4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
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o adjoint with OpenAD: |
8 |
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- move OpenAD-specific files from verification/OpenAD/code_oad_all to a new |
9 |
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package openad. This package has to be compiled for all runs with OpenAD |
10 |
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instead of specifying code_oad_all as a modification directory. |
11 |
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- link the fortran templates from tools/OAD_support to the build directory |
12 |
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for preprocessing to avoid conflicts between different setups compiled |
13 |
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simultaneously and simplify cleanup. |
14 |
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o pkg/exf: |
15 |
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- in exf_getforcing.F: comment out most of the EXCH calls (fields used by |
16 |
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main model or other pkgs are exchanged in EXF_MAPFIELDS). |
17 |
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o model/src: |
18 |
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- do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline |
19 |
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(similar to do_fields_blocking_exchanges.F). |
20 |
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o tools/genmake2: |
21 |
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- remove TAF output src code just before calling staf (when not doing a fresh |
22 |
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built, will stop if things go wrong with staf). |
23 |
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- fix target "adobj" (left from TAF version-2 transition) |
24 |
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o pkg/diagnostics: |
25 |
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- add a parameter to track the status of pkg/diagnostics activation; |
26 |
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this replace/extend the use of logical param "settingDiags" (to check |
27 |
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when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call. |
28 |
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New S/R to print error message and stop when pkgStatus is not right. |
29 |
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- to try: add a warning when "data.diagnostics" exist but useDiagnostics=F. |
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|
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checkpoint64m (2013/08/13) |
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o model/inc: |
33 |
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- move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from |
34 |
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8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) |
35 |
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o pkg/kpp & aim_v23: |
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- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
37 |
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o pkg/seaice: |
38 |
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- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
39 |
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undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
40 |
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- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
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o eesupp/src: |
42 |
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- fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) |
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in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). |
44 |
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o switch to TAF version-2: |
45 |
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- add flow directives to "freeze" naming convention for ad-routines that |
46 |
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are used in I/O routines of adjoint state and associated common blocks |
47 |
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that are used in adcommon.h (backward compatible with version-1) |
48 |
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- update all ad-optfiles (in tools/adjoint_options + few local to some |
49 |
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verification exp) to switch to latest TAF version (currently 2.5.5); |
50 |
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merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented |
51 |
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out except for diva). |
52 |
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- the major change with TAF version-2 is that both the differentiated |
53 |
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routines and the forward routines (new) are returned as part of the TAF |
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output source code. Update genmake2 accordingly. |
55 |
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- new output for AD experiment tutorial_global_oce_biogeo (better AD gradient |
56 |
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with version-2 when compared to TLM or FWD gradient); other experiments |
57 |
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output show minor changes (machine truncation level); update the few AD & |
58 |
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TLM output with 12 matching digits only (some prior to version-2 switch). |
59 |
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|
60 |
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checkpoint64l (2013/08/05) |
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o model/src: |
62 |
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- in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F |
63 |
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- main_do_loop.F: no longer includes additional (AUTODIFF) header files |
64 |
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when using TAF but only if using OpenAD. |
65 |
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o pkg/mom_common+fluxform+vecinv: |
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- always set horiz. viscosity arrays to background value before calling |
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MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC |
68 |
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only when using variable horiz. viscosity (useVariableVisc=T); |
69 |
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- simplify mom_vecinv.F (only 1 block for momViscosity). |
70 |
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o pkg/mom_common: variable horiz. viscosity in NH code |
71 |
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- move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F) |
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from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h |
73 |
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- store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, |
74 |
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useBiharmonicVisc & useVariableVisc. |
75 |
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- fix old bug (already in 1rst implementation of variable horizontal viscosity |
76 |
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in calc_gw.F, version 1.27, 2006/06/20): |
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horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 |
78 |
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even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. |
79 |
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- change background horiz viscosity in vertical momentum (gW) to always be |
80 |
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viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using |
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any type of variable viscosity, e.g., viscAh/4Grid) |
82 |
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- change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of |
83 |
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viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing |
84 |
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horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since |
85 |
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default viscAh,viscA4 is zero). |
86 |
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o model/src: |
87 |
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- extend length of drC & recip_drC from Nr to Nr+1. |
88 |
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o Divided Adjoint (DIVA) with MPI: |
89 |
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- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
90 |
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- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
91 |
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and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h. |
92 |
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|
93 |
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checkpoint64k (2013/07/23) |
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o tools/OAD_support: |
95 |
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- avoid the need for file "oadtempflile" in insertTemplateDir.bash |
96 |
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and remove it from genmake2. |
97 |
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o tools/build_options: |
98 |
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- remove MPI_HEADER_FILES_INC setting (no longer used) and comment out |
99 |
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MPI_HEADER_FILES list (let genmake2 find the missing headers) |
100 |
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o verification/halfpipe_streamice: |
101 |
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- change to driving stress formulation; update both Fwd & AD output. |
102 |
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o tools/genmake2 and Divided Adjoint with MPI: |
103 |
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- remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken); |
104 |
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- only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set; |
105 |
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- add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in |
106 |
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Makefile, which is set by genmake2, and check which mpi-headers are needed. |
107 |
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Note: need to update adjoint_options/adjoint_diva_mpi accordingly. |
108 |
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- update target "CLEAN" (to also remove ./mpi_headers/ dir). |
109 |
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o testreport: |
110 |
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- changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, |
111 |
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perform additional runs (number of additional runs is "add_DIVA_runs" taken |
112 |
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from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h"). |
113 |
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o verification/lab_sea (AD test): |
114 |
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- change to test Divided Adjoint Run in this set-up (both standard AD test |
115 |
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and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test. |
116 |
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o pkg atm_ & ocn_compon_interf: |
117 |
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- remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old |
118 |
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staggerTimeStep implementation) and disable (retired) corresponding |
119 |
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parameter. |
120 |
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o pkg/offline: |
121 |
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- comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01]; |
122 |
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- add S/R OFFLINE_CHECK to print offline parameter summary |
123 |
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and stop if loading a file that is not used; |
124 |
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- enable to calculate GMRedi tensor, KPP mixing and convective index |
125 |
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when the corresponding file(s) is/are not specified (but pkg is used). |
126 |
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- comment out resetting of monitorFreq (to endTime) since it still useful |
127 |
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for monitoring CFL numbers and checking offline fields. |
128 |
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o OpenAD: |
129 |
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- do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get |
130 |
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smaller standard output) and generate new (smaller) output (on baudelaire |
131 |
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using gfortran with -ieee) for exp. tutorial_tracer_adjsens |
132 |
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o model/src: |
133 |
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- call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F), |
134 |
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(where external_forcing_adjust was called) and change list of arguments; |
135 |
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- merge external_forcing_adjust.F into external_forcing_surf.F |
136 |
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- put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F) |
137 |
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which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX, |
138 |
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previously in file "balance_relax.F", now removed); remove corresponding |
139 |
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arrays in FFIELDS.h. |
140 |
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- EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement |
141 |
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a hack for getting back surfaceForcingS (loaded from file) when using |
142 |
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ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up. |
143 |
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- update output of AD test experiment global_ocean.cs32x15.seaice_dynmix |
144 |
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(was getting only 11 digits for AD-grad, due to different truncation |
145 |
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error in AD code). |
146 |
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|
147 |
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checkpoint64j (2013/07/04) |
148 |
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o pkg/offline: |
149 |
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- to enable the use of other features with pkg offline (e.g., obcs), |
150 |
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also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come. |
151 |
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- comment out "allowFreezing" (now active) in 2 offline testing exp. |
152 |
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o pkg/exf ALLOW_RUNOFTEMP |
153 |
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- fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL |
154 |
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- ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice |
155 |
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- changes verification/global_ocean.cs32x15/results/output.seaice.txt |
156 |
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o pkg/atm_phys: |
157 |
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- allows to add some damping on uVel,vVel (strength only function of k). |
158 |
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o verification, ad-tests: |
159 |
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- reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, |
160 |
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global_ocean_ebm and offline_exf_seaice.thsice. |
161 |
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o verification/halfpipe_streamice: |
162 |
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- found a bug in s/r pkg/streamice/streamice_advect_thickness which caused |
163 |
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flux input boundary conditions to be ignored; a fix for this bug changed |
164 |
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verification results for forward test. |
165 |
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- add adjoint test. |
166 |
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o pkg/ptracers: |
167 |
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- allow to restart without SOM pickup (resetting SOM to zero). |
168 |
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o pkg/gmredi: |
169 |
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- New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added. |
170 |
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- It uses mixing length theory and suppression by steering level effects to |
171 |
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calculate a diffusivity used in the Redi tensor (see Bates et al., submitted |
172 |
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to JPO, for more details). |
173 |
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- It also uses the diffusivity to calculate an eddy induced streamfunction |
174 |
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based on a PV closure (rather than a buoyancy closure as in GM). |
175 |
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- New files added to pkg/gmredi: |
176 |
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gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy |
177 |
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induced overturning streamfunction (called from gmredi_calc_tensor) |
178 |
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gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required |
179 |
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for use in gmredi_k3d |
180 |
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gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate |
181 |
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the eddy diffusivity |
182 |
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|
183 |
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checkpoint64i (2013/06/18) |
184 |
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o pkg/cheapaml: |
185 |
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- take src files from MITgcm_contrib/verification_other/offline_cheapaml/code |
186 |
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that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics) |
187 |
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with pkg/cheapaml. |
188 |
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o utils/python: add subpackage for cubed sphere function, first example is |
189 |
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simple cs.pcol to plot 2D fields on a map |
190 |
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o pkg/streamice: |
191 |
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- This is a new package in MITgcm, which solves dynamic equations for ice |
192 |
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sheets and ice streams |
193 |
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- At the moment it is independent of atmosphere/ocean dynamics, or any |
194 |
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other physical packages in MITgcm, even ShelfIce (although it is anticipat- |
195 |
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ed that this will change) |
196 |
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- There is a new verification exercise that tests it, halfpipe_streamice, |
197 |
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evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a |
198 |
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rectangular embayment |
199 |
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- halfpipe_streamice is forward-only for now, will have TAF test soon |
200 |
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- for questions, email dgoldber@mit.edu |
201 |
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o pkg/thsice: |
202 |
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- fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing |
203 |
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of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40); |
204 |
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- remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new |
205 |
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call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect ); |
206 |
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- allow precip from pkg/cheapaml to make snow over seaice. |
207 |
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o pkg/cfc: |
208 |
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- move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC |
209 |
|
- remove atmos CFC 2-D arrays from common bloc (now local variables) |
210 |
|
- change some hard-coded constant to run time parameter for reading and |
211 |
|
and interpolating atmospheric CFC ; keep same default as previously. |
212 |
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- more flexible reading of Atmos CFC (number of records no longer hard-coded) |
213 |
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- put arguments in standard order: myTime, myIter, myThid |
214 |
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- use standard S/R GET_PERIODIC_INTERVAL for time interpolation of |
215 |
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atmospheric CFC ; fix for the case myIter < PTRACERS_iter0. |
216 |
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- fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf |
217 |
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- new routine to print summary of CFC params and check for consistency. |
218 |
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o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff, |
219 |
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similar to thsice_advdiff. |
220 |
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Note that for the B-grid case the routine parameters uc/vc are overwritten. |
221 |
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o pkg/cfc: |
222 |
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- change time interpolation for atmospheric CFC-11 (now same as for CFC-12); |
223 |
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update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline. |
224 |
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- fix interpolation of atmphspheric CFC between Sorthern and Northern |
225 |
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hemisphere value. |
226 |
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o pkg/seaice: |
227 |
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- allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml) |
228 |
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o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics; |
229 |
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so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE. |
230 |
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- requires an additional time level that is stored in the pickup |
231 |
|
- you can start with AB2 from a pickup without this time level with |
232 |
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pickupStrictlyMatch = .false. |
233 |
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|
234 |
|
checkpoint64h (2013/05/26) |
235 |
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o pkg/cheapaml: |
236 |
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- replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux); |
237 |
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affect machine truncation (but exp cheapAML_box still pass with 13 digits). |
238 |
|
- consistent treatment of uWind,vWind location: assume everywhere in |
239 |
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pkg/cheapaml that they are on C-grid (@ uVel,vVel location) |
240 |
|
(Note: was already the case for Tair,Qair advection); |
241 |
|
add option (INCONSISTENT_WIND_LOCATION) to recover old results. |
242 |
|
- compute diabatic forcing only in the interior (excluding overlap regions) |
243 |
|
- fill in array "Qsw" (for short-wave heating); |
244 |
|
- add diagnostic for precip ; fill-in diagnostics for cheapAML state vars |
245 |
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before any update (consistent with MITgcm state var diagnostics); |
246 |
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- cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if |
247 |
|
non periodic ; + adjusted for uWind,vWind (C-grid). |
248 |
|
o pkg/seaice: |
249 |
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- remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and |
250 |
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add explicitly pkg/exf in experiments that currently use pkg/seaice. |
251 |
|
- allows to compile pkg/seaice without pkg/exf. |
252 |
|
o tools/OAD_support: |
253 |
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- use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds |
254 |
|
of array "ourStepOf" in function rvNextAction (revolve.F90). |
255 |
|
o pkg/aim_compon_interf renamed to pkg/atm_compon_interf |
256 |
|
- change pkg name (to be used with other atmospheric physics pkg) |
257 |
|
but by-pass CVS when making the new pkg so that we keep the CVS history. |
258 |
|
o pkg/offline: |
259 |
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- call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F |
260 |
|
(previously called from pkg/dic_surfforcing_init.F) |
261 |
|
o model/src: |
262 |
|
- re-order sequence of calls within packages_init_variables.F, using |
263 |
|
standard order, except for: |
264 |
|
DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top), |
265 |
|
CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom) |
266 |
|
o new pkg: atm_phys |
267 |
|
- add entry point and source code (previously in contrib |
268 |
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verification_other/atm_gray/code_gray/) for new pkg "atm_phys" |
269 |
|
(atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008). |
270 |
|
- re-order sequence of calls within packages_readparms.F, |
271 |
|
packages_init_fixed.F and packages_write_pickup.F |
272 |
|
(but skip packages_init_variables.F because of TAF issues). |
273 |
|
- update contrib/*/atm_gray/ experiment. |
274 |
|
o pkg/seaice (ITD code): |
275 |
|
- simplify and fix the writing of pickup-files for ITD case |
276 |
|
o pkg/seaice (ITD code): |
277 |
|
- introduce floe size dependent lateral melt for ITD case; |
278 |
|
- cleaning (avoid division by zero, change to f77 syntax, remove tabs) |
279 |
|
- update seaice_itd experiment main output. |
280 |
|
o pkg/thsice: |
281 |
|
- remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and |
282 |
|
declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F; |
283 |
|
changed accordingly pkg/atm2d. |
284 |
|
|
285 |
|
checkpoint64g (2013/05/01) |
286 |
|
o pkg/exf ALLOW_RUNOFTEMP |
287 |
|
- if defined, river and glacier runoff temperature can be read-in from |
288 |
|
runoftempfile; runoftempfile needs to have same format as runofffile |
289 |
|
o pkg/thsice (& pkg/bulk_force): |
290 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
291 |
|
for energy content of Precip + RunOff & Evap (like with pkg/exf). |
292 |
|
- change computation domain to always be the interior (without overlap). |
293 |
|
- fix bug (wrong overlap) when using EXF and stressReduction > 0. |
294 |
|
o verification/tutorial_global_oce_biogeo: |
295 |
|
- add preliminary OpenAD setup (still has problems) |
296 |
|
o pkg/seaice: |
297 |
|
- turn some parameters for choosing the convergence criterion of |
298 |
|
the inexact Newton method (JFNK) into runtime parameters for convenience |
299 |
|
- clean up seaice_calc_viscosities.F: remove/retire two options for |
300 |
|
SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes |
301 |
|
the results of lab_sea/input because a division has been replaced by |
302 |
|
a multiplication with the reciprocal (sumNorm) |
303 |
|
- modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve |
304 |
|
convergence of solver (changes results, of course), and to test some |
305 |
|
new features |
306 |
|
o model/src: |
307 |
|
- remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call. |
308 |
|
- remove unused forcing field "dQdT" and associated parameter "dQdTFile". |
309 |
|
- move forcing adjustment (balancing surface forcing) in specific S/R |
310 |
|
where might also be applied exchanges (if needed) to forcing arrays. |
311 |
|
o pkg/shelfice: |
312 |
|
- allow to specify the Ice-Shelf mass per unit area (instead of |
313 |
|
shelficeLoadAnomaly) and do the conversion from one to the other |
314 |
|
- move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA |
315 |
|
to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and |
316 |
|
(b) will be loaded in time (before calling INI_PRESSURE) in case it is |
317 |
|
needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc |
318 |
|
- update isomip experiment forward output (get machine truncation error |
319 |
|
from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly) |
320 |
|
o verification/offline_exf_seaice: |
321 |
|
revise data.seaice in input.thermo and input_ad and update results accordingly |
322 |
|
HO = 0.2, SEAICE_areaLossFormula = 2, |
323 |
|
SEAICE_growMeltByConv = .TRUE., |
324 |
|
SEAICE_doOpenWaterMelt = .TRUE., |
325 |
|
Improve consistency with input.thsice and fix the spurious 500m ice corners |
326 |
|
o verification/global_ocean.cs32x15: |
327 |
|
- set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0., |
328 |
|
in icedyn (thsice+seaice-dyn) test and update output. |
329 |
|
o verification/offline_exf_seaice: |
330 |
|
- adjust list of tested variables (with testreport) and update |
331 |
|
standard test output with better slection of monitored fields. |
332 |
|
o pkg/cd_code: |
333 |
|
- swtich off Adams-Bashforth on the 1rst iteration. Update output of |
334 |
|
experiment lab_sea.hb87 |
335 |
|
o tools/genmake2: |
336 |
|
- change default makedepend from the system default to tools/xmakedepend: |
337 |
|
When no makedepend is specified, select tools/xmakedepend it the test pass, |
338 |
|
otherwise select the system default (if exist and pass the test) or |
339 |
|
try to build cyrus-makedepend ; stop if none of the 3 works. |
340 |
|
o pkg/exf & pkg/thsice: |
341 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
342 |
|
for energy content of Precip + RunOff & Evap. Assumes: |
343 |
|
1) Rain has same temp as Air. |
344 |
|
2) Snow has no heat capacity (consistent with seaice & thsice pkgs) |
345 |
|
3) Run-Off comes at the temp of surface water (with same Cp) |
346 |
|
4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be |
347 |
|
put directly into Latent Heat flux & should use water-vapor heat capacity. |
348 |
|
5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent |
349 |
|
with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL). |
350 |
|
o pkg/seaice: simplify the use of CPP flags in JFNK-related files |
351 |
|
(compile when SEAICE_ALLOW_JFNK is defined) |
352 |
|
o pkg/thsice: |
353 |
|
- fix oceanic flux diagnostics & timeave (left from new sequence of calls |
354 |
|
implementation): move THSICE_AVE call after the advection (called directly |
355 |
|
from thsice_do_advect.F). |
356 |
|
o verification/global_ocean.90x40x15 and OpenAD: |
357 |
|
New experiment for OpenAD is identical to the one in input_ad except that |
358 |
|
multiDimAdvection=.FALSE., |
359 |
|
There is still an issue with this. |
360 |
|
o pkg/thsice: |
361 |
|
- account for ice velocity (ocean relative velocity) in turbulent heat flux |
362 |
|
at the base of the ice; update output of global_ocean.cs32x15 (icedyn) |
363 |
|
and offline_exf_seaice (main test). |
364 |
|
|
365 |
|
checkpoint64f (2013/03/31) |
366 |
|
o verification/OpenAD: |
367 |
|
- new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran. |
368 |
|
o verification/isomip, pkg/shelfice and OpenAD: |
369 |
|
- add OpenAD setup to this exp and make shelfice package work with OpenAD |
370 |
|
o verification/tutorial_global_oce_biogeo: |
371 |
|
- update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h) |
372 |
|
o verification/offline_exf_seaice: |
373 |
|
- replace adjoint experiment (now similar to fwd input.thermo/ setup). |
374 |
|
o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD: |
375 |
|
- add OpenAD setup to this exp and make ptracers package work with OpenAD |
376 |
|
o pkg/seaice/seaice_evp.F: |
377 |
|
mask the asymmetric contribution of the ice-ocean stress (when |
378 |
|
the turningAngle is non-zero) over open water to avoid stripes |
379 |
|
in the EVP-solutions after many EVP-substeps. This does not change |
380 |
|
the verification experiment (because turningAngle=0 in that experiment), |
381 |
|
but will affect other EVP solutions with turningAngle.ne.0 |
382 |
|
o verification, AD & TLM output: |
383 |
|
- new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple |
384 |
|
additions and multiplications which affect results at machine truncation |
385 |
|
level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5, |
386 |
|
lab_sea.noseaicedyn & offline_exf_seaice) and TLM output |
387 |
|
(1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12 |
388 |
|
digits of matching. |
389 |
|
o pkg/seaice: |
390 |
|
modify lsr-algorithm so that it vectorizes AND converges by using a |
391 |
|
"zebra" method: split vector loop into two with step size 2; this |
392 |
|
solves a general convergence problem for the JFNK solver on a vector |
393 |
|
computer. It has the potential to even improve convergence for |
394 |
|
non-vector machines, but it does change the results so it is turned |
395 |
|
off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and |
396 |
|
SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h |
397 |
|
|
398 |
|
checkpoint64e (2013/03/05) |
399 |
|
o pkg/ecco and several verification experiments: |
400 |
|
Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F |
401 |
|
from ecco package, and revert to unified routine in model/src/ |
402 |
|
Adjust verification experiments accordingly, especially gloal_oce_llc90 |
403 |
|
Should conclude long-standing work by Gael to reconsile the_main_loop with |
404 |
|
ECCO and will enable OpenAD's revolve loop in ECCO setup. |
405 |
|
o pkg/generic_advdiff: |
406 |
|
- implement compressible flow method for multi-dim advection (similar to |
407 |
|
gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since |
408 |
|
TAF generates many recomputations) to use it; no yet coded with implicit |
409 |
|
vertical advection. |
410 |
|
- change experiment advect_cs (new output) and advect_xy (same output) |
411 |
|
to test compressible flow multi-dim advection. |
412 |
|
o pkg/generic_advdiff: |
413 |
|
- fix SOM advection for unusual cases (linear Free-Surf in r*, other |
414 |
|
cases where linear Free-Surf is not @ k=1, e.g., useShelfIce) |
415 |
|
o pkg/seaice: |
416 |
|
- fix bug in the no-slip implementation in seaice_calc_strainrates.F, this |
417 |
|
bug affects two verification experiments (lab_sea and lab_sea.hb87), |
418 |
|
recover old (wrong) results by setting noSlipFac = 2. in |
419 |
|
seaice_calc_strainrates.F; |
420 |
|
- add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0 |
421 |
|
- add runtime parameter SEAICE_JFNKepsilon for that finite difference |
422 |
|
gradient in the Jacobian times vector operation (s/r seaice_jacvec) |
423 |
|
- fix line search in seaice_jfnk.F (s/r seaice_jfnk_update) |
424 |
|
o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code: |
425 |
|
- new subroutines seaice_lsr_tridiagu/v |
426 |
|
- introduce loop bounds i/jmin/max to be able to use a restricted |
427 |
|
additive Schwarz method, but not used for now. |
428 |
|
- rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS |
429 |
|
- use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner |
430 |
|
o OpenAD support |
431 |
|
Reorganize S/R call for overall time-stepping loop to facilitate |
432 |
|
OpenAD revolve loop replacement |
433 |
|
(new S/R main_do_loop.F) |
434 |
|
o model/src: |
435 |
|
- add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3; |
436 |
|
- pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R |
437 |
|
ADAMS_BASHFORTH2. |
438 |
|
o pkg/cheapaml: |
439 |
|
- add new parameter (default=F, same as before) to disable full domain |
440 |
|
(including land) periodicity in X & Y dir. |
441 |
|
- new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of |
442 |
|
prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer |
443 |
|
into single S/R CHEAPAML_TIMESTEP. |
444 |
|
|
445 |
|
checkpoint64d (2013/02/17) |
446 |
|
o pkg/monitor (angular momentum): |
447 |
|
- do not add Eta contribution to the total AM if using rigid-lid; |
448 |
|
- correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta). |
449 |
|
- horizontal discretisation: compute Zonal wind contribution separately for |
450 |
|
each component (instead of from cell centered averaged) and use the 4 |
451 |
|
grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part. |
452 |
|
- Check that AM is conserved with linear dynamics (momAdvection=F and linear |
453 |
|
FreeSurf) if using vectorInvariant momentum. |
454 |
|
o model/src (horizontal grid): |
455 |
|
- move initialisation of all horizontal grid arrays to null value |
456 |
|
from specific horizontal grid S/R to main S/R INI_GRID; |
457 |
|
- add 2 new arrays to project model C-grid velocity on to zonal direction |
458 |
|
(similar to AngleCosC & -AngleSinC but at U and V point location) and |
459 |
|
compute them in S/R CALC_GRID_ANGLES. |
460 |
|
o pkg/seaice: replace a hard coded parameter by a runtime parameter |
461 |
|
SEAICE_JFNK_tolIter |
462 |
|
o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in |
463 |
|
preconditioner for JFNK (run LSR into the overlaps as far as possible, |
464 |
|
i.e OLx/y-2, but overwrite the solution in the overlaps) |
465 |
|
- extend loop range in seaice_calc_viscosity |
466 |
|
- add new parameters SEAICE_OLx/y (default = OLx/y-2) |
467 |
|
- add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs |
468 |
|
- slightly modify loops in tridiagonal solver lsr-preconditioner |
469 |
|
- by default remove the extra exchange in seaice_preconditioner with a |
470 |
|
replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE |
471 |
|
- modify offline_exf_seaice so that old results without RAS are reproduced |
472 |
|
for output.dyn_jfnk.txt |
473 |
|
in seaice_fgmres.F (unrelated to RAS) |
474 |
|
- add a cpp-flag option for a re-ordered mapping (potentially more |
475 |
|
efficient), but because this changes the results, turn it off by |
476 |
|
default |
477 |
|
- replace the save statement by local common blocks |
478 |
|
o utils/matlab: |
479 |
|
- fix tile-offset in rdmnc.m when output was produced using EXCH2. |
480 |
|
- update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab) |
481 |
|
instead of local script "load_cs.m". |
482 |
|
o pkg/seaice: |
483 |
|
- fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected |
484 |
|
to the scalarProductMetric and the unrolling. By chance this does not |
485 |
|
change the verification experiment, because of the particular domain |
486 |
|
decomposition |
487 |
|
o pkg/diagnostics: |
488 |
|
- change default missing_value from UNSET_RL to -999. |
489 |
|
o pkg/layers: improve vectorization of layers_fluxcalc.F |
490 |
|
- step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu |
491 |
|
time spent in this routine by more than a factor of 3 on an NEC-SX8 |
492 |
|
- step 2: replace search algorithm by a bisection algorithm found in |
493 |
|
Press et al. Numerical Recipes in Fortran. This algorithm can be |
494 |
|
vectorized and finds the correct bin in approx. log2(Nlayers) steps. |
495 |
|
For now, use this algorithm only for TARGET_NEC_SX defined. |
496 |
|
- moved the search algorithm into a separate subroutine, that is kept |
497 |
|
within the same file for automatic inlining. |
498 |
|
- modified catching potential errors |
499 |
|
o pkg/ecco: |
500 |
|
- add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY. |
501 |
|
o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk : |
502 |
|
- modifications for ALLOW_GENTIM2D_CONTROL |
503 |
|
-- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes. |
504 |
|
-- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid ) |
505 |
|
-- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc |
506 |
|
-- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F |
507 |
|
o model/src: |
508 |
|
- account for moist thermodynamics in (dry) potential temperature equation; |
509 |
|
update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev) |
510 |
|
and cpl_aim+ocn. |
511 |
|
- also switch to standard compiler (gfortran, was using ifort previously) |
512 |
|
for fizhi-cs experiments reference output. |
513 |
|
o pkg/ctrl: |
514 |
|
- 1st step toward generic time-varying control variable (2D) via CPP option |
515 |
|
ALLOW_GENTIM2D_CONTROL |
516 |
|
- note new namelist ctrl_nml_genarr in data.ctrl |
517 |
|
o verification/global_ocean.cs32x15: |
518 |
|
- switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new |
519 |
|
thsice calling sequence and update "output.icedyn.txt" output file. |
520 |
|
o pkg/ptracers: |
521 |
|
- from Ryan A.: code to allow to restart a tracer at regular time interval |
522 |
|
specifying a reset frequency and a reset-phase (for each tracers). |
523 |
|
o pkg/thsice: |
524 |
|
- implement new sequence of calls for thsice+seaice: |
525 |
|
previously: ice-Dyn,ice-Advect,ice-Thermo(thsice) |
526 |
|
new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect |
527 |
|
- allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE" |
528 |
|
in CPP_OPTIONS.h) to recover old sequence; |
529 |
|
- update diagnostics for Intermediate State thsice diagnostics: now filled |
530 |
|
just before advection (instead of just after advection in old sequence); |
531 |
|
- update output of experiment offline_exf_seaice (standard test); |
532 |
|
- in global_ocean.cs32x15 exp., postpone output.icedyn.txt update |
533 |
|
by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h |
534 |
|
o pkg/aim_v23: |
535 |
|
- use tiled array for aim_CO2 and surface wind speed for export to coupler; |
536 |
|
- use standard pkg/mdsio routines to read & write CO2 pickup file; |
537 |
|
- in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F; |
538 |
|
- Implement new sequence of calls for seaice advection (with thsice and |
539 |
|
seaice diffusion): do ice advection after ice-Thermodynamic (previously |
540 |
|
was done before); change aim_do_physics.F (split the bi,bj loops block); |
541 |
|
- use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence; |
542 |
|
o pkg/thsice: |
543 |
|
- add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case |
544 |
|
where just seaice diffusion is used without seaice-dynamics. |
545 |
|
|
546 |
|
checkpoint64c (2013/01/18) |
547 |
|
o pkg/seaice: |
548 |
|
- add a parameter JFNKres_tFac that can replace JFNKres_t |
549 |
|
(= JFNKres_tFac*JFNKresidual before JFNK solver) |
550 |
|
- add a line search option to the JFNK solver |
551 |
|
- move update of u/vIce and computation of initial residual into a separate |
552 |
|
routine (same file); makes the code a little easier to read (?) |
553 |
|
- the line search requires computation of the residual and for some reason |
554 |
|
I cannot do the update of u/vIce at the beginning of the Newton loop |
555 |
|
without changing the results, so we move computation of the new residual |
556 |
|
also to the end of the Newton loop, even without the line search |
557 |
|
o pkg/mdsio: |
558 |
|
- write missing value (corresponding to undefined array value) to meta files; |
559 |
|
skip this if missing value is one (UNSET_RL would be a better value for the |
560 |
|
case of undefined missing value but it's current the default missing-value); |
561 |
|
Also update mdsio_read_meta.F (reading timeInterval & missing-value). |
562 |
|
o pkg/exf & thsice: |
563 |
|
- for diagnostics purpose, fill-up and update Qsw array (+ fill the |
564 |
|
diagnostics) even when SHORTWAVE_HEATING is #undef; |
565 |
|
o verification/cfc_example: |
566 |
|
- turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to |
567 |
|
illustrate how to use it). |
568 |
|
o verification/offline_exf_seaice: |
569 |
|
in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing |
570 |
|
files to only one time-record. |
571 |
|
in input.thermo: narrow the 2 bands of low initial ice-concentration near |
572 |
|
N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for |
573 |
|
snapshot output; same mcPheePiston value as in thsice with |
574 |
|
surf-current=0.2m/s. |
575 |
|
in input.thsice: similar set-up as in input.thermo (channel with same seaice |
576 |
|
initial conditions). |
577 |
|
o verification/cfc_example: |
578 |
|
- update file "data" with more standard choice (default rotationPeriod, |
579 |
|
exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F, |
580 |
|
set deltaTFreeSurf to deltaTtracer) and update the output. |
581 |
|
o pkg/layers: |
582 |
|
- fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC; |
583 |
|
- ensure that "layers_bolus" is switched to False when useGMRedi=False. |
584 |
|
o verification/offline_exf_seaice: |
585 |
|
- set all {field}period to zero for constant-in-time forcing (not tested |
586 |
|
anywhere else). |
587 |
|
o verification/offline_exf_seaice: |
588 |
|
- dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice; |
589 |
|
- dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice. |
590 |
|
o model/src: |
591 |
|
- implement Finite-Volume method for (hydrostatic) presure gradient |
592 |
|
from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate. |
593 |
|
o pkg/seaice: implement EVP* by Lemieux et al. (2012). |
594 |
|
- In order to be compatible with the default EVP code, this requires changing |
595 |
|
the EVP code around a little; and because any small change immediately |
596 |
|
breaks the lab_sea.hb87 verification experiment, the reference output is |
597 |
|
updated two times (each time the remaining aggrement was only 2 digits): |
598 |
|
- after replacing 1/dt by 1*recip_dt with a precomputed recip_dt |
599 |
|
- after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt |
600 |
|
The adjoint test lab_sea.evp also needed to be updated. |
601 |
|
- Turn on EVP* by setting SEAICE_deltaTevp as before, and setting |
602 |
|
SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be |
603 |
|
a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps |
604 |
|
explicitly with SEAICEnEVPstarSteps (thereby overriding the default of |
605 |
|
INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately |
606 |
|
kept obscure, because I need to test it a little more. |
607 |
|
o pkg/cheapaml: |
608 |
|
- fix few incorrect type (_RL/_RS) in subroutine calls. |
609 |
|
o pkg/seaice: |
610 |
|
- new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays |
611 |
|
to _RL vector; this fixes JFNK code when compiling with "-use_r4" option. |
612 |
|
o model/src: |
613 |
|
- add a warning if using select_rStar=2 with nonlinFreeSurf <> 4; |
614 |
|
change (in input_ad*/data) select_rStar from 2 to 1 for AD verification |
615 |
|
experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output) |
616 |
|
o pkg/cheapaml: |
617 |
|
- replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and |
618 |
|
update output of experiment cheapAML_box. |
619 |
|
- store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity, |
620 |
|
and set them only in one place (cheapaml_readparms.F). |
621 |
|
- replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI" |
622 |
|
- remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms) |
623 |
|
and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia). |
624 |
|
o model/src/the_main_loop.F: |
625 |
|
- fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION. |
626 |
|
o pkg/seaice: |
627 |
|
- remove legacy branch code. |
628 |
|
- retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly. |
629 |
|
o verification/*/code*/SEAICE_OPTIONS.h: |
630 |
|
- remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY, |
631 |
|
SEAICE_CAP_HEFF). |
632 |
|
o pkg/cheapaml: |
633 |
|
- use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time |
634 |
|
to load new forcing fields. |
635 |
|
- add missing "_d 0" where it's needed; + some editing (improve indentation). |
636 |
|
- remove switch to "-r8" compiler option (no longer needed) in verification |
637 |
|
cheapAML_box, keep same output (small trucation error differences). |
638 |
|
o verification/offline_exf_seaice: |
639 |
|
- add thermodynamics only test. |
640 |
|
o verification/cheapAML_box: |
641 |
|
- split the domain in 8 (2x4) tiles; add MPI and multi-threaded test; |
642 |
|
keep same output (same 14 digits for cg2d). |
643 |
|
- switch on "-r8" compiler option (some numerical values are missing |
644 |
|
the "_d 0") and update output (only 6 digits for cg2d were preserved). |
645 |
|
|
646 |
|
checkpoint64b (2012/12/24) |
647 |
|
o pkg/cheapaml: |
648 |
|
- remove un-used variables (Qnet,EmPmR) from pickup files. |
649 |
|
- store tendency of advected variables into cheapaml pickup file |
650 |
|
and fix the AB-2 restart. |
651 |
|
o verification/offline_exf_seaice and lab_sea adjoint: |
652 |
|
- switch to new code (#undef SEAICE_GROWTH_LEGACY). |
653 |
|
- switch to 4 time steps in offline, consistent with lab_sea. |
654 |
|
- match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice. |
655 |
|
- update results after change of experiment seaice. |
656 |
|
o pkg/seaice: |
657 |
|
- remove option SEAICE_MULTICATEGORY; has been replaced with run-time |
658 |
|
parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is |
659 |
|
still defined since SEAICE_multDim needs to be set to MULTDIM value (from |
660 |
|
SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default. |
661 |
|
o model/src: |
662 |
|
- add run-time parameter to select CG2D solver minimum-residual solution |
663 |
|
(in case of a poor convergence). |
664 |
|
o pkg/seaice/seaice_lsr.F |
665 |
|
- move calculation of matrix coefficients into new |
666 |
|
S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same |
667 |
|
file; the main purpose of this change is to be able to reuse the code |
668 |
|
in S/R SEAICE_PRECONDITIONER |
669 |
|
- modify the computation of the residual so that the mass of sea-ice |
670 |
|
is not used twice; this simplifies the calculations, but since |
671 |
|
the residual is never used except when LSR_mixIniGuess.ge.4---and this is |
672 |
|
not tested in testreport---this does not affect the testreport results. |
673 |
|
o verification/seaice_obcs: |
674 |
|
- disable SEAICE_GROWTH_LEGACY; reset input files to match those of |
675 |
|
verification/lab_sea/input.salt_plume; changes results/output.txt* |
676 |
|
o model/src: |
677 |
|
- adapt quasi-hydrostatic formulation to work with p or p* coordinate. |
678 |
|
o pkg/seaice: |
679 |
|
- improve description of parameters in seaice_fgmres.F and start |
680 |
|
cleaning up the code |
681 |
|
- change name of SCALPROD to SEAICE_SCALPROD and modify meaning of |
682 |
|
second argument |
683 |
|
- add a metric based on grid cell area to SEAICE_SCALPROD; update |
684 |
|
results of offline_exf_seaice.dyn_jfnk |
685 |
|
- compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD |
686 |
|
o pkg/aim_v23: |
687 |
|
- fix an other bug in dissipation heating (grid-cell area was missing). |
688 |
|
o model/src + pkg/seaice: |
689 |
|
- add global (multi-tile) linear solver for pair of tri-diagonal system |
690 |
|
along X and Y lines, respectively for U and V component. |
691 |
|
Note: 1) MPI and cube-exchange not yet coded. |
692 |
|
2) probably not accurate for poorly conditioned / large size problem. |
693 |
|
- add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver; |
694 |
|
default: not compiled and not used. |
695 |
|
o pkg/seaice: |
696 |
|
- first attempt at a multi-threaded fgmres solver for the JFNK solver: |
697 |
|
introduce bi/bj loops and use global_sum_tile_rl instead of |
698 |
|
mpi_allreduce in seaice_fgmres.F |
699 |
|
- improve diagnostics output for fgmres solver (seaice_fgmres.F) |
700 |
|
- replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F) |
701 |
|
- add a verification experiment for JFNK in offline_exf_seaice |
702 |
|
o verification: |
703 |
|
- change (for now, only fwd test) offline_exf_seaice experiment: |
704 |
|
use a re-entrant channel with idealized coastline (trapezoidal shape) |
705 |
|
at southern boundary to explore seaice dynamics and thermodynamics |
706 |
|
with simple forcing. Main set-up has dynamics+thermo and SST relaxation; |
707 |
|
secondary test (input.thsice) use thermodynamics only with SST relaxation. |
708 |
|
- add seaice-dynamics only secondary test using LSR and pkg/thsice advection. |
709 |
|
o pkg/exf: |
710 |
|
- disable "sstExtrapol" when Nr=1 |
711 |
|
o verification: |
712 |
|
- add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble) |
713 |
|
to test pkg/cheapaml. |
714 |
|
o pkg/aim_v23 & pkg/shap_filt: |
715 |
|
- fix dissipation heating (erroneous gravity multiplication factor). |
716 |
|
o pkg/seaice: |
717 |
|
- remove unused field pressPre from jfnk solver |
718 |
|
- rename two subroutines in seaice_preconditioner.F |
719 |
|
o eesupp/src: |
720 |
|
- S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...) |
721 |
|
o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again |
722 |
|
- remove wrong parts of the rhs and the lhs (were in there |
723 |
|
because I did not understand the concept of this preconditioner) |
724 |
|
- add an exchange between u- and v-sweep. This increases communication |
725 |
|
by a factor of two but improves the convergence of jfnk. Ideally, |
726 |
|
one would like the u- and v-sweep to be independent. So far within |
727 |
|
undocumented ifdefs |
728 |
|
- reorganize the extra computations for printing the residuals |
729 |
|
o tools/genmake2: |
730 |
|
- comment out the "mpif.h" include in NetCDF test programm (for MPI built) |
731 |
|
since it's not necessary (and was preventing to use MNC in some cases). |
732 |
|
|
733 |
|
checkpoint64a (2012/11/16) |
734 |
|
o pkg/autodiff: |
735 |
|
- improve pkg-internal logical parameter switch (inAd/inFwd mode) so that |
736 |
|
autodiff_readparms.F no longer depends on calling order (within |
737 |
|
packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h): |
738 |
|
rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd |
739 |
|
and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd. |
740 |
|
o pkg/obcs: |
741 |
|
- adding tidal velocity forcing capability to obcs |
742 |
|
for usage example, see verification/seaice_obcs/input.tides |
743 |
|
o pkg/seaice: |
744 |
|
- turn the LSR-relaxation parameters WFAU/V into runtime parameters |
745 |
|
SEAICE_LSRrelaxU/V |
746 |
|
- introduce runtime parameter SEAICEetaZmethod (=0 by default) |
747 |
|
o pkg/aim_v23: |
748 |
|
- implement heating from friction (bottom friction and stratospheric drag). |
749 |
|
o pkg/shap_filt: |
750 |
|
- fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from |
751 |
|
dissipation but only for Shap_funct=2, active when addFrictionHeating=T. |
752 |
|
o model/src: |
753 |
|
- move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in |
754 |
|
time-constant addMass field from file (addMassFile); |
755 |
|
- support for heating due to friction (and Kinetic Energy dissipation): |
756 |
|
add option, run-time switch and 3-D field array + support code ; each pkg |
757 |
|
or S/R can add heating contribution (if there is a sink of KE); the sum is |
758 |
|
accounted for as a Temperature tendency term (EXTERNAL_FORCING_T). |
759 |
|
o pkg/seaice: |
760 |
|
- complete merge of ITD code into seaice_growth.F |
761 |
|
from MITgcm_contrib/torge/itd/code/ |
762 |
|
no verification so far, but Torge Martin tested |
763 |
|
"1-D test case and Beaufort set up; |
764 |
|
deliver okay results after 1 model year." |
765 |
|
- complete merge of SEAICE_SIZE.h into all relevant routines |
766 |
|
- move computation of eta at Z-points into calc_viscosities |
767 |
|
+ introduce global field etaZ |
768 |
|
+ add different methods for computing etaZ, for now the old |
769 |
|
method (simple averages of eta to Z-points) is hardwired |
770 |
|
+ replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual, |
771 |
|
seaice_preconditioner |
772 |
|
- simplify computations for SEAICE_ZETA_SMOOTHREG |
773 |
|
- seaice_preconditioner: |
774 |
|
+ replace one remaining press by pressLoc (mistake) |
775 |
|
+ adjust printing of residuals |
776 |
|
- improve I/O of diagnostics of JFNK in seaice_jfnk.F: |
777 |
|
+ add (SEAICE.h) and rename some counters (initiliased in |
778 |
|
seaice_init_fixed.F) |
779 |
|
+ add _BEGIN/END_MASTER (myThid) around print statements |
780 |
|
+ print total number of iterations and failures over SEAICE_monFreq |
781 |
|
interval to STDOUT |
782 |
|
- move control over output-messages by fgmres to seaice_jfnk to save |
783 |
|
some operations |
784 |
|
- move resetting initial guess for fgmres outside of seaice_fgmres_driver |
785 |
|
in order to make restarts with sol .ne. zero (fgmres with restarts) |
786 |
|
(seaice_jfnk.F, seaice_fgmres.F) |
787 |
|
- seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes |
788 |
|
a serious convergence problem when open boundaries are involved |
789 |
|
o pkg/ggl90: fix computation of control volumes for the case of |
790 |
|
ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes |
791 |
|
up half a grid cell from C-centered to W-centered (pointed out by C. Eden) |
792 |
|
o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC |
793 |
|
o pkg/autodiff |
794 |
|
- Add inAdMode switch for SEAICEuseDYNAMICS: |
795 |
|
SEAICEuseDYNAMICSinAdMode |
796 |
|
(extend logic in ADAUTODIFF_INADMODE_SET) |
797 |
|
o pkg/seaice |
798 |
|
- Step 1 of merging ice-thickness distribution (ITD) code from |
799 |
|
MITgcm_contrib/torge/itd/ (author: Torge Martin) |
800 |
|
The code implements concept laid out in Thorndike et al. (1975); |
801 |
|
code is enabled via CPP flag SEAICE_ITD |
802 |
|
nITD (in SEAICE_SIZE.h) defines number of ice thickness categories; |
803 |
|
code is not complete yet!! |
804 |
|
- SEAICE_SIZE.h now included in almost all seaice routines |
805 |
|
o verification (using seaice): |
806 |
|
- switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp. |
807 |
|
global_ocean.cs32x15.seaice ; update results. |
808 |
|
- compile B-grid dynamics in FW test exp 1D_ocean_ice_column ; |
809 |
|
- compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp |
810 |
|
offline_exf_seaice (previously compiling B-grid). |
811 |
|
o pkg/exf: |
812 |
|
- fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow |
813 |
|
to specify neither just 1 comp of wind or wind-stress, nor no surface momentum |
814 |
|
forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind. |
815 |
|
o pkg/layers (adjust changes from Sept 19): |
816 |
|
- do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F) |
817 |
|
this allows to remove "layers_maxNum" dimension from all layers arrays. |
818 |
|
o pkg/layers (adjust changes from Sept 19): |
819 |
|
- remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ; |
820 |
|
- snap-shot extended to all type of layers (not just the 1rst type); |
821 |
|
- remove layers variables when corresponding CPP option is undef. |
822 |
|
o pkg/layers: |
823 |
|
- rename pkg/layers variable and add new output (layer exist & un-weighted |
824 |
|
velocity in layer) |
825 |
|
o pkg/seaice: |
826 |
|
- simplify (?) ocean-drag coefficent computations by using |
827 |
|
the same routine in all three solvers (saves some code lines) |
828 |
|
- remove global fields DRAGA and DRAGS from C-grid code and |
829 |
|
declare them locally in lsr.F (the only place where they are |
830 |
|
still used) |
831 |
|
- update AD output of lab_sea.evp (very sensitive anyway). |
832 |
|
o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics |
833 |
|
(Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK |
834 |
|
and SEAICEuseJFNK=.true. A few things to note: |
835 |
|
- involves a FGMRES, that is parallel but very inefficient, |
836 |
|
because of many scalar products (global sums) in the Gram-Schmidt |
837 |
|
orthogonalization method. Needs to be replaced. Original code |
838 |
|
from J.-F. Lemieux |
839 |
|
- preconditioner for FGMRES is a stripped down version of LSOR |
840 |
|
- SOLV_MAX_ITERS is now used for LSOR as a solver and as a |
841 |
|
preconditioner. For the preconditioner, the default is set to 10. |
842 |
|
- Jacobian times vector is computed with finite differences |
843 |
|
- marginally related to JFNK-solver: add a smooth regularization for |
844 |
|
zeta with tanh that will improve convergence (Lemieux and Tremblay, |
845 |
|
2009) for any implicit solver (not implemented for EVP because EVP |
846 |
|
does not need this regularization in the first place). Define |
847 |
|
SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use. |
848 |
|
o eesupp/src: |
849 |
|
- check in genmake2 that intrinsic S/R flush is available. |
850 |
|
- add S/R to flush IO unit (if intrinsic S/R flush is available) |
851 |
|
- flush standard & error msg unit before MPI termination |
852 |
|
- if debugMode, flush IO unit after printing msg |
853 |
|
o pkg/ctrl: |
854 |
|
- ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call |
855 |
|
to ctrl_set_unpack_xyz. |
856 |
|
|
857 |
|
checkpoint64 (2012/10/09) |
858 |
|
o pkg/shelfice |
859 |
|
- in mom_fluxform.F, mom_vecinv.F: |
860 |
|
CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid) |
861 |
|
Bug fix KappaRU -> KappaRV |
862 |
|
does not change verification/isomip but may change other setups |
863 |
|
(presumably constant KappaRU=KappaRV) |
864 |
|
- fix diagnostics SHIU/Vdrag (thanks to Tom Millgate) |
865 |
|
o pkg/obcs: |
866 |
|
- fixed some indexing bugs in obcs_seaice_sponge.F |
867 |
|
- added obcs relaxation subroutines for HSALT and HSNOW |
868 |
|
- changes verification/seaice_obcs/results/obcs_seaice_sponge.F |
869 |
|
o pkg/seaice: |
870 |
|
- add "multicategory" parameterization for snow in analogy to ice, |
871 |
|
default is off for now. |
872 |
|
o pkg/obcs: |
873 |
|
- added obcs_seaice_sponge.F for obcs relaxation of seaice variables; |
874 |
|
see verification/seaice_obcs/input.seaiceSponge for example application. |
875 |
|
- remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB |
876 |
|
index setting by master-thread. This fix multi-threads Pb in previous modifs. |
877 |
|
o pkg/layers : |
878 |
|
- add diagnostics to pkg/layers |
879 |
|
- move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F |
880 |
|
(from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly. |
881 |
|
o pkg/generic_advdiff/gad_implicit_r.F : |
882 |
|
- fix ADVr diagnostics in case of both implicit vertical advection and diffusion. |
883 |
|
o pkg/seaice/seaice_growth.F: |
884 |
|
- fix SItflux diagnostics in virtual salt flux + balanceEmpmr case. |
885 |
|
o pkg/obcs: |
886 |
|
- change default setting of OBCS_UVICE_OLD from defined to undef; |
887 |
|
- use new parameter OB_indexNone for null index value (instead of hard-coded 0) |
888 |
|
in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F; |
889 |
|
- pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z; |
890 |
|
- change OB null index value (OB_indexNone) to -99 ; this fix the problem |
891 |
|
with Southern & Western OB at a tile edge (at least in a simple set-up). |
892 |
|
o pkg/obcs: |
893 |
|
- change settings of OB index in case OB coincides with tile edge (shared by |
894 |
|
2 tiles), so that common OB location is registered by both tiles (instead of |
895 |
|
only 1). However, for Southern and Western OB, index value = 0 is not |
896 |
|
recognized as valid OB index (=default null value) and needs to be fixed. |
897 |
|
- modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting) |
898 |
|
- new parameter "OB_indexNone" for null index value (for now, still zero) |
899 |
|
to replace hard-coded null index value of zero. |
900 |
|
o pkg/exch2: |
901 |
|
- improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON: |
902 |
|
always check buffer-size (but outside the loop); move checking for valid |
903 |
|
index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON, |
904 |
|
print each tile and point connection only if |W2_printMsg|>= 2 and 3. |
905 |
|
o pkg/ctrl (pack & unpack): |
906 |
|
- in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable |
907 |
|
(locally defined) for different variables (+ remove the variable-specific |
908 |
|
file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL |
909 |
|
(to be extended to other local file names in ctrl.h). |
910 |
|
o pkg/flt: |
911 |
|
- add a FLT_Iter0 option (similar to PTRACERS_Iter0). |
912 |
|
o pkg/mdsio: |
913 |
|
- fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing |
914 |
|
o tools/genmake2: |
915 |
|
- add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE |
916 |
|
(added by Alistair in version 1.51 for building without make depend); |
917 |
|
- remove Header files list (H_SRC_FILES) from the dependence of targets |
918 |
|
ad_input_code.f & ftl_input_code.f (not clear why it was added in the first |
919 |
|
place in version 1.23): this save going through staf when unrelated header |
920 |
|
file has been modified. |
921 |
|
Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without |
922 |
|
"make depend" step, still need to do "make links" before "make adtaf". |
923 |
|
o eesupp/src (+ few pkg src files) & genmake2: |
924 |
|
- finish to remove ALWAYS_USE_MPI in source code that TAF does not see; |
925 |
|
- no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2). |
926 |
|
- improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish |
927 |
|
upper/lower case ; account for space between "#" and undef/define) |
928 |
|
o pkg/flt (with exch2): |
929 |
|
- cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F; |
930 |
|
- simplify threads synchronisation; fix (many issues) multi-threaded with MPI. |
931 |
|
|
932 |
|
checkpoint63s (2012/09/05) |
933 |
|
o pkg/ecco: |
934 |
|
- remove #ifdef ALLOW_SMOOTH_CORREL3D brackets. |
935 |
|
- add more relevant #ifdef ALLOW_SMOOTH ones. |
936 |
|
- sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D. |
937 |
|
o pkg/ctrl: |
938 |
|
- CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D, |
939 |
|
ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D. |
940 |
|
- ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag, |
941 |
|
doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and |
942 |
|
ctrlSmoothCorrel3D (new). |
943 |
|
The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP. |
944 |
|
- ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist. |
945 |
|
- ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress |
946 |
|
controls when useAtmWind, and vice versa. |
947 |
|
- ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers. |
948 |
|
- ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with |
949 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH. |
950 |
|
- ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with |
951 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH. |
952 |
|
- ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F: |
953 |
|
replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D. |
954 |
|
o pkg/smooth: |
955 |
|
- remove un-necessary includes. |
956 |
|
- remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets. |
957 |
|
Those CPP options were never defined, and not necessary. |
958 |
|
o model/src: |
959 |
|
- fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi). |
960 |
|
- standard treatment of useSMOOTH. |
961 |
|
o pkg/autodiff: |
962 |
|
- add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode, |
963 |
|
useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint. |
964 |
|
o pkg/exch2: |
965 |
|
- add "if usingMPI" where it was missing (in exch2_rx?_cube*.template) |
966 |
|
+ start to remove ALWAYS_USE_MPI in source code that TAF does not see. |
967 |
|
- make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag |
968 |
|
and tiles to process mapping. |
969 |
|
- re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h) |
970 |
|
moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h; |
971 |
|
rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX |
972 |
|
from w2_eeboot.F to w2_readparms.F. |
973 |
|
o eesupp/src: |
974 |
|
- set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of |
975 |
|
ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F; |
976 |
|
also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F |
977 |
|
- in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI |
978 |
|
is defined (remove condition on usingMPI) to match cases where MPI_INIT |
979 |
|
has been called. |
980 |
|
- fix bug I put in previous modif of exch_sm_3d_rx.template (not much used); |
981 |
|
- change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings |
982 |
|
(so that on 1 proc, get same myPid independently of usingMPI) |
983 |
|
- add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and |
984 |
|
useCubedSphereExchange with EXCH-1 (safer). |
985 |
|
- add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI). |
986 |
|
o pkg/ggl90: |
987 |
|
- fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call) |
988 |
|
used in ALLOW_GGL90_SMOOTH code. |
989 |
|
o pkg/flt: |
990 |
|
- fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping |
991 |
|
floats at the Southern end of the domain). |
992 |
|
o eesupp/inc: |
993 |
|
- add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h); |
994 |
|
but not used (and not to be used) anywhere, just for documentation. |
995 |
|
o pkg/autodiff, exf, ptracers & seaice (AD & TL output): |
996 |
|
- comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since: |
997 |
|
a) can damage previously written records in any other multi-record files. |
998 |
|
b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S. |
999 |
|
o tools/genmake2: |
1000 |
|
- define variable MAKE within Makefile and use it in place of 'make'; |
1001 |
|
- update AD_CONFIG.h (if needed) before building any of the executable |
1002 |
|
(forward, adjoint or tangent-lin); this involves a 2nd invocation of make; |
1003 |
|
and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h; |
1004 |
|
- always print usual warning comment 'this file is automatically generated' |
1005 |
|
from script convert_cpp_cmd2defines (+ remove this warning from genmake2). |
1006 |
|
o pkg/cheapaml: |
1007 |
|
- updated to correspond to the code used in accepted paper (Nico Wienders). |
1008 |
|
o pkg/exf: |
1009 |
|
added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch. |
1010 |
|
ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F) |
1011 |
|
and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h). |
1012 |
|
o pkg/exf, autodiff, ctrl, ecco and seaice: |
1013 |
|
remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones. |
1014 |
|
o pkg/ctrl, ecco: |
1015 |
|
allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL. |
1016 |
|
Depending on useAtmWind, one is inactive, and the other is active (see |
1017 |
|
exf_getffields.F/exf_getsurfacefluxes.F). |
1018 |
|
o tools/genmake2: |
1019 |
|
- improve error msg when failing in 2nd test of check_for_broken_Ff |
1020 |
|
- fix option '-makefile' short-name (-mf according to genmake2 -help) |
1021 |
|
- source local config file "genmake_local" just after processing the genmake2 |
1022 |
|
command arguments (previously done before processing arg). |
1023 |
|
o pkg/grdchk: |
1024 |
|
- add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call |
1025 |
|
to this routine from cost_final has been dropped in g_cost_final) |
1026 |
|
- improve printed information (more explicit msg, no longer using "print *," |
1027 |
|
fix fcpertminus printed value). |
1028 |
|
o model/src: |
1029 |
|
- move call to COST_INIT_VARIA out of packages_init_variables.F directly |
1030 |
|
into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES): |
1031 |
|
this prevents getting cost-funct reset in adinitialise_varia recomputations. |
1032 |
|
o pkg/dic: |
1033 |
|
- move initialisation of "freefe" array from from dic_biotic_forcing.F to |
1034 |
|
fe_chem.F: this prevents TAF from dropping this initialisation in TLM code. |
1035 |
|
o pkg/grdchk: |
1036 |
|
- grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid ) |
1037 |
|
- grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0 |
1038 |
|
o pkg/autodiff/ctrl/grdchk : |
1039 |
|
- attempt to sort out what works and what does not, |
1040 |
|
with regard to I/O, and to warn/stop accordingly. |
1041 |
|
o pkg/grdchk: |
1042 |
|
- attempt to fix grdchk in the case of useSingleCpuIO. |
1043 |
|
- "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )" |
1044 |
|
statements were moved from grdchk_main.F and into |
1045 |
|
grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F. |
1046 |
|
- a global sum is applied to record numbers icvrec/layer |
1047 |
|
out of grdchk_loc so that they be passed to I/O routines. |
1048 |
|
o pkg/smooth: |
1049 |
|
- fix recomputation that appeared with nlfs : use smooth_recip_hFacC, |
1050 |
|
smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case. |
1051 |
|
o verification/testreport: |
1052 |
|
- add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive); |
1053 |
|
- can also use compressed (gzip) reference output file; |
1054 |
|
- change format (in pkg/grdchk) of TLM output (+ add forward gradient) |
1055 |
|
to be easier to collect by testreport. |
1056 |
|
- update existing TLM output (half out-of-date by more than 3 yrs). |
1057 |
|
- report NETCDF & LAPACK settings (from genmake2) in output dir. |
1058 |
|
- report run-time in each individual summary (previously only for AD test); |
1059 |
|
for TLM test, add also TAF version. |
1060 |
|
- add daily TLM test on (old) aces cluster + weekly test on baudelaire. |
1061 |
|
|
1062 |
|
checkpoint63r (2012/08/15) |
1063 |
|
o tools/genmake2: |
1064 |
|
- fix Makefile for target ftlall (+ update files to clean after make ftlall) |
1065 |
|
o pkg/ecco/ecco_cost_final.F : |
1066 |
|
- fix fc print statements (to stdout and costfunction0000) so |
1067 |
|
that the printed value is always after the global sum. |
1068 |
|
o pkg/seaice/seaice_dynsolver.F : |
1069 |
|
- fix ice strength assymptote at SEAICE_area_max<1 |
1070 |
|
(no change for the standard case of SEAICE_area_max=1) |
1071 |
|
o some cleaning: |
1072 |
|
- pkg source files: ensure that all *.F files from each pkg included the |
1073 |
|
corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which |
1074 |
|
only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment |
1075 |
|
code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding |
1076 |
|
includes; |
1077 |
|
- model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used. |
1078 |
|
- ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR |
1079 |
|
is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when |
1080 |
|
ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop. |
1081 |
|
- update option-file CPP_OPTIONS.h of all AD experiments: |
1082 |
|
* no longer include PACKAGES_CONFIG.h ; |
1083 |
|
* includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ; |
1084 |
|
* def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before |
1085 |
|
including ECCO_CPPOPTIONS.h). |
1086 |
|
o pkg/cost, pkg/ctrl, pkg/ecco option-file: |
1087 |
|
- clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into |
1088 |
|
separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h, |
1089 |
|
not necessary accurate). |
1090 |
|
- add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in |
1091 |
|
pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to |
1092 |
|
deliberately break compilation (a remainder that it needs to be customized) |
1093 |
|
- in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h |
1094 |
|
- rename COST_CPPOPTIONS.h to COST_OPTIONS.h |
1095 |
|
- rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h |
1096 |
|
o tools/genamke2: |
1097 |
|
- check for lapack. |
1098 |
|
o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies. |
1099 |
|
- pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions |
1100 |
|
jointly. The exclusive ifdefs were removed, to add costs terms (when defined) |
1101 |
|
from both packages. |
1102 |
|
- the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly. |
1103 |
|
- for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs. |
1104 |
|
- pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes |
1105 |
|
of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly. |
1106 |
|
o pkg/cost : add comments to explain special and/or untested setups. |
1107 |
|
o pkg/exf: |
1108 |
|
- use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h |
1109 |
|
(previously, ALLOW_AUTODIFF_TAMC was controling this switch). |
1110 |
|
o verification/*/code_ad: |
1111 |
|
mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file: |
1112 |
|
- reccord when this file is included (define ECCO_CPPOPTIONS_H) |
1113 |
|
- remove the most obvious obsolete features (e.g., #define ALLOW_COST not |
1114 |
|
allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h) |
1115 |
|
o pkg/seaice : |
1116 |
|
- added possibility to change ice strength/PRESS0 relationship to |
1117 |
|
HEFF, according to the following run time parameters |
1118 |
|
SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0) |
1119 |
|
SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0) |
1120 |
|
SEAICEpresH0 :: HEFF threshold for ice strength (m) |
1121 |
|
o pkg/ggl90 : |
1122 |
|
- added run time flag mxlSurfFlag to include the code that ensure |
1123 |
|
mixing between first and second level (previously included as a comment) |
1124 |
|
o verification/1D_ocean_ice_column/input_ad/data.autodiff : |
1125 |
|
- add test of newly added dumpAdByRec=T option where |
1126 |
|
we write all records to one file per variable. |
1127 |
|
o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h : |
1128 |
|
- switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES |
1129 |
|
to check that this code is ok with taf and compiles in adjoint. |
1130 |
|
o pkg/autodiff : |
1131 |
|
- added run time param dumpAdByRec : ad dump format switch. |
1132 |
|
If true then write all records to one file per variable. |
1133 |
|
Else write one file per record (remains the default). |
1134 |
|
- revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly. |
1135 |
|
o pkg/seaice: |
1136 |
|
- Added SEAICEuseTILT run time switch : if set to |
1137 |
|
false then omit the tilt term in seaice dynamics. |
1138 |
|
- Fix free drift calculation. |
1139 |
|
o pkg/shelfice: |
1140 |
|
When initializing SHELFICEDragQuadratic, set default to be |
1141 |
|
consistent with shiCdrag in case SHELFICEuseGammaFrict is used, |
1142 |
|
but retain option to set it independently |
1143 |
|
(inconsistenty spotted by Veronique Dansereau) |
1144 |
|
o eesupp/inc: |
1145 |
|
- in EEPARAMS.h, add real-type constant for some frequently used simple number |
1146 |
|
(0,1,2,1/2), with name explicitly referring to RS/RL type. |
1147 |
|
o model/src: |
1148 |
|
- move balancing of relaxation terms to new S/R balance_relax.F. |
1149 |
|
o pkg/autodiff: |
1150 |
|
re-write active I/O high-level (control) S/R: |
1151 |
|
- rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL |
1152 |
|
- add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R. |
1153 |
|
- use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and |
1154 |
|
MDS_READ/WRITE_FIELD); change loops to multi-threads. |
1155 |
|
- update and merge active_file_control_slice.flow into active_file_control.flow |
1156 |
|
- update the calls in lower level S/R (active_file.F, active_file_g.F and |
1157 |
|
active_file_ad.F) keeping the argument list and function unchanged. |
1158 |
|
- also update lower-level "_LOC" version (call same S/R with "useCurrentDir |
1159 |
|
=.TRUE.") and remove high-level (control) _loc version (not called anymore). |
1160 |
|
- new low-level active I/O routines, one for each type (RL/RS), for active var |
1161 |
|
of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr); |
1162 |
|
fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the |
1163 |
|
right type. |
1164 |
|
o autodiff and RS=real*4: |
1165 |
|
- call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf |
1166 |
|
ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ; |
1167 |
|
- change argument type of 3-D mask argument to _RS to match type in the call |
1168 |
|
(in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued. |
1169 |
|
o pkg/thsice: |
1170 |
|
- re-anable balanceEmPmR when useSEAICE=T with useThSIce=T. |
1171 |
|
- option to correct ocean fresh-water flux for imbalance of Atmos+Land |
1172 |
|
fresh-water flux: uniform correction or proportional to local precip. |
1173 |
|
o pkg/ctrl: |
1174 |
|
- new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D |
1175 |
|
- redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to |
1176 |
|
ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC |
1177 |
|
- verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL |
1178 |
|
|
1179 |
|
checkpoint63q (2012/07/30) |
1180 |
|
o pkg/autodiff: |
1181 |
|
note about monitor and snap-shot of ad-variables: |
1182 |
|
a) need to apply ADEXCH before monitor or output of ad-vars to include |
1183 |
|
overlap contributions (was done for adjDump but missing for monitor). |
1184 |
|
b) since ADEXCH implies adding overlap values to interior array, machine |
1185 |
|
truncation error is expected when adding an ADEXCH call in the middle of |
1186 |
|
the time-stepping (although mathematically identical). |
1187 |
|
modifs: |
1188 |
|
- fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars |
1189 |
|
declaration (adEddyPsiX,adEddyPsiY in adcommon.h). |
1190 |
|
- add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to |
1191 |
|
apply ADEXCH before monitor or snap-shot of ad-variables: |
1192 |
|
=0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy. |
1193 |
|
- implement new method (copy+adexch) for snap-shot and monitor of main model |
1194 |
|
ad-vars (initially not used by default -> output unchanged). |
1195 |
|
- change default (set to 2) to use new method and update few output_adm.txt |
1196 |
|
with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo |
1197 |
|
and both tutorial_tracer_adjsens tests). |
1198 |
|
- switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice) |
1199 |
|
and turn off momDissip_In_AB in the 2 other (needed for stable AB-3). |
1200 |
|
o pkg/ctrl: |
1201 |
|
enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of |
1202 |
|
generic control variables via |
1203 |
|
#define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL |
1204 |
|
Only required customization should be S/R ctrl_map_ini_genarr.F |
1205 |
|
(routine in repository contains example) |
1206 |
|
o pkg/exf: |
1207 |
|
- fix and refine checking of surface-relaxation setting when using EXF |
1208 |
|
o verification (adjoint exp): |
1209 |
|
- reduce length of simulation by half for experiment global_ocean.cs32x15 |
1210 |
|
(std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output. |
1211 |
|
o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag) |
1212 |
|
- replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers |
1213 |
|
of KE that can occur with aggressive optimization |
1214 |
|
+ put quadratic bottom drag calculation in separated loops (only done if |
1215 |
|
using bottomDragQuadratic) |
1216 |
|
o model/src: CG2D_NSA |
1217 |
|
- clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF |
1218 |
|
and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE. |
1219 |
|
- in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens), |
1220 |
|
change cg2d residual target to be expressed in Wunits (=> do not normalise |
1221 |
|
RHS ; this fix global_max Pb with TAF); update output. |
1222 |
|
o verification/tutorial_tracer_adjsens: |
1223 |
|
improve parameter consistency (and get rid of warnings): |
1224 |
|
- use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf); |
1225 |
|
- switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical) |
1226 |
|
- use staggerTimeStep (for stability) in som81; use default rotation period. |
1227 |
|
o pkg/exch2: |
1228 |
|
- with empty facet: fix compact-format (W2_mapIO=1) definition (was previously |
1229 |
|
reset to 0 = 1 long line in X) |
1230 |
|
o pkg/mdsio: |
1231 |
|
- fix reading of dimensions from meta file for large-size domain |
1232 |
|
o model/src: |
1233 |
|
- fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long); |
1234 |
|
- to refine CS-grid check, add logical flag "hasWetCSCorners": true if using |
1235 |
|
Cubed-Sphere Exch with CS-corners inside the domain; |
1236 |
|
make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate |
1237 |
|
globalArea and to set hasWetCSCorners. |
1238 |
|
- add warning if usingCurvilinearGrid and momAdvection in flux-form (missing |
1239 |
|
metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form. |
1240 |
|
- re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if |
1241 |
|
useCDscheme and useCubedSphereExchange). |
1242 |
|
o pkg/seaice/seaice_growth.F : |
1243 |
|
- compute the SEAICE_DISABLE_HEATCONSFIX term accordingly |
1244 |
|
for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0) |
1245 |
|
when the previous code was not correct. |
1246 |
|
- in all cases diagnoze the boundary condition mismatch to SIaaflux |
1247 |
|
- in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add |
1248 |
|
that term to QNET (essentially to set the melt/freeze water to 0degC). |
1249 |
|
when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed. |
1250 |
|
o verification/global_ocean.cs32x15/input.seaice : |
1251 |
|
- add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget. |
1252 |
|
- add diagnostics (commented out) for budget test using my matlab codes (gcmfaces). |
1253 |
|
- update results (output.seaice.txt) accordingly. |
1254 |
|
o verification/lab_sea/input/data.seaice : |
1255 |
|
- remove SEAICEheatConsFix, which is now be tested |
1256 |
|
in global_ocean.cs32x15. The presently coded fix |
1257 |
|
is only consistent with real fresh water + nlfs. |
1258 |
|
- update results (output.txt) accordingly. |
1259 |
|
o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd). |
1260 |
|
o AD_CONFIG.h file: |
1261 |
|
- in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h; |
1262 |
|
- remove #include "AD_CONFIG.h" from all included OPTIONS files and |
1263 |
|
add it explicitly in each fortran src file where it is needed. |
1264 |
|
motivation: header file AD_CONFIG.h is generated/modified after "make depend" |
1265 |
|
thus introducing potentially wrong dependency; therefore, better to include |
1266 |
|
it only where it's really needed, and after any other included OPTIONS file |
1267 |
|
(less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN |
1268 |
|
or ALLOW_TANGENTLINEAR_RUN). |
1269 |
|
|
1270 |
|
checkpoint63p (2012/07/06) |
1271 |
|
o pkg/autodiff: |
1272 |
|
- rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ; |
1273 |
|
- create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters |
1274 |
|
which are now read from new parameter file "data.autodiff" (inAdExact |
1275 |
|
previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg) |
1276 |
|
- add file "data.autodiff" in all verification/*/input_ad/ directories. |
1277 |
|
- add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward |
1278 |
|
mode (used in global_ocean.cs32x15.seaice_dynmix test exp.) |
1279 |
|
o verification/tutorial_tracer_adjsens/ |
1280 |
|
- add extra sub-verification which uses "SOM" advection scheme |
1281 |
|
(2nd Order-Moment Advection Scheme, Prather Limiter) with |
1282 |
|
#define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h |
1283 |
|
and in data: |
1284 |
|
multiDimAdvection=.TRUE., |
1285 |
|
tempAdvScheme=81, |
1286 |
|
saltAdvScheme=81, |
1287 |
|
o model/src: |
1288 |
|
- introduce ALLOW_BALANCE_RELAX which allow the removal |
1289 |
|
of the global mean of relaxation terms by setting |
1290 |
|
balanceThetaClimRelax and balanceSaltClimRelax |
1291 |
|
- disable balanceEmPmR and balanceQnet in the case when useSeaice. |
1292 |
|
This case is now treated appropriately in seaice_growth.F |
1293 |
|
o pkg/seaice: |
1294 |
|
- do balanceEmPmR and balanceQnet based on the net fluxes |
1295 |
|
(SItflux) that enter the ocean+ice system rather than QNET |
1296 |
|
and EMPMR. Works best in real fresh water. |
1297 |
|
- SIatmFW, SIatmQnet, and SItflux computations had to be moved |
1298 |
|
out of the diagnotics bloc, and stored in global arrays. |
1299 |
|
|
1300 |
|
checkpoint63o (2012/06/29) |
1301 |
|
o vertical mixing schemes: |
1302 |
|
- remove unused S/R CALC_BUOYANCY (left from branch-atmos merging) |
1303 |
|
- replace computation of density (in Function STATE1, opps_calc.F) by a call |
1304 |
|
to S/R FIND_RHO_SCALAR |
1305 |
|
- pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC |
1306 |
|
and use it for N^2 calculation in ggl90_calc.F (save 2 density computations); |
1307 |
|
affects output (vermix.ggl90) at truncation level. |
1308 |
|
o testreport: |
1309 |
|
- change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles |
1310 |
|
(nSx,nSy) for the number of threads (from eedata.mth) |
1311 |
|
o model/src: |
1312 |
|
- remove 2nd set of calls at the top of initialise_varia.F (Adjoint part) |
1313 |
|
related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary). |
1314 |
o verification/tutorial_tracer_adjsens/ |
o verification/tutorial_tracer_adjsens/ |
1315 |
- compile with ALLOW_CG2D_NSA |
- compile with ALLOW_CG2D_NSA |
1316 |
- run with nonlinFreeSurf=3 |
- run with nonlinFreeSurf=3 |