4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o verification/global_ocean.cs32x15: |
8 |
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- switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new |
9 |
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thsice calling sequence and update "output.icedyn.txt" output file. |
10 |
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o pkg/ptracers: |
11 |
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- from Ryan A.: code to allow to restart a tracer at regular time interval |
12 |
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specifying a reset frequency and a reset-phase (for each tracers). |
13 |
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o pkg/thsice: |
14 |
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- implement new sequence of calls for thsice+seaice: |
15 |
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previously: ice-Dyn,ice-Advect,ice-Thermo(thsice) |
16 |
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new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect |
17 |
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- allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE" |
18 |
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in CPP_OPTIONS.h) to recover old sequence; |
19 |
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- update diagnostics for Intermediate State thsice diagnostics: now filled |
20 |
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just before advection (instead of just after advection in old sequence); |
21 |
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- update output of experiment offline_exf_seaice (standard test); |
22 |
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- in global_ocean.cs32x15 exp., postpone output.icedyn.txt update |
23 |
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by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h |
24 |
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o pkg/aim_v23: |
25 |
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- use tiled array for aim_CO2 and surface wind speed for export to coupler; |
26 |
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- use standard pkg/mdsio routines to read & write CO2 pickup file; |
27 |
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- in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F; |
28 |
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- Implement new sequence of calls for seaice advection (with thsice and |
29 |
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seaice diffusion): do ice advection after ice-Thermodynamic (previously |
30 |
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was done before); change aim_do_physics.F (split the bi,bj loops block); |
31 |
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- use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence; |
32 |
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o pkg/thsice: |
33 |
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- add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case |
34 |
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where just seaice diffusion is used without seaice-dynamics. |
35 |
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|
36 |
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checkpoint64c (2013/01/18) |
37 |
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o pkg/seaice: |
38 |
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- add a parameter JFNKres_tFac that can replace JFNKres_t |
39 |
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(= JFNKres_tFac*JFNKresidual before JFNK solver) |
40 |
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- add a line search option to the JFNK solver |
41 |
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- move update of u/vIce and computation of initial residual into a separate |
42 |
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routine (same file); makes the code a little easier to read (?) |
43 |
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- the line search requires computation of the residual and for some reason |
44 |
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I cannot do the update of u/vIce at the beginning of the Newton loop |
45 |
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without changing the results, so we move computation of the new residual |
46 |
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also to the end of the Newton loop, even without the line search |
47 |
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o pkg/mdsio: |
48 |
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- write missing value (corresponding to undefined array value) to meta files; |
49 |
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skip this if missing value is one (UNSET_RL would be a better value for the |
50 |
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case of undefined missing value but it's current the default missing-value); |
51 |
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Also update mdsio_read_meta.F (reading timeInterval & missing-value). |
52 |
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o pkg/exf & thsice: |
53 |
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- for diagnostics purpose, fill-up and update Qsw array (+ fill the |
54 |
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diagnostics) even when SHORTWAVE_HEATING is #undef; |
55 |
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o verification/cfc_example: |
56 |
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- turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to |
57 |
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illustrate how to use it). |
58 |
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o verification/offline_exf_seaice: |
59 |
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in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing |
60 |
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files to only one time-record. |
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in input.thermo: narrow the 2 bands of low initial ice-concentration near |
62 |
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N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for |
63 |
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snapshot output; same mcPheePiston value as in thsice with |
64 |
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surf-current=0.2m/s. |
65 |
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in input.thsice: similar set-up as in input.thermo (channel with same seaice |
66 |
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initial conditions). |
67 |
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o verification/cfc_example: |
68 |
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- update file "data" with more standard choice (default rotationPeriod, |
69 |
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exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F, |
70 |
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set deltaTFreeSurf to deltaTtracer) and update the output. |
71 |
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o pkg/layers: |
72 |
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- fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC; |
73 |
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- ensure that "layers_bolus" is switched to False when useGMRedi=False. |
74 |
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o verification/offline_exf_seaice: |
75 |
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- set all {field}period to zero for constant-in-time forcing (not tested |
76 |
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anywhere else). |
77 |
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o verification/offline_exf_seaice: |
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- dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice; |
79 |
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- dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice. |
80 |
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o model/src: |
81 |
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- implement Finite-Volume method for (hydrostatic) presure gradient |
82 |
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from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate. |
83 |
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o pkg/seaice: implement EVP* by Lemieux et al. (2012). |
84 |
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- In order to be compatible with the default EVP code, this requires changing |
85 |
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the EVP code around a little; and because any small change immediately |
86 |
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breaks the lab_sea.hb87 verification experiment, the reference output is |
87 |
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updated two times (each time the remaining aggrement was only 2 digits): |
88 |
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- after replacing 1/dt by 1*recip_dt with a precomputed recip_dt |
89 |
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- after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt |
90 |
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The adjoint test lab_sea.evp also needed to be updated. |
91 |
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- Turn on EVP* by setting SEAICE_deltaTevp as before, and setting |
92 |
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SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be |
93 |
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a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps |
94 |
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explicitly with SEAICEnEVPstarSteps (thereby overriding the default of |
95 |
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INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately |
96 |
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kept obscure, because I need to test it a little more. |
97 |
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o pkg/cheapaml: |
98 |
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- fix few incorrect type (_RL/_RS) in subroutine calls. |
99 |
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o pkg/seaice: |
100 |
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- new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays |
101 |
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to _RL vector; this fixes JFNK code when compiling with "-use_r4" option. |
102 |
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o model/src: |
103 |
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- add a warning if using select_rStar=2 with nonlinFreeSurf <> 4; |
104 |
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change (in input_ad*/data) select_rStar from 2 to 1 for AD verification |
105 |
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experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output) |
106 |
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o pkg/cheapaml: |
107 |
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- replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and |
108 |
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update output of experiment cheapAML_box. |
109 |
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- store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity, |
110 |
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and set them only in one place (cheapaml_readparms.F). |
111 |
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- replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI" |
112 |
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- remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms) |
113 |
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and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia). |
114 |
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o model/src/the_main_loop.F: |
115 |
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- fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION. |
116 |
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o pkg/seaice: |
117 |
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- remove legacy branch code. |
118 |
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- retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly. |
119 |
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o verification/*/code*/SEAICE_OPTIONS.h: |
120 |
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- remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY, |
121 |
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SEAICE_CAP_HEFF). |
122 |
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o pkg/cheapaml: |
123 |
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- use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time |
124 |
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to load new forcing fields. |
125 |
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- add missing "_d 0" where it's needed; + some editing (improve indentation). |
126 |
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- remove switch to "-r8" compiler option (no longer needed) in verification |
127 |
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cheapAML_box, keep same output (small trucation error differences). |
128 |
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o verification/offline_exf_seaice: |
129 |
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- add thermodynamics only test. |
130 |
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o verification/cheapAML_box: |
131 |
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- split the domain in 8 (2x4) tiles; add MPI and multi-threaded test; |
132 |
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keep same output (same 14 digits for cg2d). |
133 |
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- switch on "-r8" compiler option (some numerical values are missing |
134 |
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the "_d 0") and update output (only 6 digits for cg2d were preserved). |
135 |
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|
136 |
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checkpoint64b (2012/12/24) |
137 |
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o pkg/cheapaml: |
138 |
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- remove un-used variables (Qnet,EmPmR) from pickup files. |
139 |
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- store tendency of advected variables into cheapaml pickup file |
140 |
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and fix the AB-2 restart. |
141 |
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o verification/offline_exf_seaice and lab_sea adjoint: |
142 |
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- switch to new code (#undef SEAICE_GROWTH_LEGACY). |
143 |
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- switch to 4 time steps in offline, consistent with lab_sea. |
144 |
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- match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice. |
145 |
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- update results after change of experiment seaice. |
146 |
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o pkg/seaice: |
147 |
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- remove option SEAICE_MULTICATEGORY; has been replaced with run-time |
148 |
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parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is |
149 |
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still defined since SEAICE_multDim needs to be set to MULTDIM value (from |
150 |
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SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default. |
151 |
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o model/src: |
152 |
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- add run-time parameter to select CG2D solver minimum-residual solution |
153 |
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(in case of a poor convergence). |
154 |
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o pkg/seaice/seaice_lsr.F |
155 |
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- move calculation of matrix coefficients into new |
156 |
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S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same |
157 |
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file; the main purpose of this change is to be able to reuse the code |
158 |
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in S/R SEAICE_PRECONDITIONER |
159 |
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- modify the computation of the residual so that the mass of sea-ice |
160 |
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is not used twice; this simplifies the calculations, but since |
161 |
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the residual is never used except when LSR_mixIniGuess.ge.4---and this is |
162 |
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not tested in testreport---this does not affect the testreport results. |
163 |
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o verification/seaice_obcs: |
164 |
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- disable SEAICE_GROWTH_LEGACY; reset input files to match those of |
165 |
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verification/lab_sea/input.salt_plume; changes results/output.txt* |
166 |
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o model/src: |
167 |
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- adapt quasi-hydrostatic formulation to work with p or p* coordinate. |
168 |
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o pkg/seaice: |
169 |
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- improve description of parameters in seaice_fgmres.F and start |
170 |
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cleaning up the code |
171 |
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- change name of SCALPROD to SEAICE_SCALPROD and modify meaning of |
172 |
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second argument |
173 |
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- add a metric based on grid cell area to SEAICE_SCALPROD; update |
174 |
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results of offline_exf_seaice.dyn_jfnk |
175 |
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- compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD |
176 |
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o pkg/aim_v23: |
177 |
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- fix an other bug in dissipation heating (grid-cell area was missing). |
178 |
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o model/src + pkg/seaice: |
179 |
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- add global (multi-tile) linear solver for pair of tri-diagonal system |
180 |
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along X and Y lines, respectively for U and V component. |
181 |
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Note: 1) MPI and cube-exchange not yet coded. |
182 |
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2) probably not accurate for poorly conditioned / large size problem. |
183 |
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- add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver; |
184 |
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default: not compiled and not used. |
185 |
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o pkg/seaice: |
186 |
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- first attempt at a multi-threaded fgmres solver for the JFNK solver: |
187 |
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introduce bi/bj loops and use global_sum_tile_rl instead of |
188 |
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mpi_allreduce in seaice_fgmres.F |
189 |
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- improve diagnostics output for fgmres solver (seaice_fgmres.F) |
190 |
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- replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F) |
191 |
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- add a verification experiment for JFNK in offline_exf_seaice |
192 |
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o verification: |
193 |
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- change (for now, only fwd test) offline_exf_seaice experiment: |
194 |
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use a re-entrant channel with idealized coastline (trapezoidal shape) |
195 |
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at southern boundary to explore seaice dynamics and thermodynamics |
196 |
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with simple forcing. Main set-up has dynamics+thermo and SST relaxation; |
197 |
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secondary test (input.thsice) use thermodynamics only with SST relaxation. |
198 |
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- add seaice-dynamics only secondary test using LSR and pkg/thsice advection. |
199 |
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o pkg/exf: |
200 |
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- disable "sstExtrapol" when Nr=1 |
201 |
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o verification: |
202 |
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- add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble) |
203 |
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to test pkg/cheapaml. |
204 |
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o pkg/aim_v23 & pkg/shap_filt: |
205 |
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- fix dissipation heating (erroneous gravity multiplication factor). |
206 |
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o pkg/seaice: |
207 |
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- remove unused field pressPre from jfnk solver |
208 |
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- rename two subroutines in seaice_preconditioner.F |
209 |
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o eesupp/src: |
210 |
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- S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...) |
211 |
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o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again |
212 |
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- remove wrong parts of the rhs and the lhs (were in there |
213 |
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because I did not understand the concept of this preconditioner) |
214 |
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- add an exchange between u- and v-sweep. This increases communication |
215 |
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by a factor of two but improves the convergence of jfnk. Ideally, |
216 |
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one would like the u- and v-sweep to be independent. So far within |
217 |
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undocumented ifdefs |
218 |
|
- reorganize the extra computations for printing the residuals |
219 |
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o tools/genmake2: |
220 |
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- comment out the "mpif.h" include in NetCDF test programm (for MPI built) |
221 |
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since it's not necessary (and was preventing to use MNC in some cases). |
222 |
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|
223 |
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checkpoint64a (2012/11/16) |
224 |
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o pkg/autodiff: |
225 |
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- improve pkg-internal logical parameter switch (inAd/inFwd mode) so that |
226 |
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autodiff_readparms.F no longer depends on calling order (within |
227 |
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packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h): |
228 |
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rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd |
229 |
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and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd. |
230 |
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o pkg/obcs: |
231 |
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- adding tidal velocity forcing capability to obcs |
232 |
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for usage example, see verification/seaice_obcs/input.tides |
233 |
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o pkg/seaice: |
234 |
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- turn the LSR-relaxation parameters WFAU/V into runtime parameters |
235 |
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SEAICE_LSRrelaxU/V |
236 |
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- introduce runtime parameter SEAICEetaZmethod (=0 by default) |
237 |
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o pkg/aim_v23: |
238 |
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- implement heating from friction (bottom friction and stratospheric drag). |
239 |
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o pkg/shap_filt: |
240 |
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- fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from |
241 |
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dissipation but only for Shap_funct=2, active when addFrictionHeating=T. |
242 |
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o model/src: |
243 |
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- move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in |
244 |
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time-constant addMass field from file (addMassFile); |
245 |
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- support for heating due to friction (and Kinetic Energy dissipation): |
246 |
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add option, run-time switch and 3-D field array + support code ; each pkg |
247 |
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or S/R can add heating contribution (if there is a sink of KE); the sum is |
248 |
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accounted for as a Temperature tendency term (EXTERNAL_FORCING_T). |
249 |
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o pkg/seaice: |
250 |
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- complete merge of ITD code into seaice_growth.F |
251 |
|
from MITgcm_contrib/torge/itd/code/ |
252 |
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no verification so far, but Torge Martin tested |
253 |
|
"1-D test case and Beaufort set up; |
254 |
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deliver okay results after 1 model year." |
255 |
|
- complete merge of SEAICE_SIZE.h into all relevant routines |
256 |
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- move computation of eta at Z-points into calc_viscosities |
257 |
|
+ introduce global field etaZ |
258 |
|
+ add different methods for computing etaZ, for now the old |
259 |
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method (simple averages of eta to Z-points) is hardwired |
260 |
|
+ replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual, |
261 |
|
seaice_preconditioner |
262 |
|
- simplify computations for SEAICE_ZETA_SMOOTHREG |
263 |
|
- seaice_preconditioner: |
264 |
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+ replace one remaining press by pressLoc (mistake) |
265 |
|
+ adjust printing of residuals |
266 |
|
- improve I/O of diagnostics of JFNK in seaice_jfnk.F: |
267 |
|
+ add (SEAICE.h) and rename some counters (initiliased in |
268 |
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seaice_init_fixed.F) |
269 |
|
+ add _BEGIN/END_MASTER (myThid) around print statements |
270 |
|
+ print total number of iterations and failures over SEAICE_monFreq |
271 |
|
interval to STDOUT |
272 |
|
- move control over output-messages by fgmres to seaice_jfnk to save |
273 |
|
some operations |
274 |
|
- move resetting initial guess for fgmres outside of seaice_fgmres_driver |
275 |
|
in order to make restarts with sol .ne. zero (fgmres with restarts) |
276 |
|
(seaice_jfnk.F, seaice_fgmres.F) |
277 |
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- seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes |
278 |
|
a serious convergence problem when open boundaries are involved |
279 |
|
o pkg/ggl90: fix computation of control volumes for the case of |
280 |
|
ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes |
281 |
|
up half a grid cell from C-centered to W-centered (pointed out by C. Eden) |
282 |
|
o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC |
283 |
|
o pkg/autodiff |
284 |
|
- Add inAdMode switch for SEAICEuseDYNAMICS: |
285 |
|
SEAICEuseDYNAMICSinAdMode |
286 |
|
(extend logic in ADAUTODIFF_INADMODE_SET) |
287 |
|
o pkg/seaice |
288 |
|
- Step 1 of merging ice-thickness distribution (ITD) code from |
289 |
|
MITgcm_contrib/torge/itd/ (author: Torge Martin) |
290 |
|
The code implements concept laid out in Thorndike et al. (1975); |
291 |
|
code is enabled via CPP flag SEAICE_ITD |
292 |
|
nITD (in SEAICE_SIZE.h) defines number of ice thickness categories; |
293 |
|
code is not complete yet!! |
294 |
|
- SEAICE_SIZE.h now included in almost all seaice routines |
295 |
|
o verification (using seaice): |
296 |
|
- switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp. |
297 |
|
global_ocean.cs32x15.seaice ; update results. |
298 |
|
- compile B-grid dynamics in FW test exp 1D_ocean_ice_column ; |
299 |
|
- compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp |
300 |
|
offline_exf_seaice (previously compiling B-grid). |
301 |
|
o pkg/exf: |
302 |
|
- fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow |
303 |
|
to specify neither just 1 comp of wind or wind-stress, nor no surface momentum |
304 |
|
forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind. |
305 |
|
o pkg/layers (adjust changes from Sept 19): |
306 |
|
- do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F) |
307 |
|
this allows to remove "layers_maxNum" dimension from all layers arrays. |
308 |
|
o pkg/layers (adjust changes from Sept 19): |
309 |
|
- remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ; |
310 |
|
- snap-shot extended to all type of layers (not just the 1rst type); |
311 |
|
- remove layers variables when corresponding CPP option is undef. |
312 |
|
o pkg/layers: |
313 |
|
- rename pkg/layers variable and add new output (layer exist & un-weighted |
314 |
|
velocity in layer) |
315 |
|
o pkg/seaice: |
316 |
|
- simplify (?) ocean-drag coefficent computations by using |
317 |
|
the same routine in all three solvers (saves some code lines) |
318 |
|
- remove global fields DRAGA and DRAGS from C-grid code and |
319 |
|
declare them locally in lsr.F (the only place where they are |
320 |
|
still used) |
321 |
|
- update AD output of lab_sea.evp (very sensitive anyway). |
322 |
|
o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics |
323 |
|
(Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK |
324 |
|
and SEAICEuseJFNK=.true. A few things to note: |
325 |
|
- involves a FGMRES, that is parallel but very inefficient, |
326 |
|
because of many scalar products (global sums) in the Gram-Schmidt |
327 |
|
orthogonalization method. Needs to be replaced. Original code |
328 |
|
from J.-F. Lemieux |
329 |
|
- preconditioner for FGMRES is a stripped down version of LSOR |
330 |
|
- SOLV_MAX_ITERS is now used for LSOR as a solver and as a |
331 |
|
preconditioner. For the preconditioner, the default is set to 10. |
332 |
|
- Jacobian times vector is computed with finite differences |
333 |
|
- marginally related to JFNK-solver: add a smooth regularization for |
334 |
|
zeta with tanh that will improve convergence (Lemieux and Tremblay, |
335 |
|
2009) for any implicit solver (not implemented for EVP because EVP |
336 |
|
does not need this regularization in the first place). Define |
337 |
|
SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use. |
338 |
|
o eesupp/src: |
339 |
|
- check in genmake2 that intrinsic S/R flush is available. |
340 |
|
- add S/R to flush IO unit (if intrinsic S/R flush is available) |
341 |
|
- flush standard & error msg unit before MPI termination |
342 |
|
- if debugMode, flush IO unit after printing msg |
343 |
|
o pkg/ctrl: |
344 |
|
- ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call |
345 |
|
to ctrl_set_unpack_xyz. |
346 |
|
|
347 |
|
checkpoint64 (2012/10/09) |
348 |
|
o pkg/shelfice |
349 |
|
- in mom_fluxform.F, mom_vecinv.F: |
350 |
|
CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid) |
351 |
|
Bug fix KappaRU -> KappaRV |
352 |
|
does not change verification/isomip but may change other setups |
353 |
|
(presumably constant KappaRU=KappaRV) |
354 |
|
- fix diagnostics SHIU/Vdrag (thanks to Tom Millgate) |
355 |
|
o pkg/obcs: |
356 |
|
- fixed some indexing bugs in obcs_seaice_sponge.F |
357 |
|
- added obcs relaxation subroutines for HSALT and HSNOW |
358 |
|
- changes verification/seaice_obcs/results/obcs_seaice_sponge.F |
359 |
|
o pkg/seaice: |
360 |
|
- add "multicategory" parameterization for snow in analogy to ice, |
361 |
|
default is off for now. |
362 |
|
o pkg/obcs: |
363 |
|
- added obcs_seaice_sponge.F for obcs relaxation of seaice variables; |
364 |
|
see verification/seaice_obcs/input.seaiceSponge for example application. |
365 |
|
- remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB |
366 |
|
index setting by master-thread. This fix multi-threads Pb in previous modifs. |
367 |
|
o pkg/layers : |
368 |
|
- add diagnostics to pkg/layers |
369 |
|
- move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F |
370 |
|
(from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly. |
371 |
|
o pkg/generic_advdiff/gad_implicit_r.F : |
372 |
|
- fix ADVr diagnostics in case of both implicit vertical advection and diffusion. |
373 |
|
o pkg/seaice/seaice_growth.F: |
374 |
|
- fix SItflux diagnostics in virtual salt flux + balanceEmpmr case. |
375 |
|
o pkg/obcs: |
376 |
|
- change default setting of OBCS_UVICE_OLD from defined to undef; |
377 |
|
- use new parameter OB_indexNone for null index value (instead of hard-coded 0) |
378 |
|
in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F; |
379 |
|
- pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z; |
380 |
|
- change OB null index value (OB_indexNone) to -99 ; this fix the problem |
381 |
|
with Southern & Western OB at a tile edge (at least in a simple set-up). |
382 |
|
o pkg/obcs: |
383 |
|
- change settings of OB index in case OB coincides with tile edge (shared by |
384 |
|
2 tiles), so that common OB location is registered by both tiles (instead of |
385 |
|
only 1). However, for Southern and Western OB, index value = 0 is not |
386 |
|
recognized as valid OB index (=default null value) and needs to be fixed. |
387 |
|
- modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting) |
388 |
|
- new parameter "OB_indexNone" for null index value (for now, still zero) |
389 |
|
to replace hard-coded null index value of zero. |
390 |
|
o pkg/exch2: |
391 |
|
- improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON: |
392 |
|
always check buffer-size (but outside the loop); move checking for valid |
393 |
|
index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON, |
394 |
|
print each tile and point connection only if |W2_printMsg|>= 2 and 3. |
395 |
|
o pkg/ctrl (pack & unpack): |
396 |
|
- in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable |
397 |
|
(locally defined) for different variables (+ remove the variable-specific |
398 |
|
file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL |
399 |
|
(to be extended to other local file names in ctrl.h). |
400 |
|
o pkg/flt: |
401 |
|
- add a FLT_Iter0 option (similar to PTRACERS_Iter0). |
402 |
|
o pkg/mdsio: |
403 |
|
- fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing |
404 |
|
o tools/genmake2: |
405 |
|
- add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE |
406 |
|
(added by Alistair in version 1.51 for building without make depend); |
407 |
|
- remove Header files list (H_SRC_FILES) from the dependence of targets |
408 |
|
ad_input_code.f & ftl_input_code.f (not clear why it was added in the first |
409 |
|
place in version 1.23): this save going through staf when unrelated header |
410 |
|
file has been modified. |
411 |
|
Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without |
412 |
|
"make depend" step, still need to do "make links" before "make adtaf". |
413 |
|
o eesupp/src (+ few pkg src files) & genmake2: |
414 |
|
- finish to remove ALWAYS_USE_MPI in source code that TAF does not see; |
415 |
|
- no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2). |
416 |
|
- improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish |
417 |
|
upper/lower case ; account for space between "#" and undef/define) |
418 |
|
o pkg/flt (with exch2): |
419 |
|
- cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F; |
420 |
|
- simplify threads synchronisation; fix (many issues) multi-threaded with MPI. |
421 |
|
|
422 |
|
checkpoint63s (2012/09/05) |
423 |
|
o pkg/ecco: |
424 |
|
- remove #ifdef ALLOW_SMOOTH_CORREL3D brackets. |
425 |
|
- add more relevant #ifdef ALLOW_SMOOTH ones. |
426 |
|
- sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D. |
427 |
|
o pkg/ctrl: |
428 |
|
- CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D, |
429 |
|
ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D. |
430 |
|
- ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag, |
431 |
|
doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and |
432 |
|
ctrlSmoothCorrel3D (new). |
433 |
|
The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP. |
434 |
|
- ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist. |
435 |
|
- ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress |
436 |
|
controls when useAtmWind, and vice versa. |
437 |
|
- ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers. |
438 |
|
- ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with |
439 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH. |
440 |
|
- ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with |
441 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH. |
442 |
|
- ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F: |
443 |
|
replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D. |
444 |
|
o pkg/smooth: |
445 |
|
- remove un-necessary includes. |
446 |
|
- remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets. |
447 |
|
Those CPP options were never defined, and not necessary. |
448 |
|
o model/src: |
449 |
|
- fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi). |
450 |
|
- standard treatment of useSMOOTH. |
451 |
|
o pkg/autodiff: |
452 |
|
- add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode, |
453 |
|
useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint. |
454 |
|
o pkg/exch2: |
455 |
|
- add "if usingMPI" where it was missing (in exch2_rx?_cube*.template) |
456 |
|
+ start to remove ALWAYS_USE_MPI in source code that TAF does not see. |
457 |
|
- make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag |
458 |
|
and tiles to process mapping. |
459 |
|
- re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h) |
460 |
|
moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h; |
461 |
|
rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX |
462 |
|
from w2_eeboot.F to w2_readparms.F. |
463 |
|
o eesupp/src: |
464 |
|
- set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of |
465 |
|
ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F; |
466 |
|
also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F |
467 |
|
- in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI |
468 |
|
is defined (remove condition on usingMPI) to match cases where MPI_INIT |
469 |
|
has been called. |
470 |
|
- fix bug I put in previous modif of exch_sm_3d_rx.template (not much used); |
471 |
|
- change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings |
472 |
|
(so that on 1 proc, get same myPid independently of usingMPI) |
473 |
|
- add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and |
474 |
|
useCubedSphereExchange with EXCH-1 (safer). |
475 |
|
- add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI). |
476 |
|
o pkg/ggl90: |
477 |
|
- fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call) |
478 |
|
used in ALLOW_GGL90_SMOOTH code. |
479 |
|
o pkg/flt: |
480 |
|
- fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping |
481 |
|
floats at the Southern end of the domain). |
482 |
|
o eesupp/inc: |
483 |
|
- add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h); |
484 |
|
but not used (and not to be used) anywhere, just for documentation. |
485 |
|
o pkg/autodiff, exf, ptracers & seaice (AD & TL output): |
486 |
|
- comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since: |
487 |
|
a) can damage previously written records in any other multi-record files. |
488 |
|
b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S. |
489 |
|
o tools/genmake2: |
490 |
|
- define variable MAKE within Makefile and use it in place of 'make'; |
491 |
|
- update AD_CONFIG.h (if needed) before building any of the executable |
492 |
|
(forward, adjoint or tangent-lin); this involves a 2nd invocation of make; |
493 |
|
and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h; |
494 |
|
- always print usual warning comment 'this file is automatically generated' |
495 |
|
from script convert_cpp_cmd2defines (+ remove this warning from genmake2). |
496 |
|
o pkg/cheapaml: |
497 |
|
- updated to correspond to the code used in accepted paper (Nico Wienders). |
498 |
|
o pkg/exf: |
499 |
|
added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch. |
500 |
|
ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F) |
501 |
|
and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h). |
502 |
|
o pkg/exf, autodiff, ctrl, ecco and seaice: |
503 |
|
remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones. |
504 |
|
o pkg/ctrl, ecco: |
505 |
|
allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL. |
506 |
|
Depending on useAtmWind, one is inactive, and the other is active (see |
507 |
|
exf_getffields.F/exf_getsurfacefluxes.F). |
508 |
|
o tools/genmake2: |
509 |
|
- improve error msg when failing in 2nd test of check_for_broken_Ff |
510 |
|
- fix option '-makefile' short-name (-mf according to genmake2 -help) |
511 |
|
- source local config file "genmake_local" just after processing the genmake2 |
512 |
|
command arguments (previously done before processing arg). |
513 |
|
o pkg/grdchk: |
514 |
|
- add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call |
515 |
|
to this routine from cost_final has been dropped in g_cost_final) |
516 |
|
- improve printed information (more explicit msg, no longer using "print *," |
517 |
|
fix fcpertminus printed value). |
518 |
|
o model/src: |
519 |
|
- move call to COST_INIT_VARIA out of packages_init_variables.F directly |
520 |
|
into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES): |
521 |
|
this prevents getting cost-funct reset in adinitialise_varia recomputations. |
522 |
|
o pkg/dic: |
523 |
|
- move initialisation of "freefe" array from from dic_biotic_forcing.F to |
524 |
|
fe_chem.F: this prevents TAF from dropping this initialisation in TLM code. |
525 |
|
o pkg/grdchk: |
526 |
|
- grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid ) |
527 |
|
- grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0 |
528 |
|
o pkg/autodiff/ctrl/grdchk : |
529 |
|
- attempt to sort out what works and what does not, |
530 |
|
with regard to I/O, and to warn/stop accordingly. |
531 |
|
o pkg/grdchk: |
532 |
|
- attempt to fix grdchk in the case of useSingleCpuIO. |
533 |
|
- "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )" |
534 |
|
statements were moved from grdchk_main.F and into |
535 |
|
grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F. |
536 |
|
- a global sum is applied to record numbers icvrec/layer |
537 |
|
out of grdchk_loc so that they be passed to I/O routines. |
538 |
|
o pkg/smooth: |
539 |
|
- fix recomputation that appeared with nlfs : use smooth_recip_hFacC, |
540 |
|
smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case. |
541 |
|
o verification/testreport: |
542 |
|
- add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive); |
543 |
|
- can also use compressed (gzip) reference output file; |
544 |
|
- change format (in pkg/grdchk) of TLM output (+ add forward gradient) |
545 |
|
to be easier to collect by testreport. |
546 |
|
- update existing TLM output (half out-of-date by more than 3 yrs). |
547 |
|
- report NETCDF & LAPACK settings (from genmake2) in output dir. |
548 |
|
- report run-time in each individual summary (previously only for AD test); |
549 |
|
for TLM test, add also TAF version. |
550 |
|
- add daily TLM test on (old) aces cluster + weekly test on baudelaire. |
551 |
|
|
552 |
|
checkpoint63r (2012/08/15) |
553 |
|
o tools/genmake2: |
554 |
|
- fix Makefile for target ftlall (+ update files to clean after make ftlall) |
555 |
|
o pkg/ecco/ecco_cost_final.F : |
556 |
|
- fix fc print statements (to stdout and costfunction0000) so |
557 |
|
that the printed value is always after the global sum. |
558 |
|
o pkg/seaice/seaice_dynsolver.F : |
559 |
|
- fix ice strength assymptote at SEAICE_area_max<1 |
560 |
|
(no change for the standard case of SEAICE_area_max=1) |
561 |
|
o some cleaning: |
562 |
|
- pkg source files: ensure that all *.F files from each pkg included the |
563 |
|
corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which |
564 |
|
only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment |
565 |
|
code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding |
566 |
|
includes; |
567 |
|
- model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used. |
568 |
|
- ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR |
569 |
|
is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when |
570 |
|
ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop. |
571 |
|
- update option-file CPP_OPTIONS.h of all AD experiments: |
572 |
|
* no longer include PACKAGES_CONFIG.h ; |
573 |
|
* includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ; |
574 |
|
* def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before |
575 |
|
including ECCO_CPPOPTIONS.h). |
576 |
|
o pkg/cost, pkg/ctrl, pkg/ecco option-file: |
577 |
|
- clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into |
578 |
|
separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h, |
579 |
|
not necessary accurate). |
580 |
|
- add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in |
581 |
|
pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to |
582 |
|
deliberately break compilation (a remainder that it needs to be customized) |
583 |
|
- in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h |
584 |
|
- rename COST_CPPOPTIONS.h to COST_OPTIONS.h |
585 |
|
- rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h |
586 |
|
o tools/genamke2: |
587 |
|
- check for lapack. |
588 |
|
o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies. |
589 |
|
- pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions |
590 |
|
jointly. The exclusive ifdefs were removed, to add costs terms (when defined) |
591 |
|
from both packages. |
592 |
|
- the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly. |
593 |
|
- for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs. |
594 |
|
- pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes |
595 |
|
of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly. |
596 |
|
o pkg/cost : add comments to explain special and/or untested setups. |
597 |
|
o pkg/exf: |
598 |
|
- use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h |
599 |
|
(previously, ALLOW_AUTODIFF_TAMC was controling this switch). |
600 |
|
o verification/*/code_ad: |
601 |
|
mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file: |
602 |
|
- reccord when this file is included (define ECCO_CPPOPTIONS_H) |
603 |
|
- remove the most obvious obsolete features (e.g., #define ALLOW_COST not |
604 |
|
allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h) |
605 |
|
o pkg/seaice : |
606 |
|
- added possibility to change ice strength/PRESS0 relationship to |
607 |
|
HEFF, according to the following run time parameters |
608 |
|
SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0) |
609 |
|
SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0) |
610 |
|
SEAICEpresH0 :: HEFF threshold for ice strength (m) |
611 |
|
o pkg/ggl90 : |
612 |
|
- added run time flag mxlSurfFlag to include the code that ensure |
613 |
|
mixing between first and second level (previously included as a comment) |
614 |
|
o verification/1D_ocean_ice_column/input_ad/data.autodiff : |
615 |
|
- add test of newly added dumpAdByRec=T option where |
616 |
|
we write all records to one file per variable. |
617 |
|
o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h : |
618 |
|
- switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES |
619 |
|
to check that this code is ok with taf and compiles in adjoint. |
620 |
|
o pkg/autodiff : |
621 |
|
- added run time param dumpAdByRec : ad dump format switch. |
622 |
|
If true then write all records to one file per variable. |
623 |
|
Else write one file per record (remains the default). |
624 |
|
- revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly. |
625 |
|
o pkg/seaice: |
626 |
|
- Added SEAICEuseTILT run time switch : if set to |
627 |
|
false then omit the tilt term in seaice dynamics. |
628 |
|
- Fix free drift calculation. |
629 |
|
o pkg/shelfice: |
630 |
|
When initializing SHELFICEDragQuadratic, set default to be |
631 |
|
consistent with shiCdrag in case SHELFICEuseGammaFrict is used, |
632 |
|
but retain option to set it independently |
633 |
|
(inconsistenty spotted by Veronique Dansereau) |
634 |
|
o eesupp/inc: |
635 |
|
- in EEPARAMS.h, add real-type constant for some frequently used simple number |
636 |
|
(0,1,2,1/2), with name explicitly referring to RS/RL type. |
637 |
|
o model/src: |
638 |
|
- move balancing of relaxation terms to new S/R balance_relax.F. |
639 |
|
o pkg/autodiff: |
640 |
|
re-write active I/O high-level (control) S/R: |
641 |
|
- rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL |
642 |
|
- add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R. |
643 |
|
- use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and |
644 |
|
MDS_READ/WRITE_FIELD); change loops to multi-threads. |
645 |
|
- update and merge active_file_control_slice.flow into active_file_control.flow |
646 |
|
- update the calls in lower level S/R (active_file.F, active_file_g.F and |
647 |
|
active_file_ad.F) keeping the argument list and function unchanged. |
648 |
|
- also update lower-level "_LOC" version (call same S/R with "useCurrentDir |
649 |
|
=.TRUE.") and remove high-level (control) _loc version (not called anymore). |
650 |
|
- new low-level active I/O routines, one for each type (RL/RS), for active var |
651 |
|
of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr); |
652 |
|
fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the |
653 |
|
right type. |
654 |
|
o autodiff and RS=real*4: |
655 |
|
- call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf |
656 |
|
ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ; |
657 |
|
- change argument type of 3-D mask argument to _RS to match type in the call |
658 |
|
(in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued. |
659 |
|
o pkg/thsice: |
660 |
|
- re-anable balanceEmPmR when useSEAICE=T with useThSIce=T. |
661 |
|
- option to correct ocean fresh-water flux for imbalance of Atmos+Land |
662 |
|
fresh-water flux: uniform correction or proportional to local precip. |
663 |
|
o pkg/ctrl: |
664 |
|
- new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D |
665 |
|
- redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to |
666 |
|
ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC |
667 |
|
- verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL |
668 |
|
|
669 |
|
checkpoint63q (2012/07/30) |
670 |
|
o pkg/autodiff: |
671 |
|
note about monitor and snap-shot of ad-variables: |
672 |
|
a) need to apply ADEXCH before monitor or output of ad-vars to include |
673 |
|
overlap contributions (was done for adjDump but missing for monitor). |
674 |
|
b) since ADEXCH implies adding overlap values to interior array, machine |
675 |
|
truncation error is expected when adding an ADEXCH call in the middle of |
676 |
|
the time-stepping (although mathematically identical). |
677 |
|
modifs: |
678 |
|
- fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars |
679 |
|
declaration (adEddyPsiX,adEddyPsiY in adcommon.h). |
680 |
|
- add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to |
681 |
|
apply ADEXCH before monitor or snap-shot of ad-variables: |
682 |
|
=0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy. |
683 |
|
- implement new method (copy+adexch) for snap-shot and monitor of main model |
684 |
|
ad-vars (initially not used by default -> output unchanged). |
685 |
|
- change default (set to 2) to use new method and update few output_adm.txt |
686 |
|
with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo |
687 |
|
and both tutorial_tracer_adjsens tests). |
688 |
|
- switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice) |
689 |
|
and turn off momDissip_In_AB in the 2 other (needed for stable AB-3). |
690 |
|
o pkg/ctrl: |
691 |
|
enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of |
692 |
|
generic control variables via |
693 |
|
#define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL |
694 |
|
Only required customization should be S/R ctrl_map_ini_genarr.F |
695 |
|
(routine in repository contains example) |
696 |
|
o pkg/exf: |
697 |
|
- fix and refine checking of surface-relaxation setting when using EXF |
698 |
|
o verification (adjoint exp): |
699 |
|
- reduce length of simulation by half for experiment global_ocean.cs32x15 |
700 |
|
(std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output. |
701 |
|
o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag) |
702 |
|
- replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers |
703 |
|
of KE that can occur with aggressive optimization |
704 |
|
+ put quadratic bottom drag calculation in separated loops (only done if |
705 |
|
using bottomDragQuadratic) |
706 |
|
o model/src: CG2D_NSA |
707 |
|
- clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF |
708 |
|
and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE. |
709 |
|
- in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens), |
710 |
|
change cg2d residual target to be expressed in Wunits (=> do not normalise |
711 |
|
RHS ; this fix global_max Pb with TAF); update output. |
712 |
|
o verification/tutorial_tracer_adjsens: |
713 |
|
improve parameter consistency (and get rid of warnings): |
714 |
|
- use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf); |
715 |
|
- switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical) |
716 |
|
- use staggerTimeStep (for stability) in som81; use default rotation period. |
717 |
|
o pkg/exch2: |
718 |
|
- with empty facet: fix compact-format (W2_mapIO=1) definition (was previously |
719 |
|
reset to 0 = 1 long line in X) |
720 |
|
o pkg/mdsio: |
721 |
|
- fix reading of dimensions from meta file for large-size domain |
722 |
|
o model/src: |
723 |
|
- fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long); |
724 |
|
- to refine CS-grid check, add logical flag "hasWetCSCorners": true if using |
725 |
|
Cubed-Sphere Exch with CS-corners inside the domain; |
726 |
|
make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate |
727 |
|
globalArea and to set hasWetCSCorners. |
728 |
|
- add warning if usingCurvilinearGrid and momAdvection in flux-form (missing |
729 |
|
metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form. |
730 |
|
- re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if |
731 |
|
useCDscheme and useCubedSphereExchange). |
732 |
|
o pkg/seaice/seaice_growth.F : |
733 |
|
- compute the SEAICE_DISABLE_HEATCONSFIX term accordingly |
734 |
|
for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0) |
735 |
|
when the previous code was not correct. |
736 |
|
- in all cases diagnoze the boundary condition mismatch to SIaaflux |
737 |
|
- in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add |
738 |
|
that term to QNET (essentially to set the melt/freeze water to 0degC). |
739 |
|
when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed. |
740 |
|
o verification/global_ocean.cs32x15/input.seaice : |
741 |
|
- add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget. |
742 |
|
- add diagnostics (commented out) for budget test using my matlab codes (gcmfaces). |
743 |
|
- update results (output.seaice.txt) accordingly. |
744 |
|
o verification/lab_sea/input/data.seaice : |
745 |
|
- remove SEAICEheatConsFix, which is now be tested |
746 |
|
in global_ocean.cs32x15. The presently coded fix |
747 |
|
is only consistent with real fresh water + nlfs. |
748 |
|
- update results (output.txt) accordingly. |
749 |
|
o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd). |
750 |
|
o AD_CONFIG.h file: |
751 |
|
- in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h; |
752 |
|
- remove #include "AD_CONFIG.h" from all included OPTIONS files and |
753 |
|
add it explicitly in each fortran src file where it is needed. |
754 |
|
motivation: header file AD_CONFIG.h is generated/modified after "make depend" |
755 |
|
thus introducing potentially wrong dependency; therefore, better to include |
756 |
|
it only where it's really needed, and after any other included OPTIONS file |
757 |
|
(less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN |
758 |
|
or ALLOW_TANGENTLINEAR_RUN). |
759 |
|
|
760 |
|
checkpoint63p (2012/07/06) |
761 |
|
o pkg/autodiff: |
762 |
|
- rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ; |
763 |
|
- create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters |
764 |
|
which are now read from new parameter file "data.autodiff" (inAdExact |
765 |
|
previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg) |
766 |
|
- add file "data.autodiff" in all verification/*/input_ad/ directories. |
767 |
|
- add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward |
768 |
|
mode (used in global_ocean.cs32x15.seaice_dynmix test exp.) |
769 |
|
o verification/tutorial_tracer_adjsens/ |
770 |
|
- add extra sub-verification which uses "SOM" advection scheme |
771 |
|
(2nd Order-Moment Advection Scheme, Prather Limiter) with |
772 |
|
#define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h |
773 |
|
and in data: |
774 |
|
multiDimAdvection=.TRUE., |
775 |
|
tempAdvScheme=81, |
776 |
|
saltAdvScheme=81, |
777 |
|
o model/src: |
778 |
|
- introduce ALLOW_BALANCE_RELAX which allow the removal |
779 |
|
of the global mean of relaxation terms by setting |
780 |
|
balanceThetaClimRelax and balanceSaltClimRelax |
781 |
|
- disable balanceEmPmR and balanceQnet in the case when useSeaice. |
782 |
|
This case is now treated appropriately in seaice_growth.F |
783 |
|
o pkg/seaice: |
784 |
|
- do balanceEmPmR and balanceQnet based on the net fluxes |
785 |
|
(SItflux) that enter the ocean+ice system rather than QNET |
786 |
|
and EMPMR. Works best in real fresh water. |
787 |
|
- SIatmFW, SIatmQnet, and SItflux computations had to be moved |
788 |
|
out of the diagnotics bloc, and stored in global arrays. |
789 |
|
|
790 |
|
checkpoint63o (2012/06/29) |
791 |
|
o vertical mixing schemes: |
792 |
|
- remove unused S/R CALC_BUOYANCY (left from branch-atmos merging) |
793 |
|
- replace computation of density (in Function STATE1, opps_calc.F) by a call |
794 |
|
to S/R FIND_RHO_SCALAR |
795 |
|
- pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC |
796 |
|
and use it for N^2 calculation in ggl90_calc.F (save 2 density computations); |
797 |
|
affects output (vermix.ggl90) at truncation level. |
798 |
|
o testreport: |
799 |
|
- change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles |
800 |
|
(nSx,nSy) for the number of threads (from eedata.mth) |
801 |
|
o model/src: |
802 |
|
- remove 2nd set of calls at the top of initialise_varia.F (Adjoint part) |
803 |
|
related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary). |
804 |
|
o verification/tutorial_tracer_adjsens/ |
805 |
|
- compile with ALLOW_CG2D_NSA |
806 |
|
- run with nonlinFreeSurf=3 |
807 |
|
- update reference output_adm.txt |
808 |
|
o tools/genmake2: |
809 |
|
- add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ; |
810 |
|
refine usePROFILES switching off (only when NetCDF is not available). |
811 |
|
o verification (atmospheric set-up): |
812 |
|
- change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration |
813 |
|
o pkg/profiles : refine profiles and files handling. |
814 |
|
o model/src and pkg/ecco : introduce run-time switch usePROFILES. |
815 |
|
o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h : |
816 |
|
- changes to use model/src/the_main_loop.F rather than the ecco version |
817 |
|
in ecco type adjoint runs. |
818 |
|
o model/src: |
819 |
|
- move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID |
820 |
|
- move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC |
821 |
|
- update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL) |
822 |
|
o model/src: |
823 |
|
- fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before); |
824 |
|
update output of test experiment bottom_ctrl_5x5. |
825 |
|
o pkg/generic_advdiff: |
826 |
|
- implement vertical bi-harmonic diffusion (for now, only for T & S and |
827 |
|
only explicitly). |
828 |
|
o verification/bottom_ctrl_5x5/ |
829 |
|
update reference output (results changed quite some time ago, |
830 |
|
not sure when; but new reference results look ok in terms of grdchk) |
831 |
|
o verification/1D_ocean_ice_column/ |
832 |
|
For verification purposes, the exact adjoint rather than an approx. |
833 |
|
should be used (e.g., to comare against F.D. or TLM). |
834 |
|
removed autodiff_inadmode*_ad.F routines in code_ad/ |
835 |
|
Update results/ accordingly. |
836 |
|
o pkg/cal: |
837 |
|
- change cal_getdate.F so that output date is function of input time only |
838 |
|
(less ambiguous, not mixed up with input iteration number). |
839 |
|
- fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP). |
840 |
|
o pkg/diagnostics: |
841 |
|
- implement calendarDumps also for stats-diags |
842 |
|
- implement calendarDumps also for snap-shot output (negative freq) |
843 |
|
- for now, ignores calendarDumps if non-zero phase-lag. |
844 |
|
|
845 |
|
checkpoint63n (2012/06/04) |
846 |
|
o model/src: |
847 |
|
- recompute rSurfW & S to ensure consistent column thickness (needed for rStar) |
848 |
|
between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice; |
849 |
|
- use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more |
850 |
|
similar to calc_r_star.F); update results of experiment internal_wave and |
851 |
|
tutorial_global_oce_in_p (affected @ truncation level). |
852 |
|
o pkg/shelfice: |
853 |
|
- add parameterisation of advective-diffusive flux into the ice shelf |
854 |
|
according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd |
855 |
|
- simply eps3/3a computation |
856 |
|
o eesupp: |
857 |
|
- add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange |
858 |
|
between tiles, just fill-in edges assuming locally periodic subdomain) and |
859 |
|
add corresponding exchange subroutines (EXCH0); |
860 |
|
- new CG-solver version (_EX0) for disconnected-tiles special case. |
861 |
|
o model/src (CG-solvers): |
862 |
|
- modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached |
863 |
|
(similar final residual output and max-Iter number as with standard version); |
864 |
|
- allows to store and use lowest-residual solution (standard & _SR versions); |
865 |
|
- cleaning up (remove old, commented out code, LETS_MAKE_JAM ...). |
866 |
|
- by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h) |
867 |
|
o eesup/src: |
868 |
|
- global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef |
869 |
|
ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012) |
870 |
|
o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn |
871 |
|
|
872 |
|
checkpoint63m (2012/04/27) |
873 |
|
o pkg/shelfice: |
874 |
|
- account for partical cells in surface level below ice-shelf for hydrostatic |
875 |
|
pressure calculion (set uniformFreeSurfLev to F); update isomip experiments. |
876 |
|
o ad test experiments: |
877 |
|
- update and rename to "ad_optfile.local" local AD-optfile specific to a |
878 |
|
particular adjoint verification experiment (in verification/*/code_ad/) |
879 |
|
o pkg/seaice & pkg/exf: |
880 |
|
- Part two of ECCO-CLIVAR code merges. |
881 |
|
Completes merge of seaice area relax. code. |
882 |
|
Requires unified CPP option EXF_ALLOW_SEAICE_RELAX |
883 |
|
to be set in EXF_OPTIONS.h since this pkg controls its I/O |
884 |
|
(and avoids second CPP option in SEAICE_OPTIONS.h) |
885 |
|
- change default value of costIceStart & costIceEnd to a valid date. |
886 |
|
- add snowPrecip to HSNOW in seaice_growth |
887 |
|
o pkg/ptracers: |
888 |
|
- move ptracers summary and setup check into separated S/R ; add a check for |
889 |
|
valid PTRACERS_Iter0 value (error+stop or just warning). |
890 |
|
o pkg/cal (+ pkg/ecco): |
891 |
|
- avoid calling a S/R with 2 times the same arg (FWD: unless both are only used |
892 |
|
as input; and for AD, unless both are not differentiable (e.g., k index)). |
893 |
|
o model/src: |
894 |
|
- define internal flag "uniformFreeSurfLev" (=T when free-surface level-index |
895 |
|
is everywhere k=1) to speed-up some calculations (by pass kSurf reference); |
896 |
|
temporary set to usingZCoords value (to be changed to F when using shelfice). |
897 |
|
- hydrostatic pressure: implement partial cell near the surface also for |
898 |
|
Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on |
899 |
|
usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code). |
900 |
|
o pkg/ctrl/ctrl_init.F: |
901 |
|
- add a formal parameter to s/r ctrl_init_rec to print |
902 |
|
xx_$(ctrl_valiable)_file for easier debugging |
903 |
|
- move call of cal_* routines into the if-block where they are really |
904 |
|
needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having |
905 |
|
to specify a startdate |
906 |
|
o pkg/seaice: |
907 |
|
- update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and |
908 |
|
global_ocean.cs32x15/code versions). |
909 |
|
- turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for |
910 |
|
verification experiment global_ocean.cs32x15.seaice and update results. |
911 |
|
o pkg/exf: |
912 |
|
- new S/R EXF_GETFIELD_START to return starting-time of a forcing field |
913 |
|
(according to useExfYearlyFields). |
914 |
|
o pkg/cal: |
915 |
|
- move calendar setting & summary (previously in cal_readparams.F) into new |
916 |
|
S/R CAL_INIT_FIXED to be called later in the initialisation process, once |
917 |
|
length of the simulation is set (after SET_PARMS call); This is an attempt |
918 |
|
to fix Pb when, e.g.: pkg/longstep, modifies the length of the run. |
919 |
|
- For safety: keep a record of pkg/cal parameter settings status |
920 |
|
to allow to STOP if one pkg/cal S/R is called too early. |
921 |
|
- add a stop in all basic pkg/cal subroutines if called before setting is done. |
922 |
|
- modify cal_getdate.F: stop when nothing was returned; |
923 |
|
if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2); |
924 |
|
this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F. |
925 |
|
|
926 |
|
checkpoint63l (2012/04/04) |
927 |
|
o pkg/bbl: |
928 |
|
- fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc); |
929 |
|
update global_with_exf output.yearly.txt file. |
930 |
|
o pkg/cal: |
931 |
|
- start to clean-up cal_set.F ; fix for the case where baseTime is non-zero. |
932 |
|
- remove 2 unsused and very short (1 line only) functions ; |
933 |
|
- remove unsused subroutines from AD-Diff list. |
934 |
|
o model/src: |
935 |
|
- start to implement clean wait to stop in initialization S/R (config_check.F, |
936 |
|
packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage) |
937 |
|
o folowing PRINT_MESSAGE changes: |
938 |
|
- remove reminder multiple print to the same file (STDOUT) when multi-threads. |
939 |
|
o pkg/bbl: |
940 |
|
- modification so it can work with z* |
941 |
|
- replace deltaT with dTtracerLev(k) for asynchronous time stepping |
942 |
|
- global_with_exf/input.yearly verification; changes output.yearly.txt |
943 |
|
o eesupp/src: |
944 |
|
- PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR); |
945 |
|
writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1 |
946 |
|
- CHECK_THREADS: specific code if using OpenMP threading: improve checking of |
947 |
|
# of threads across processors (e.g., different env OMP_NUM_THREADS setting) |
948 |
|
- improve special preliminary call to EESET_PARMS (if eedata is read 2 times). |
949 |
|
- when using MPI, always set usingMPI=T ; set default accordingly and stop |
950 |
|
if not consistent. |
951 |
|
- ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread |
952 |
|
argument is zero (in case called within single-thread section). |
953 |
|
o pkg/fizhi: |
954 |
|
clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored |
955 |
|
in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO. |
956 |
|
o pkg/exch2: |
957 |
|
- add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to |
958 |
|
activate EXCH_IGNORE_CORNERS in vector EXCH S/R). |
959 |
|
- switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS) |
960 |
|
but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data |
961 |
|
with bad ones coming from a not-yet-updated halo. |
962 |
|
This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx. |
963 |
|
o pkg/frazil: |
964 |
|
move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F |
965 |
|
http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html |
966 |
|
o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy |
967 |
|
o verification/lab_sea |
968 |
|
* #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING |
969 |
|
* #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL |
970 |
|
* nTimeSteps 3 -> 4 |
971 |
|
* changed reference output accordingly |
972 |
|
o pkg/ctrl: |
973 |
|
* fix ctrl_get_gen for xx_sst, xx_sss |
974 |
|
o pkg/fizhi: |
975 |
|
- fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F |
976 |
|
update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d) |
977 |
|
- by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE); |
978 |
|
fix few out-of-bounds indices in referencing vars (initialise igrd to 1); |
979 |
|
clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array). |
980 |
|
o pkg/gmredi: |
981 |
|
- add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp |
982 |
|
o pkg/fizhi: |
983 |
|
- fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the |
984 |
|
(old)aces open64 tuv test. |
985 |
|
o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F |
986 |
|
o pkg/mom_vecinv: |
987 |
|
- fix 1 loop range in mom_vecinv.F to be like all the other loops which |
988 |
|
set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv |
989 |
|
with non-lin free-surf). |
990 |
|
o model/src: move k-loop outside of i/j-loops when (re-)computing R_low |
991 |
|
in ini/update_masks_etc.F in order to avoid -O3 optimization problems with |
992 |
|
some compilers (gfortran 4.6.0 on MacOS) |
993 |
|
o momentum: |
994 |
|
- separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM |
995 |
|
& MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised |
996 |
|
fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control. |
997 |
|
|
998 |
|
checkpoint63k (2012/03/17) |
999 |
|
o model/src: |
1000 |
|
- selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum |
1001 |
|
flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations. |
1002 |
|
- SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version |
1003 |
|
(#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp. |
1004 |
|
o model/src: solve_*diagonal.F |
1005 |
|
- replace division with multiplication by inverse (similar to original version) |
1006 |
|
update output of AD exp. global_ocean.90x40x15. |
1007 |
|
- fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F |
1008 |
|
to enable the use of the vectorized & differentiable solve_tridiagonal.F |
1009 |
|
- test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for |
1010 |
|
vertical advection (to get solve_tridiagonal tested in AD mode). |
1011 |
|
o pkg/seaice: ECCO-CLIVAR merge: |
1012 |
|
1. seaice AREA relaxation |
1013 |
|
* CPP option: SEAICE_ALLOW_AREA_RELAXATION |
1014 |
|
* runtime flag: SEAICE_tauAreaObsRelax |
1015 |
|
2. modified global mean cost imbalance code: CPP option |
1016 |
|
ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION |
1017 |
|
o another iteration on solve_*diagonal.F |
1018 |
|
Make choices independent of AUTODIFF |
1019 |
|
Default will be the adjoinable vectorized version. |
1020 |
|
Alternative choices are: |
1021 |
|
* non-adjoinable original version with low memory footprint: |
1022 |
|
#define SOLVE_DIAGONAL_LOWMEMORY |
1023 |
|
* still adjoinable but does not vectorize (k as inner-most loop): |
1024 |
|
#define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef) |
1025 |
|
o testreport |
1026 |
|
- add option to use a home made wrapper around "make" |
1027 |
|
- remove MITGCM_IEEE env. variable (no longer active) |
1028 |
|
o pkg/shelfice |
1029 |
|
- improve computation of friction velocity for velocity dependent |
1030 |
|
exchange coefficients: include velocities into SHELFICEBoundaryLayer |
1031 |
|
block to average velocities vertically |
1032 |
|
- add TAF store directives for SHI_ALLOW_GAMMAFRICT |
1033 |
|
o Modify diagonal solvers, now three versions (upon request): |
1034 |
|
#ifndef SOLVE_DIAGONAL_AUTODIFF |
1035 |
|
1. default version (dating back a while ago) |
1036 |
|
#else /* def SOLVE_DIAGONAL_AUTODIFF */ |
1037 |
|
# ifdef SOLVE_DIAGONAL_KINNER |
1038 |
|
2. adjoinable version with k-innermost loop (G. Forget) |
1039 |
|
# else |
1040 |
|
3. adjoinable vectorized version of 2. |
1041 |
|
# endif |
1042 |
|
#endif /* SOLVE_DIAGONAL_AUTODIFF */ |
1043 |
|
All flags are currently set within routines, but could/should be moved to CPP-options. |
1044 |
|
Array bounds for 1. are as before, for 2.,3. cover the entire domain |
1045 |
|
(could be changed for 1. too). |
1046 |
|
o verification/lab_sea (fwd): |
1047 |
|
- update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY, |
1048 |
|
use 7 categories (except hb87), new solve4temp params (except salt_plume), |
1049 |
|
constant salinity (=4) or variable salinity (salt_plume) done through |
1050 |
|
SItracer. |
1051 |
|
o pkg/seaice: |
1052 |
|
- rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0; |
1053 |
|
- remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t, |
1054 |
|
SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz) |
1055 |
|
from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when |
1056 |
|
SEAICE_freeze got retired) but already better than previously with |
1057 |
|
SEAICE_freeze=123456.7 deg.C; |
1058 |
|
- move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS |
1059 |
|
(safer multi-threaded setting); always set SEAICEuseEVP; |
1060 |
|
- setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to |
1061 |
|
SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report); |
1062 |
|
stop if multiple specifications for the same coeff; make sure default |
1063 |
|
SEAICE_mcPheePiston is compatible with drF(1) & deltaT. |
1064 |
|
o pkg/obcs: |
1065 |
|
- allow to switch to upwind 1rst order advection scheme for the advective |
1066 |
|
flux computation at the open-boundary; disabled for adjoint built. |
1067 |
|
o pkg/ptracers: |
1068 |
|
- rename PTRACERS_RESTART.h -> PTRACERS_START.h |
1069 |
|
- rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F |
1070 |
|
- add parameter to decide when to start a tracer; use internal flag to |
1071 |
|
know which tracer to step-forward; switch this internal flag at the top |
1072 |
|
of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled |
1073 |
|
for adjoint built. |
1074 |
|
o pkg/seaice: |
1075 |
|
- add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ; |
1076 |
|
- move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ; |
1077 |
|
- keep experiment offline_exf_seaice truly single category (set MULTDIM=1). |
1078 |
|
o pkg/ecco: |
1079 |
|
- fix writing of output file DiagnosCost_ClimSalt/Theta |
1080 |
|
and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc). |
1081 |
|
o pkg/seaice: |
1082 |
|
- add missing initialisation of COR_ICE array in dynsolver.F |
1083 |
|
- merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is |
1084 |
|
compiled either way, and is tested in all exps (multidim was only tested |
1085 |
|
in lab_sea ad before). |
1086 |
|
- cosmetic change to prepare for future addition of ITD. no change to results. |
1087 |
|
no defaults change. |
1088 |
|
- added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise). |
1089 |
|
- by lack of adequate verification experiments, I further used custom versions |
1090 |
|
of global_ocean.cs32x15 to test multicat or not, with pickup or not. All |
1091 |
|
should be correct. |
1092 |
|
- avoid recomputations in ad. |
1093 |
|
o array initialisation in adjoint mode: |
1094 |
|
1) pkg/mom_common/mom_calc_ke.F: |
1095 |
|
add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC): |
1096 |
|
The S/R which calls MOM_CALC_KE initialises KE but in some recomputation |
1097 |
|
part this initialisation is gone, resulting in Floating Point Exception |
1098 |
|
(caught by open64 compiler with debug option). |
1099 |
|
2) model/src/convective_weights.F |
1100 |
|
set output convectCount over the full array range (instead of doing |
1101 |
|
an update): this fix a similar issue when called within recomputation (adjoint) |
1102 |
|
which could by-pass the initialisation (normally done in the caller S/R). |
1103 |
|
o pkg/seaice: |
1104 |
|
- final version of turbulent flux params, as agreed at MIT ice meet: |
1105 |
|
SEAICE_mcPheePiston (default is ~ 0.000875) |
1106 |
|
SEAICE_mcPheeTaper (default is 0.) |
1107 |
|
SEAICE_frazilFrac (defualt is 1.) |
1108 |
|
SEAICE_mcPheeStepFunc (default is false) |
1109 |
|
- changes results at trunction error level |
1110 |
|
- ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo |
1111 |
|
o added pkg/frazil: |
1112 |
|
- see frazil_description.tex for details |
1113 |
|
- verification experiment is global_with_exf/input.yearly; changes output.yearly.txt |
1114 |
|
o pkg/shelfice/shelfice_thermodynamics.F |
1115 |
|
- fix exponents for velocity dependent exchange coefficients: change |
1116 |
|
from 2/3(=0) to 0.66666666666666667 |
1117 |
|
- move computation of velocity dependent exchange coefficients into |
1118 |
|
separate loop, so that it applies to both thermodynamics |
1119 |
|
- move some divisions by constants out of loops |
1120 |
|
|
1121 |
|
checkpoint63j (2012/02/16) |
1122 |
|
o pkg/seaice: |
1123 |
|
- overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc. |
1124 |
|
- SItracer: added run time params, and allow coupling to ocn salinity. |
1125 |
|
o pkg/seaice: remove (almost) all divisions by constants within loops |
1126 |
|
in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d |
1127 |
|
results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only |
1128 |
|
those, caused by 1/QI -> recip_QI) -> update output.seaice.txt, |
1129 |
|
output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt |
1130 |
|
o pkg/seaice : |
1131 |
|
- simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula |
1132 |
|
= 1 or 2, using newly added run time parameter SEAICE_availHeatTaper. |
1133 |
|
- fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148. |
1134 |
|
- add permanent SItflux diag that corresponds to TFLUX but includes |
1135 |
|
ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget. |
1136 |
|
- allow activation/testing of a fix for suspected missing term in |
1137 |
|
ocn-ice heat budget (to be confirmed). To test this, you want to |
1138 |
|
undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param |
1139 |
|
SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic. |
1140 |
|
- no change in results, fwd or ad. |
1141 |
|
o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below: |
1142 |
|
- switch to variable freezing point. |
1143 |
|
Results change : cg2d -> 1 digits; ad -> 3-6-6 digits. |
1144 |
|
- bug fix : the sublimation term that was missing is now activated. |
1145 |
|
Results change : cg2d -> 2 digits; ad -> 8-6-6 digits. |
1146 |
|
- bug fix : flooding sign term for SIsal0.NE.0. |
1147 |
|
Result change : cg2d -> 8 digits; ad -> 11-12-9 digits. |
1148 |
|
o pkg/seaice: |
1149 |
|
- unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT |
1150 |
|
is now the default, and the old default constant freezing point is recovered |
1151 |
|
with SEAICE_tempFrz0 = -1.96, |
1152 |
|
SEAICE_dTempFrz_dS = 0., |
1153 |
|
- retire SEAICE_freeze (= the old way of specifycing the constant freezing point) |
1154 |
|
- remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there. |
1155 |
|
- bug fix (thanks to M. Losch) : the sublimation term that was missing is now |
1156 |
|
activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM. |
1157 |
|
- bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211) |
1158 |
|
was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail). |
1159 |
|
- bug fix (thanks to O. Jahn) : area loss for melting got messed up in |
1160 |
|
seaice_growth r149 for legacy branch (no results change). |
1161 |
|
- introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code |
1162 |
|
from I. Fenty). |
1163 |
|
- results did not change except for global_ocean.cs32x15, mostly due to the |
1164 |
|
switch to variable freezing point (see above item for detail). |
1165 |
|
o pkg/thsice: |
1166 |
|
- fix and simplify interface to salt_plume pkg ; diagnose directly amount of |
1167 |
|
seawater freezing in thsice_calc_thickn (not used). |
1168 |
|
o pkg/seaice: turbulent flux term specification via run time params. |
1169 |
|
- replace CPP switches with run time switches to facilitate testing |
1170 |
|
- retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, |
1171 |
|
GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR |
1172 |
|
- added runtime parameter : SEAICEturbFluxFormula |
1173 |
|
- move Mcphee constants to SEAICE_PARAMS.h |
1174 |
|
- seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula; |
1175 |
|
SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); |
1176 |
|
remove seaice_summary call (moved to seaice_init_fixed) |
1177 |
|
- seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on |
1178 |
|
SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms) |
1179 |
|
- seaice_summary.F : add missing report of read turbulent flux term set up |
1180 |
|
and SITRACER. |
1181 |
|
- seaice_check.F : check range; inform and stop if retired CPPs are used |
1182 |
|
(incl. SEAICE_AGE). |
1183 |
|
- seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without |
1184 |
|
CPP switch, same computation as before for the different options. |
1185 |
|
- change results at the truncation level. |
1186 |
|
o pkg/seaice: |
1187 |
|
- remove un-used parameters LAD & MAX_TICE ; add new run-time parameters: |
1188 |
|
useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and |
1189 |
|
SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY. |
1190 |
|
- update verification/*/input*/data.seaice: |
1191 |
|
to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY |
1192 |
|
code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ; |
1193 |
|
and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code, |
1194 |
|
set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0. |
1195 |
|
o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY): |
1196 |
|
- remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same |
1197 |
|
algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0); |
1198 |
|
difference in results only due to machine truncation. |
1199 |
|
- remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using |
1200 |
|
MaykutPolySatVap; keep MIN_LWDOWN. |
1201 |
|
- adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation. |
1202 |
|
- update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87, |
1203 |
|
+ 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits). |
1204 |
|
o pkg/salt_plume: |
1205 |
|
- isolate saltPlumeFlux array exch into a specific S/R called from |
1206 |
|
do_oceanic_phys.F |
1207 |
|
- add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice. |
1208 |
|
o verification: |
1209 |
|
- move untested set-up to MITgcm_contrib/verification_other. |
1210 |
|
o pkg/seaice: |
1211 |
|
- retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER. |
1212 |
|
o pkg/seaice: |
1213 |
|
- seaice_solve4temp.F (keeping results unchanged): |
1214 |
|
* add 2 future run-time params to select which saturation vapor pressure |
1215 |
|
formula is used and how post-iteration fluxes are set. |
1216 |
|
Temporary set these 2 params according to option SOLVE4TEMP_LEGACY; |
1217 |
|
* New piece of code (not used) to update surf. atmos. heat flux F_ia using |
1218 |
|
the linearized expression to stay consistent with tsurf finding. |
1219 |
|
- seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x |
1220 |
|
can be < 0. |
1221 |
|
o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef): |
1222 |
|
- remove from F_ia (and from it's derivative dFiDTs1) the contribution of |
1223 |
|
conductive heat flux F_c , and add it explicitly when updating tsurf as |
1224 |
|
solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf |
1225 |
|
so that now F_ia has a consistent meaning through the entire routine. |
1226 |
|
This causes differences at truncation level: update output of fwd exp. |
1227 |
|
global_ocean.cs32x15.seaice. |
1228 |
|
o pkg/seaice: |
1229 |
|
- lots of editing/cleaning in seaice_solve4temp.F + better documentation |
1230 |
|
of arrays, sign/direction of fluxes; no effect on results. |
1231 |
|
- replace hard coded 273.16 (=previous value of celsius2K) by celsius2K |
1232 |
|
in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part); |
1233 |
|
note: this should have been done before changing celsius2K default. |
1234 |
|
- to keep results unchanged, add back old value of celsius2K in verification |
1235 |
|
exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs |
1236 |
|
- replace hard coded seawater freezing temp in seaice_solve4temp.F (part |
1237 |
|
SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default |
1238 |
|
value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater |
1239 |
|
freezing temp is consistent with value in seaice_growth.F ; this causes |
1240 |
|
differences at machine truncation level: update lab_sea AD output (3/4). |
1241 |
|
o pkg/seaice: |
1242 |
|
- mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask |
1243 |
|
and climsst/sss even when using seaice (to prevent calculation that might |
1244 |
|
use SST on land); does not affect any verification exp. |
1245 |
|
- apply mask to taux,tauy (in seaice_get_dynforcing.F); update output |
1246 |
|
of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix. |
1247 |
|
o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness |
1248 |
|
over land (non-legacy code) |
1249 |
|
o vectorize salt_plume package: |
1250 |
|
- add extra code to salt_plume_frac and salt_plume_tendency_apply_s |
1251 |
|
- this code computes plumebk everywhere (also over land), thus requires |
1252 |
|
code to avoid divisions by zero and catch the case of kLev=Nr. |
1253 |
|
- efficiency of salt_plume_frac is still sub-optimal |
1254 |
|
o tools (genmake2): |
1255 |
|
- fix makefile NAME specification (option: -makefile NAME) by adding |
1256 |
|
"-f $MAKEFILE" in few places where it was missing including makedepend |
1257 |
|
command (contribution from Paul). |
1258 |
|
|
1259 |
|
checkpoint63i (2012/01/24) |
1260 |
|
o model/src: |
1261 |
|
- add factorized versions of some EOS code to find_rho.F, |
1262 |
|
define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX) |
1263 |
|
o model/src: |
1264 |
|
- add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h; |
1265 |
|
- change default celsius2K from 273.16 to 273.15 |
1266 |
|
- to keep results unchanged, add back old value of celsius2K in verification |
1267 |
|
exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd), |
1268 |
|
global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm). |
1269 |
|
o model/src: add a little initialisation trick to find_rho.F and find_alpha.F |
1270 |
|
to make TAF generate vectorizable code |
1271 |
|
o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows. |
1272 |
|
Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers |
1273 |
|
have flags that do this more efficiently. |
1274 |
|
o pkg/diagnostics/diagstats_calc.F |
1275 |
|
- for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact |
1276 |
|
o pkg/obcs (with exch2): |
1277 |
|
- derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F) |
1278 |
|
and remove code (in obcs_readparms.F) which was based on EXCH of indices |
1279 |
|
(through buffer) and did not account for exch2 (e.g., CS-grid) topology. |
1280 |
|
o pkg/exf and seaice exp: |
1281 |
|
- change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0) |
1282 |
|
so that switching off area & heff advection flags does not affect results. |
1283 |
|
- change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h |
1284 |
|
- keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef |
1285 |
|
EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update |
1286 |
|
results of verification experiments: 1D_ocean_ice_column(fwd), |
1287 |
|
global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8) |
1288 |
|
and offline_exf_seaice (all 4). |
1289 |
|
o pkg/seaice: |
1290 |
|
- remove array YNEG, RIVER, TMIX (replaced by local var) from common block; |
1291 |
|
remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef. |
1292 |
|
- fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY) |
1293 |
|
but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and |
1294 |
|
not multi-dim advection; |
1295 |
|
- fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and |
1296 |
|
SHORTWAVE_HEATING #undef. |
1297 |
|
o optim: make Makefile more robust (?) |
1298 |
|
o pkg/obcs: |
1299 |
|
* fix treatment of obcs_read_pickup for TAF |
1300 |
|
o pkg/shelfice: |
1301 |
|
* add missing initialisation of num_shifwflx |
1302 |
|
* new adjoint verification exp. for isomip |
1303 |
|
* change Prandtl and Schmidt numbers from generic formulations |
1304 |
|
(in terms of model diffus. and visc.) to separate runtime |
1305 |
|
parameters, with Holland and Jenkins (1999) default values. |
1306 |
|
o pkg/exf (interpolation): |
1307 |
|
- extended input field (2 rows) near the N & S poles: |
1308 |
|
* fill in with the symetric value (when even Nb of data in longitude) |
1309 |
|
* add average value at the poles only for scalar quantities ; for vector |
1310 |
|
component interpolation, skip the averaging and keep duplicated values, |
1311 |
|
unless the 2 components have same location (uvInterp=T) in which case |
1312 |
|
interpolate the 2 components together using S/R EXF_INTERP_UV. |
1313 |
|
- new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field |
1314 |
|
together: this allows to account properly for local orientation when |
1315 |
|
averaging at N & S pole. |
1316 |
|
- add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding |
1317 |
|
exf-interpolation near N & S poles. Undef by default. |
1318 |
|
- add debug check/print on 1rst iter if debugLevel >=2. |
1319 |
|
o pkg/exf: |
1320 |
|
- change masking flags definition (no longer "parameter"), put them in |
1321 |
|
common block and set them in S/R EXF_INIT_FIXED. |
1322 |
|
- change recognized masking flag from s,u,v to c,w,s since the mask |
1323 |
|
to use (maskC,W,S) depends on position on model grid and has little to |
1324 |
|
do with scalar/vector difference; fix masking if using P-coordinates. |
1325 |
|
- fix masking of wind-stress (was wrong if interpolated or read on A-grid) |
1326 |
|
and update results of exp. global_with_exf (x2). |
1327 |
|
- fix setting of zenith-angle table when SHORTWAVE_HEATING is undef. |
1328 |
|
o pkg/obcs |
1329 |
|
- S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate) |
1330 |
|
o pkg/exf (interpolation): |
1331 |
|
- assume periodicity in X only if input field cover full longitude range. |
1332 |
|
- improve search for lat. index (supposed to be faster, in ~log2(ny) steps, |
1333 |
|
and should vectorise). |
1334 |
|
- fix input lat of the 2 added row (in case we provide N.pole data). |
1335 |
|
|
1336 |
|
checkpoint63h (2011/12/30) |
1337 |
|
o pkg/seaice: |
1338 |
|
- change declaration of UVM from _RL to _RS in order to get B-grid |
1339 |
|
uIce,vIce monitor when _RS = real*4 |
1340 |
|
o pkg/offline: |
1341 |
|
- new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags); |
1342 |
|
- compute vertical velocity if not read from file (switch on exactConserv |
1343 |
|
& staggerTimeStep); |
1344 |
|
- fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq. |
1345 |
|
o verification: |
1346 |
|
- update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input) |
1347 |
|
with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m": |
1348 |
|
fix Pb in yG definition @ 2 missing corners (previously yG was averaged); |
1349 |
|
- update output of exp. global_ocean.cs32x15.viscA4 after changing |
1350 |
|
grid-file angles (used here for coriolis-3d); |
1351 |
|
- remove (or gzip) few files not needed to run fizhi-cs experiments. |
1352 |
|
o pkg/exf (vector interpolation): |
1353 |
|
- rotate vector component toward local grid-axis orientation using grid-angles |
1354 |
|
(stored in GRID.h) instead of locally computed rotation angle; keep old code |
1355 |
|
available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default). |
1356 |
|
o pkg/seaice: |
1357 |
|
- allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION |
1358 |
|
undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined. |
1359 |
|
o pkg/PKG_OPTIONS.h files: |
1360 |
|
- move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h", |
1361 |
|
outside of the #ifdef ALLOW_THISPKG / #endif block. |
1362 |
|
- update verification/*/code/PKG_OPTIONS.h files. |
1363 |
|
o add a verification experiment (offline_exf_seaice/input.seaice) that test |
1364 |
|
the B-grid LSOR solver |
1365 |
|
o pkg/seaice: sort out emissivity and long wave radiation step 2: |
1366 |
|
- add emissivity for snow and ice as new run-time parameters |
1367 |
|
(unfortunately) that default to the corresponding exf values; this |
1368 |
|
changes results in most verification experiments so that for backward |
1369 |
|
compatibility these parameter have to be set explicitly to inconsistent |
1370 |
|
values (ugly); |
1371 |
|
- the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired |
1372 |
|
emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp |
1373 |
|
until we agree how to handle this bug properly |
1374 |
|
o pkg/exf (interpolation): |
1375 |
|
- add a set of run-time param ({inputfield}_interpMethod), one for |
1376 |
|
each interpolated input field, to select the interpolation method |
1377 |
|
with a value of zero switching off the interpolation; |
1378 |
|
- print interpolation parameters to standard output; |
1379 |
|
- refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined |
1380 |
|
(to use instead runoff_interpMethod=0 in data.exf). |
1381 |
|
- simplify default setting of interpolation parameters (for all fields, |
1382 |
|
set position to match model grid cell-center position, leading to trivial |
1383 |
|
interpolation in case of regular Lat-Lon grid) and fix for the case of |
1384 |
|
non-uniform delY. |
1385 |
|
o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for |
1386 |
|
within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1. |
1387 |
|
this factor is absolutely required, because the lw exitance (= out-going |
1388 |
|
long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown, |
1389 |
|
where the reflectivity rho = 1-emissivity for conservation reasons. Once |
1390 |
|
this is established, we can remove the CPP-Flag (if we want to). |
1391 |
|
o pkg/seaice: |
1392 |
|
- qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and |
1393 |
|
ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined |
1394 |
|
- sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity |
1395 |
|
what the name implies (and not emissivity*BoltzmannConstant), this means |
1396 |
|
the old default value of 5.5e-8 now means |
1397 |
|
5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in |
1398 |
|
S/R exf_readparms |
1399 |
|
- FV-discretization of the B-grid LSOR solver, turn on with |
1400 |
|
SEAICE_LSRBNEW. This new solver also involves a slight re-organization |
1401 |
|
of the calling routine dynsolver, so that B and C-grid code look a |
1402 |
|
little more alike. |
1403 |
|
- fix index bugs in ostres.F (B-grid code) |
1404 |
|
o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better |
1405 |
|
o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the |
1406 |
|
default for SEAICE_emissivity, if useEXF; requires setting a wrong |
1407 |
|
parameter value in global_ocean.cs32x15/input.seaice/data.seaice for |
1408 |
|
backward compatiblity |
1409 |
|
o model/src: use sigmaR in calc_ivdc |
1410 |
|
|
1411 |
|
checkpoint63g (2011/12/16) |
1412 |
|
o pkg/seaice/seaice_growth.F: |
1413 |
|
fix heat conservation of the coupled ocean-seaice system. |
1414 |
|
when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of |
1415 |
|
solid vs liquid water treatment is resolved via QNET. |
1416 |
|
o pkg/seaice/seaice_growth.F: |
1417 |
|
add missing term for sublimation in saltFlux, which was breaking conservation. |
1418 |
|
o pkg/seaice/seaice_model.F: |
1419 |
|
Remove this patholigical case treatment in evolution branch, |
1420 |
|
where it is un-necessary and breaks conservation. |
1421 |
|
Update global_ocean.cs32x15/results accordingly for |
1422 |
|
output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt |
1423 |
|
o model/src: |
1424 |
|
useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in |
1425 |
|
external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE. |
1426 |
|
o pkg/obcs: |
1427 |
|
modify Stevens boundary conditions so that S/R obcs_calc_stevens computes |
1428 |
|
tendency for temperature and salinity that is then applied to update |
1429 |
|
theta and salt in S/R obcs_apply_ts; this requires proper masking of all |
1430 |
|
horizontal advection and diffusion contributions on the boundary (in |
1431 |
|
S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and |
1432 |
|
removing the mask in S/R timestep_tracer. The advantage of this approach is |
1433 |
|
that the updated tracer values include contributions from the surface |
1434 |
|
forcing and vertical diffusion. |
1435 |
|
This modification changes exp4.stevens because of vertical diffusion. |
1436 |
|
o model/src: |
1437 |
|
change non-curvilinear grid setting to also work with exch2 + blank tiles: |
1438 |
|
- move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst |
1439 |
|
face dimensions. |
1440 |
|
- new S/R INI_LOCAL_GRID to define model tile-local grid (using same units |
1441 |
|
as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID |
1442 |
|
and INI_SPHERICAL_POLAR_GRID. |
1443 |
|
change test-experiment global_ocean.90x40x15: |
1444 |
|
- split the domain in many more tiles (9x4 tiles of 10x10 each); |
1445 |
|
- switch to exch2 and remove 1 blank-tile (but only for MPI test). |
1446 |
|
- update results of both test (std & dwnslp). |
1447 |
|
o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in |
1448 |
|
tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation |
1449 |
|
o model/src: |
1450 |
|
- take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS |
1451 |
|
and fix initialisation when using sigma-coords. |
1452 |
|
o model/src: |
1453 |
|
- improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc. |
1454 |
|
to their current value at the beginning of forward_step.F": add a new run-time |
1455 |
|
switch "doResetHFactors" (default=false) and use it to do (or not) the resetting. |
1456 |
|
- set doResetHFactors=T in the following test exp: |
1457 |
|
global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS), |
1458 |
|
global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS) |
1459 |
|
and tutorial_global_oce_in_p (nonLinFS in p) |
1460 |
|
o pkg/ecco |
1461 |
|
- added IES cost term |
1462 |
|
o verification/advect_xz |
1463 |
|
- scale down the depth by 1/100 (from 200 km to just 2.km) |
1464 |
|
- add secondary test using divergent flow, r-star and implicit vertical advection. |
1465 |
|
- add note (check_conserve_TS.txt) and matlab script to check global |
1466 |
|
conservation of T & S with NonLin-FreeSurf and Adams-Bashforth. |
1467 |
|
o pkg/rbcs: |
1468 |
|
- add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F). |
1469 |
|
o pkg/obcs (Stevens BCs): |
1470 |
|
- fix various problems in the phase speed computations of the Stevens |
1471 |
|
boundary conditions: |
1472 |
|
- sign error for western and southern boundaries, |
1473 |
|
- time tendencies were underestimated by factor of dTracerLev and some just |
1474 |
|
zero (for multidim advection schemes) -> now estimate time tendencies |
1475 |
|
from difference between previous (n) time level and the one before (n-1); |
1476 |
|
this requires storing a field per tracer per boundary, also in the pickup |
1477 |
|
files. |
1478 |
|
- replace deltaTmom in cflMer/Zon computation with dTracerLev |
1479 |
|
- set default phase velocity to cflMer/Zon |
1480 |
|
- update verification experiment exp4.stevens |
1481 |
|
o pkg/generic_advdiff (implicit_r): |
1482 |
|
- fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf |
1483 |
|
(remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F); |
1484 |
|
- fix implicit vertical diffusion or advection with NonLin FreeSurf |
1485 |
|
(was using current recip_hFacC instead of future recip_hFacC): set future |
1486 |
|
recip_hFac in thermodynamics.F and pass & use it in all vertical implicit |
1487 |
|
solver S/R ; |
1488 |
|
- fill diagnostics of vertical advective fluxes (computed from tendency) |
1489 |
|
when using implicit vert. advection; |
1490 |
|
- update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion: |
1491 |
|
global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD), |
1492 |
|
tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD) |
1493 |
|
and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5. |
1494 |
|
o pkg/diagnostics: |
1495 |
|
- add diags for T & S tendency which goes through Adams-Bashforth. |
1496 |
|
|
1497 |
|
checkpoint63f (2011/11/30) |
1498 |
|
o pkg/obcs/obcs_calc_stevens.F: |
1499 |
|
- join some loops to reduce number of if-statements |
1500 |
|
- fix a bug in code for northern and southern boundaries. |
1501 |
|
o pkg/seaice/seaice_init_varia.F |
1502 |
|
- undo resetting UVM=0 that has slipped in unnoticed in r1.49 and |
1503 |
|
caused zero ice-velocities for the B-grid code |
1504 |
|
o pkg/seaice/seaice_init_fixed.F |
1505 |
|
- fix a bug in the initialisation of the second metric terms |
1506 |
|
k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0. |
1507 |
|
- this affects all seaice configurations with useCurviLinearGrid = .true. |
1508 |
|
and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms |
1509 |
|
= .true. (default) |
1510 |
|
- the only verification experiment affected is global_ocean.cs32x15: |
1511 |
|
icedyn, seaice, and seaice_dynmix (AD) |
1512 |
|
o pkg/thsice/thsice_diagnostics_state.F |
1513 |
|
- only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does |
1514 |
|
not contain garbage that can lead to surprises in diagstats_calc.F |
1515 |
|
o model/src: |
1516 |
|
- move bi,bj loops inside INTEGR_CONTINUITY ; |
1517 |
|
- call INTEGR_CONTINUITY directly from forward_step.F |
1518 |
|
(previously called from momentum_correction_step.F) |
1519 |
|
- call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F, |
1520 |
|
forward_step.F and pkg/ecco/the_main_loop.F |
1521 |
|
o model/src/do_oceanic_phys.F: |
1522 |
|
- reset addMass to zero only if useICEFRONT ; |
1523 |
|
- separated k-loop for rhoInSitu calculation ; |
1524 |
|
- add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P) |
1525 |
|
and at constant T,S (= WdRHOdP); |
1526 |
|
NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport |
1527 |
|
of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical |
1528 |
|
transport of locally-referenced potential density); |
1529 |
|
to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP) |
1530 |
|
o gluemnc: |
1531 |
|
- replace ncrcat with ncks when adding variables to *.glob.nc |
1532 |
|
- change the way variables without record dimensions are handled so that |
1533 |
|
files that have variables with and without record variables can be glued: |
1534 |
|
add a record dimension with a new unique name to be able to differentiate |
1535 |
|
between variable with and without a-prior record dimensions. Remove |
1536 |
|
this record dimension before adding the variable to the *.glob.nc file. |
1537 |
|
This procedure automatically works also for grid.*.nc files that do not |
1538 |
|
have any record dimension. |
1539 |
|
o verification/cpl_aim+ocn: |
1540 |
|
- generate new reference output on baudelaire (gfortran, mpich2) (previously |
1541 |
|
from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script. |
1542 |
|
o pkg/obcs/obcs_calc_stevens.F: |
1543 |
|
- add code for northern and southern boundaries. |
1544 |
|
- reorder some loops to save some operations and so that drFBar can be scalar |
1545 |
|
o model/src: |
1546 |
|
- re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine |
1547 |
|
truncation) and add diagnostics for Adams-Bashforth tendency increment. |
1548 |
|
- update test-exp. AD output: |
1549 |
|
1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl; |
1550 |
|
and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20, |
1551 |
|
front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5), |
1552 |
|
global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4), |
1553 |
|
matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre, |
1554 |
|
tutorial_global_oce_in_p, tutorial_global_oce_latlon and |
1555 |
|
tutorial_plume_on_slope. |
1556 |
|
o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX |
1557 |
|
that vectorises. This code uses 3 extra 2D fields, F90 array assignments |
1558 |
|
and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX |
1559 |
|
does not even come with an F77 compiler anymore, this should not be |
1560 |
|
a limitation |
1561 |
|
|
1562 |
|
checkpoint63e (2011/11/06) |
1563 |
|
o pkg/seaice adjoint of LSR: |
1564 |
|
- substantially rework STORE dirs. |
1565 |
|
- add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED |
1566 |
|
this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields |
1567 |
|
and only perform SOLV_MAX_FIXED adjoint iters. |
1568 |
|
If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration |
1569 |
|
always goes to same record, meaning that the last forward field will be |
1570 |
|
the one used in the adjoint - an approximation. |
1571 |
|
- now produces non-zero LSR-related gradients, and acceptable gradients for |
1572 |
|
An's zonal (x-z) test case (to be checked in) |
1573 |
|
- lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR |
1574 |
|
(but these are screwed up by the thermodynamics in the first place); |
1575 |
|
reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution; |
1576 |
|
output_adm.txt also reflects changes to seaice_lsr |
1577 |
|
- global_ocean.cs32x15: |
1578 |
|
* the "default" input_ad.seaice has been re-defined to always exclude dynamics |
1579 |
|
(output_adm.seaice.txt was updated) |
1580 |
|
* new input_ad.seaice_dynmix tests a forward LSR / backward free-drift |
1581 |
|
(output_adm.seaice_dynmix.txt) |
1582 |
|
o test-exp. exp4+stevens: |
1583 |
|
- switch off pTracers and nonHydrostatic (restart problems with NH); update output |
1584 |
|
o pkg/seaice (lsr solver): |
1585 |
|
- put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only); |
1586 |
|
update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15 |
1587 |
|
- fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD) |
1588 |
|
- new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution |
1589 |
|
into initial guess for linearised solver; use weight ~ (1/err)^2,4. |
1590 |
|
- compute (with new S/R) and print initial (+ free-driff sol. if available) |
1591 |
|
and final residual of linearised system. |
1592 |
|
o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity |
1593 |
|
(requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F) |
1594 |
o pkg/obcs: Stevens BCs (still only for east and west) |
o pkg/obcs: Stevens BCs (still only for east and west) |
1595 |
- fix Stevens BCs by using intermediate velocities of previous |
- fix Stevens BCs by using intermediate velocities of previous |
1596 |
time step as "baroclinic" contribution rather velocity of one grid cell |
time step as "baroclinic" contribution rather velocity of one grid cell |
1597 |
inside the boundaries; more consistent but makes the entire treatment |
inside the boundaries; more consistent but makes the entire treatment |
1598 |
more complicated, requires new pickup files and two new S/Rs: |
more complicated, requires new pickup files and two new S/Rs: |
1599 |
obcs_copy_uv_n and obcs_save_uv_n |
obcs_copy_uv_n and obcs_save_uv_n |
1600 |
keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY |
keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY |
1601 |
(undefined by default) |
(undefined by default) |
1602 |
- silently move computation of some grid factors into separate loops to |
- silently move computation of some grid factors into separate loops to |
1603 |
save some recomputations |
save some recomputations |
1604 |
- add a hack for non-linear free surface |
- add a hack for non-linear free surface |
1605 |
- add a verification experiment to exp4 that tests this code |
- add a verification experiment to exp4 that tests this code |