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 pkg/autodiff : |
8 |
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- introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and |
9 |
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viscFacInAd : run time parameters allowing for adjoint switches |
10 |
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note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F |
11 |
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o pkg/ecco : |
12 |
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- introduce cost_gencost_boxmean.F that computes a box mean |
13 |
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temperature (for use in adjoint sensitivity studies). |
14 |
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o model/src/set_defaults.F : initialize viscFacAdj to 1. |
15 |
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o pkg/mom_common/mom_calc_visc.F : |
16 |
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- ifdef ALLOW_AUTODIFF then include viscFacAdj factor. |
17 |
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o pkg/seaice/seaice_summary.F : |
18 |
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- statement for SEAICEadjMODE now in autodiff_readparms.F |
19 |
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o pkg/seaice |
20 |
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- remove unnecessary u/vTmp from subroutine call of |
21 |
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seaice_lsr_tridiagu/v |
22 |
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- remove some store directives and add new ones in an effort to get |
23 |
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finally rid off the recomputation warnings. This is successful |
24 |
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when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are |
25 |
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defined (i.e. no extensive recomputation warnings left), but there |
26 |
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are still too many recomputations on the solver iteration level |
27 |
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- define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h |
28 |
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- move definition of MPSEUDOTIMESTEPS into TAMC-block in |
29 |
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SEAICE_SIZE.h |
30 |
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- add a store directive in S/R seaice_calc_viscosities |
31 |
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o pkg/seaice (ITD code): |
32 |
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- fix definition of Hlimit for multi-threaded case |
33 |
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- use double precision arithmetic to compute Hlimit: this affects results; |
34 |
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update output of experiment seaice_itd. |
35 |
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o replace content of verification/seaice_itd |
36 |
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- instead of a 1D column use the configuration of offline_exf_seaice |
37 |
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to test the ice thickness distribution code with ridging |
38 |
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- this is a first shot at this experiment |
39 |
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- change of some defaults of ridging parameters SEAICEhStar (from |
40 |
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100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F |
41 |
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and lot of new comments. |
42 |
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|
43 |
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checkpoint64y (2014/06/20) |
44 |
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o pkg/seaice/seaice_reg_ridge.F: |
45 |
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- modify the regularization of very small volumes of ice; only check |
46 |
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total volume HEFF, and do not apply correction to individual ice |
47 |
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classes because that leads to funny patterns in the heat and fw-fluxes |
48 |
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into the ocean. Adjust seaice_itd/results/output.txt |
49 |
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- replace nITD by SEAICE_multDim in loop-ranges |
50 |
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o pkg/exf: |
51 |
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- add code to process the case field period = -12. with UV interpolation. |
52 |
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- move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec |
53 |
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into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F) |
54 |
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o verification/global_with_exf: |
55 |
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- switch all fields period to -12. (was previously untested) in input/data.exf |
56 |
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(but keep secondary test ".yearly" unchanged); update the reference output. |
57 |
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o pkg/cal: |
58 |
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- new calendar type "noLeapYear" for 365 days calendar without any leap year. |
59 |
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o pkg/exf: |
60 |
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- new integer parameter "exf_debugLev" (default set to main model debugLevel) |
61 |
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to replace logical switch "exf_verbose" |
62 |
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- report in STDOUT when loading a new record (if exf_debugLev >= 3) |
63 |
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o pkg/sbo: |
64 |
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- update from Katherine Quinn: evaluate mass directly from density and SSH |
65 |
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(budget using Finite Volume method) instead of from bottom pressure. |
66 |
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- allow testreport to collect few selected SBO output ; tested in exp. |
67 |
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global_ocean.90x40x15 (after updating the results, to include SBO output). |
68 |
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- fix some multi-threading issues (in output part). |
69 |
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o model/src & most packages: |
70 |
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- always call {PKG}_READPARMS even if corresponding use{PKG}=F; |
71 |
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- in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R |
72 |
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PACKAGES_UNUSED_MSG to print a weak warning when parameter file |
73 |
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"data.{pkg}" exist ; and leave the S/R (return) just after. |
74 |
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- more standard LAND pkg interface (land_init_fixed.F, land_check.F). |
75 |
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+ call LAND_READPARMS from packages_readparms.F |
76 |
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o pkg/seaice: |
77 |
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- remove code that resets useThSice in S/R seaice_readparms and |
78 |
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replace it by a warning in S/R seaice_check |
79 |
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- remove parameter MULTDIM, replace with nITD and runtime |
80 |
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parameter SEAICE_multDim (still hard-wired to nITD if |
81 |
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SEAICE_ITD is defined) |
82 |
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|
83 |
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checkpoint64x (2014/05/24) |
84 |
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o verification/lab_sea: |
85 |
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- update adjoint and TLM output following changes to pkg/salt_plume |
86 |
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- un-do the update after putting back local recip_Cp in few places. |
87 |
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o pkg/salt_plume: modifications by An Nguyen: |
88 |
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- add capability to do brine rejection (salt-plume) as function of |
89 |
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volume+tracers (instead of only salinity tracer). |
90 |
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- conserve volume by exchanging volume from each kLev to above to |
91 |
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accommodate in-coming brine volume |
92 |
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- store surface and klev exchanged fraction + volume in 4 new 3-d arrays |
93 |
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- switch KPP surf buoyancy due to brine forcing to 3-d |
94 |
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(3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume) |
95 |
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- add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t |
96 |
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- unrelatedly, also add ad-hoc capability to vary salt_plume scheme |
97 |
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in East/West Arctic. |
98 |
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o pkg/sbo: |
99 |
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- incorporate modifications from Katherine Quinn to enable the use of sbo |
100 |
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pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like |
101 |
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output for future testreport verification (unfinished). |
102 |
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o pkg/atm_phys: |
103 |
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- change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R: |
104 |
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skip the reseting of t_ref & q_ref to initial t & q ; this preserve the |
105 |
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output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics. |
106 |
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o pkg/seaice |
107 |
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seaice_calc_ice_strength.F: modify expression to avoid divisions |
108 |
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(affects truncation) |
109 |
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seaice_do_ridging.F: clean up the insectarium |
110 |
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- fix a bug that was compensated by areaScaling (-> remove areaScaling code) |
111 |
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- added SEAICEsnowFracRidge to redistributed snow (2nd bug) |
112 |
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- set closing/openingRate to zero where no extra iteration is need (3rd bug) |
113 |
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- add some debugging information and error messages (warnings) |
114 |
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o model/src: modifications relatd to atmosphere p*: |
115 |
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- Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F) |
116 |
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- With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead |
117 |
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of vertical profile tRef in geopotential background and anomaly. |
118 |
|
- Acount for true p* correction in theta <-> T conversion in pkg/aim_v23 |
119 |
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and pkg/atm_phys. |
120 |
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- Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40, |
121 |
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fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn. |
122 |
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o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt |
123 |
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o pkg/ptracers: compute ptracer source/sink due to linear free surface. |
124 |
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not used right now, but can be used in BGC packages to fix conservation. |
125 |
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o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by |
126 |
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other packages too. |
127 |
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o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by |
128 |
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SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix) |
129 |
|
o model/src: |
130 |
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- since we have several heat capacity (even in model/src), define "recip_Cp" |
131 |
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as local variable (no longer in common block) to avoid any confusion. |
132 |
|
- add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords). |
133 |
|
o pkg/exf: |
134 |
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- from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local |
135 |
|
air density as function of air Temp, Humidity and atm pressure. |
136 |
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|
137 |
|
checkpoint64w (2014/05/02) |
138 |
|
o verification: |
139 |
|
- update output_adm.txt files for experiment global_ocean.cs32x15 (seaice & |
140 |
|
seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing |
141 |
|
code from seaice_growth.F & seaice_advdiff.F to new ridging routines |
142 |
|
seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient |
143 |
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(down to 8-7 matching digits for global_ocean and 5-6 for lab_sea). |
144 |
|
o model/src: for atmosphere in p* coords: |
145 |
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- store factor rStarFacC**atm_kappa (= pStarFacK) in common block |
146 |
|
- implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F), |
147 |
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but not yet activated. |
148 |
|
o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation: |
149 |
|
- move computation of opnWtrFrac = 1-AREA to before computing ice strength |
150 |
|
- this changes the results (but not for any verification experiment, because |
151 |
|
none tests this), but avoids having an extra field in the restart files |
152 |
|
o pkg/seaice: remove global variable TICE (not needed) |
153 |
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- replace by TICES or local variable where necessary (cost_seaice_test, |
154 |
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seaice_diagnostics_state) |
155 |
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- move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup |
156 |
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- use specific read/write routines for reading and writing individual leves |
157 |
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of a multilevel field |
158 |
|
o pkg/ctrl & model/inc: |
159 |
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- move additional anomaly fields of control vars (related to options: |
160 |
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ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL) |
161 |
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from DYNVARS.h into new header file: CTRL_FIELDS.h |
162 |
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o pkg/seaice: some small modifications to the ridging code |
163 |
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- make fw2ObyRidge a global variable and add the freshwater flux to |
164 |
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seaice_growth |
165 |
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- pass actual thickness from seaice_prepare_ridging, so that it is |
166 |
|
computed only in one place and compute it in the same way as in |
167 |
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seaice_growth |
168 |
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- initialise more fields in seaice_do_ridging that where cause floating |
169 |
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point exceptions over land |
170 |
|
o pkg/seaice: preparations for ridging code and first real ridging code |
171 |
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- move most of "PART 1" of S/R seaice_growth into a new and separate |
172 |
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S/R seaice_reg_ridge that will both regularize the state variable after |
173 |
|
advection call the actual ridging routine; |
174 |
|
- requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG, |
175 |
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d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust; |
176 |
|
- remove ridging code from seaice_advdiff |
177 |
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- clean up remaining part 1 of seaice_growth in an attempt to make it |
178 |
|
more readable (this is probably subjective) |
179 |
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- call seaice_itd_redist once in the initialisation phase to have the initial |
180 |
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conditions in the correct category |
181 |
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- finally: add new ridging routine for ITD code |
182 |
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|
183 |
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checkpoint64v (2014/04/11) |
184 |
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o pkg/ecco: |
185 |
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- add runtime parameters mdt[start,end]date[1,2] |
186 |
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- rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile" |
187 |
|
o pkg/seaice: |
188 |
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- make deltaC a global variable, so that it can be used in ridging code |
189 |
|
- first step towards ridging: introduce new routines that compute |
190 |
|
ice strength based on ridging parameters |
191 |
|
- add diagnostic for HSNOWITD |
192 |
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- add opnWtrFrac as a global variable (required for ridging scheme) |
193 |
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o pkg/salt_plume + pkg/seaice/seaice_growth.F |
194 |
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- add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice |
195 |
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AREA exceeds a threshold (code contributed by I.Fenty in 2011) |
196 |
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o verification/hs94.1x64x5: |
197 |
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- leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h |
198 |
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- do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests. |
199 |
|
o autodiff: |
200 |
|
- Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, |
201 |
|
and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h) |
202 |
|
For now, only in pkgs used in verification/hs94.1x64x5. |
203 |
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- Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage |
204 |
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which are specific to TAF/TAMC). |
205 |
|
- Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD: |
206 |
|
since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad |
207 |
|
is compiled), this simplifies/reduces which *_OPTIONS.h file to include. |
208 |
|
- OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when |
209 |
|
building mitgcmuv_ad (make adAll). |
210 |
|
o pkg/ecco: |
211 |
|
- cost_gencost_seaicev4.F: |
212 |
|
reformulate proxy cost as function of sst and local param SEAICE_freeze |
213 |
|
change cost names from siv4-[sst,vol] to siv4-[deconc,exconc] |
214 |
|
- add stop statement if old names siv4-[sst,vol] are used |
215 |
|
- add snapshots + cost reports for atmospheric longwave |
216 |
|
- remove factor 0.1 in front of wtau[u,v] |
217 |
|
- replace never used flag ALLOW_TMI_COST_CONTRIBUTION with |
218 |
|
ALLOW_TMI_SST_COST_CONTRIBUTION |
219 |
|
o pkg/atm_phys: |
220 |
|
- add some diagnostics for Short-wave and for convection S/R. |
221 |
|
o pkg/seaice/seaice_growth: |
222 |
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- fix a bug in the lateral melt parameterization for SEAICE_ITD |
223 |
|
in seaice_growth; tempFrz needs to be computed inside the i/j-loop |
224 |
|
- rearrange loop order for better vector code in the same code block |
225 |
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- rewrite the floeDiameter formula to have fewer divisions |
226 |
|
- (miraculously) none of this changes the results of seaice_itd |
227 |
|
o pkg/smooth: |
228 |
|
- move param smooth2Ddiffnbt to pkg/ecco |
229 |
|
o pkg/salt_plume: |
230 |
|
- salt_plume_frac.F: |
231 |
|
clean up local param names |
232 |
|
reformulate (1-frac) to frac; original 1-frac was based on swfrac code |
233 |
|
o pkg/rw: |
234 |
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- add RS version of S/R READ_MFLDS_LEV. |
235 |
|
o pkg/streamice: |
236 |
|
- fix the restart test by writing/reading pickup_streamice files. |
237 |
|
o pkg/seaice: |
238 |
|
- refine checks for jfnk-related parameters |
239 |
|
- comment out if statement with SEAICEuseIMEX parameter as long as there |
240 |
|
is no IMEX code to avoid confusion and surprises |
241 |
|
|
242 |
|
checkpoint64u (2014/03/07) |
243 |
|
o verification/MLAdjust: |
244 |
|
- rename secondary test suffix: |
245 |
|
1.leith -> A4FlxF + switch to flux-form & add side-drag |
246 |
|
0.leithD -> AhFlxF + switch to flux-form |
247 |
|
0.smag -> AhVrDv (use Vorticity-Div. visc form) + add side-drag |
248 |
|
0.leith -> AhStTn (use Strain-Tension visc form) + add side-drag |
249 |
|
o pkg/mom_vecinv: |
250 |
|
- remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used |
251 |
|
to be before mom_calc_visc.F) |
252 |
|
- skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed. |
253 |
|
- add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip): |
254 |
|
this is simpler for the adjoint and for diagnostics. |
255 |
|
o model/src + pkg/momentum: |
256 |
|
- add input files for 2-D additional Western and Southern cell-edge wall |
257 |
|
(e.g., to add "thin-wall" where it is =1). |
258 |
|
- fix sideDrag option for thin-walls with Non-Lin Free-Surf |
259 |
|
using 2nd hFacZ that is computed from initial (fix domain) hFac |
260 |
|
- known limitations of thin wall implementation: not yet coded for sigma |
261 |
|
coords; not working with CD-scheme neither. |
262 |
|
o pkg/seaice: |
263 |
|
- rename recently introduced parameters from (wrong name) AB to |
264 |
|
BDF (backward difference time discretisation) |
265 |
|
- retire runtime parameters SEAICEuseAB2, SEAICE_abEps |
266 |
|
o tools/adjoint_options: |
267 |
|
- remove setting of "OPENAD=true" (now set by command line "genmake2 -oad") |
268 |
|
|
269 |
|
checkpoint64t (2014/02/01) |
270 |
|
o pkg/ecco |
271 |
|
- add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and |
272 |
|
runtime logical flag gencost_timevaryweight to read daily sea-ice sigma |
273 |
|
- replace hard-coded record number and period which only work for monthly |
274 |
|
with read-in runtime param that works for other periods (month,day,year) |
275 |
|
o pkg/thsice |
276 |
|
- corrected store directive fixes thsice adjoint gradient checks |
277 |
|
o genmake2 & testreport: |
278 |
|
- add genmake2 option "-oad" to generate a Makefile for OpenAD built and |
279 |
|
in this case, use tools/adjoint_options/adjoint_oad as default AD optfile. |
280 |
|
Update testreport accordingly. No need to set "export OPENAD=true" |
281 |
|
in adjoint_options/adjoint_oad anymore (will be removed later). |
282 |
|
o pkg/shelfice: |
283 |
|
- put T & S shelfice forcing into model surfaceForcing_T,_S (for now, |
284 |
|
only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F |
285 |
|
so that surface forcing applies to k=kSurf if using pkg/shelfice. |
286 |
|
o pkg/ctrl, pkg/grdchk, pkg/ecco: |
287 |
|
- Changes to make GENARR more modular (i.e. invisible if not used) |
288 |
|
o model/src/temp_integrate.F and salt_integrate.F |
289 |
|
- re-include store directives that were removed on Dec 27th. |
290 |
|
o model/src/external_forcing_surf.F |
291 |
|
- add storage directives for EmPmR and PmEpR to avoid recomputation of |
292 |
|
seaice_model in the adjoint that is problematic when seaice_model is |
293 |
|
turned off in the adjoint. The resolved issue dated back to July when |
294 |
|
EXTERNAL_FORCING_SURF call was moved. |
295 |
|
Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly. |
296 |
|
o pkg/exf/exf_check.F |
297 |
|
- fix a small bug again (originally found by Wentao Liu, now found again) |
298 |
|
- streamline error output |
299 |
|
o pkg/streamice and aim_v23: |
300 |
|
- replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that |
301 |
|
Apple's /usr/bin/cpp knows what to do: |
302 |
|
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) |
303 |
|
Target: x86_64-apple-darwin13.0.0 |
304 |
|
|
305 |
|
checkpoint64s (2014/01/05) |
306 |
|
o tools/adjoint_options: |
307 |
|
- switch to fastopt.net TAF server (instead of default fastopt.de) for |
308 |
|
AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default). |
309 |
|
o model/src: |
310 |
|
- remove some unnecessary TAF storage directives in forward_step.F and |
311 |
|
in dynamics.F (note: not always removed by TAF, e.g., double storage |
312 |
|
of kappaRU,kappaRV in former version of dynamics.F). |
313 |
|
o model/src & pkg/ptracers: |
314 |
|
- call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F |
315 |
|
salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F) |
316 |
|
and remove ptracers_dwnslp_apply.F & ptracers_implicit.F |
317 |
|
- call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F) |
318 |
|
- add fZon & fMer as output argument of S/R GAD_CALC_RHS. |
319 |
|
- update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad). |
320 |
|
o useSingleCpuInput separates single-CPU input from single-CPU output; |
321 |
|
for now only implemented for in exf_interp_read.F |
322 |
|
o verification/advect_xy: |
323 |
|
- fix missing EXCH call in local version of ini_salt.F and update output. |
324 |
|
o momentum diagnostics: |
325 |
|
- fix which deltaT is used in Total-Tendency diagnostics. |
326 |
|
- fix typo in diagnostics for momentum tendency from AB. |
327 |
|
o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the |
328 |
|
SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8 |
329 |
|
|
330 |
|
checkpoint64r (2013/12/08) |
331 |
|
o verification/*/results: |
332 |
|
- Update reference output of experiments that were passing with just 13 digits |
333 |
|
(make it easier to detect future changes in results) |
334 |
|
o model/src & pkg/ptracers: |
335 |
|
- move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to |
336 |
|
inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F |
337 |
|
to inside ptracers_integrate.F ; remove ptracers_advection.F |
338 |
|
o coupling interface pkgs: |
339 |
|
[atm_compon_interf, ocn_compon_interf & atm_ocn_coupler] |
340 |
|
- change the config check to test the agreement of Ocean Depth |
341 |
|
with ATM land/sea mask (instead of ATM orography); |
342 |
|
- send to coupler the number of coupler time-steps to do for this run: |
343 |
|
this allows to check for consistency and don't need anymore to be |
344 |
|
specified in parameter file "data"; |
345 |
|
in coupler: |
346 |
|
- check consistency of RunOff map versus Ocean Depth and ATM land/sea mask. |
347 |
|
- improve report to log-file of config setting (pass log-file unit to few S/R) |
348 |
|
o pkg/compon_communic: |
349 |
|
- add coupling send/receive for non-tiled integer vector; |
350 |
|
- add S/R to check and stop if any proc has an error (similar to |
351 |
|
eesupp/src/stop_if_error.F but single thread and across Comm_World). |
352 |
|
o pkg/exch2: |
353 |
|
- in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search |
354 |
|
through list of all tiles my proc owns. |
355 |
|
o model/src: |
356 |
|
- AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying |
357 |
|
from rTrans) to simplify dependencies (no need to store rTrans anymore in |
358 |
|
calling S/R); this affects AD results at machine truncation level: |
359 |
|
update AD-output (TAF) of experiments: 1D_ocean_ice_column, |
360 |
|
bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad). |
361 |
|
o tools/build_options: |
362 |
|
- simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran |
363 |
|
o coupling interface pkgs: |
364 |
|
[compon_communic, atm_compon_interf & ocn_compon_interf] |
365 |
|
- move declaration of local array "ibuf" out of header file "CPLR_SIG.h" |
366 |
|
to each S/R that needs it; remove un-used variables. |
367 |
|
- change component tile registration (cpl_register.F in both compon_interf |
368 |
|
and mitcomponent_tile_register.F) to pass the full list of tiles |
369 |
|
information (including bi,bj) in 1 vector (instead of in a bi,bj matrix). |
370 |
|
- with pkg/exch2: adopt the same convention used for I/O to define mapping |
371 |
|
towards coupler global array (unless W2_useE2ioLayOut=F): |
372 |
|
a) can now use different tiling between atm & ocn comp. |
373 |
|
b) no needs to modify the run-Off map when changing tiling (was needed |
374 |
|
even if using the same tiling between atm & ocn). |
375 |
|
c) will allow to run with blank-tiles in 1 component (e.g., for ocean |
376 |
|
full land tiles); not yet tested. |
377 |
|
- check for valid mapping from comp. tile to coupler global array |
378 |
|
- improve report of tile registration results to log file. |
379 |
|
o pkg/exch2: |
380 |
|
- in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler |
381 |
|
tile-registration (CPL_REGISTER); |
382 |
|
- activate (un-comment) definition and setting of "W2_tileIndex" list to |
383 |
|
store the local bi,bj indices of each tile; |
384 |
|
- also print bi,bj in local report to log file; |
385 |
|
- fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from |
386 |
|
Jun 2009 modif of pkg/exch2). |
387 |
|
o testing on baudelaire: |
388 |
|
- run 2 tests at a time: no significant slow down (since enough cpu) and |
389 |
|
get the full set of test done earlier |
390 |
|
- switch the ifort test to "-devel" ; run the OpenAD test everyday. |
391 |
|
o model/src/thermodynamics.F and routines called from it: |
392 |
|
- pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F & |
393 |
|
gmredi_calc_wflow.F) to update eulerian velocity (input) into residual |
394 |
|
velocity (outp) by adding bolus velocity. |
395 |
|
- model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute |
396 |
|
mass transport from velocity + lateral grid cell area |
397 |
|
- rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER) |
398 |
|
- rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER) |
399 |
|
in thermodynamics.F |
400 |
|
- remove k from thermodynamics.F and move it to temp_integrate.F |
401 |
|
salt_integrate.F and ptracers_integrate.F (now done inside the tracer |
402 |
|
loop). |
403 |
|
- compute locally (in thermodynamics.F) 3-D velocity field that is used to |
404 |
|
advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT, |
405 |
|
PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE, |
406 |
|
GAD_IMPLICIT_R and PTRACERS_IMPLICIT |
407 |
|
- update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column, |
408 |
|
global_ocean.90x40x15, tutorial_global_oce_biogeo and |
409 |
|
tutorial_tracer_adjsens (+ TLM output). |
410 |
|
o tools/OAD_support and (verification/*/) code_oad: |
411 |
|
- OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to |
412 |
|
module conversion ; remove unneeded CPP_EEOPTIONS.h. |
413 |
|
- code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard |
414 |
|
version (closer to model/inc/CPP_OPTIONS.h). |
415 |
|
o model/src: |
416 |
|
- remove parameter "useOldFreezing" from PARAMS.h and push it to the |
417 |
|
retired list of parameters (routine FREEZE has been replace by surface |
418 |
|
freezing (10.yrs ago) and by pkg/frazil (interior freezing). |
419 |
|
o pkg/gmredi: |
420 |
|
- add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from |
421 |
|
velocity (same scheme but affects machine truncation) for GM_AdvForm. |
422 |
|
- update output of FWD experiments: front_relax.bvp, |
423 |
|
global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce. |
424 |
|
|
425 |
|
checkpoint64q (2013/11/17) |
426 |
|
o verification: |
427 |
|
- generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments |
428 |
|
tutorial_global_oce_biogeo and global_ocean.90x40x15. |
429 |
|
- generate new output (growth & melt) for seaice_itd experiment after |
430 |
|
updating the input pickup_seaice files (previously wrong). |
431 |
|
o pkg/cost: |
432 |
|
- define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL |
433 |
|
(instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads: |
434 |
|
o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL |
435 |
|
cannot be applied to var in common block). |
436 |
|
o allows to get results independent of tile-per-proc setting (if using |
437 |
|
slower GLOBAL_SUM_SEND_RECV option). |
438 |
|
- update accordingly: seaice_cost_final.F, shelfice_cost_final.F, |
439 |
|
thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea |
440 |
|
forward gradients: update output). |
441 |
|
- update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL |
442 |
|
S/R and, for most exp., also comment out GLOBAL_SUM_R8. |
443 |
|
o pkg/mom_common: |
444 |
|
- move to pkg/mom_common and model/src (previously in tutorial_deep_convection |
445 |
|
code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and |
446 |
|
viscosity are locally declared in dynmics.F and pass as argument to CALC_GW; |
447 |
|
ensure that all field value that are used are set. |
448 |
|
o tutorial_deep_convection (smag3d): |
449 |
|
- add missing scaling in mom_calc_smag_3d.F; |
450 |
|
- set smag3D_coeff in input.smag3d such that results do not change. |
451 |
|
o pkg/dic: |
452 |
|
- change dic_cost.F to compute cost on each tile first and then apply |
453 |
|
GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments |
454 |
|
tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output. |
455 |
|
- remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea. |
456 |
|
o eesupp/src & pkg/mdsio: |
457 |
|
- remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F |
458 |
|
(from pkg/mdsio) since they are no longer used for tape IO. |
459 |
|
- move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src |
460 |
|
(+ keep a copy in pkg/atm_ocn_coupler). |
461 |
|
o verification/isomip: |
462 |
|
- split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests. |
463 |
|
o tools/build_options: |
464 |
|
- optfile linux_amd64_ifort11, fast (no ieee) case: |
465 |
|
to get a working restart for all experiments, add "-fp-model source" |
466 |
|
to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default). |
467 |
|
|
468 |
|
checkpoint64p (2013/10/20) |
469 |
|
o pkg/autodiff: |
470 |
|
- adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO |
471 |
|
criteria, return to simple (default) tape IO format. |
472 |
|
o pkg/mdsio (+ eesupp/src): |
473 |
|
- rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace |
474 |
|
previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8); |
475 |
|
- fix globalFile and singleCpuIO options using simpler global mapping. |
476 |
|
- new pairs of scatter/gather vector S/R (one for each type, generated from |
477 |
|
template) corresponding to simpler global mapping. |
478 |
|
- adread_write.F: switch to new S/R (but leave old calls commented) and write |
479 |
|
to globalFile when parameter globalFiles is set to True. |
480 |
|
- switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip. |
481 |
|
o pkg/autodiff: |
482 |
|
- adread_adwrite.F: add a hack for RS arrays (when RS=real*4); |
483 |
|
with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is |
484 |
|
missing, just add a STOP if array type do not match. |
485 |
|
o pkg/exf: |
486 |
|
- to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice: |
487 |
|
rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION |
488 |
|
and rename array obsSIce to exf_iceFraction. |
489 |
|
o tutorial_deep_convection: |
490 |
|
- add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe), |
491 |
|
for now all in this exp. code dir. |
492 |
|
- add secondary test using Smag-3D viscosity (keep very low backgroud visc for |
493 |
|
testing) and flux-limter advection scheme for Temp. (no explicit diffusion). |
494 |
|
o eesupp/src: |
495 |
|
- added SINGLE_DISK_IO option because reading of parameter files on |
496 |
|
very large number of processors did not work with existing set-up |
497 |
|
|
498 |
|
checkpoint64o (2013/09/25) |
499 |
|
o pkg/atm_phys & atm_compon_interf: |
500 |
|
- allows for coupling of gray-atmosphere (atm_phys) with ocean. |
501 |
|
o tools/build_options: |
502 |
|
- switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran |
503 |
|
& linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also |
504 |
|
remove CPP setting (was identical to genmake2 default). |
505 |
|
o pkg/gmredi & model/src: Some updating and work done on the residual model. |
506 |
|
- created new file model/src/calc_eddy_stress.F to calculate the eddy stress. |
507 |
|
- fixed up the calculation of the eddy stress and how it is added to the |
508 |
|
external forcing via taueddy_external_forcing.F |
509 |
|
- at the moment, it is very experimental and only works with the variable eddy |
510 |
|
diffusivity calculated in gmredi_k3d.F |
511 |
|
o pkg/seaice/seaice_check.F: add a check to catch the case of specifying |
512 |
|
lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice |
513 |
|
o testreport (& tools/do_tst_2+2): |
514 |
|
- for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}' |
515 |
|
o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11: |
516 |
|
- remove CPP='cpp -traditional -P' (this is genmake2 default) |
517 |
|
- add switch (for big setups) to use 'medium' memory-model (but leave it |
518 |
|
commented out for now). Note: needed with FC 19 to compile big setups. |
519 |
|
o pkg/atm_compon_interf: |
520 |
|
- regroup per field origin (model & pkgs) the coupling storage routines |
521 |
|
(which accumalate in time each coupling field) |
522 |
|
- move bi,bj loops inside atm_store_my_data.F and store also wind-stress; |
523 |
|
update accordingly + simplify aim_do_physics.F |
524 |
|
|
525 |
|
checkpoint64n (2013/08/26) |
526 |
|
o pkg/bbl: |
527 |
|
- update formulation to reduce dispersion of tracer properties in bbl |
528 |
|
- replaced horizontal and vertical transport parameters with velocities |
529 |
|
- changes results for verification/global_with_exf.yearly |
530 |
|
o verification/halfpipe_streamice: |
531 |
|
- change to matrix construction; update both Fwd & AD output. |
532 |
|
o verification/tutorial_tracer_adjsens: |
533 |
|
- OpenAD test: switch to vector-invariant momentum since fluxform with |
534 |
|
rStar causes problems with OpenAD; update output. |
535 |
|
o tools: |
536 |
|
- genmake2: define a common prefix for all temp-file names ; move them |
537 |
|
to local /tmp disk (but would be easy to move them back); |
538 |
|
- xmakedepend: apply the same switch for temp-files. |
539 |
|
o pkg/offline: |
540 |
|
- changes for use with rStar (NLFS): assume that we continue to provide |
541 |
|
UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid |
542 |
|
output files) and apply r* scaling at each time-step (function of the time |
543 |
|
varying Eta field); use normal pickup files (needed for restart with NLFS). |
544 |
|
o adjoint with OpenAD: |
545 |
|
- move OpenAD-specific files from verification/OpenAD/code_oad_all to a new |
546 |
|
package openad. This package has to be compiled for all runs with OpenAD |
547 |
|
instead of specifying code_oad_all as a modification directory. |
548 |
|
- link the fortran templates from tools/OAD_support to the build directory |
549 |
|
for preprocessing to avoid conflicts between different setups compiled |
550 |
|
simultaneously and simplify cleanup. |
551 |
|
o pkg/exf: |
552 |
|
- in exf_getforcing.F: comment out most of the EXCH calls (fields used by |
553 |
|
main model or other pkgs are exchanged in EXF_MAPFIELDS). |
554 |
|
o model/src: |
555 |
|
- do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline |
556 |
|
(similar to do_fields_blocking_exchanges.F). |
557 |
|
o tools/genmake2: |
558 |
|
- remove TAF output src code just before calling staf (when not doing a fresh |
559 |
|
built, will stop if things go wrong with staf). |
560 |
|
- fix target "adobj" (left from TAF version-2 transition) |
561 |
|
o pkg/diagnostics: |
562 |
|
- add a parameter to track the status of pkg/diagnostics activation; |
563 |
|
this replace/extend the use of logical param "settingDiags" (to check |
564 |
|
when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call. |
565 |
|
New S/R to print error message and stop when pkgStatus is not right. |
566 |
|
- to try: add a warning when "data.diagnostics" exist but useDiagnostics=F. |
567 |
|
|
568 |
|
checkpoint64m (2013/08/13) |
569 |
|
o model/inc: |
570 |
|
- move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from |
571 |
|
8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) |
572 |
|
o pkg/kpp & aim_v23: |
573 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
574 |
o pkg/seaice: |
o pkg/seaice: |
575 |
- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
576 |
undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
577 |
- only call DIAGNOSTICS_FILL when useDiagnostics=T. |
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
578 |
|
o eesupp/src: |
579 |
|
- fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) |
580 |
|
in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). |
581 |
o switch to TAF version-2: |
o switch to TAF version-2: |
582 |
- add flow directives to "freeze" naming convention for ad-routines that |
- add flow directives to "freeze" naming convention for ad-routines that |
583 |
are used in I/O routines of adjoint state and associated common blocks |
are used in I/O routines of adjoint state and associated common blocks |