4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
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|
7 |
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o pkg/seaice/seaice_growth: |
8 |
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- catch potential division by zero in ITD code, does not change |
9 |
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verification results |
10 |
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o pkg/ecco: |
11 |
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- retire old codes to the Attic. The calls to retired |
12 |
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functions are left in a commented form in case they |
13 |
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ever need to be re-activated. |
14 |
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- ecco_check.F: issue warning if any old CPP option is |
15 |
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defined that corresponds to retired codes -- then stop. |
16 |
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o pkg/atm_compon_interf: |
17 |
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- change seaice fraction (use for OCN dic surf.flux) stored and sent to |
18 |
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coupler: use last time-step value instead of average over cplSendFrq_iter |
19 |
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time-step, similar to what is done for seaIceMass. |
20 |
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This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up. |
21 |
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o eesupp & genmake2: |
22 |
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- from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME); |
23 |
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<= remove until a fix is found for some ifort version on ia32 machine. |
24 |
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o pkg/seaice/seaice_evp: |
25 |
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- refine residual computation |
26 |
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|
27 |
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checkpoint65q (2015/11/18) |
28 |
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o pkg/seaice/seaice_evp: |
29 |
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- fix residual computations so that they no longer affect the actual |
30 |
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simulation code |
31 |
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- fix seaice_readparams to be able to actually set new parameters |
32 |
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SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little |
33 |
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o model/src: |
34 |
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- fix wrong truncation (single prec) from "FLOAT" function in expressions |
35 |
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like: deltaT*FLOAT(myIter) when myIter is large: |
36 |
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a) replaced by DFLOAT (if not seen by TAF); |
37 |
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b) remove "FLOAT" and use implicit type conversion (if seen by TAF). |
38 |
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o pkg/aim_v23: |
39 |
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- write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading |
40 |
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when pickupSuff is set ; do write rolling pickups + at the end of the run. |
41 |
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o pkg/atm_ocn_coupler + ocn_compon_interf: |
42 |
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- in prep for using pkg/seaice Dyn in coupled set-up, implement sequential |
43 |
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coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ; |
44 |
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add corresponding call in DO_OCEANIC_PHYS. |
45 |
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o coupler pkgs: |
46 |
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Start a new way to set-up optionally-exchanged variables (previously, only |
47 |
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there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler |
48 |
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data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ; |
49 |
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send switch to ATM & OCN compon before reading their own "data.cpl" (so that |
50 |
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compononent param default can be set accordingly). |
51 |
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Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch |
52 |
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but rather applies to a group a fields (going both ways like for DIC) |
53 |
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and corresponds to an option of coupling config. |
54 |
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coupler (pkg/atm_ocn_coupler): |
55 |
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- change parameter file from "data" to "data.cpl" (in cpl_read_params.F), |
56 |
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and read namelist directly (without eessup S/R calls) instead of |
57 |
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in the very un-flexible old way, 1 param per line, in fixed order; |
58 |
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- add error-counter to track errors (e.g., missing "data.cpl") and to stop |
59 |
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cleanly in CPL_CHECK_CPLCONFIG |
60 |
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- add new coupling-exchange selectors (some not yet active) including |
61 |
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cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h |
62 |
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and ocnCpl_exchange_DIC=T in OCNIDS.h); |
63 |
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- add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each |
64 |
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component ; called directly from coupler.F, after comp. registrations; |
65 |
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- rename few variable-ID names (in ATMIDS.h & OCNIDS.h): |
66 |
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atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name -> |
67 |
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-> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName |
68 |
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components (pkg/atm_ & ocn_compon_interf): |
69 |
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- add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding |
70 |
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CPP header file in all pkg source files. |
71 |
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- move checking of comp. configs out of cpl_exch_configs.F into new S/R |
72 |
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ATM/OCN_CHECK_CPLCONFIG; |
73 |
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- add error-counter to track errors (e.g., in "data.cpl") and to stop |
74 |
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cleanly in ATM/OCN_CHECK_CPLCONFIG; |
75 |
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- add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors |
76 |
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from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and |
77 |
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before PACKAGES_READPARMS; |
78 |
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verification/cpl_aim+ocn/: |
79 |
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- update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file |
80 |
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"data.cpl" for coupler (in input_cpl). |
81 |
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o eesupp/inc: |
82 |
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- change the MPI-global-sum default (in CPP_EEOPTIONS.h) to: |
83 |
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#define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F) |
84 |
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to always cumulate tile local-sum in the same order (still uses |
85 |
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MPI_Allreduce like standard code). |
86 |
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- in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files |
87 |
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that are now identical to standard version (in eesupp/inc). |
88 |
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o pkg/shelfice: |
89 |
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- add SHELFICETransCoeffTFile for initializing spatially varying |
90 |
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heat and salt transfer coefficients |
91 |
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o pkg/atm_compon_interf & ocn_compon_interf: |
92 |
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- combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous |
93 |
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S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA |
94 |
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- move bi,bj loops inside S/R OCN_STORE_MY_DATA |
95 |
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o pkg/atm_ocn_coupler: |
96 |
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- initialise to zero ATMVARS.h & OCNVARS.h arrays. |
97 |
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o pkg/rbcs: |
98 |
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- select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows |
99 |
|
to compile with maskLEN=1 when all tracers use the same RBCS-mask. |
100 |
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- add a short report (to STDOUT) about RBCS-mask settings. |
101 |
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|
102 |
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checkpoint65p (2015/10/23) |
103 |
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o pkg/seaice/seaice_evp.F: fix store directives and key computations, since |
104 |
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there is no adjoint test for EVP, we don't know what it does to the adjoint |
105 |
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solution, but at least there are no more recomputation warnings left |
106 |
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o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands |
107 |
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a chance of giving the same results as a fully converged VP (JFNK) solver |
108 |
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o tools/adjoint_options/adjoint_diva: |
109 |
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- fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA |
110 |
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o pkg/streamice: |
111 |
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- spotted bug in streamice_driving_stress using dyG where should have been dxG |
112 |
|
o pkg/exf: |
113 |
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- remove STOP statement that prevented to use wind or (wind-)stress |
114 |
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interpolation for constant-in-time forcing fields (wind/stress period = 0). |
115 |
|
o pkg/seaice: |
116 |
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- replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires |
117 |
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5 additionals 2D fields and 6 new store directives |
118 |
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- change logic in seaice_readparms.F: EVP code can now be turned on in |
119 |
|
various ways, setting SEAICE_deltaTev is no longer required, |
120 |
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alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev, |
121 |
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or SEAICEaEVPcoeff |
122 |
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o pkg/shelfice/shelfice_thermodynamics.F |
123 |
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- redefining uLoc/vLoc to u/v, instead of 2u/v |
124 |
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o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz |
125 |
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- this is an intermediate state of a truely converging EVP that has |
126 |
|
the potential of outperforming implicit VP methods, I do not recommend |
127 |
|
using it yet. |
128 |
|
- for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION |
129 |
|
and all parameters are hardwired |
130 |
|
- for convergence it still requires very smooth regularisations, that means, |
131 |
|
if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is |
132 |
|
different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also |
133 |
|
specific averaging appears to be required, still subject to tuning |
134 |
|
- still needs cleaning and I need to turn parameter into runtime parameters |
135 |
|
- add code to compute and print residuals of iteration, compile with |
136 |
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defining ALLOW_SEAICE_EVP_RESIDUAL to enable it |
137 |
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o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq) |
138 |
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that entered with r1.54 on Sep04, 2015, -> update results |
139 |
|
|
140 |
|
checkpoint65o (2015/09/14) |
141 |
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o pkg/mom_vecinv & mom_common: |
142 |
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- add deep-atmosphere geometry factor in mom_calc_visc.F + in routines |
143 |
|
called from there. |
144 |
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- add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this |
145 |
|
allows to use Vector-Invariant form in deep atmos and anelastic formulation |
146 |
|
o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015) |
147 |
|
and Koenig-Beatty+Holland (2012) |
148 |
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- two new parameters SEAICE_tensilFac and SEAICE_tensilDepth |
149 |
|
- global 2D field tensileStrength, computed in seaice_calc_ice_strength |
150 |
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- requires an extra input argument for S/R seaice_calc_viscosities |
151 |
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- tensileStrength's depth dependence is different from Itkin et al. (2015) |
152 |
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(to be changed and played with, for now exponential) |
153 |
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o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.) |
154 |
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- if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice |
155 |
|
by AREA according to Connelly et al. (2004), JPO. |
156 |
|
- For EVP and the LSR solver, the implicit part of the drag term is |
157 |
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the only non-zero term in the denominator when there is no ice (which |
158 |
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prevented running the model with zero ice-ocean drag). If |
159 |
|
SEAICEscaleSurfStress = .TRUE., this results in a division by zero |
160 |
|
(or zero main diagonals BU/BV) which need to be caught. A practical |
161 |
|
consequence is that for open water, the momentum equation reduce |
162 |
|
to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if |
163 |
|
they happen to be zero, often leading to a non-zero solution over |
164 |
|
open water. |
165 |
|
o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more |
166 |
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efficient EVP method. |
167 |
|
- introduce area-weighted averages for e12 (analogously to |
168 |
|
seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits |
169 |
|
remain, but also changing the order of terms in the previous average |
170 |
|
changed the results as much) -> update experiment |
171 |
|
- add SEAICE_DELTA_SMOOTHREG code |
172 |
|
- disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for |
173 |
|
TEM-code |
174 |
|
- adjust loop bounds so that only required fields are computed |
175 |
|
- add new averaging code for zetaZ/deltaZ (again similar to |
176 |
|
seaice_calc_viscosities.F), inactive by default for now (will change |
177 |
|
results again), but will replace old code eventually |
178 |
|
o eesupp/src: |
179 |
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- add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F) |
180 |
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to always cumulate tile local-sum in the same order |
181 |
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(option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h). |
182 |
|
Still uses MPI_Allreduce (like standard code) but on array of tiles |
183 |
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and should be faster than GLOBAL_SUM_SEND_RECV code. |
184 |
|
- switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV |
185 |
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(defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead. |
186 |
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- add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.: |
187 |
|
aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40, |
188 |
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fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example, |
189 |
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natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre, |
190 |
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tutorial_baroclinic_gyre and tutorial_held_suarez_cs. |
191 |
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|
192 |
|
checkpoint65n (2015/07/29) |
193 |
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o pkg/thsice: |
194 |
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- add a warning when used with pkg/aim but without updating SST |
195 |
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(stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ). |
196 |
|
o pkg/offline: |
197 |
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- change where Offline-Fields are loaded, from load_fields_driver.F to |
198 |
|
directly within FORWARD_STEP, just after updating iter number and time; |
199 |
|
- move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new |
200 |
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S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS; |
201 |
|
These changes allow: |
202 |
|
a) to recover exactly on-line results using deltaToffline=deltaTClock, |
203 |
|
tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2) |
204 |
|
both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous |
205 |
|
time-step, both with GM & KPP files and with recomputing these fields; |
206 |
|
b) no needs to switch on staggerTimeStep anymore; |
207 |
|
c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf. |
208 |
|
- update output of experiment tutorial_dic_adjoffline (only 3 digits left). |
209 |
|
o pkg/offline: |
210 |
|
- change (rarely used) offset-iteration parameter to an offset time (in s): |
211 |
|
can easily recover previous offset-iter effect by setting offset-time |
212 |
|
(offlineTimeOffset) to offset-iter x deltaToffline; |
213 |
|
- do not turn-off Temp & Salinity surface relaxation when using KPP (used |
214 |
|
in KPP as part of surface buoyancy forcing) in offline run. |
215 |
|
- fix ptracers KPP non-local term in the case where KPP is re-computed. |
216 |
|
o OpenAD |
217 |
|
- Adding preliminary ggl90 test to OpenAD verification. |
218 |
|
Config. with ggl90 currently diverges after 64 time steps |
219 |
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so will need more work to become more stable |
220 |
|
- Adding preliminary kpp test to OpenAD verification. |
221 |
|
required small tweakes in kpp_routines.F |
222 |
|
- Merge and update from Krishna Narayanan's contrib area: |
223 |
|
* Add one variable for preliminary OpenAD DIVA |
224 |
|
* Add replacement time-stepping for OpenAD DIVA |
225 |
|
* genmake2 flag -diva (but only for OpenAD; preliminary) |
226 |
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* required modifs for OAD_support |
227 |
|
successful preliminary test for tutorial_global_oce_biogeo/ |
228 |
|
o pkg/seaice: |
229 |
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- initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr |
230 |
|
- add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising |
231 |
|
delta with a smooth function in s/r seaice_calc_viscosity |
232 |
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(no effect on EVP) |
233 |
|
- rename local suffix "sqr" into "sq" for more consistent variable names |
234 |
|
o pkg/seaice: |
235 |
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add new parameter SEAICE_deltaMin that is used ***only*** |
236 |
|
for regularizing Delta (and nothing else, like the parameter |
237 |
|
which is also used for all sorts of things SEAICE_EPS). |
238 |
|
Defaults to SEAICE_EPS for backward compatibility only. |
239 |
|
o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with |
240 |
|
the wrong key by inialising it before use -> fixes a recomputation |
241 |
|
problem but does not fix the gradient |
242 |
|
o pkg/layers: |
243 |
|
- move resetting of flux arrays to outside the iLa loop |
244 |
|
(this caused layers_diapycnal to not work with more than one layer coord.) |
245 |
|
- fix bug in calculation of layers_recip_delta in layers_init_fixed.F |
246 |
|
o pkg/layers: |
247 |
|
- remove from common block 3D layers fields (used to diagnose transport |
248 |
|
in tracer coords) and declare them as local arrays in layers_calc.F |
249 |
|
o pkg/seaice: |
250 |
|
- Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it |
251 |
|
in lab_sea forward experiment (changes results -> updated) |
252 |
|
- update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v |
253 |
|
o pkg/seaice: modify seaice_lsr.F in order to improve the gradient |
254 |
|
computations; for SEAICE_VECTORIZE_LSR |
255 |
|
- move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v) |
256 |
|
sweep to the outside, |
257 |
|
- remove store directives and add "CADJ loop sequential" directives |
258 |
|
in analogy to model/src/solve_tridiagonal.F |
259 |
|
- replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop |
260 |
|
boundaries to yield more readable code. This has also the charming side |
261 |
|
effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without |
262 |
|
SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in |
263 |
|
seaice_lsr_tridiagu/v now requires either of these flags, vectorization |
264 |
|
still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as |
265 |
|
an additional option) |
266 |
|
The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F |
267 |
|
but the adjoint gradients (which are affected by this change) still explode. |
268 |
|
o coupler (atm & ocn _compon_interf): |
269 |
|
- avoid using Exch2 IO mapping if not suitable. |
270 |
|
|
271 |
|
checkpoint65m (2015/06/15) |
272 |
|
o pkg/layers: |
273 |
|
- clean-up old parameters setting (from Sep 2012): |
274 |
|
+ remove old parameters setting from common block (declared locally); |
275 |
|
+ stop if any old parameter is mixed with new parameters; |
276 |
|
+ check for valid or consistent parameter setting (e.g., layers_name) |
277 |
|
- check that layers_bounds for Pot.Density are in the right range; |
278 |
|
this is supposed to catch un-updated setting after recently shifting |
279 |
|
potential density field "prho" by -1000 (now in "sigma" scale). |
280 |
|
o pkg/layers: |
281 |
|
- Added missing call to layers_fill for keeping track of tottend in |
282 |
|
pkg/diagnostics/diagnostics_fill_state.F |
283 |
|
o pkg/layers: |
284 |
|
- added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning |
285 |
|
of diapycnal fluxes |
286 |
|
o pkg/layers: |
287 |
|
- reverted changes to interpolation to previous treatment; there |
288 |
|
was never actually a problem |
289 |
|
o pkg/layers: |
290 |
|
- fix interpolation of layers tracers in the presence of partial cells |
291 |
|
- add lots of new functionality to compute water mass transformation |
292 |
|
(enabled by CPP flag LAYERS_THERMODYNAMICS) |
293 |
|
- add new calls from main code (diags_oceanic_surf_flux.F, |
294 |
|
thermodynamics.F, impldiff.F) and gad to save the necessary fields |
295 |
|
for layers_thermodynamics calculations |
296 |
|
o pkg/ptracers: |
297 |
|
- add capability of stepping a passive tracer forward without advection |
298 |
|
by setting PTRACERS_advScheme to 0. |
299 |
|
o pkg/diagnostics: |
300 |
|
- add few (threads) _BARRIER around any update of "diag_pkgStatus". |
301 |
|
o pkg/layers: |
302 |
|
- shift potential density field "prho" by -1000 for density layer averaging so |
303 |
|
that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000); |
304 |
|
Note that density bin boundaries (layers_bounds in data.layers) have |
305 |
|
to be set accordingly (i.e., shifted, in sigma scale). |
306 |
|
o pkg/layers: |
307 |
|
- fix snap-shot output of layer thickness @ V.pt and output of pot.density |
308 |
|
- fix calculation of layer non-weighted velocity and layer probability |
309 |
|
- add diagnostics for pot.density used for layer averaging |
310 |
|
o pkg/seaice: |
311 |
|
- seaice_calc_viscosity.F: change computation of deltaC**2 to ensure |
312 |
|
positiveness, modify a few comments and improve variable names, |
313 |
|
- the changed computation of deltaC affects most seaice-related |
314 |
|
experiments at the truncation level. |
315 |
|
seaice_itd.thermo is affected by far the most, with |
316 |
|
only 7 digits of agreement remaining; update experiments. |
317 |
|
|
318 |
|
checkpoint65l (2015/05/04) |
319 |
|
o pkg/shelfice: |
320 |
|
- in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set |
321 |
|
factor drKp1 to zero where it is negative (ie. do not use |
322 |
|
SHELFICEBoundaryLayer if hFacC>1) |
323 |
|
- the same for factor drLoc in shelfice_forcing.F |
324 |
|
o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem |
325 |
|
with modules in ptracers, when using testreport option "-small_f" |
326 |
|
o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD) |
327 |
|
- replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1)) |
328 |
o verification/testreport |
o verification/testreport |
329 |
- add new option -small_f |
- add new option -small_f |
330 |
with this option testreport first makes the target small_f (*.f files) |
with this option testreport first makes the target small_f (*.f files) |
331 |
before running make (all). This is useful for explicit inlining when |
before running make (all). This is useful for explicit inlining when |
332 |
all sources need to be full available. |
all sources need to be full available. |
333 |
|
o pkg/exf/exf_interp.F: |
334 |
|
remove previous changes related to reverse (decreasing) input grids latitude |
335 |
|
|
336 |
checkpoint65k (2015/04/01) |
checkpoint65k (2015/04/01) |
337 |
o pkg/ecco: |
o pkg/ecco: |