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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
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7 |
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o model/src/ini_curvilinear_grid.F: |
8 |
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compute angleSin/CosC when they are not read from a file |
9 |
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o pkg/seaice: |
10 |
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add pseudo time stepping for LSOR |
11 |
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o pkg/exch2: |
12 |
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temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW |
13 |
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o pkg/seaice: |
14 |
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Adding separate sea ice albedo and drag coefficients in Southern Ocean |
15 |
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from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h |
16 |
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o SingleCpuIO: |
17 |
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fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used. |
18 |
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o pkg/seaice: |
19 |
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put exchanged variable in (local) common block for MPI+Multi-Threads |
20 |
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to work (necessary with exch1, and for now with exch2 too). |
21 |
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o verification: to get more experiments tested with mpi, mth and mpi+mth, |
22 |
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change tiling of: |
23 |
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aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15, |
24 |
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hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope |
25 |
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update output of exp: |
26 |
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exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5), |
27 |
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tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod) |
28 |
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+ ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU |
29 |
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(note: output.txt generated on faulks using only 1 tile) |
30 |
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o eesupp & mdsio (SingleCpuIO): |
31 |
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- remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time |
32 |
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parameter "W2_useE2ioLayOut" (read from file "data.exch2"). |
33 |
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Note: was not effective for globalFile & useSingleCpuIO=F; now fixed. |
34 |
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- move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc). |
35 |
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- fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same |
36 |
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gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array). |
37 |
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o pkg/exch2: |
38 |
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- new code to set-up W2-Exch2 topology (replace matlab-topology-generator): |
39 |
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read parameter file "data.exch2" if it exists; otherwise try default regular |
40 |
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cube without blank-tile; new header file "W2_EXCH2_SIZE.h"; |
41 |
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- update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible |
42 |
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with new code (not to be used, just as a backup solution). |
43 |
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- add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2" |
44 |
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in utils/exch2/input. |
45 |
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|
46 |
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checkpoint61n |
47 |
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o eesupp & mdsio (SingleCpuIO): |
48 |
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- move mapping to global io-buffer inside gather_2d/scater_2d: this save |
49 |
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memory (1 less 2D global RL array); skip 1 buffer copy; and only send/ |
50 |
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receive real*4 array (instead of real*8) to read/write 32.bit files. |
51 |
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(new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S |
52 |
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and remove new mapping S/R) |
53 |
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o pkg/mdsio: in preparation for topology-generator within pkg/exch2: |
54 |
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- Change declaration of SingleCpuIO buffer, reduced to only 1 dim.: |
55 |
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xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h |
56 |
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when using exch2. Add S/R to map global io-buffer to global model array. |
57 |
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- uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt. |
58 |
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|
59 |
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checkpoint61m |
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o write_utils : change WRITE_1D_R8 to WRITE_1D_RL |
61 |
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and add 3 other S/R for other types (R4,R8,RS). |
62 |
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Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument. |
63 |
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o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros): |
64 |
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- ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ; |
65 |
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- reduce number of macro definitions (keep only those which are used); |
66 |
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can always call directly the corrresponding S/R if needed. |
67 |
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- everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix |
68 |
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_R4/_R8 to _RS/_RL when applied to _RS/_RL variable. |
69 |
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Fixed wrong type of arg in: |
70 |
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atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F |
71 |
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ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F |
72 |
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To fix: global_sum of var in common block is wrong (multi-threaded) in: |
73 |
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dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F |
74 |
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To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops) |
75 |
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o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd |
76 |
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"nlfs" mpi test is going to stop when checking for unconnected tile egdes. |
77 |
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o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error |
78 |
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o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile |
79 |
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edges are closed (zero depth); might happen with "blank tiles"; |
80 |
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for now, disabled if using OBCS. |
81 |
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o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi": |
82 |
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link *_mpi files from "MODS" dir) to return to a strait-forward behavior. |
83 |
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o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D) |
84 |
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to reduce length of 1.D array print in STDOUT. |
85 |
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o adjustment.cs-32x32x1: changed to oceanic test with 1 continent |
86 |
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+ use 48 tiles (16x8): this will allow to test "blank tiles". |
87 |
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o start to test MPI + multi-threaded (change testreport to skip tests |
88 |
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where number of tiles do not match). |
89 |
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o genmake2: add option "-omp" to turn on Open-MP ; |
90 |
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passed to testreport (if using -mth) ; merge few (*+mth) optfiles. |
91 |
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o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them) |
92 |
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and keep the original tile numbering. Note: compatible with old |
93 |
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W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files. |
94 |
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|
95 |
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checkpoint61l |
96 |
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o Overlaps had been forgotten in calculating ijk keys : fixed |
97 |
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o fix cyrus makedepend for gcc 4.4 |
98 |
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o experiment fizhi-cs-aqualev20: |
99 |
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switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE) |
100 |
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and generate new output. Note: new output is much closer to the old |
101 |
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one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from |
102 |
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the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007. |
103 |
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o pkg/fizhi: |
104 |
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- change to avoid indices going deliberately over array-bounds |
105 |
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- remove unnecessary MPI stuff |
106 |
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- perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY" |
107 |
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- new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE: |
108 |
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does not go over array-bounds and therefore returns reliable output. |
109 |
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- in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls: |
110 |
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this S/R has 4 output arguments, which are used inside "get_alarm"; |
111 |
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when it is called with the same variable "ndum" in place of several |
112 |
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output arguments, this produces weird side effect inside "get_alarm" |
113 |
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(e.g., datein=dates(n) is overwritten by timein=times(n) since both |
114 |
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datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum" |
115 |
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address) and produces error. |
116 |
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o tools/gemake2: (March 27-29 2009) |
117 |
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with option "-mpi": link *_mpi files from "MODS" dir (this is what |
118 |
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testreport does). |
119 |
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o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output |
120 |
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o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F: |
121 |
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update lab_sea.lsr & lab_sea.salt_plume results |
122 |
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o pkg/seaice: |
123 |
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Major overhaul of the LSOR solver: change discretization from original |
124 |
|
finite differences to finite volume. The old routine is still in the |
125 |
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file seaice_lsr.F and can be turned on with the CPP-flag |
126 |
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SEAICE_OLD_AND_BAD_DISCRETIZATION |
127 |
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Along with this change, the discretization of the strain rates is changed. |
128 |
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The same flag turns on the old discretization in seaice_calc_strainrates.F |
129 |
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All verification experiments with seaice are affected (except for |
130 |
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seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old |
131 |
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results by setting the above flag. |
132 |
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Further changes involve changes in defaults: |
133 |
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- ALLOW_FLOODING is defined and turned on by default |
134 |
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- SEAICEadvSnow = .true. is now the default |
135 |
|
- SEAICEadvSalt = .true. is now the default |
136 |
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- SEAICEadvAge = .true. is now the default |
137 |
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- SEAICE_clipVelocities = .false. is now the default |
138 |
|
(as per J. Zhang's recommendation) |
139 |
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- B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE |
140 |
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is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS |
141 |
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- seaice_growth: replace computation of UG by a simple copy from wspeed |
142 |
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|
143 |
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checkpoint61k |
144 |
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o pkg/seaice: a few bug fixes mostly concerning the metric terms: |
145 |
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seaice_lsr: fixed a few metric terms, |
146 |
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affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs |
147 |
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add more debugging diagnostics |
148 |
|
seaice_evp: removed superfluous many metric terms of FV discretization |
149 |
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of stress divergence |
150 |
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affects lab_sea, lab_sea.hb87 |
151 |
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seaice_ocean_stress: removed superfluous many metric terms of FV discretization |
152 |
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of stress divergence for non-evp solver |
153 |
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(this part is not tested anywhere) |
154 |
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seaice_calc_strainrates: fixed a bug in no-slip boundary conditions, |
155 |
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they were effectively only half slip |
156 |
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affects lab_sea.hb87 |
157 |
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updated all relevant verification experiments (except lab_sea//output_adm.txt |
158 |
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which was left over, but fails at level 7 & 6) |
159 |
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|
160 |
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checkpoint61j |
161 |
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o pkg/seaice: turn a few hard wired parameters into run time parameters |
162 |
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o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model |
163 |
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time in seconds as promised by the usints in seaice_monitor and exf_monitor |
164 |
|
o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids |
165 |
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that are not cubed-sphere grids |
166 |
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o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR |
167 |
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o pkg/ctrl: |
168 |
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fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low) |
169 |
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o non-hydrostatic (calc_gw.F): |
170 |
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fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec |
171 |
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update output of exp. global_ocean.cs32x15.viscA4 |
172 |
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o remove backward compatibility for thetaMin,phiMin |
173 |
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(replaced by xgOrigin,ygOrigin on Jan 27, 2009) |
174 |
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o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the |
175 |
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interpolated wind field not only for curvilineargrid=.true., but also |
176 |
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for a rotated grid (rotateGrid=.true.) |
177 |
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o pkg/exf: add capability to bypass interpolation for runoff |
178 |
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by setting yet another CPP-flag |
179 |
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o eesupp/src, B-grid exchange: |
180 |
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add simple (6 tiles, non MPI) CS exch + standard interface S/R. |
181 |
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o autodiff |
182 |
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new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV |
183 |
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allows to switch to single-prec common blocks; |
184 |
|
corresponding switch occurs in tamc.h, integer isbyte |
185 |
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TAF store directivs "byte" and "kind" seem equivalent; |
186 |
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Most tamc.h have been updated correspondingly. |
187 |
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|
188 |
|
checkpoint61i |
189 |
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o autodiff: |
190 |
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fix autodiff_sore/_restore indices for obcs |
191 |
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(spotted by I. Hoteit, M. Mazloff) |
192 |
|
o pkg/autodiff, pkg/ctrl: |
193 |
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Add flag to reduce all tapelev I/O to single-prec. |
194 |
|
In data.ctrl set |
195 |
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doSinglePrecTapelev = .TRUE. |
196 |
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o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2: |
197 |
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check in hack for SX8 compiler (for dxV, dyU); remove it afterwards. |
198 |
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o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for |
199 |
|
real fresh water flux (not yet) |
200 |
|
o pkg/mdsio & rw: |
201 |
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- add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta) |
202 |
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- add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX. |
203 |
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o pkg/flt: |
204 |
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- replace FLT_INIT by 3-steps standard initialization S/R: readparms, |
205 |
|
init_fixed & ini_varia. |
206 |
|
- clean-up & simplify linear interpolation S/R: |
207 |
|
move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid. |
208 |
|
- fix some indices (mainly vertical index) ; add IMPLICIT NONE. |
209 |
|
- more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R. |
210 |
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- add vert. coordinate & horiz. indices to output files. |
211 |
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- change vertical position in initial condition, from index to depth [m]. |
212 |
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- store horizontal (decimal) indices i,j in common block (instead of coord. x,y) |
213 |
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(easier to get to a curvilinear grid) ; delX,delY no longer used. |
214 |
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o pkg/ggl90: a few modifications: |
215 |
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- fix bottom boundary condition, and interpolation of KappaE |
216 |
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near top and bottom |
217 |
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- use same set of viscosity/diffusivity for TKE/momnetum/tracer |
218 |
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- add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH) |
219 |
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- add a few options for mixing-length upper limit (--> mxlMaxFlag) |
220 |
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o rename thetaMin,phiMin -> xgOrigin,ygOrigin |
221 |
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(maintain temporary backward compatibility, until next checkpoint) |
222 |
|
|
223 |
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checkpoint61h |
224 |
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o pkg/diagnostics with "periodic averaging diagnostics": |
225 |
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fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. |
226 |
|
o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82 |
227 |
|
o pkg/obcs: fix loop ranges for balancing code |
228 |
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o pkg/flt: |
229 |
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- improve criteria for finding which tile owns a float. |
230 |
|
- fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case. |
231 |
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o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg |
232 |
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aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling |
233 |
|
with ocean biogeo) |
234 |
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o pkg/flt: |
235 |
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- do some cleaning and fix the restart ; |
236 |
|
- add output.txt in flt_example/results to get this pkg tested. |
237 |
|
o genmake2: add an EXTENDED_SRC option and flag. |
238 |
|
for now, cannot be turned on on command line (only through genmake_local) |
239 |
|
o pkg/mdsio: read/write vector: |
240 |
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- singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS |
241 |
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- singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR |
242 |
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& MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. |
243 |
|
- affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) |
244 |
|
(drop to 4 digits matching for grad). But this test does not look very |
245 |
|
reliable (was already failling on eddy, fc5, at 6.digits). Update output. |
246 |
|
|
247 |
|
checkpoint61g |
248 |
|
o pkg/flt: |
249 |
|
- move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) |
250 |
|
+ make OPTIONS file more standard. |
251 |
|
- rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) |
252 |
|
- fix _BYTESWAPIO CPP-Flag |
253 |
|
- standard reading of file-parameter "data.flt" |
254 |
|
- fix argument list of S/R FLT_RESTART |
255 |
|
still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F |
256 |
|
o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell |
257 |
|
o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to |
258 |
|
a still unfixed compiler/optimization bug |
259 |
|
|
260 |
|
checkpoint61f |
261 |
|
o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; |
262 |
|
update results of global_ocean.cs32x15.icedyn test. |
263 |
|
o move getcon.F from model/src to pkg/fizhi. |
264 |
|
o pkg/exf: add parameter for extrapolation of temp up to the surface |
265 |
|
and option to prevent negative evap (in bulk_largeyeager04 only). |
266 |
|
o Prather Advection scheme: fix tracer conservation for divergent flow |
267 |
|
(e.g., when using NonLin Free-Surface). |
268 |
|
o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead |
269 |
|
o gmredi (Visbeck-variable-K): |
270 |
|
- add more parameters to Visbeck-variable-K. |
271 |
|
- use a 5 points average for dSigmaR in Visbeck-K calculation |
272 |
|
(more "homogenous": same stencil and same weights as in dSigmaH) |
273 |
|
- update output of ideal_2D_oce experiment. |
274 |
|
o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 |
275 |
|
(#undef REAL4_IS_SLOW) |
276 |
|
- pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 |
277 |
|
coordinate variable |
278 |
|
- pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables |
279 |
|
(surface forcing fields), removes some of the functionality |
280 |
|
- model/src/write_grid.F: write _RS variables as RS-netcdf variables |
281 |
|
- model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but |
282 |
|
probably not all: copy _RS surface flux fields to RL field before |
283 |
|
calling DIAGNOSTICS_FILL |
284 |
|
- model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into |
285 |
|
real*4 (CALL EXCH_*_RS) versions. |
286 |
|
- tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 |
287 |
|
(generate new output). |
288 |
|
|
289 |
|
checkpoint61e |
290 |
|
o gmredi (Visbeck-variable-K): |
291 |
|
- fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h |
292 |
|
- change computation of Visbeck-K where Slope > Smax : |
293 |
|
now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct) |
294 |
|
previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output. |
295 |
|
o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic |
296 |
|
to be the same as with Z-coord. (i.e., m/s & no-units respectively). |
297 |
|
o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc) |
298 |
|
o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz |
299 |
|
does not become too large (to avoid precision problems in implicit-diffusion |
300 |
|
solver); update ideal_2D_oce output. |
301 |
|
o pkg ggl90: |
302 |
|
- in ggl90_cal.F: compute only one set of visc/diff, used to |
303 |
|
step forward TKE/T/S/momentum |
304 |
|
- default value of GGL90viscMax/GGL90diffMax larger and equal (to |
305 |
|
have Prandlt =1) |
306 |
|
o gmredi (fm07): |
307 |
|
- add lower limit on Transition layer thickness + lower limit on 1/lambda |
308 |
|
- allow to set few more params from data.gmredi |
309 |
|
o pkg ggl90: |
310 |
|
- add missing sqrt(2) factor in computation of mixing length |
311 |
|
scale in ggl90_calc.F |
312 |
|
(see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) |
313 |
|
|
314 |
|
checkpoint61d |
315 |
|
o adjoint modifs |
316 |
|
- adapt to new field rhoInSitu |
317 |
|
- allow to revert from StoreDynVars2D, StoreDynVars3D |
318 |
|
to individual fields |
319 |
|
(switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) |
320 |
|
o store 3-D (in-situ) density in commom block (DYNVARS.h) |
321 |
|
- save 1 rho computation. |
322 |
|
- no longer modify T & S inland when using down_slope pkg. |
323 |
|
o gad_som : allow to switch to SOM advection for T & S without corresponding |
324 |
|
pickup files (using new S/R: MDS_CHECK4FILE). |
325 |
|
o keep removing _BEGIN/_END_MASTER between MDSIO S/R call |
326 |
|
(for useSingleCpuIO to work in multi-threaded) |
327 |
|
o pkg/shelfice: |
328 |
|
- disentangle parameters: retire shelfIceFile in data/PARM05 and substitute |
329 |
|
with SHELFICEtopoFile in data.shelfice |
330 |
|
- move code for reading ice shelf topography and modifying hFacC into separate |
331 |
|
subroutines of the shelfice package |
332 |
|
- separate initialisation of "fixed" and "variable" variables |
333 |
|
- kTopC is not (yet) replaced by kSurfC, although this is possible |
334 |
|
o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
335 |
|
o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
336 |
|
and rename: |
337 |
|
ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
338 |
|
ini_reference_state.F --> load_ref_files.F (- set anelastic factors) |
339 |
|
o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) |
340 |
|
|
341 |
|
checkpoint61c |
342 |
|
o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" |
343 |
|
to add mass source/sink of fluid in the interior (3-D generalisation |
344 |
|
of oceanic real-fresh water flux). |
345 |
|
o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) |
346 |
|
o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) |
347 |
|
o new pkg: down_slope |
348 |
|
density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). |
349 |
|
- presently, modify T & S inland (dwnslp_calc_rho.F). |
350 |
|
can be avoided if rho was stored in common bloc and used in calc_phi_hyd. |
351 |
|
- implementation for ocean in P-coords not tested. |
352 |
|
- add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. |
353 |
|
o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) |
354 |
|
(to facilitate conversion of oceanic pkg to p-coordinate). |
355 |
|
o change FIND_RHO to FIND_RHO_2D : |
356 |
|
pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. |
357 |
|
o new pkg: cheapaml |
358 |
|
|
359 |
|
checkpoint61b |
360 |
|
o exch2: |
361 |
|
change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) |
362 |
|
- no longer depend on the order sequence (N,S,E,W). |
363 |
|
- 3rd exchange no longer needed (tested with 24 tiles). |
364 |
|
- same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) |
365 |
|
- exch_UV_A-grid readily available (but not yet tested). |
366 |
|
comment out 3rd exch call and remove copy of V to U at SE & NE face-corners |
367 |
|
(both are no longer needed) in exch_uv: no effect in forward run; but |
368 |
|
get truncation error differences with adjoint exch. |
369 |
|
o exch2: |
370 |
|
- change index-bounds storage (moved from target to local tile, |
371 |
|
more intuitive this way) ; rename/remove some variables. |
372 |
|
- change utils/exch2/matlab-topology-generator & code_mods accordingly. |
373 |
|
|
374 |
|
checkpoint61a |
375 |
|
o exch2/matlab-topology-generator: |
376 |
|
fix bug in index bounds for N-S internal exchange (hard to tell if this |
377 |
|
had any effect on the solution). |
378 |
|
o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf |
379 |
|
is exceeded |
380 |
|
o testreport: modify syntax of awk, so that it works also with |
381 |
|
awk, and not only with nawk and gawk |
382 |
|
|
383 |
|
checkpoint61 |
384 |
|
o autodiff |
385 |
|
Change default for TAF usage by removing argument '-nonew_arg' |
386 |
|
This changes TAF subroutine argument list (ordering of active var.) |
387 |
|
Omission of this flag leads to incompatibility w.r.t. TAMC |
388 |
|
To restore TAMC-compatibility, need following modifs: |
389 |
|
* use adoptfile tools/adjoint_options/adjoint_tamc_compatibility |
390 |
|
* use CPP option #define AUTODIFF_TAMC_COMPATIBILITY |
391 |
|
Tested TAF version is 1.9.22 |
392 |
|
N.B.: exch2 hand-written adjoint code currently not TAMC compatible |
393 |
|
|
394 |
|
checkpoint60 |
395 |
|
--->>> This is the last checkpoint for which generating the adjoint |
396 |
|
--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" |
397 |
|
--->>> by default. |
398 |
|
--->>> Future checkpoints will ommit this flag by default. |
399 |
|
o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. |
400 |
|
o pkg/grdchk: Add gradient check to etan0 perturbations. |
401 |
|
o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). |
402 |
|
o pkg/autodiff: more flexibility in zeroadj. |
403 |
|
model/src: modifying do_oceanic_phys.F accordingly. |
404 |
|
o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. |
405 |
|
o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option |
406 |
|
special setup of gmredi for which the adjoint is stable |
407 |
|
enough for parameter optimization. |
408 |
|
o bridging the gap between eddy stress and GM. |
409 |
|
-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) |
410 |
|
along with a change in CPP option (now ALLOW_EDDYPSI). |
411 |
|
-> when using GM w/ GM_AdvForm: |
412 |
|
The total eddy streamfunction (Psi = eddyPsi + K x Slope) |
413 |
|
is applied either in the tracer Eq. or in momentum Eq. |
414 |
|
depending on data.gmredi (intro. GM_InMomAsStress). |
415 |
|
-> ALLOW_EDDYPSI_CONTROL for estimation purpose. |
416 |
|
The key modifications are in model/src/taueddy_external_forcing.F |
417 |
|
pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F |
418 |
|
|
419 |
|
checkpoint59r |
420 |
|
o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array |
421 |
|
from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); |
422 |
|
fix option to read coriolis(@ cell-corner) from files with CS-grid. |
423 |
|
o pkg/mnc: add some attributes to standard 1D-coordinate variables |
424 |
|
o pkg/diagnostics: enforce missing_value attribute for scalar variables at |
425 |
|
mass points, when using mnc for output |
426 |
|
- add runtime parameter (missing_value, missing_value_int) to override |
427 |
|
default (which is the value of getcon('UNDEF')) |
428 |
|
o pkg/mnc: prepare mnc for the actual use of missing values with the |
429 |
|
diagnostics package: small fix in mnc_cw_readwrite.template and more |
430 |
|
initialisation of never used fields |
431 |
|
- replace mnc_common.h and mnc_id_header.h with corresponding upper case |
432 |
|
versions |
433 |
|
o pkg/thsice/thsice_ini_vars.F added default initial values so that |
434 |
|
thermodynamics sea ice solver does not blow up when some initial fields |
435 |
|
are missing. |
436 |
|
o move from external_forcing_surf.F to ini_forcing.F |
437 |
|
the p-coord. hack consisting in using pLoad to set phi0surf ; |
438 |
|
update output of tutorial_global_oce_in_p (affected @ truncation level). |
439 |
|
o Freshen up a bit hs94.1x64x5, notably: |
440 |
|
remove rotationPeriod and tRef=5*0. (adjoint only), and add |
441 |
|
exactConserv=.TRUE. |
442 |
|
o pkg/generic_advdiff: |
443 |
|
change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
444 |
|
applies to files where Temperature & Salinity 2nd Order moments are used. |
445 |
|
o pkg/ptracers: add second-order moment advection schemes (80 and 81); |
446 |
|
this uses a dynamically allocated internal state data structure |
447 |
|
(#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) |
448 |
|
and requires a fortran 90 compiler |
449 |
|
|
450 |
|
checkpoint59q |
451 |
|
o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) |
452 |
|
(from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) |
453 |
|
o Refresh tutorial_global_oce_biogeo, notably: |
454 |
|
- change bathymetry (put back seamounts in ACC, use hFacs) |
455 |
|
- change EOS (POLY3 --> JMD95Z) |
456 |
|
- use Bryan-Lewis vertical diffusivity |
457 |
|
- use multidimensional advection |
458 |
|
- remove old virtual virtual in dic pkg, now done through ptracer pkg |
459 |
|
- change a couple of parameters in dic pkg |
460 |
|
o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F |
461 |
|
o pkg/obcs: change default to OBCSfixTopo = .true., |
462 |
|
- set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result |
463 |
|
- replace "debugMode" with "debugLevel .GE. debLevB" |
464 |
|
o implementation of TAF directives for gchem,cfc,dic |
465 |
|
o remove "exp5" (replaced by tutorial_deep_convection). |
466 |
|
o pkg/obcs: add code to fix topography gradients normal to open boundaries; |
467 |
|
this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; |
468 |
|
the code can be turned on by setting OBCSfixTopo = .true. in data.obcs |
469 |
|
--> changes results in exp4, seaice_obcs |
470 |
|
o tutorial_deep_convection : |
471 |
|
update the set-up and increase resolution and domain size ; start |
472 |
|
from pseudo initial conditions = output at t=120mn in order to see |
473 |
|
something happening when running testreport. |
474 |
|
o pkg/seaice: add os7mp as an advection scheme |
475 |
|
add check for advection schemes |
476 |
|
add a flag for restoring T and S underneath sea ice |
477 |
|
o pkg/my82: add netcdf-support and diagnostics |
478 |
|
o thsice pkg: |
479 |
|
- Now hsMax limits snow height by turning it into ice following |
480 |
|
flooding scheme (and now conserving energy) |
481 |
|
- Slight rewriting of the formula in thsice_calc_thick.F |
482 |
|
- Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos |
483 |
|
--> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice |
484 |
|
|
485 |
|
checkpoint59p |
486 |
|
o gchem / dic / cfc : |
487 |
|
- add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); |
488 |
|
- add new parameter files: "data.dic" & "data.cfc" ; |
489 |
|
- various re-arrangement in initialisation & header file ; |
490 |
|
- fix tutorial_global_oce_biogeo for multi-threaded test. |
491 |
|
o pkg/dic: test for "pickup_dic" file when restarting ; |
492 |
|
if no pickup-file, can restart with a re-initialised pH (same as it did |
493 |
|
before) providing pickupStrictlyMatch is set to False. |
494 |
|
o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP |
495 |
|
+ fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP |
496 |
|
o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2 |
497 |
|
and staggerTimeStep is off (needed for stability of Internal-wave dynamics). |
498 |
|
o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax, |
499 |
|
& lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers |
500 |
|
(note: not clear to me what lambdaTr1ClimRelax is still used for ...) |
501 |
|
o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which |
502 |
|
scheme to use for vorticty-term ; |
503 |
|
- compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F |
504 |
|
(with default selectVortScheme, return to original discretisation) |
505 |
|
- remove weird combination (e.g.: upwindVorticity & highOrderVorticity) |
506 |
|
o pkg/seaice: add a line to the summary to indicate grid type (B/C) |
507 |
|
o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the |
508 |
|
bottom ; only used with variable horizontal viscosity and non-hydrostatic. |
509 |
|
also fix diagnostics VISCAHW & VISCA4W. |
510 |
|
|
511 |
|
checkpoint59o |
512 |
|
o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). |
513 |
|
o change the loop ordering in most gad_*_adv_x.F to improve vectorization: |
514 |
|
move a few statemens out the main loop into separate loops |
515 |
|
o pkg/shelfice: |
516 |
|
- sort out freshwater flux; convert freshwater fluxes to mass fluxes |
517 |
|
(kg/m^2/s), does not break tests, because in verification/isomip, |
518 |
|
rhoConstFresh=rhoConst (by accident) |
519 |
|
- rearrange computation of tLoc, sLoc, pLoc to make code more efficient |
520 |
|
- move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into |
521 |
|
new file model/src/seawater.F, so that they are available for all pkgs. |
522 |
|
- convert potential temperature into in-situ temperature. This changes the |
523 |
|
isomip tests => update tests |
524 |
|
o add a flag writePickupAtEnd (default=true) to be able to suppress |
525 |
|
writing a pickup at the last timestep |
526 |
|
o tools/mpack-1.6 : |
527 |
|
- disable automake (not working) and autoconf (not needed). |
528 |
|
- update to version 1.6.4 which fix MD5 code on some 64 bits platforms |
529 |
|
also cleaner with much less compilation warnings. |
530 |
|
o pkg/profiles: |
531 |
|
rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg |
532 |
|
(for "less than 32 characters name" compiler requirement) |
533 |
|
o pkg/obcs and pkg/exf: added capability to specify seaice open boundary |
534 |
|
conditions that have a different sampling frequency than S/T/U/V obcs |
535 |
|
o pkg/diagnostics (stats-diags): |
536 |
|
- fix global Min/Max in case 1 processor get only empty tiles |
537 |
|
o genmake2: replace (4 times) |
538 |
|
make genmake_tc_1.o >> genmake_warnings 2>&1 |
539 |
|
with |
540 |
|
COMM="$CC $CFLAGS -c genmake_tc_1.c" |
541 |
|
echo $COMM >> genmake_warnings |
542 |
|
$COMM >> genmake_warnings 2>&1 |
543 |
|
to make genmake2 always see the value of CC as specified in the optfile. |
544 |
|
o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid. |
545 |
|
- add diagnostics for 1srt & 2nd Order moments and sub-grid variance. |
546 |
|
- modify verification advect_cs test to test SOM-advection on CS-grid. |
547 |
|
o pkg/ctrl: |
548 |
|
- Rewrite of ctrl_map_ini_ecco.F, |
549 |
|
introducing a generic routine (ctrl_map_ini_gen.F). |
550 |
|
- Modification of ctrl_bound/adctrl_bound handling control vector bounds. |
551 |
|
|
552 |
|
checkpoint59n |
553 |
|
o pkg/diagnostics: for large number of diagnostics, store diagnostic mate |
554 |
|
number in dedicate array "hdiag": |
555 |
|
- new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST |
556 |
|
with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST. |
557 |
|
- many small changes (integer format) for large number of diagnostics |
558 |
|
- start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with |
559 |
|
a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23. |
560 |
|
o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For |
561 |
|
usingSphericalGrid, this allows to define the rotated grid coordinates |
562 |
|
via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the |
563 |
|
geographical coordinates according to the inverse of the rotation defined |
564 |
|
by the Euler angles, so that Coriolis parameter and online-interpolation by |
565 |
|
exf works with the geographical coordinates on XC/YC/XG/YG. |
566 |
|
Naturally, this feature does not work with all packages, so some |
567 |
|
combinations are prohibited in config_summary (flt, flt_zonal, ecco, |
568 |
|
profiles), because there the coordinates are assumed to be regular |
569 |
|
spherical grid coordinates. |
570 |
|
o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc: |
571 |
|
- introduce isopycnal diffusion coefficient control. |
572 |
|
o tools/adjoint_options: |
573 |
|
- additional control vector components. |
574 |
|
o pkg/mnc: have mnc create marginally meaning full coordinate variables |
575 |
|
(that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 |
576 |
|
o pkg/mypackage: |
577 |
|
- add example of read/write pickup for state-var ; |
578 |
|
- add entry points to the main code for state-vars diags & write-pickup. |
579 |
|
o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year |
580 |
|
transitions for useExfYearlyFields |
581 |
|
- add new subroutine that determines the file to read from for |
582 |
|
use*YearlyFields = .TRUE. and .FALSE. |
583 |
|
- add a verification experiment to global_with_exf that tests |
584 |
|
useExfYearlyFields with USE_EXF_INTERPOLATION defined |
585 |
|
o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in |
586 |
|
analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new |
587 |
|
subroutines (which could be generated from a template, because they are |
588 |
|
almost identical), for now they are included in obcs_prescribe_read.F for |
589 |
|
simplicity |
590 |
|
o pkg/exf: |
591 |
|
- add a little more diagnostic to exf_interp_read (in analogy to |
592 |
|
mds_read_field, can be turned off with debugLevel < debugLevA=1) |
593 |
|
- improve vectorizability of exf_interp for TARGET_NEC_SX, makes code |
594 |
|
ugly but fast by unrolling short inner loops, inserting a unroll=8 |
595 |
|
directive in routine lagran, and splitting a loop and making do while the |
596 |
|
outermost loop (the latter requires the intoduction of index arrays) |
597 |
|
o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice |
598 |
|
o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver |
599 |
|
http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html |
600 |
|
o verification/seaice_obcs: updated for restart test and latest options |
601 |
|
o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different |
602 |
|
ice rheology (so-called truncated ellipse, that gets rid of tensile stress); |
603 |
|
for now this is only available for the C-grid code and also within |
604 |
|
#ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code |
605 |
|
|
606 |
|
checkpoint59m |
607 |
|
o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) |
608 |
|
and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature |
609 |
|
o gad_som : fix flux output (& diagnostics) to have same units as other |
610 |
|
advection scheme fluxes (was previously multiplied by deltaT). |
611 |
|
o added verification/seaice_obcs both to test seaice open boundaries |
612 |
|
and to provide an example matlab scrpt for generating them |
613 |
|
o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume |
614 |
|
o pkg/salt_plume: clean up salt_plume_frac.F to |
615 |
|
remove redundancy in PlumeMethod 1 and 4 |
616 |
|
o pkg/kpp: added saltplume diagnostics |
617 |
o pkg/obcs and pkg/seaice: |
o pkg/obcs and pkg/seaice: |
618 |
- do not set uice and vice to zero when OB*icefile are unspecified |
- do not set uice and vice to zero when OB*icefile are unspecified |
619 |
- OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default |
- OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default |
2540 |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
2541 |
- these scheme operate in a similar manner as KPP (without ghat, of |
- these scheme operate in a similar manner as KPP (without ghat, of |
2542 |
course), however there is only one diffusivity that is used for both |
course), however there is only one diffusivity that is used for both |
2543 |
temperature and salinity (and passive tracers)ç |
temperature and salinity (and passive tracers) |
2544 |
o add offline package |
o add offline package |
2545 |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
2546 |
provided by Stephanie Dutkiewicz |
provided by Stephanie Dutkiewicz |