, because the lw exitance (= out-going |
1796 |
|
long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown, |
1797 |
|
where the reflectivity rho = 1-emissivity for conservation reasons. Once |
1798 |
|
this is established, we can remove the CPP-Flag (if we want to). |
1799 |
|
o pkg/seaice: |
1800 |
|
- qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and |
1801 |
|
ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined |
1802 |
|
- sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity |
1803 |
|
what the name implies (and not emissivity*BoltzmannConstant), this means |
1804 |
|
the old default value of 5.5e-8 now means |
1805 |
|
5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in |
1806 |
|
S/R exf_readparms |
1807 |
|
- FV-discretization of the B-grid LSOR solver, turn on with |
1808 |
|
SEAICE_LSRBNEW. This new solver also involves a slight re-organization |
1809 |
|
of the calling routine dynsolver, so that B and C-grid code look a |
1810 |
|
little more alike. |
1811 |
|
- fix index bugs in ostres.F (B-grid code) |
1812 |
|
o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better |
1813 |
|
o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the |
1814 |
|
default for SEAICE_emissivity, if useEXF; requires setting a wrong |
1815 |
|
parameter value in global_ocean.cs32x15/input.seaice/data.seaice for |
1816 |
|
backward compatiblity |
1817 |
|
o model/src: use sigmaR in calc_ivdc |
1818 |
|
|
1819 |
|
checkpoint63g (2011/12/16) |
1820 |
|
o pkg/seaice/seaice_growth.F: |
1821 |
|
fix heat conservation of the coupled ocean-seaice system. |
1822 |
|
when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of |
1823 |
|
solid vs liquid water treatment is resolved via QNET. |
1824 |
|
o pkg/seaice/seaice_growth.F: |
1825 |
|
add missing term for sublimation in saltFlux, which was breaking conservation. |
1826 |
|
o pkg/seaice/seaice_model.F: |
1827 |
|
Remove this patholigical case treatment in evolution branch, |
1828 |
|
where it is un-necessary and breaks conservation. |
1829 |
|
Update global_ocean.cs32x15/results accordingly for |
1830 |
|
output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt |
1831 |
|
o model/src: |
1832 |
|
useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in |
1833 |
|
external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE. |
1834 |
|
o pkg/obcs: |
1835 |
|
modify Stevens boundary conditions so that S/R obcs_calc_stevens computes |
1836 |
|
tendency for temperature and salinity that is then applied to update |
1837 |
|
theta and salt in S/R obcs_apply_ts; this requires proper masking of all |
1838 |
|
horizontal advection and diffusion contributions on the boundary (in |
1839 |
|
S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and |
1840 |
|
removing the mask in S/R timestep_tracer. The advantage of this approach is |
1841 |
|
that the updated tracer values include contributions from the surface |
1842 |
|
forcing and vertical diffusion. |
1843 |
|
This modification changes exp4.stevens because of vertical diffusion. |
1844 |
|
o model/src: |
1845 |
|
change non-curvilinear grid setting to also work with exch2 + blank tiles: |
1846 |
|
- move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst |
1847 |
|
face dimensions. |
1848 |
|
- new S/R INI_LOCAL_GRID to define model tile-local grid (using same units |
1849 |
|
as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID |
1850 |
|
and INI_SPHERICAL_POLAR_GRID. |
1851 |
|
change test-experiment global_ocean.90x40x15: |
1852 |
|
- split the domain in many more tiles (9x4 tiles of 10x10 each); |
1853 |
|
- switch to exch2 and remove 1 blank-tile (but only for MPI test). |
1854 |
|
- update results of both test (std & dwnslp). |
1855 |
|
o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in |
1856 |
|
tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation |
1857 |
|
o model/src: |
1858 |
|
- take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS |
1859 |
|
and fix initialisation when using sigma-coords. |
1860 |
|
o model/src: |
1861 |
|
- improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc. |
1862 |
|
to their current value at the beginning of forward_step.F": add a new run-time |
1863 |
|
switch "doResetHFactors" (default=false) and use it to do (or not) the resetting. |
1864 |
|
- set doResetHFactors=T in the following test exp: |
1865 |
|
global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS), |
1866 |
|
global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS) |
1867 |
|
and tutorial_global_oce_in_p (nonLinFS in p) |
1868 |
|
o pkg/ecco |
1869 |
|
- added IES cost term |
1870 |
|
o verification/advect_xz |
1871 |
|
- scale down the depth by 1/100 (from 200 km to just 2.km) |
1872 |
|
- add secondary test using divergent flow, r-star and implicit vertical advection. |
1873 |
|
- add note (check_conserve_TS.txt) and matlab script to check global |
1874 |
|
conservation of T & S with NonLin-FreeSurf and Adams-Bashforth. |
1875 |
|
o pkg/rbcs: |
1876 |
|
- add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F). |
1877 |
|
o pkg/obcs (Stevens BCs): |
1878 |
|
- fix various problems in the phase speed computations of the Stevens |
1879 |
|
boundary conditions: |
1880 |
|
- sign error for western and southern boundaries, |
1881 |
|
- time tendencies were underestimated by factor of dTracerLev and some just |
1882 |
|
zero (for multidim advection schemes) -> now estimate time tendencies |
1883 |
|
from difference between previous (n) time level and the one before (n-1); |
1884 |
|
this requires storing a field per tracer per boundary, also in the pickup |
1885 |
|
files. |
1886 |
|
- replace deltaTmom in cflMer/Zon computation with dTracerLev |
1887 |
|
- set default phase velocity to cflMer/Zon |
1888 |
|
- update verification experiment exp4.stevens |
1889 |
|
o pkg/generic_advdiff (implicit_r): |
1890 |
|
- fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf |
1891 |
|
(remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F); |
1892 |
|
- fix implicit vertical diffusion or advection with NonLin FreeSurf |
1893 |
|
(was using current recip_hFacC instead of future recip_hFacC): set future |
1894 |
|
recip_hFac in thermodynamics.F and pass & use it in all vertical implicit |
1895 |
|
solver S/R ; |
1896 |
|
- fill diagnostics of vertical advective fluxes (computed from tendency) |
1897 |
|
when using implicit vert. advection; |
1898 |
|
- update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion: |
1899 |
|
global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD), |
1900 |
|
tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD) |
1901 |
|
and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5. |
1902 |
|
o pkg/diagnostics: |
1903 |
|
- add diags for T & S tendency which goes through Adams-Bashforth. |
1904 |
|
|
1905 |
|
checkpoint63f (2011/11/30) |
1906 |
|
o pkg/obcs/obcs_calc_stevens.F: |
1907 |
|
- join some loops to reduce number of if-statements |
1908 |
|
- fix a bug in code for northern and southern boundaries. |
1909 |
|
o pkg/seaice/seaice_init_varia.F |
1910 |
|
- undo resetting UVM=0 that has slipped in unnoticed in r1.49 and |
1911 |
|
caused zero ice-velocities for the B-grid code |
1912 |
|
o pkg/seaice/seaice_init_fixed.F |
1913 |
|
- fix a bug in the initialisation of the second metric terms |
1914 |
|
k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0. |
1915 |
|
- this affects all seaice configurations with useCurviLinearGrid = .true. |
1916 |
|
and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms |
1917 |
|
= .true. (default) |
1918 |
|
- the only verification experiment affected is global_ocean.cs32x15: |
1919 |
|
icedyn, seaice, and seaice_dynmix (AD) |
1920 |
|
o pkg/thsice/thsice_diagnostics_state.F |
1921 |
|
- only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does |
1922 |
|
not contain garbage that can lead to surprises in diagstats_calc.F |
1923 |
|
o model/src: |
1924 |
|
- move bi,bj loops inside INTEGR_CONTINUITY ; |
1925 |
|
- call INTEGR_CONTINUITY directly from forward_step.F |
1926 |
|
(previously called from momentum_correction_step.F) |
1927 |
|
- call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F, |
1928 |
|
forward_step.F and pkg/ecco/the_main_loop.F |
1929 |
|
o model/src/do_oceanic_phys.F: |
1930 |
|
- reset addMass to zero only if useICEFRONT ; |
1931 |
|
- separated k-loop for rhoInSitu calculation ; |
1932 |
|
- add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P) |
1933 |
|
and at constant T,S (= WdRHOdP); |
1934 |
|
NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport |
1935 |
|
of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical |
1936 |
|
transport of locally-referenced potential density); |
1937 |
|
to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP) |
1938 |
|
o gluemnc: |
1939 |
|
- replace ncrcat with ncks when adding variables to *.glob.nc |
1940 |
|
- change the way variables without record dimensions are handled so that |
1941 |
|
files that have variables with and without record variables can be glued: |
1942 |
|
add a record dimension with a new unique name to be able to differentiate |
1943 |
|
between variable with and without a-prior record dimensions. Remove |
1944 |
|
this record dimension before adding the variable to the *.glob.nc file. |
1945 |
|
This procedure automatically works also for grid.*.nc files that do not |
1946 |
|
have any record dimension. |
1947 |
|
o verification/cpl_aim+ocn: |
1948 |
|
- generate new reference output on baudelaire (gfortran, mpich2) (previously |
1949 |
|
from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script. |
1950 |
|
o pkg/obcs/obcs_calc_stevens.F: |
1951 |
|
- add code for northern and southern boundaries. |
1952 |
|
- reorder some loops to save some operations and so that drFBar can be scalar |
1953 |
|
o model/src: |
1954 |
|
- re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine |
1955 |
|
truncation) and add diagnostics for Adams-Bashforth tendency increment. |
1956 |
|
- update test-exp. AD output: |
1957 |
|
1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl; |
1958 |
|
and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20, |
1959 |
|
front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5), |
1960 |
|
global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4), |
1961 |
|
matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre, |
1962 |
|
tutorial_global_oce_in_p, tutorial_global_oce_latlon and |
1963 |
|
tutorial_plume_on_slope. |
1964 |
|
o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX |
1965 |
|
that vectorises. This code uses 3 extra 2D fields, F90 array assignments |
1966 |
|
and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX |
1967 |
|
does not even come with an F77 compiler anymore, this should not be |
1968 |
|
a limitation |
1969 |
|
|
1970 |
|
checkpoint63e (2011/11/06) |
1971 |
|
o pkg/seaice adjoint of LSR: |
1972 |
|
- substantially rework STORE dirs. |
1973 |
|
- add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED |
1974 |
|
this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields |
1975 |
|
and only perform SOLV_MAX_FIXED adjoint iters. |
1976 |
|
If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration |
1977 |
|
always goes to same record, meaning that the last forward field will be |
1978 |
|
the one used in the adjoint - an approximation. |
1979 |
|
- now produces non-zero LSR-related gradients, and acceptable gradients for |
1980 |
|
An's zonal (x-z) test case (to be checked in) |
1981 |
|
- lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR |
1982 |
|
(but these are screwed up by the thermodynamics in the first place); |
1983 |
|
reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution; |
1984 |
|
output_adm.txt also reflects changes to seaice_lsr |
1985 |
|
- global_ocean.cs32x15: |
1986 |
|
* the "default" input_ad.seaice has been re-defined to always exclude dynamics |
1987 |
|
(output_adm.seaice.txt was updated) |
1988 |
|
* new input_ad.seaice_dynmix tests a forward LSR / backward free-drift |
1989 |
|
(output_adm.seaice_dynmix.txt) |
1990 |
|
o test-exp. exp4+stevens: |
1991 |
|
- switch off pTracers and nonHydrostatic (restart problems with NH); update output |
1992 |
|
o pkg/seaice (lsr solver): |
1993 |
|
- put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only); |
1994 |
|
update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15 |
1995 |
|
- fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD) |
1996 |
|
- new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution |
1997 |
|
into initial guess for linearised solver; use weight ~ (1/err)^2,4. |
1998 |
|
- compute (with new S/R) and print initial (+ free-driff sol. if available) |
1999 |
|
and final residual of linearised system. |
2000 |
|
o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity |
2001 |
|
(requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F) |
2002 |
|
o pkg/obcs: Stevens BCs (still only for east and west) |
2003 |
|
- fix Stevens BCs by using intermediate velocities of previous |
2004 |
|
time step as "baroclinic" contribution rather velocity of one grid cell |
2005 |
|
inside the boundaries; more consistent but makes the entire treatment |
2006 |
|
more complicated, requires new pickup files and two new S/Rs: |
2007 |
|
obcs_copy_uv_n and obcs_save_uv_n |
2008 |
|
keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY |
2009 |
|
(undefined by default) |
2010 |
|
- silently move computation of some grid factors into separate loops to |
2011 |
|
save some recomputations |
2012 |
|
- add a hack for non-linear free surface |
2013 |
|
- add a verification experiment to exp4 that tests this code |
2014 |
|
o make gluemnc/xplodemnc work with (moron) non-GNU shell tools |
2015 |
|
|
2016 |
|
checkpoint63d (2011/10/25) |
2017 |
|
o pkg/obcs + seaice-dynamics: |
2018 |
|
- new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before |
2019 |
|
solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB |
2020 |
|
values (consistent with an implicit method). |
2021 |
|
- add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to |
2022 |
|
return to older implementation (same results as before); note that none of |
2023 |
|
the "experimental" OBCS_SEAICE options are implemented in the new version. |
2024 |
|
- switch test exp. seaice_obcs to use new version (update output). |
2025 |
|
o pkg/seaice: |
2026 |
|
- add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS) |
2027 |
|
- add parenthesis in Water-Ice drag calculations (evp & lsr); |
2028 |
|
- in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1; |
2029 |
|
and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice) |
2030 |
|
- update output of test exp lab_sea that uses evp or lsr (fwd+ad) |
2031 |
|
and global_ocean.cs32x15 (icedyn & seaice fwd+ad). |
2032 |
|
o pkg/layers: |
2033 |
|
- Include potential density as new coordinate (Thanks to David Munday) |
2034 |
|
o pkg/dic: |
2035 |
|
- Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add |
2036 |
|
carbonate computation/output to CALC_PCO2_APPROX |
2037 |
|
o pkg/generic_advdiff |
2038 |
|
- make TAF generate code that vectorizes: |
2039 |
|
gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F |
2040 |
|
o model/src: |
2041 |
|
- improve vectorization also for adjoint code of |
2042 |
|
solve_tridiagonal and solve_pentadiagonal. As this requires up to |
2043 |
|
5 new 3D-fields, this code is only turned on for the combination of |
2044 |
|
ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message |
2045 |
|
for singular matrix check (only for TARGET_NEC_SX). |
2046 |
|
- remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to |
2047 |
|
ALLOW_AUTODIFF. This flag now needs to be set outside of |
2048 |
|
solve_tri/pentadiagonal.F |
2049 |
|
o pkg/exf: |
2050 |
|
- fix previous modif in exf_readparms.F (revision 1.66: treatment of |
2051 |
|
optional namelist EXF_NML_OBCS). |
2052 |
|
- add many debug-print (to trace down where pkg/cal error msg comes from) |
2053 |
|
o pkg/mom_vecinv/mom_vi_hdissip.F |
2054 |
|
- rearrange loops so that vectorization is improved and in particular |
2055 |
|
the adjoint routine vectorizes. The code is a little longer now, but I |
2056 |
|
think easier to read. |
2057 |
|
Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested. |
2058 |
|
o pkg/seaice: |
2059 |
|
- allow to specify initial seaice velocity from files (uIceFile,vIceFile) |
2060 |
|
o pkg/exch2: |
2061 |
|
- alternative code (without tile x tile matrix) for cumulated (global) sum; |
2062 |
|
used as default; keep using matrix version in adjustment.cs-32x32x1. |
2063 |
|
o tools/build_options: |
2064 |
|
- after merging some MPI and/or multi-threads specific optfiles so that |
2065 |
|
the modified default optfile support both built (using genmake2 -mpi |
2066 |
|
for the MPI built, using genmake2 -omp for OpenMP built), |
2067 |
|
move now obsolete optfiles to tools/build_options/unsupported/ |
2068 |
|
(add copy of email sent to support list in doc/optfiles_changes.txt) |
2069 |
|
|
2070 |
|
checkpoint63c (2011/09/28) |
2071 |
|
o pkg/ebm: |
2072 |
|
- fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of |
2073 |
|
test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d) |
2074 |
|
o pkg/seaice (SItracer pickup) |
2075 |
|
* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER) |
2076 |
|
To be done: |
2077 |
|
- thorough testing of missing fields in S/R seaice_read_pickup |
2078 |
|
- thorough matching between generic tracers and specific fields used |
2079 |
|
(e.g. volume-weighted age, area-weighted age, salinity, ...) |
2080 |
|
o pkg/grdchk: |
2081 |
|
- all procs calculate and print finite-difference gradient (for testreport) |
2082 |
|
- change description output used by testreport; |
2083 |
|
- AD testing: also compare and report Finite-difference gradient; |
2084 |
|
=> update all output_adm*.txt |
2085 |
|
o test exp. global_ocean_ebm: |
2086 |
|
- switch back useRealFreshWaterFlux (no problem anymore with run-off); |
2087 |
|
and turn on exactConserve; update (fwd) output. |
2088 |
|
o pkg/seaice (LSR): |
2089 |
|
- print to STDOUT number of solver iterations at SEAICE_monFreq interval. |
2090 |
|
- modify solver to deal cleanly with u/v switch at face edges (CS-grid): |
2091 |
|
* identical results with non-CS topology (but save up to half of EXCH calls) |
2092 |
|
* no much changes in cs-32 verification tests since no ice at face edges |
2093 |
|
(differences due to convergence criteria, since nb of iterations changed) |
2094 |
|
* expect some differences on lat-lon-cap grid. |
2095 |
|
update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice) |
2096 |
|
o pkg/exch2: |
2097 |
|
- add new CPP option to disable Cumul-Sum matrix (to save storage when using |
2098 |
|
many tiles); until alternative coding is added, just add a stop. |
2099 |
|
o pkg/kpp: |
2100 |
|
- move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F |
2101 |
|
to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list). |
2102 |
|
o optfiles: |
2103 |
|
- merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles |
2104 |
|
into corresponding standard one, which now support different build: |
2105 |
|
(when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built) |
2106 |
|
- add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael) |
2107 |
|
o pkg/obcs (seaice): |
2108 |
|
- add missing EXCH for uIce,vIce after applying OBCS; |
2109 |
|
- remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding |
2110 |
|
argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R |
2111 |
|
EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F; |
2112 |
|
- fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared) |
2113 |
|
- verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi |
2114 |
|
and eedata.mth for MPI and mutlti-threaded testing. |
2115 |
|
o pkg/flt: |
2116 |
|
- make FLT EXCH working with multi-threads (and MPI + multi-threads); |
2117 |
|
- use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h; |
2118 |
|
- fix pickup and trajectories + profiles output with multi-threads; |
2119 |
|
- add parameter to select group of fields to write along trajectory and |
2120 |
|
profile (default unchanged); |
2121 |
|
- only call PORT_RAND* function when flt_noise <> 0; |
2122 |
|
- add multi-threaded test for verification exp. flt_example. |
2123 |
|
o eesupp/src: |
2124 |
|
- fix S/R ALL_PROC_DIE for MPI+multi-threads. |
2125 |
|
- USE_OMP_THREADING: check that number of threads (from eedata) matches |
2126 |
|
actual number (from env.var. setting). |
2127 |
|
o pkg/ebm: |
2128 |
|
- fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file. |
2129 |
|
- add multi-threaded test for verification exp. global_ocean_ebm |
2130 |
|
|
2131 |
|
checkpoint63b (2011/08/29) |
2132 |
|
o pkg/ebm: |
2133 |
|
- fix sign of runoff; |
2134 |
|
- update directly forcing fields (Qnet,EmPmR) to use standard |
2135 |
|
external_forcing_surf.F (remove ebm_forcing_surf.F); |
2136 |
|
- avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F); |
2137 |
|
- set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm) |
2138 |
|
and apply relaxation towards corresponding SST field (2-D map or ZonAver). |
2139 |
|
- update global_ocean_ebm parameters file data and update output (fwd+ad). |
2140 |
|
o verification/matrix_example: |
2141 |
|
- split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for |
2142 |
|
MPI and mutlti-threaded testing. |
2143 |
|
o pkg/matrix: |
2144 |
|
- change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ; |
2145 |
|
- fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter); |
2146 |
|
- fix for multi-threaded (remove DATA statement); |
2147 |
|
- use standard DIFFERENT_MULTIPLE function; |
2148 |
|
- add MATRIX_OPTIONS.h |
2149 |
|
o verification/matrix_example: |
2150 |
|
To allow to split the domain in several tiles, change the domain size |
2151 |
|
from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on |
2152 |
|
Western side) of land points. |
2153 |
|
o (*_)write_pickup: |
2154 |
|
- fix few bugs in mypackage_read/write_pickup.F |
2155 |
|
- in MDS_WR_METAFILES calls, replace "myTime" by a local copy into |
2156 |
|
array of length 1 (was caught by compiler syntax-check). |
2157 |
|
o pkg/diagnostics (velocity potential solver): |
2158 |
|
- fix initialisation of main diagonal matrix (for overlap values) |
2159 |
|
o tools/build_options: |
2160 |
|
- towards single optfile for MPI and non-MPI built: merge few +mpi optfile |
2161 |
|
into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11) |
2162 |
|
- linux_amd64_gfortran: merge +mpi_generic version into standard optfile: |
2163 |
|
* move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ; |
2164 |
|
* FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list; |
2165 |
|
and use "-devel" testreport option for standard testing on baudelaire. |
2166 |
|
o pkg/grdchk: |
2167 |
|
- Assume that all gradient-check position are within the same tile |
2168 |
|
corresponding to global indices (iGloTile,jGloTile) and that |
2169 |
|
positions (i,j indices or nbeg) are local to this tile; |
2170 |
|
- set tile local-indices and proc. number according to tile global-indices; |
2171 |
|
- remove grdchkwhichproc from namelist (retired param); |
2172 |
|
- send adjoint gradient to all procs so that all procs print it to STDOUT; |
2173 |
|
- switch on MPI test for global_ocean.90x40x15 AD test experiment. |
2174 |
|
o adding package bbl (Bottom Boundary Layer) |
2175 |
|
description in MITgcm/pkg/bbl/bbl_description.tex |
2176 |
|
example/test experiment in MITgcm_contrib/bbl |
2177 |
|
o adjoint verifications |
2178 |
|
- changed 5 experiments to multi-tiles |
2179 |
|
* global_ocean.90x40x15 |
2180 |
|
* obcs_ctrl |
2181 |
|
* offline_exf_seaice |
2182 |
|
* tutorial_dic_adjoffline |
2183 |
|
* tutorial_tracer_adjsens |
2184 |
|
changed reference output for those that crossed tile boundaries |
2185 |
|
(changed choices of gradient check positions) |
2186 |
|
- with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi) |
2187 |
|
- temporary bug fix in grdchk_loc.F for obcs |
2188 |
|
o genmake2 & testreport |
2189 |
|
- add target "obj" (just for OBJFILES files) to Makefile; |
2190 |
|
- add option to specify FEXTRAFLAGS on command line. |
2191 |
|
o pkg/mypackage: |
2192 |
|
- remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS |
2193 |
|
|
2194 |
|
checkpoint63a (2011/08/02) |
2195 |
|
o pkg/diagnostics (velocity potential): |
2196 |
|
- fix velocity-potential calculation when using OBCS: balance net inflow |
2197 |
|
at each level (new S/R OBCS_DIAG_BALANCE). |
2198 |
|
- fix some of the problems with OBCS in stream-function calculation. |
2199 |
|
o pkg/exf/exf_readparms.F |
2200 |
|
- make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF, |
2201 |
|
EXF_NML_OBCS) more consistent, so that you need not have these lists |
2202 |
|
in data.exf when they are not used. |
2203 |
|
o optim/optim_readdata.F: |
2204 |
|
- add some output about obcs variables that might help debugging |
2205 |
|
- add a check about nvarlength |
2206 |
|
o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec |
2207 |
|
o pkg/diagnostics (velocity potential): |
2208 |
|
- fix mask for OBCS (still problems in stream-function with OBCS); |
2209 |
|
- add specific parameter (default = main code CG2D params) for solver; |
2210 |
|
- in case of poor convergence, use solution corresponding to lowest residual. |
2211 |
|
o pkg/seaice/seaice_growth.F: small changes that permit vectorizable |
2212 |
|
adjoint code. In general statements like tmpscal=fld(i,j) are problematic |
2213 |
|
and should be avoided where possible. |
2214 |
|
o model/src (rStar): |
2215 |
|
- include r* effect on reference-state (PhiRef) in totPhiHyd |
2216 |
|
(so that it's really the potential anomaly at the cell center); |
2217 |
|
affect solution only if z* with full pressure in EOS. |
2218 |
|
- test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and |
2219 |
|
update output (because of z* in totPhiHyd and viscA4 changes); |
2220 |
|
- keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly |
2221 |
|
@ constant r) until interpolation at constant r is implemented. |
2222 |
|
o pkg/diagnostics |
2223 |
|
- fix RCENTER diagnostics in case cell center is not at interface middle |
2224 |
|
o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use |
2225 |
|
this eos with eosType = 'TEOS10', in data (PARM01). This eos implies |
2226 |
|
that THETA and SALT are "conservative temperature" and "absolute |
2227 |
|
salinity" |
2228 |
|
o pkg/ctrl |
2229 |
|
- fix computation of endrec in s/r ctrl_init_rec |
2230 |
|
- ctrl_pack/unpack_*: remove unused variables and some obsolete code |
2231 |
|
o pkg/seaice/seaice_growth.F |
2232 |
|
- fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code, |
2233 |
|
remove then obsolete STORE directives |
2234 |
|
- fix STORE directives for tice and tices, so that only the |
2235 |
|
appropriate part of the fields are stored (and not the entire |
2236 |
|
field); update global_ocean.cs32x15.seaice AD output. |
2237 |
|
- cosmetic changes: adjust CPP flags and indentation for better |
2238 |
|
legibilty |
2239 |
|
o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by |
2240 |
|
Chris Wilson) |
2241 |
|
o pkg/gmredi: |
2242 |
|
Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF), |
2243 |
|
and test it in verification exp. "front_relax.bvp" (update output.bvp.txt) |
2244 |
|
|
2245 |
|
checkpoint63 (2011/07/11) |
2246 |
|
o pkg/exch2: |
2247 |
|
- rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h |
2248 |
|
- exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the |
2249 |
|
(2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y |
2250 |
|
increments, calculates Cumul-Sum @ tile origin and sends results to each tile. |
2251 |
|
o pkg/diagnostics: |
2252 |
|
- deal with pairs of post-processed diags which are computed together; in |
2253 |
|
particular, re-order list of diags within 1 file to save 2nd computation. |
2254 |
|
- add S/R to compute velocity stream-function (called after velocity-potential |
2255 |
|
calculation) from divergence free transport -> new diagnostics "PsiVEL". |
2256 |
|
- add parameter to select grid-point location where PsiVEL == 0. |
2257 |
|
o eesupp/src: |
2258 |
|
new S/R to calculate cumulated sum on tiled array, corner grid-cell location |
2259 |
|
(specific S/R needed with exch2 topology - for now, just print an error msg) |
2260 |
|
o pkg/shelfice |
2261 |
|
- Implement friction velocity-dependent transfer coefficients following |
2262 |
|
Holland and Jenkins, JPO, 1999 |
2263 |
|
Original code by M. Losch with small modifs. |
2264 |
|
Enable with CPP option SHI_ALLOW_GAMMAFRICT |
2265 |
|
and runtime flag SHELFICEuseGammaFrict |
2266 |
|
o verification lab_sea & global_ocean.cs32x15: |
2267 |
|
- use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local): |
2268 |
|
does not miss some dependencies (but is slower) and also works with many files |
2269 |
|
(default makedepend limitation for AD built). |
2270 |
|
- use cyrus_makedepend in adjustment.128x64x1 (so that it still tested). |
2271 |
|
o pkg/diagnostics: |
2272 |
|
- add run-time parameter "useMissingValue" (def=False) to fill land-point |
2273 |
|
(i.e., where mask=0) with MissingValue ; used only in MNC output file. |
2274 |
|
This replaces CPP-option DIAGNOSTICS_MISSING_VALUE. |
2275 |
|
- Extend the use of "missing_value" setting from data.diagnostics for the case |
2276 |
|
of counter-diagnostics (where fraction-weight is zero). This applies both to |
2277 |
|
MNC and MDS output files. |
2278 |
|
o pkg/seaice/seaice_growth.F: |
2279 |
|
- add 'a priori' cap of latent heat flux based on actual mass considerations |
2280 |
|
when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the |
2281 |
|
non-legacy seaice_solve4temp. |
2282 |
|
- add diagnostic of the residual sublimation freshwater flux (the freshwater |
2283 |
|
flux taken from the ocean if the total actual latent heat fluxes exceed |
2284 |
|
the maximum) |
2285 |
|
- remove the CPP switch around the *_FWbySublim unit change and move diagnostic |
2286 |
|
fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F. |
2287 |
|
- add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef |
2288 |
|
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim). |
2289 |
|
- bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET. |
2290 |
|
- bug fix : missing part to Martin's r_FWbySublim pathological case fix. |
2291 |
|
o verification 1D_ocean_ice_column: |
2292 |
|
made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet |
2293 |
|
update results |
2294 |
|
o pkg/diagnostics: |
2295 |
|
- Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P') |
2296 |
|
which are not filled-up but computed from other diags ; In this case, the mate |
2297 |
|
diag points to the primary (filled-up) diag to used for post processing. |
2298 |
|
- Update Velocity-potential computation using post-processed diag framework. |
2299 |
|
==> Change the ordering of fields and time-periods in MDS output file |
2300 |
|
when using periodic averaging: now writes one time record with the full set |
2301 |
|
of fields for this time period, then the next time reccord (it used to be |
2302 |
|
one field with the full set of time records then the next field). |
2303 |
|
Note: this is now similar to NetCDF (MNC) output file. <== |
2304 |
|
|
2305 |
|
checkpoint62z (2011/06/21) |
2306 |
|
o adjoint monitor: |
2307 |
|
- Add adjoint monitor output for packages exf, seaice |
2308 |
|
and update relevant testreport output |
2309 |
|
o pkg/seaice: |
2310 |
|
- re-order diags inits so that they appear in order in available_diagnostics.log |
2311 |
|
- added diags: hsnow thermo. rates of change, area preceeding ridiging process, |
2312 |
|
area/heff/hsnow preceeding thermodynamic growth/melt. |
2313 |
|
- modified diag: SIdA; output actual effect, as the description states. |
2314 |
|
- modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. |
2315 |
|
- retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. |
2316 |
|
(SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; |
2317 |
|
and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) |
2318 |
|
- modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. |
2319 |
|
- added diagnostics for seaice generic tracers (SItr*). |
2320 |
|
- added SItrUnit and SItrNameLong run time param (for SItr* diags). |
2321 |
|
- in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. |
2322 |
|
I. Fenty: 18-Jun-2011: |
2323 |
|
Minor changes to seaice package: |
2324 |
|
1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and |
2325 |
|
added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) |
2326 |
|
- Differentiated "regularization variables" from "floor variables" |
2327 |
|
* areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor |
2328 |
|
* hiceMin became SEAICE_hice_reg (old hiceMin) |
2329 |
|
(with _reg meaning regularization variable) |
2330 |
|
- SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion |
2331 |
|
so as to ensure energy conservation when going between phases |
2332 |
|
- A22 was not used anywhere |
2333 |
|
2) Changed regularization procedure for heffActual and hsnowActual to ensure |
2334 |
|
well-boundedness and smooth adjoint in seaice_growth.F |
2335 |
|
3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells |
2336 |
|
because the old regularization always set heffActual >= 0.05 cm |
2337 |
|
4) Changed the model so that the default behavior is to put a small (10^-5) "floor" |
2338 |
|
on AREA when HEFF > 0. |
2339 |
|
- went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to |
2340 |
|
requiring that DISABLE_AREA_FLOOR *not* be defined |
2341 |
|
Affected verifications: |
2342 |
|
- 1D_ocean_ice_column (output.txt output_adm.txt) |
2343 |
|
- global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) |
2344 |
|
o pkg/diagnostics: |
2345 |
|
- move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). |
2346 |
|
- rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument |
2347 |
|
(was _RL, now integer) with option = 0 to retrieve all levels. |
2348 |
|
- add pieces of code to compute velocity potential at each level (new diagnostics |
2349 |
|
PhiVEL, works only when UVELMASS & VVELMASS are also turned on); |
2350 |
|
for now, using same params as CG2D (target-resisual, max Nb of iter ...). |
2351 |
|
- fix few issues with counter diagnostics in diagnostics_setdiag.F & |
2352 |
|
diagstats_setdiag.F (if diagnostic counter is itself a counter diag) |
2353 |
|
and in diagnostics_fract_fill.F (do not need a valid pointer for the |
2354 |
|
diagnostics counter-mate); check that definition of counter-diagnostic |
2355 |
|
includes a valid counter-mate (in diagnostics_set_levels.F). |
2356 |
|
o model/src (rStar): |
2357 |
|
- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
2358 |
|
affect solution only if z* with full pressure in EOS; |
2359 |
|
update output of test-exp global_ocean.90x40x15. |
2360 |
|
o pkg/seaice: |
2361 |
|
- introduce siEps=1e-5 parameter |
2362 |
|
- use areaMax in AREA update (part 4), consistent with ridging step (part 2.5). |
2363 |
|
- re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code. |
2364 |
|
- introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer. |
2365 |
|
For now it covers, and was tested for, ice salinity and age (attached to HEFF), |
2366 |
|
as well as ice cover age and ridging index (attached to AREA). |
2367 |
|
For now the run time parameters (in data.seaice/SEAICE_PARM03) are |
2368 |
|
SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA'). |
2369 |
|
Up to SItrMaxNum=3 tracers can be used simultaneously. |
2370 |
|
o pkg/salt_plume: |
2371 |
|
-introduce SPsalFRAC run time parameter that sets the fraction of the |
2372 |
|
salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically) |
2373 |
|
that gets vertically redistributed (fluxed down) by pkg/salt_plume. |
2374 |
|
o model debug options: |
2375 |
|
- Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored |
2376 |
|
in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h). |
2377 |
|
- Refine debug-msg printing selection (3 new levels): |
2378 |
|
debugMode : controls printing of debug messages (sequence of S/R calls). |
2379 |
|
debugLevel : controls printing of algorithm-relevant auxiliary/debug messages |
2380 |
|
debLevZero = 0 ; /* level of disabled aux. msg printing */ |
2381 |
|
debLevA = 1 ; /* level of minimum aux. msg printing */ |
2382 |
|
debLevB = 2 ; /* level of low aux. print (report read-file opening)*/ |
2383 |
|
debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */ |
2384 |
|
debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */ |
2385 |
|
debLevE = 5 ; /* level of extensive debug printing */ |
2386 |
|
New debugLevel default: with default debugMode value (=F), |
2387 |
|
= 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.; |
2388 |
|
and if debugMode=T, default debugLevel = 4 (debLevD). |
2389 |
|
Relation with previous settings: |
2390 |
|
debLevB (=2) corresponds to former debLevA (=1) |
2391 |
|
debLevD (=4) corresponds to former debLevB (=2) |
2392 |
|
Note: |
2393 |
|
a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before); |
2394 |
|
b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs); |
2395 |
|
to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5) |
2396 |
|
- Add new parameter (printResidualFreq, read from PARM02 namelist) to print |
2397 |
|
detailed CG solvers convergence; off (=0) by default, except if debugLevel=5. |
2398 |
|
o pkg/obcs: |
2399 |
|
- change OBCSfixTopo default from True to False (should not change the results); |
2400 |
|
keep OBCSfixTopo=T in verification-exp. seaice_obcs. |
2401 |
|
o pkg/thsice: |
2402 |
|
- fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in |
2403 |
|
2nd layer seaice sublimation (unlikely to happen) |
2404 |
|
- use Interior mask for OBCS in thsice_advection.F (similar to what is |
2405 |
|
done in gad_advection & seaice_advection). |
2406 |
|
o adjoint: |
2407 |
|
bug fix spotted by Gael Forget: |
2408 |
|
seaice_advection and thsice_advection still had |
2409 |
|
legacy CPP options to avoid CS corner updates for adjoint |
2410 |
|
o pkg/seaice: |
2411 |
|
=> Change some of the defaults (2011/05/29): |
2412 |
|
- change SEAICEuseFluxForm default (from False to True) |
2413 |
|
- change DIFF1 default (from 0.004 m/s to 0. m/s) |
2414 |
|
And print warnings if DIFF1 is not set in data.seaice and centered |
2415 |
|
avection scheme is used without any diffusion. |
2416 |
|
also: |
2417 |
|
- fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F; |
2418 |
|
- set SEAICEdiffKh[] default in the same way as SEAICEadvSch[] |
2419 |
|
- stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any |
2420 |
|
other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with |
2421 |
|
#undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE. |
2422 |
|
update results of test exp.: |
2423 |
|
lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20) |
2424 |
|
output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200) |
2425 |
|
output_adm.noseaicedyn (SEAICEuseFluxForm=T) |
2426 |
|
offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T) |
2427 |
|
seaice_obcs: output (SEAICEuseFluxForm=T) |
2428 |
|
and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004) |
2429 |
|
for standard fwd & AD lab_sea tests (to keep the same output). |
2430 |
|
o pkg/seaice/seaice_growth.F: |
2431 |
|
- use Ian Fenty's capping formulas for actual ice |
2432 |
|
thickness thoughout EVOLUTION branch. |
2433 |
|
- put treatment pathological case #2) in CPP brackets |
2434 |
|
(ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). |
2435 |
|
- update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. |
2436 |
|
o pkg/seaice: |
2437 |
|
- seaice_diffusion.F : remove the min(DX,DY) factor permanently; |
2438 |
|
pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter; |
2439 |
|
also pass fac as a param, which can be 1. (to update the tendency |
2440 |
|
field) or the time step (to update the field itself). |
2441 |
|
- seaice_advdiff.F: for multidim, call seaice_diffusion with |
2442 |
|
e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call |
2443 |
|
seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. |
2444 |
|
- SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : |
2445 |
|
hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
2446 |
|
o pkg/seaice: |
2447 |
|
diffusion with centered advection scheme (diffus.F & advect.F): |
2448 |
|
- simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) |
2449 |
|
to just compute the laplacian of input-field. |
2450 |
|
- unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call. |
2451 |
|
- fix flux-form version in diffus.F to conserve tracer. |
2452 |
|
update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects |
2453 |
|
machine truncation) and lab_sea.salt_plume (conservative flux-form modif) |
2454 |
|
|
2455 |
|
checkpoint62y (2011/05/26) |
2456 |
|
o pkg/seaice: |
2457 |
|
- seaice_growth.F : in EVOLUTION branch, always include |
2458 |
|
a_QSWbyATM_cover in qnet (as it should be). |
2459 |
|
- verification/global_ocean.cs32x15 : update results accordingly |
2460 |
|
(output.seaice.txt output_adm.seaice.txt). |
2461 |
|
o pkg/seaice + obcs: |
2462 |
|
- use maskInW & maskInS in multi-dim advection and biharmonic diffusion: |
2463 |
|
equivalent of assuming no tracer gradient outside the OB region. |
2464 |
|
update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion) |
2465 |
|
- remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed |
2466 |
|
after changes above); |
2467 |
|
- obcs+seaice cleaning: apply seaice-tracer OB values to tracer field |
2468 |
|
only at OB location (instead of over a band of OLx width). |
2469 |
|
o pkg/seaice: |
2470 |
|
- fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F |
2471 |
|
(dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid) |
2472 |
|
o pkg/obcs: |
2473 |
|
- split header file "OBCS.h" into 4 separated files: |
2474 |
|
OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h |
2475 |
|
Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h |
2476 |
|
(contain no conditional statement which depends on OBCS options). |
2477 |
|
- move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h) |
2478 |
|
to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h). |
2479 |
|
o ctrl, cost, grdchk & autodiff pkgs: |
2480 |
|
- make options file more standard (like other {PKG}_OPTIONS.h file but |
2481 |
|
with AD_CONFIG.h); clean-up some of the included header files. |
2482 |
|
o pkg/obcs: |
2483 |
|
- do not mask tracer when applying OB (tracer == 0 could generate problems) |
2484 |
|
- apply tracer OB values to tracer field only at OB location (instead of |
2485 |
|
over a band of OLx width) |
2486 |
|
- clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R) |
2487 |
|
- remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove |
2488 |
|
obcs_apply_tloc.F & obcs_apply_sloc.F |
2489 |
|
o obcs in model/src: |
2490 |
|
- call OBCS_APPLY_W only if NonHydrostatic. |
2491 |
|
- call OBCS_APPLY_ETA only if NonLinFreeSurf. |
2492 |
|
- reset dEtaHdt and wVel to zero outside OB interior region ; |
2493 |
|
- leave tracer unchanged outside OB interior region: This has no effect |
2494 |
|
on the solution but just to prevent unrealistic tracer value outside OB. |
2495 |
|
- zero out velocity outside OB interior region: This has no effect on |
2496 |
|
the solution but just to prevent unrealistic velocity outside OB. |
2497 |
|
o obcs and non-lin free-surf: |
2498 |
|
move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F |
2499 |
|
and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F |
2500 |
|
+ add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR: |
2501 |
|
this fixes missing EXCH + get consistent eta OB value (+ fix restart). |
2502 |
|
update results of test-exp. exp4(nlfs). |
2503 |
|
o exp4 (nlfs) test-exp: |
2504 |
|
use OBC for Eta at Western & Eastern OB (to test prescribing Eta |
2505 |
|
with NonLin-FreeSurf); update output.nlfs.txt |
2506 |
|
o obcs and 2d/3d solver norm: |
2507 |
|
use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB |
2508 |
|
and outside OB interior region (will allow to place OB further inside the |
2509 |
|
domain). Depending on the domain, can affects cg2d-Norm (previous |
2510 |
|
cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl, |
2511 |
|
and cg3d-Norm (previous Norm was computed before canceling OB terms), |
2512 |
|
e.g. in tutorial_plume_on_slope. |
2513 |
|
- update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope. |
2514 |
|
o pkg rbcs: |
2515 |
|
- split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h |
2516 |
|
- add capability to apply relaxation to horizontal velocity uVel & vVel. |
2517 |
|
o pkg/grdchk: add gradient check for control variable xx_shifwflx |
2518 |
|
o pkg/shelfice/shelfice_init_fixed.F |
2519 |
|
fix CPP-flag combinations |
2520 |
|
o pkg/seaice: Merge iceage code of Pierre Rampal |
2521 |
|
* update/change/correct ice age calculations |
2522 |
|
* add age updates for pathological cases |
2523 |
|
Probably needs more testing... |
2524 |
|
|
2525 |
|
checkpoint62x (2011/05/13) |
2526 |
|
o pkg/mom_vecinv: |
2527 |
|
high-order vorticity scheme: use interior masks (maskInW & S) |
2528 |
|
to zero-out (outside OB) gradient of vorticity. |
2529 |
|
o verification exp.: |
2530 |
|
turn on "useEnergyConservingCoriolis" (better discretisation) in exp. |
2531 |
|
hs94.128x64x5 and seaice_obcs ; update results. |
2532 |
|
o pkg/obcs: |
2533 |
|
fix bug in OBeta for YZ sections in obcs_exf_load.F |
2534 |
|
o pkg/ctrl, pkg/shelfice, and optim: |
2535 |
|
- add new control variable xx_shifwflx (fresh water flux underneath ice |
2536 |
|
shelves). This is almost as tedious as obcs-ctrl, because the |
2537 |
|
variables needs its own mask. |
2538 |
|
- add a cost function term that penalizes the deviation of xx_shifwflx |
2539 |
|
from the first guess (zero) in analogy to other control variables |
2540 |
|
o pkg/shelfice: |
2541 |
|
- start basic adjoint |
2542 |
|
o pkg/ctrl: |
2543 |
|
- remove extra 2D field "for good measure" when initializing in |
2544 |
|
ctrl_set_globfld_[xy/xz/yz].F |
2545 |
|
- replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec |
2546 |
|
- improve error messages in ctrl_set_unpack_* |
2547 |
|
o OBC implementation in momentum: |
2548 |
|
use interior masks (maskInC,W & S) in momentum S/R: |
2549 |
|
- multiply divergence, tension and some del^i.u or del^j.v by maskInC |
2550 |
|
- multiply del2u,del2v by maskInW/S (biharmonic viscosity) |
2551 |
|
- multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) |
2552 |
|
- multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) |
2553 |
|
Motivation: fix/clean implementation of OBC with biharmonic-viscosity |
2554 |
|
(and also with Leith/Smagorinsky harmonic-viscosity). |
2555 |
|
Update output of experiment dome and exp4 (+nlfs). |
2556 |
|
o exp4 test-exp: |
2557 |
|
- turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) |
2558 |
|
and prescribe time-varying OB (without pkg/exf) for zonal-velocity |
2559 |
|
at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
2560 |
|
time-varying OB at Western-side for wVel (NonHyd); update output. |
2561 |
|
- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
2562 |
|
and biharmonic-viscosity ; also use prescribed time varying OB. |
2563 |
|
o pkg/obcs: |
2564 |
|
fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
2565 |
|
o model/src: |
2566 |
|
- fix startTime setting when baseTime<>0 & nIter0=0 are specified ; |
2567 |
|
- initialise startTime & nIter0 with unlikely values: allows to set one |
2568 |
|
from the other without ambiguity. |
2569 |
|
o seaice_obcs test-exp.: |
2570 |
|
add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output. |
2571 |
|
o pkg/obcs: |
2572 |
|
- remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: |
2573 |
|
no longer needed with maskInC,W,S in pkg/generic_advdiff. |
2574 |
|
o pkg/seaice: |
2575 |
|
- retired SEAICE_SALINITY and SEAICE_salinity in favor of |
2576 |
|
SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively. |
2577 |
|
- fixed bug in the initialization of sea ice salinity variable HSALT |
2578 |
|
in seaice_init_varia.F (removed dependence on ICE2WATR) |
2579 |
|
o fizhi-cs test exp.: |
2580 |
|
switch reference output convention for these 2 non-standard test-exp, |
2581 |
|
from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5) |
2582 |
|
to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11) |
2583 |
|
reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran |
2584 |
|
o model/inc: |
2585 |
|
- change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4") |
2586 |
|
of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS) |
2587 |
|
o pkg/seaice: |
2588 |
|
- fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY |
2589 |
|
o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15 |
2590 |
|
- updated output*.txt files due to bug fixes in salt, saltPlumeFlux, |
2591 |
|
and initial HSALT |
2592 |
|
|
2593 |
|
checkpoint62w (2011/04/26) |
2594 |
|
o pkg/mom_fluxform: |
2595 |
|
- fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf. |
2596 |
|
- use parameter "sideDragFactor" in no-slip BC side-drag part. |
2597 |
|
- update output of exp. global_ocean.90x40x15 |
2598 |
|
o pkg/mom_vecinv: |
2599 |
|
mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform) |
2600 |
|
o update seaice exp.: |
2601 |
|
use more consistent parameter values (remove "backward compatability only": |
2602 |
|
ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh) |
2603 |
|
related to thermodynamics seaice. Update output (fwd+AD) of exp.: |
2604 |
|
1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs |
2605 |
|
o update test-exp global_ocean.90x40x15: |
2606 |
|
o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis). |
2607 |
|
o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.) |
2608 |
|
o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params) |
2609 |
|
o turn on zStar & viscA4 in standard set-up (dir input/) |
2610 |
|
and update output files: output.txt & output.dwnslp.txt |
2611 |
|
o new AD-test experiment: obcs_ctrl |
2612 |
|
(From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector. |
2613 |
|
o pkg/dic: |
2614 |
|
fix two bugs in handling water vapour pressure in carbonate chemistry |
2615 |
|
and air-sea fluxes. Found by Val Bennington and Galen McKinley |
2616 |
|
(add DIC Option = WATERVAP_BUG to recover old results) |
2617 |
|
update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline |
2618 |
|
o adding allowInteriorFreezing option to check for water below freezing point |
2619 |
|
at depth and bring the negative heat anomaly to the surface level |
2620 |
|
o pkgs _fields_load: |
2621 |
|
- extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs) |
2622 |
|
- use new S/R GET_PERIODIC_INTERVAL in pkgs: |
2623 |
|
bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and |
2624 |
|
rbcs to get interpolation weights and time reccord number. |
2625 |
|
- fix multi-threading in aim_fields_load.F |
2626 |
|
- apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F |
2627 |
|
o external_fields_load: |
2628 |
|
new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear |
2629 |
|
interpolation weights) to use in a periodic time-series ; do not divide by |
2630 |
|
time-step to convert to integer: |
2631 |
|
- this fixes case where externForcingPeriod is not multiple of time-step |
2632 |
|
(Thanks to Christopher L. Wolfe) |
2633 |
|
- this fixes case where externForcingPeriod is an odd multiple of time-step |
2634 |
|
(was wrong by half of time-step); update results of tutorial_global_oce_in_p. |
2635 |
|
store index of time-record which is currently loaded: |
2636 |
|
- works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ; |
2637 |
|
- needed for the adjoint but not yet used because of extensive recomputations; |
2638 |
|
(to be fixed soon) |
2639 |
|
|
2640 |
|
checkpoint62v (2011/04/02) |
2641 |
|
o verification/1D_ocean_ice_column added to test Ian Fenty's |
2642 |
|
pkg/seaice_growth.F modifications for improving sea ice code differentiability |
2643 |
|
o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope |
2644 |
|
(new velocity statistics after changing maskInW & maskInS definition) |
2645 |
|
o pkg/generic_advdiff with OBCS: |
2646 |
|
use maksInW & maskInS in advective flux and in biharmonic diffusion calculation: |
2647 |
|
equivalent to assumption of no tracer gradient outside the OB region. |
2648 |
|
This will affect the results if using obcs+biharmonic diffusion. |
2649 |
|
update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc) |
2650 |
|
o pkg/obcs: |
2651 |
|
change definition of maskInW & maskInS: leave OB edges inside (maskIn=1) |
2652 |
|
(e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still |
2653 |
|
in Interior region. No impact on solution but affects Velocity monitor stats. |
2654 |
|
o pkg/ptracers (adjoint) |
2655 |
|
New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate |
2656 |
|
tape file for each tracer |
2657 |
|
o model/inc/src and pkg/autodiff: add parameters that allow to turn |
2658 |
|
of parts of the adjoint code at run time. For now, there are only |
2659 |
|
useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These |
2660 |
|
parameters are set in data.pkg. |
2661 |
|
This is the lazy coward's version of doing this, but still useful for |
2662 |
|
debugging. In order to do it right, everything needs to be moved to |
2663 |
|
pkg/autodiff. |
2664 |
|
o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at |
2665 |
|
the end; this fixes the adjoint balancing code for open boundaries. |
2666 |
|
o pkg/ctrl: |
2667 |
|
- change behavior of xx_${varname}period to be analogous to exf-conventions: |
2668 |
|
xx_${varname}period = 0., means time-independent control part |
2669 |
|
xx_${varname}period = -12., means one-year-periodic monthly control part |
2670 |
|
- introduce helper routine ctrl_init_rec (part of ctrl_init.F) to |
2671 |
|
clean up ctrl_init a little, remove unused variables |
2672 |
|
- ctrl_init: fixed the handling of the start/endrec for obcs-variables |
2673 |
|
- move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec |
2674 |
|
|
2675 |
|
checkpoint62u (2011/03/15) |
2676 |
|
o model/src: |
2677 |
|
- for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in |
2678 |
|
h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ; |
2679 |
|
- in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to |
2680 |
|
INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF. |
2681 |
|
o pkg/ctrl/obcs/ecco: |
2682 |
|
- remove obsolete, unused, and partially broken code: |
2683 |
|
ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within |
2684 |
|
ALLOW_CTRL_OBCS_BALANCE |
2685 |
|
- put a stop statement into ecco/cost_obcsvol.F, but also add |
2686 |
|
cost_obcsvol to ecco_ad_diff.list |
2687 |
|
o pkg/ecco: fix counting cost function contributions for obcs (code |
2688 |
|
by Matt M.) and diffkr for diagnostics |
2689 |
|
o pkg/ecco, pkg/ctrl, pkg/grdchk: |
2690 |
|
add cost penalty terms for initial uvel, vvel, eta controls |
2691 |
|
and I/O for prior error files |
2692 |
|
o pkg/mdsio: |
2693 |
|
move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option |
2694 |
|
(new argument) to check for tiled file in mdsioLocalDir : this fix the |
2695 |
|
restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir. |
2696 |
|
o pkg/ctrl: |
2697 |
|
- ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by |
2698 |
|
ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove |
2699 |
|
unused and superfluous variables |
2700 |
|
- ctrl_get_gen_rec.F: catch the case of xx_genperiod=0. |
2701 |
|
o pkg/ecco |
2702 |
|
- enable adjoint of Stevens OB |
2703 |
|
o pkg/ctrl/ecco/grdchk: |
2704 |
|
- remove global declaration of tmpfldx/yz and tmpfldx/yz2. |
2705 |
|
Fortunately, we do not have any tests for the numerous cpp-flagged |
2706 |
|
option of "obcs as control parameters" so we will never know |
2707 |
|
if this is an improvement (but at least now things compile). |
2708 |
|
- remove an obsolete initialization from ecco_cost_init_barfiles.F |
2709 |
|
- fix some problems within never used ifdefs to make the code compile |
2710 |
|
o pkg/obcs: |
2711 |
|
- Refine Interior mask definition to work with more complex OB (e.g. |
2712 |
|
if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to |
2713 |
|
read in Interior mask from file. Check if Interior mask is consistent |
2714 |
|
with OB list of indices. |
2715 |
|
o pkg/seaice |
2716 |
|
- beginning code for a seaice tracer package, |
2717 |
|
but currently only used for seaice age: SEAICE_AGE |
2718 |
|
SEAICE_num = 4 |
2719 |
|
iTracer = 1: area-weighted ice age |
2720 |
|
= 2: volume-weighted ice age |
2721 |
|
= 3, 4: template for one-year vs. multi-year ice |
2722 |
|
data.seaice has new namelist SEAICE_PARM03 for arrays related to |
2723 |
|
SEAICE_num |
2724 |
|
|
2725 |
|
checkpoint62t (2011/03/05) |
2726 |
|
o pkg/obcs: |
2727 |
|
- obcs_apply_uv.F: change to a 2 steps method, first tangential component; |
2728 |
|
then normal component. This ensures that the normal component is set |
2729 |
|
correctly even when it conficts with tangential setting from an other OB. |
2730 |
|
Affects results of test-experiment seaice_obcs: update the output.txt |
2731 |
|
o pkg/obcs: |
2732 |
|
- add code to monitor statistics of dynamical fields at OB. |
2733 |
|
- take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW : |
2734 |
|
- fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection). |
2735 |
|
- change default: balance the Net inflow through all OB (instead of balancing |
2736 |
|
each OB separately); keep the old method if setting OBC_balanceFacX < 0. |
2737 |
|
- switch on useOBCSbalance in dome experiment: only correct Western OB outflow |
2738 |
|
to match Nortern OB inflow (OBCS_balanceFacN=0). |
2739 |
|
o pkg/seaice: |
2740 |
|
- redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL |
2741 |
|
o pkg/seaice (seaice_growth v 1.113): |
2742 |
|
- reverting seaice_growth to v 1.111 in order to have code with exact bit |
2743 |
|
compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge |
2744 |
|
CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced |
2745 |
|
runtime flag SEAICEareaFormula is kept but is inactive |
2746 |
|
o model/src: |
2747 |
|
- add new param to scale curvilinear grid distance and area when using |
2748 |
|
a different sphere radius from the grid-files. |
2749 |
|
- test/check multi-threads EXCH applied to local variable (cg2d_x) |
2750 |
|
o adjoint: |
2751 |
|
- enable adjoint of Stevens OB |
2752 |
|
- add dummy_in_dynamics to enable extraction of ADJrhoinsitu |
2753 |
|
(a bit delicate because of potentially modified adj. common block structure; |
2754 |
|
current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later) |
2755 |
|
|
2756 |
|
checkpoint62s (2011/02/15) |
2757 |
|
o pkg/seaice (seaice_growth v 1.112): |
2758 |
|
- introduce SEAICEareaFormula run time parameter, which selects the recipe for |
2759 |
|
computing the ice cover tendency from effective thickness tendencies. Include |
2760 |
|
Ian Fenty's formula. |
2761 |
|
- remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using |
2762 |
|
SEAICEareaFormula. |
2763 |
|
- simplify notations for the various d_HEFF/d_AREA terms. |
2764 |
|
o pkg/gmredi: |
2765 |
|
- add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code |
2766 |
|
from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative; |
2767 |
|
add a verification test-run (front_relax.bvp) to test GM_useBVP. |
2768 |
|
o pkg/seaice (seaice_growth v 1.111): |
2769 |
|
- for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's. |
2770 |
|
- the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to |
2771 |
|
also melt ice. |
2772 |
|
o pkg/seaice: |
2773 |
|
- McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty). |
2774 |
|
- can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h |
2775 |
|
o pkg/cheapaml: |
2776 |
|
- from Nico Wienders: New version of this package. |
2777 |
|
o pkg/flt: |
2778 |
|
- add CPP options to prevent floats to re-enter the opposite side of |
2779 |
|
a periodic domain (default: keep periodicity) |
2780 |
|
o pkg/gmredi: |
2781 |
|
- apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners |
2782 |
|
(needed for multi-dim advection). |
2783 |
|
- switch on GM Advective form in global_ocean.cs32x15 and update output.txt |
2784 |
|
o model/src: |
2785 |
|
- fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run. |
2786 |
|
o tutorial_tracer_adjsens |
2787 |
|
- extend to NLFS and replace maskC by hFacC |
2788 |
|
(change reference output accordingly) |
2789 |
|
|
2790 |
|
checkpoint62r (2011/01/24) |
2791 |
|
o testreport: |
2792 |
|
- add option -deloutp (-do) to remove output file after successful run |
2793 |
|
- add option -mfile (-mf) for MPI machile-file and for each test-exp, |
2794 |
|
extract exact list of procs from this file ; adjust COMMAND by |
2795 |
|
replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs. |
2796 |
|
o pkg/ecco: replace old ineffective way of penalizing deviations from |
2797 |
|
first guess (of obcs) with code by Matt Mazloff |
2798 |
|
o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without |
2799 |
|
exf/cal |
2800 |
|
- ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl |
2801 |
|
and handle case of obcs?period == 0 |
2802 |
|
Not affected by these changes: There is still an inconsistency in |
2803 |
|
the computation of start/endrec for the obcs variables for ALLOW_CAL |
2804 |
|
defined (see comment by Menemenlis, 7-Mar-2003) |
2805 |
|
- make S/R ctrl_get_gen_rec return something meaningful even if |
2806 |
|
ALLOW_CAL is not defined |
2807 |
|
- ctrl_getobcs?: simplify code so that it does not need to use |
2808 |
|
S/R exf_swapfields |
2809 |
|
o testreport: |
2810 |
|
allow to test MPI with different number of processors for each experiment: |
2811 |
|
create file "SIZE.h.mpi" in each build dir. |
2812 |
|
Note: update of "-command" argument not yet implemented. |
2813 |
|
o model/src, pkg/autodiff, pkg/ecco, pkg/seaice: |
2814 |
|
alleviate the need for additional 3D tapes when using |
2815 |
|
the non-inear free surface in the adjoint. This is done |
2816 |
|
by adding an 'update' of hfacc etc. to their current |
2817 |
|
value at the beginning of forward_step.F. |
2818 |
|
o pkg/seaice |
2819 |
|
seaice_lsr: move stress-divergence computations out of outer pseudo- |
2820 |
|
timestepping loop |
2821 |
|
o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD' |
2822 |
|
up, so that the calls of the ctrl_* subroutines are really at the end |
2823 |
|
of the routine. |
2824 |
|
o pkg/gmredi: |
2825 |
|
allow to specify a 2-D horizontal map and a 1-D vertical profil |
2826 |
|
as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity. |
2827 |
|
o pkg/seaice: |
2828 |
|
move lsr iterations from seaice_dynsolver to seaice_lsr. |
2829 |
|
o pkg/seaice: |
2830 |
|
reduce memory footprint of seaice mutldim advection tapes, |
2831 |
|
by using a 2D tape independent of the generic_advdiff ones, |
2832 |
|
and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc. |
2833 |
|
|
2834 |
|
checkpoint62q (2010/12/29) |
2835 |
|
o model/src: |
2836 |
|
- check horizontal grid-spacing for unset or zero/negative values. |
2837 |
|
- change AD test hs94.1x64x5 to be truly a 2-D set-up. |
2838 |
|
o pkg/flt: |
2839 |
|
- use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR |
2840 |
|
- precision of input and output files set according to readBinaryPrec |
2841 |
|
and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits. |
2842 |
|
- initial float position from tiled file was not converted to index space |
2843 |
|
(looks like a bug): fixed to make it similar to initial pos. global file. |
2844 |
|
o global_ocean.cs32x15: |
2845 |
|
change SIZE.h of AD set-up to get same tiling as with MPI. |
2846 |
|
Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11) |
2847 |
|
o model/src: |
2848 |
|
add flag to control printing of domain fields (bathymetry, hFac ...) in |
2849 |
|
ini_mask_etc (call to plot_fieds_xy*). |
2850 |
|
o pkg/thsice: |
2851 |
|
if useEXF, some forcing fields are not valid in overlap: fixed by computing |
2852 |
|
over the interior only + apply EXCH at the end (like with SEAICE advection). |
2853 |
|
o pkg/mdsio: |
2854 |
|
- add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer |
2855 |
|
to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS. |
2856 |
|
- change barrier call for safe multi-threads access to 3-D shared buffer. |
2857 |
|
- MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones) |
2858 |
|
- replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and |
2859 |
|
remove the 4 S/R MDS_PASS_WH_R4/8toRL/S. |
2860 |
|
o pkg/flt: |
2861 |
|
- add fourth-order Runge-Kutta integration |
2862 |
|
- add basic exch2 support (only 1 facet supported so far!) |
2863 |
|
o pkg/mdsio+rw: |
2864 |
|
new S/R to read local (or tile independent) vector (read counterpart of |
2865 |
|
mds_writevec_loc, and front-end write_glvec_rl/rs). |
2866 |
|
o global_ocean.cs32x15: additional input_ad.seaice experiment |
2867 |
|
that uses pkg/seaice rather than pkg/thsice. |
2868 |
|
(using multidim advection for seaice) |
2869 |
|
o towards more F95 syntax for array specification in namelist: |
2870 |
|
- change "data.diagnostics" (data.ptracers was changed before checkpoint62p) |
2871 |
|
of all verification experiments. |
2872 |
|
e.g.: line: fields(1,3)='ETAN ','ETANSQ ', |
2873 |
|
was changed to: fields(1:2,3)='ETAN ','ETANSQ ', |
2874 |
|
- finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles |
2875 |
|
o global_ocean.cs32x15: additional input.seaice experiment |
2876 |
|
that uses pkg/seaice rather than pkg/thsice. |
2877 |
|
|
2878 |
|
checkpoint62p (2010/12/17) |
2879 |
|
o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it |
2880 |
|
to THSICE_SIZE.h to avoid conflict with pkg/seaice. |
2881 |
|
o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint. |
2882 |
|
allow for use of multim. advection in seaice adjoint. |
2883 |
|
o pkg/seaice: add diagnostics for snow precipitation and sublimation flux |
2884 |
|
- first attempt to close budgets by taking into account the freshwater |
2885 |
|
flux implied by the sublimation of snow and ice. So far only the |
2886 |
|
volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag |
2887 |
|
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET |
2888 |
|
o eesupp/src: |
2889 |
|
new S/R with new option (NML_EXTENDED_F77) to change array specification |
2890 |
|
from F95 standard to commonly accepted extended F77 form. |
2891 |
|
This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5) |
2892 |
|
and to revert back to the original syntax (with -DNML_EXTENDED_F77) |
2893 |
|
for less tolerant f77 compiler (e.g., pgf77, g77). |
2894 |
|
o globalFiles: |
2895 |
|
commented out in parameter file "data" since it's not safe with MPI |
2896 |
|
(e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much |
2897 |
|
in this case); no longer commented out in restart test (tst_2+2). |
2898 |
|
o add adTapeDir to specify a special directory where adjoint tapes are |
2899 |
|
written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05 |
2900 |
|
and cannot be used together with mdsioLocalDir. |
2901 |
o nesting pkgs: |
o nesting pkgs: |
2902 |
- packages_init_variables : put call to OBCS_INIT_VARIABLES in last position |
- packages_init_variables : put call to OBCS_INIT_VARIABLES in last position |
2903 |
- update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) |
- update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) |