| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
| 6 |
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|
| 7 |
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o tutorial_deep_convection (smag3d): |
| 8 |
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- add missing scaling in mom_calc_smag_3d.F; |
| 9 |
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- set smag3D_coeff in input.smag3d such that results do not change. |
| 10 |
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o pkg/dic: |
| 11 |
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- change dic_cost.F to compute cost on each tile first and then apply |
| 12 |
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GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments |
| 13 |
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tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output. |
| 14 |
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o eesupp/src & pkg/mdsio: |
| 15 |
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- remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F |
| 16 |
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(from pkg/mdsio) since they are no longer used for tape IO. |
| 17 |
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- move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src |
| 18 |
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(+ keep a copy in pkg/atm_ocn_coupler). |
| 19 |
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o verification/isomip: |
| 20 |
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- split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests. |
| 21 |
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o tools/build_options: |
| 22 |
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- optfile linux_amd64_ifort11, fast (no ieee) case: |
| 23 |
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to get a working restart for all experiments, add "-fp-model source" |
| 24 |
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to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default). |
| 25 |
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|
| 26 |
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checkpoint64p (2013/10/20) |
| 27 |
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o pkg/autodiff: |
| 28 |
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- adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO |
| 29 |
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criteria, return to simple (default) tape IO format. |
| 30 |
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o pkg/mdsio (+ eesupp/src): |
| 31 |
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- rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace |
| 32 |
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previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8); |
| 33 |
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- fix globalFile and singleCpuIO options using simpler global mapping. |
| 34 |
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- new pairs of scatter/gather vector S/R (one for each type, generated from |
| 35 |
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template) corresponding to simpler global mapping. |
| 36 |
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- adread_write.F: switch to new S/R (but leave old calls commented) and write |
| 37 |
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to globalFile when parameter globalFiles is set to True. |
| 38 |
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- switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip. |
| 39 |
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o pkg/autodiff: |
| 40 |
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- adread_adwrite.F: add a hack for RS arrays (when RS=real*4); |
| 41 |
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with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is |
| 42 |
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missing, just add a STOP if array type do not match. |
| 43 |
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o pkg/exf: |
| 44 |
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- to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice: |
| 45 |
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rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION |
| 46 |
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and rename array obsSIce to exf_iceFraction. |
| 47 |
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o tutorial_deep_convection: |
| 48 |
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- add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe), |
| 49 |
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for now all in this exp. code dir. |
| 50 |
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- add secondary test using Smag-3D viscosity (keep very low backgroud visc for |
| 51 |
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testing) and flux-limter advection scheme for Temp. (no explicit diffusion). |
| 52 |
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o eesupp/src: |
| 53 |
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- added SINGLE_DISK_IO option because reading of parameter files on |
| 54 |
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very large number of processors did not work with existing set-up |
| 55 |
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|
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checkpoint64o (2013/09/25) |
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o pkg/atm_phys & atm_compon_interf: |
| 58 |
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- allows for coupling of gray-atmosphere (atm_phys) with ocean. |
| 59 |
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o tools/build_options: |
| 60 |
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- switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran |
| 61 |
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& linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also |
| 62 |
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remove CPP setting (was identical to genmake2 default). |
| 63 |
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o pkg/gmredi & model/src: Some updating and work done on the residual model. |
| 64 |
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- created new file model/src/calc_eddy_stress.F to calculate the eddy stress. |
| 65 |
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- fixed up the calculation of the eddy stress and how it is added to the |
| 66 |
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external forcing via taueddy_external_forcing.F |
| 67 |
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- at the moment, it is very experimental and only works with the variable eddy |
| 68 |
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diffusivity calculated in gmredi_k3d.F |
| 69 |
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o pkg/seaice/seaice_check.F: add a check to catch the case of specifying |
| 70 |
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lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice |
| 71 |
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o testreport (& tools/do_tst_2+2): |
| 72 |
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- for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}' |
| 73 |
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o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11: |
| 74 |
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- remove CPP='cpp -traditional -P' (this is genmake2 default) |
| 75 |
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- add switch (for big setups) to use 'medium' memory-model (but leave it |
| 76 |
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commented out for now). Note: needed with FC 19 to compile big setups. |
| 77 |
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o pkg/atm_compon_interf: |
| 78 |
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- regroup per field origin (model & pkgs) the coupling storage routines |
| 79 |
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(which accumalate in time each coupling field) |
| 80 |
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- move bi,bj loops inside atm_store_my_data.F and store also wind-stress; |
| 81 |
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update accordingly + simplify aim_do_physics.F |
| 82 |
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|
| 83 |
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checkpoint64n (2013/08/26) |
| 84 |
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o pkg/bbl: |
| 85 |
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- update formulation to reduce dispersion of tracer properties in bbl |
| 86 |
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- replaced horizontal and vertical transport parameters with velocities |
| 87 |
|
- changes results for verification/global_with_exf.yearly |
| 88 |
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o verification/halfpipe_streamice: |
| 89 |
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- change to matrix construction; update both Fwd & AD output. |
| 90 |
|
o verification/tutorial_tracer_adjsens: |
| 91 |
|
- OpenAD test: switch to vector-invariant momentum since fluxform with |
| 92 |
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rStar causes problems with OpenAD; update output. |
| 93 |
|
o tools: |
| 94 |
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- genmake2: define a common prefix for all temp-file names ; move them |
| 95 |
|
to local /tmp disk (but would be easy to move them back); |
| 96 |
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- xmakedepend: apply the same switch for temp-files. |
| 97 |
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o pkg/offline: |
| 98 |
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- changes for use with rStar (NLFS): assume that we continue to provide |
| 99 |
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UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid |
| 100 |
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output files) and apply r* scaling at each time-step (function of the time |
| 101 |
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varying Eta field); use normal pickup files (needed for restart with NLFS). |
| 102 |
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o adjoint with OpenAD: |
| 103 |
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- move OpenAD-specific files from verification/OpenAD/code_oad_all to a new |
| 104 |
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package openad. This package has to be compiled for all runs with OpenAD |
| 105 |
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instead of specifying code_oad_all as a modification directory. |
| 106 |
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- link the fortran templates from tools/OAD_support to the build directory |
| 107 |
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for preprocessing to avoid conflicts between different setups compiled |
| 108 |
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simultaneously and simplify cleanup. |
| 109 |
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o pkg/exf: |
| 110 |
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- in exf_getforcing.F: comment out most of the EXCH calls (fields used by |
| 111 |
|
main model or other pkgs are exchanged in EXF_MAPFIELDS). |
| 112 |
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o model/src: |
| 113 |
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- do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline |
| 114 |
|
(similar to do_fields_blocking_exchanges.F). |
| 115 |
|
o tools/genmake2: |
| 116 |
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- remove TAF output src code just before calling staf (when not doing a fresh |
| 117 |
|
built, will stop if things go wrong with staf). |
| 118 |
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- fix target "adobj" (left from TAF version-2 transition) |
| 119 |
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o pkg/diagnostics: |
| 120 |
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- add a parameter to track the status of pkg/diagnostics activation; |
| 121 |
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this replace/extend the use of logical param "settingDiags" (to check |
| 122 |
|
when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call. |
| 123 |
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New S/R to print error message and stop when pkgStatus is not right. |
| 124 |
|
- to try: add a warning when "data.diagnostics" exist but useDiagnostics=F. |
| 125 |
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|
| 126 |
|
checkpoint64m (2013/08/13) |
| 127 |
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o model/inc: |
| 128 |
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- move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from |
| 129 |
|
8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) |
| 130 |
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o pkg/kpp & aim_v23: |
| 131 |
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- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
| 132 |
|
o pkg/seaice: |
| 133 |
|
- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
| 134 |
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undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
| 135 |
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- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
| 136 |
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o eesupp/src: |
| 137 |
|
- fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) |
| 138 |
|
in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). |
| 139 |
|
o switch to TAF version-2: |
| 140 |
|
- add flow directives to "freeze" naming convention for ad-routines that |
| 141 |
|
are used in I/O routines of adjoint state and associated common blocks |
| 142 |
|
that are used in adcommon.h (backward compatible with version-1) |
| 143 |
|
- update all ad-optfiles (in tools/adjoint_options + few local to some |
| 144 |
|
verification exp) to switch to latest TAF version (currently 2.5.5); |
| 145 |
|
merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented |
| 146 |
|
out except for diva). |
| 147 |
|
- the major change with TAF version-2 is that both the differentiated |
| 148 |
|
routines and the forward routines (new) are returned as part of the TAF |
| 149 |
|
output source code. Update genmake2 accordingly. |
| 150 |
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- new output for AD experiment tutorial_global_oce_biogeo (better AD gradient |
| 151 |
|
with version-2 when compared to TLM or FWD gradient); other experiments |
| 152 |
|
output show minor changes (machine truncation level); update the few AD & |
| 153 |
|
TLM output with 12 matching digits only (some prior to version-2 switch). |
| 154 |
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|
| 155 |
|
checkpoint64l (2013/08/05) |
| 156 |
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o model/src: |
| 157 |
|
- in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F |
| 158 |
|
- main_do_loop.F: no longer includes additional (AUTODIFF) header files |
| 159 |
|
when using TAF but only if using OpenAD. |
| 160 |
|
o pkg/mom_common+fluxform+vecinv: |
| 161 |
|
- always set horiz. viscosity arrays to background value before calling |
| 162 |
|
MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC |
| 163 |
|
only when using variable horiz. viscosity (useVariableVisc=T); |
| 164 |
|
- simplify mom_vecinv.F (only 1 block for momViscosity). |
| 165 |
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o pkg/mom_common: variable horiz. viscosity in NH code |
| 166 |
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- move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F) |
| 167 |
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from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h |
| 168 |
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- store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, |
| 169 |
|
useBiharmonicVisc & useVariableVisc. |
| 170 |
|
- fix old bug (already in 1rst implementation of variable horizontal viscosity |
| 171 |
|
in calc_gw.F, version 1.27, 2006/06/20): |
| 172 |
|
horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 |
| 173 |
|
even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. |
| 174 |
|
- change background horiz viscosity in vertical momentum (gW) to always be |
| 175 |
|
viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using |
| 176 |
|
any type of variable viscosity, e.g., viscAh/4Grid) |
| 177 |
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- change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of |
| 178 |
|
viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing |
| 179 |
|
horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since |
| 180 |
|
default viscAh,viscA4 is zero). |
| 181 |
|
o model/src: |
| 182 |
|
- extend length of drC & recip_drC from Nr to Nr+1. |
| 183 |
|
o Divided Adjoint (DIVA) with MPI: |
| 184 |
|
- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
| 185 |
|
- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
| 186 |
|
and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h. |
| 187 |
|
|
| 188 |
|
checkpoint64k (2013/07/23) |
| 189 |
|
o tools/OAD_support: |
| 190 |
|
- avoid the need for file "oadtempflile" in insertTemplateDir.bash |
| 191 |
|
and remove it from genmake2. |
| 192 |
|
o tools/build_options: |
| 193 |
|
- remove MPI_HEADER_FILES_INC setting (no longer used) and comment out |
| 194 |
|
MPI_HEADER_FILES list (let genmake2 find the missing headers) |
| 195 |
|
o verification/halfpipe_streamice: |
| 196 |
|
- change to driving stress formulation; update both Fwd & AD output. |
| 197 |
|
o tools/genmake2 and Divided Adjoint with MPI: |
| 198 |
|
- remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken); |
| 199 |
|
- only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set; |
| 200 |
|
- add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in |
| 201 |
|
Makefile, which is set by genmake2, and check which mpi-headers are needed. |
| 202 |
|
Note: need to update adjoint_options/adjoint_diva_mpi accordingly. |
| 203 |
|
- update target "CLEAN" (to also remove ./mpi_headers/ dir). |
| 204 |
|
o testreport: |
| 205 |
|
- changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, |
| 206 |
|
perform additional runs (number of additional runs is "add_DIVA_runs" taken |
| 207 |
|
from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h"). |
| 208 |
|
o verification/lab_sea (AD test): |
| 209 |
|
- change to test Divided Adjoint Run in this set-up (both standard AD test |
| 210 |
|
and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test. |
| 211 |
|
o pkg atm_ & ocn_compon_interf: |
| 212 |
|
- remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old |
| 213 |
|
staggerTimeStep implementation) and disable (retired) corresponding |
| 214 |
|
parameter. |
| 215 |
|
o pkg/offline: |
| 216 |
|
- comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01]; |
| 217 |
|
- add S/R OFFLINE_CHECK to print offline parameter summary |
| 218 |
|
and stop if loading a file that is not used; |
| 219 |
|
- enable to calculate GMRedi tensor, KPP mixing and convective index |
| 220 |
|
when the corresponding file(s) is/are not specified (but pkg is used). |
| 221 |
|
- comment out resetting of monitorFreq (to endTime) since it still useful |
| 222 |
|
for monitoring CFL numbers and checking offline fields. |
| 223 |
|
o OpenAD: |
| 224 |
|
- do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get |
| 225 |
|
smaller standard output) and generate new (smaller) output (on baudelaire |
| 226 |
|
using gfortran with -ieee) for exp. tutorial_tracer_adjsens |
| 227 |
|
o model/src: |
| 228 |
|
- call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F), |
| 229 |
|
(where external_forcing_adjust was called) and change list of arguments; |
| 230 |
|
- merge external_forcing_adjust.F into external_forcing_surf.F |
| 231 |
|
- put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F) |
| 232 |
|
which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX, |
| 233 |
|
previously in file "balance_relax.F", now removed); remove corresponding |
| 234 |
|
arrays in FFIELDS.h. |
| 235 |
|
- EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement |
| 236 |
|
a hack for getting back surfaceForcingS (loaded from file) when using |
| 237 |
|
ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up. |
| 238 |
|
- update output of AD test experiment global_ocean.cs32x15.seaice_dynmix |
| 239 |
|
(was getting only 11 digits for AD-grad, due to different truncation |
| 240 |
|
error in AD code). |
| 241 |
|
|
| 242 |
|
checkpoint64j (2013/07/04) |
| 243 |
|
o pkg/offline: |
| 244 |
|
- to enable the use of other features with pkg offline (e.g., obcs), |
| 245 |
|
also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come. |
| 246 |
|
- comment out "allowFreezing" (now active) in 2 offline testing exp. |
| 247 |
|
o pkg/exf ALLOW_RUNOFTEMP |
| 248 |
|
- fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL |
| 249 |
|
- ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice |
| 250 |
|
- changes verification/global_ocean.cs32x15/results/output.seaice.txt |
| 251 |
|
o pkg/atm_phys: |
| 252 |
|
- allows to add some damping on uVel,vVel (strength only function of k). |
| 253 |
|
o verification, ad-tests: |
| 254 |
|
- reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, |
| 255 |
|
global_ocean_ebm and offline_exf_seaice.thsice. |
| 256 |
|
o verification/halfpipe_streamice: |
| 257 |
|
- found a bug in s/r pkg/streamice/streamice_advect_thickness which caused |
| 258 |
|
flux input boundary conditions to be ignored; a fix for this bug changed |
| 259 |
|
verification results for forward test. |
| 260 |
|
- add adjoint test. |
| 261 |
|
o pkg/ptracers: |
| 262 |
|
- allow to restart without SOM pickup (resetting SOM to zero). |
| 263 |
|
o pkg/gmredi: |
| 264 |
|
- New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added. |
| 265 |
|
- It uses mixing length theory and suppression by steering level effects to |
| 266 |
|
calculate a diffusivity used in the Redi tensor (see Bates et al., submitted |
| 267 |
|
to JPO, for more details). |
| 268 |
|
- It also uses the diffusivity to calculate an eddy induced streamfunction |
| 269 |
|
based on a PV closure (rather than a buoyancy closure as in GM). |
| 270 |
|
- New files added to pkg/gmredi: |
| 271 |
|
gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy |
| 272 |
|
induced overturning streamfunction (called from gmredi_calc_tensor) |
| 273 |
|
gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required |
| 274 |
|
for use in gmredi_k3d |
| 275 |
|
gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate |
| 276 |
|
the eddy diffusivity |
| 277 |
|
|
| 278 |
|
checkpoint64i (2013/06/18) |
| 279 |
|
o pkg/cheapaml: |
| 280 |
|
- take src files from MITgcm_contrib/verification_other/offline_cheapaml/code |
| 281 |
|
that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics) |
| 282 |
|
with pkg/cheapaml. |
| 283 |
|
o utils/python: add subpackage for cubed sphere function, first example is |
| 284 |
|
simple cs.pcol to plot 2D fields on a map |
| 285 |
|
o pkg/streamice: |
| 286 |
|
- This is a new package in MITgcm, which solves dynamic equations for ice |
| 287 |
|
sheets and ice streams |
| 288 |
|
- At the moment it is independent of atmosphere/ocean dynamics, or any |
| 289 |
|
other physical packages in MITgcm, even ShelfIce (although it is anticipat- |
| 290 |
|
ed that this will change) |
| 291 |
|
- There is a new verification exercise that tests it, halfpipe_streamice, |
| 292 |
|
evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a |
| 293 |
|
rectangular embayment |
| 294 |
|
- halfpipe_streamice is forward-only for now, will have TAF test soon |
| 295 |
|
- for questions, email dgoldber@mit.edu |
| 296 |
|
o pkg/thsice: |
| 297 |
|
- fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing |
| 298 |
|
of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40); |
| 299 |
|
- remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new |
| 300 |
|
call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect ); |
| 301 |
|
- allow precip from pkg/cheapaml to make snow over seaice. |
| 302 |
|
o pkg/cfc: |
| 303 |
|
- move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC |
| 304 |
|
- remove atmos CFC 2-D arrays from common bloc (now local variables) |
| 305 |
|
- change some hard-coded constant to run time parameter for reading and |
| 306 |
|
and interpolating atmospheric CFC ; keep same default as previously. |
| 307 |
|
- more flexible reading of Atmos CFC (number of records no longer hard-coded) |
| 308 |
|
- put arguments in standard order: myTime, myIter, myThid |
| 309 |
|
- use standard S/R GET_PERIODIC_INTERVAL for time interpolation of |
| 310 |
|
atmospheric CFC ; fix for the case myIter < PTRACERS_iter0. |
| 311 |
|
- fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf |
| 312 |
|
- new routine to print summary of CFC params and check for consistency. |
| 313 |
|
o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff, |
| 314 |
|
similar to thsice_advdiff. |
| 315 |
|
Note that for the B-grid case the routine parameters uc/vc are overwritten. |
| 316 |
|
o pkg/cfc: |
| 317 |
|
- change time interpolation for atmospheric CFC-11 (now same as for CFC-12); |
| 318 |
|
update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline. |
| 319 |
|
- fix interpolation of atmphspheric CFC between Sorthern and Northern |
| 320 |
|
hemisphere value. |
| 321 |
|
o pkg/seaice: |
| 322 |
|
- allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml) |
| 323 |
|
o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics; |
| 324 |
|
so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE. |
| 325 |
|
- requires an additional time level that is stored in the pickup |
| 326 |
|
- you can start with AB2 from a pickup without this time level with |
| 327 |
|
pickupStrictlyMatch = .false. |
| 328 |
|
|
| 329 |
|
checkpoint64h (2013/05/26) |
| 330 |
|
o pkg/cheapaml: |
| 331 |
|
- replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux); |
| 332 |
|
affect machine truncation (but exp cheapAML_box still pass with 13 digits). |
| 333 |
|
- consistent treatment of uWind,vWind location: assume everywhere in |
| 334 |
|
pkg/cheapaml that they are on C-grid (@ uVel,vVel location) |
| 335 |
|
(Note: was already the case for Tair,Qair advection); |
| 336 |
|
add option (INCONSISTENT_WIND_LOCATION) to recover old results. |
| 337 |
|
- compute diabatic forcing only in the interior (excluding overlap regions) |
| 338 |
|
- fill in array "Qsw" (for short-wave heating); |
| 339 |
|
- add diagnostic for precip ; fill-in diagnostics for cheapAML state vars |
| 340 |
|
before any update (consistent with MITgcm state var diagnostics); |
| 341 |
|
- cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if |
| 342 |
|
non periodic ; + adjusted for uWind,vWind (C-grid). |
| 343 |
|
o pkg/seaice: |
| 344 |
|
- remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and |
| 345 |
|
add explicitly pkg/exf in experiments that currently use pkg/seaice. |
| 346 |
|
- allows to compile pkg/seaice without pkg/exf. |
| 347 |
|
o tools/OAD_support: |
| 348 |
|
- use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds |
| 349 |
|
of array "ourStepOf" in function rvNextAction (revolve.F90). |
| 350 |
|
o pkg/aim_compon_interf renamed to pkg/atm_compon_interf |
| 351 |
|
- change pkg name (to be used with other atmospheric physics pkg) |
| 352 |
|
but by-pass CVS when making the new pkg so that we keep the CVS history. |
| 353 |
|
o pkg/offline: |
| 354 |
|
- call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F |
| 355 |
|
(previously called from pkg/dic_surfforcing_init.F) |
| 356 |
|
o model/src: |
| 357 |
|
- re-order sequence of calls within packages_init_variables.F, using |
| 358 |
|
standard order, except for: |
| 359 |
|
DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top), |
| 360 |
|
CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom) |
| 361 |
|
o new pkg: atm_phys |
| 362 |
|
- add entry point and source code (previously in contrib |
| 363 |
|
verification_other/atm_gray/code_gray/) for new pkg "atm_phys" |
| 364 |
|
(atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008). |
| 365 |
|
- re-order sequence of calls within packages_readparms.F, |
| 366 |
|
packages_init_fixed.F and packages_write_pickup.F |
| 367 |
|
(but skip packages_init_variables.F because of TAF issues). |
| 368 |
|
- update contrib/*/atm_gray/ experiment. |
| 369 |
|
o pkg/seaice (ITD code): |
| 370 |
|
- simplify and fix the writing of pickup-files for ITD case |
| 371 |
|
o pkg/seaice (ITD code): |
| 372 |
|
- introduce floe size dependent lateral melt for ITD case; |
| 373 |
|
- cleaning (avoid division by zero, change to f77 syntax, remove tabs) |
| 374 |
|
- update seaice_itd experiment main output. |
| 375 |
|
o pkg/thsice: |
| 376 |
|
- remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and |
| 377 |
|
declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F; |
| 378 |
|
changed accordingly pkg/atm2d. |
| 379 |
|
|
| 380 |
|
checkpoint64g (2013/05/01) |
| 381 |
|
o pkg/exf ALLOW_RUNOFTEMP |
| 382 |
|
- if defined, river and glacier runoff temperature can be read-in from |
| 383 |
|
runoftempfile; runoftempfile needs to have same format as runofffile |
| 384 |
|
o pkg/thsice (& pkg/bulk_force): |
| 385 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
| 386 |
|
for energy content of Precip + RunOff & Evap (like with pkg/exf). |
| 387 |
|
- change computation domain to always be the interior (without overlap). |
| 388 |
|
- fix bug (wrong overlap) when using EXF and stressReduction > 0. |
| 389 |
|
o verification/tutorial_global_oce_biogeo: |
| 390 |
|
- add preliminary OpenAD setup (still has problems) |
| 391 |
|
o pkg/seaice: |
| 392 |
|
- turn some parameters for choosing the convergence criterion of |
| 393 |
|
the inexact Newton method (JFNK) into runtime parameters for convenience |
| 394 |
|
- clean up seaice_calc_viscosities.F: remove/retire two options for |
| 395 |
|
SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes |
| 396 |
|
the results of lab_sea/input because a division has been replaced by |
| 397 |
|
a multiplication with the reciprocal (sumNorm) |
| 398 |
|
- modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve |
| 399 |
|
convergence of solver (changes results, of course), and to test some |
| 400 |
|
new features |
| 401 |
|
o model/src: |
| 402 |
|
- remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call. |
| 403 |
|
- remove unused forcing field "dQdT" and associated parameter "dQdTFile". |
| 404 |
|
- move forcing adjustment (balancing surface forcing) in specific S/R |
| 405 |
|
where might also be applied exchanges (if needed) to forcing arrays. |
| 406 |
|
o pkg/shelfice: |
| 407 |
|
- allow to specify the Ice-Shelf mass per unit area (instead of |
| 408 |
|
shelficeLoadAnomaly) and do the conversion from one to the other |
| 409 |
|
- move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA |
| 410 |
|
to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and |
| 411 |
|
(b) will be loaded in time (before calling INI_PRESSURE) in case it is |
| 412 |
|
needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc |
| 413 |
|
- update isomip experiment forward output (get machine truncation error |
| 414 |
|
from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly) |
| 415 |
|
o verification/offline_exf_seaice: |
| 416 |
|
revise data.seaice in input.thermo and input_ad and update results accordingly |
| 417 |
|
HO = 0.2, SEAICE_areaLossFormula = 2, |
| 418 |
|
SEAICE_growMeltByConv = .TRUE., |
| 419 |
|
SEAICE_doOpenWaterMelt = .TRUE., |
| 420 |
|
Improve consistency with input.thsice and fix the spurious 500m ice corners |
| 421 |
|
o verification/global_ocean.cs32x15: |
| 422 |
|
- set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0., |
| 423 |
|
in icedyn (thsice+seaice-dyn) test and update output. |
| 424 |
|
o verification/offline_exf_seaice: |
| 425 |
|
- adjust list of tested variables (with testreport) and update |
| 426 |
|
standard test output with better slection of monitored fields. |
| 427 |
|
o pkg/cd_code: |
| 428 |
|
- swtich off Adams-Bashforth on the 1rst iteration. Update output of |
| 429 |
|
experiment lab_sea.hb87 |
| 430 |
|
o tools/genmake2: |
| 431 |
|
- change default makedepend from the system default to tools/xmakedepend: |
| 432 |
|
When no makedepend is specified, select tools/xmakedepend it the test pass, |
| 433 |
|
otherwise select the system default (if exist and pass the test) or |
| 434 |
|
try to build cyrus-makedepend ; stop if none of the 3 works. |
| 435 |
|
o pkg/exf & pkg/thsice: |
| 436 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
| 437 |
|
for energy content of Precip + RunOff & Evap. Assumes: |
| 438 |
|
1) Rain has same temp as Air. |
| 439 |
|
2) Snow has no heat capacity (consistent with seaice & thsice pkgs) |
| 440 |
|
3) Run-Off comes at the temp of surface water (with same Cp) |
| 441 |
|
4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be |
| 442 |
|
put directly into Latent Heat flux & should use water-vapor heat capacity. |
| 443 |
|
5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent |
| 444 |
|
with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL). |
| 445 |
|
o pkg/seaice: simplify the use of CPP flags in JFNK-related files |
| 446 |
|
(compile when SEAICE_ALLOW_JFNK is defined) |
| 447 |
|
o pkg/thsice: |
| 448 |
|
- fix oceanic flux diagnostics & timeave (left from new sequence of calls |
| 449 |
|
implementation): move THSICE_AVE call after the advection (called directly |
| 450 |
|
from thsice_do_advect.F). |
| 451 |
|
o verification/global_ocean.90x40x15 and OpenAD: |
| 452 |
|
New experiment for OpenAD is identical to the one in input_ad except that |
| 453 |
|
multiDimAdvection=.FALSE., |
| 454 |
|
There is still an issue with this. |
| 455 |
|
o pkg/thsice: |
| 456 |
|
- account for ice velocity (ocean relative velocity) in turbulent heat flux |
| 457 |
|
at the base of the ice; update output of global_ocean.cs32x15 (icedyn) |
| 458 |
|
and offline_exf_seaice (main test). |
| 459 |
|
|
| 460 |
|
checkpoint64f (2013/03/31) |
| 461 |
|
o verification/OpenAD: |
| 462 |
|
- new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran. |
| 463 |
|
o verification/isomip, pkg/shelfice and OpenAD: |
| 464 |
|
- add OpenAD setup to this exp and make shelfice package work with OpenAD |
| 465 |
|
o verification/tutorial_global_oce_biogeo: |
| 466 |
|
- update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h) |
| 467 |
|
o verification/offline_exf_seaice: |
| 468 |
|
- replace adjoint experiment (now similar to fwd input.thermo/ setup). |
| 469 |
|
o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD: |
| 470 |
|
- add OpenAD setup to this exp and make ptracers package work with OpenAD |
| 471 |
|
o pkg/seaice/seaice_evp.F: |
| 472 |
|
mask the asymmetric contribution of the ice-ocean stress (when |
| 473 |
|
the turningAngle is non-zero) over open water to avoid stripes |
| 474 |
|
in the EVP-solutions after many EVP-substeps. This does not change |
| 475 |
|
the verification experiment (because turningAngle=0 in that experiment), |
| 476 |
|
but will affect other EVP solutions with turningAngle.ne.0 |
| 477 |
|
o verification, AD & TLM output: |
| 478 |
|
- new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple |
| 479 |
|
additions and multiplications which affect results at machine truncation |
| 480 |
|
level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5, |
| 481 |
|
lab_sea.noseaicedyn & offline_exf_seaice) and TLM output |
| 482 |
|
(1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12 |
| 483 |
|
digits of matching. |
| 484 |
|
o pkg/seaice: |
| 485 |
|
modify lsr-algorithm so that it vectorizes AND converges by using a |
| 486 |
|
"zebra" method: split vector loop into two with step size 2; this |
| 487 |
|
solves a general convergence problem for the JFNK solver on a vector |
| 488 |
|
computer. It has the potential to even improve convergence for |
| 489 |
|
non-vector machines, but it does change the results so it is turned |
| 490 |
|
off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and |
| 491 |
|
SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h |
| 492 |
|
|
| 493 |
|
checkpoint64e (2013/03/05) |
| 494 |
|
o pkg/ecco and several verification experiments: |
| 495 |
|
Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F |
| 496 |
|
from ecco package, and revert to unified routine in model/src/ |
| 497 |
|
Adjust verification experiments accordingly, especially gloal_oce_llc90 |
| 498 |
|
Should conclude long-standing work by Gael to reconsile the_main_loop with |
| 499 |
|
ECCO and will enable OpenAD's revolve loop in ECCO setup. |
| 500 |
|
o pkg/generic_advdiff: |
| 501 |
|
- implement compressible flow method for multi-dim advection (similar to |
| 502 |
|
gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since |
| 503 |
|
TAF generates many recomputations) to use it; no yet coded with implicit |
| 504 |
|
vertical advection. |
| 505 |
|
- change experiment advect_cs (new output) and advect_xy (same output) |
| 506 |
|
to test compressible flow multi-dim advection. |
| 507 |
|
o pkg/generic_advdiff: |
| 508 |
|
- fix SOM advection for unusual cases (linear Free-Surf in r*, other |
| 509 |
|
cases where linear Free-Surf is not @ k=1, e.g., useShelfIce) |
| 510 |
|
o pkg/seaice: |
| 511 |
|
- fix bug in the no-slip implementation in seaice_calc_strainrates.F, this |
| 512 |
|
bug affects two verification experiments (lab_sea and lab_sea.hb87), |
| 513 |
|
recover old (wrong) results by setting noSlipFac = 2. in |
| 514 |
|
seaice_calc_strainrates.F; |
| 515 |
|
- add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0 |
| 516 |
|
- add runtime parameter SEAICE_JFNKepsilon for that finite difference |
| 517 |
|
gradient in the Jacobian times vector operation (s/r seaice_jacvec) |
| 518 |
|
- fix line search in seaice_jfnk.F (s/r seaice_jfnk_update) |
| 519 |
|
o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code: |
| 520 |
|
- new subroutines seaice_lsr_tridiagu/v |
| 521 |
|
- introduce loop bounds i/jmin/max to be able to use a restricted |
| 522 |
|
additive Schwarz method, but not used for now. |
| 523 |
|
- rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS |
| 524 |
|
- use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner |
| 525 |
|
o OpenAD support |
| 526 |
|
Reorganize S/R call for overall time-stepping loop to facilitate |
| 527 |
|
OpenAD revolve loop replacement |
| 528 |
|
(new S/R main_do_loop.F) |
| 529 |
|
o model/src: |
| 530 |
|
- add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3; |
| 531 |
|
- pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R |
| 532 |
|
ADAMS_BASHFORTH2. |
| 533 |
|
o pkg/cheapaml: |
| 534 |
|
- add new parameter (default=F, same as before) to disable full domain |
| 535 |
|
(including land) periodicity in X & Y dir. |
| 536 |
|
- new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of |
| 537 |
|
prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer |
| 538 |
|
into single S/R CHEAPAML_TIMESTEP. |
| 539 |
|
|
| 540 |
|
checkpoint64d (2013/02/17) |
| 541 |
|
o pkg/monitor (angular momentum): |
| 542 |
|
- do not add Eta contribution to the total AM if using rigid-lid; |
| 543 |
|
- correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta). |
| 544 |
|
- horizontal discretisation: compute Zonal wind contribution separately for |
| 545 |
|
each component (instead of from cell centered averaged) and use the 4 |
| 546 |
|
grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part. |
| 547 |
|
- Check that AM is conserved with linear dynamics (momAdvection=F and linear |
| 548 |
|
FreeSurf) if using vectorInvariant momentum. |
| 549 |
|
o model/src (horizontal grid): |
| 550 |
|
- move initialisation of all horizontal grid arrays to null value |
| 551 |
|
from specific horizontal grid S/R to main S/R INI_GRID; |
| 552 |
|
- add 2 new arrays to project model C-grid velocity on to zonal direction |
| 553 |
|
(similar to AngleCosC & -AngleSinC but at U and V point location) and |
| 554 |
|
compute them in S/R CALC_GRID_ANGLES. |
| 555 |
|
o pkg/seaice: replace a hard coded parameter by a runtime parameter |
| 556 |
|
SEAICE_JFNK_tolIter |
| 557 |
|
o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in |
| 558 |
|
preconditioner for JFNK (run LSR into the overlaps as far as possible, |
| 559 |
|
i.e OLx/y-2, but overwrite the solution in the overlaps) |
| 560 |
|
- extend loop range in seaice_calc_viscosity |
| 561 |
|
- add new parameters SEAICE_OLx/y (default = OLx/y-2) |
| 562 |
|
- add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs |
| 563 |
|
- slightly modify loops in tridiagonal solver lsr-preconditioner |
| 564 |
|
- by default remove the extra exchange in seaice_preconditioner with a |
| 565 |
|
replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE |
| 566 |
|
- modify offline_exf_seaice so that old results without RAS are reproduced |
| 567 |
|
for output.dyn_jfnk.txt |
| 568 |
|
in seaice_fgmres.F (unrelated to RAS) |
| 569 |
|
- add a cpp-flag option for a re-ordered mapping (potentially more |
| 570 |
|
efficient), but because this changes the results, turn it off by |
| 571 |
|
default |
| 572 |
|
- replace the save statement by local common blocks |
| 573 |
|
o utils/matlab: |
| 574 |
|
- fix tile-offset in rdmnc.m when output was produced using EXCH2. |
| 575 |
|
- update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab) |
| 576 |
|
instead of local script "load_cs.m". |
| 577 |
|
o pkg/seaice: |
| 578 |
|
- fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected |
| 579 |
|
to the scalarProductMetric and the unrolling. By chance this does not |
| 580 |
|
change the verification experiment, because of the particular domain |
| 581 |
|
decomposition |
| 582 |
|
o pkg/diagnostics: |
| 583 |
|
- change default missing_value from UNSET_RL to -999. |
| 584 |
|
o pkg/layers: improve vectorization of layers_fluxcalc.F |
| 585 |
|
- step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu |
| 586 |
|
time spent in this routine by more than a factor of 3 on an NEC-SX8 |
| 587 |
|
- step 2: replace search algorithm by a bisection algorithm found in |
| 588 |
|
Press et al. Numerical Recipes in Fortran. This algorithm can be |
| 589 |
|
vectorized and finds the correct bin in approx. log2(Nlayers) steps. |
| 590 |
|
For now, use this algorithm only for TARGET_NEC_SX defined. |
| 591 |
|
- moved the search algorithm into a separate subroutine, that is kept |
| 592 |
|
within the same file for automatic inlining. |
| 593 |
|
- modified catching potential errors |
| 594 |
|
o pkg/ecco: |
| 595 |
|
- add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY. |
| 596 |
|
o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk : |
| 597 |
|
- modifications for ALLOW_GENTIM2D_CONTROL |
| 598 |
|
-- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes. |
| 599 |
|
-- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid ) |
| 600 |
|
-- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc |
| 601 |
|
-- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F |
| 602 |
|
o model/src: |
| 603 |
|
- account for moist thermodynamics in (dry) potential temperature equation; |
| 604 |
|
update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev) |
| 605 |
|
and cpl_aim+ocn. |
| 606 |
|
- also switch to standard compiler (gfortran, was using ifort previously) |
| 607 |
|
for fizhi-cs experiments reference output. |
| 608 |
|
o pkg/ctrl: |
| 609 |
|
- 1st step toward generic time-varying control variable (2D) via CPP option |
| 610 |
|
ALLOW_GENTIM2D_CONTROL |
| 611 |
|
- note new namelist ctrl_nml_genarr in data.ctrl |
| 612 |
|
o verification/global_ocean.cs32x15: |
| 613 |
|
- switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new |
| 614 |
|
thsice calling sequence and update "output.icedyn.txt" output file. |
| 615 |
|
o pkg/ptracers: |
| 616 |
|
- from Ryan A.: code to allow to restart a tracer at regular time interval |
| 617 |
|
specifying a reset frequency and a reset-phase (for each tracers). |
| 618 |
|
o pkg/thsice: |
| 619 |
|
- implement new sequence of calls for thsice+seaice: |
| 620 |
|
previously: ice-Dyn,ice-Advect,ice-Thermo(thsice) |
| 621 |
|
new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect |
| 622 |
|
- allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE" |
| 623 |
|
in CPP_OPTIONS.h) to recover old sequence; |
| 624 |
|
- update diagnostics for Intermediate State thsice diagnostics: now filled |
| 625 |
|
just before advection (instead of just after advection in old sequence); |
| 626 |
|
- update output of experiment offline_exf_seaice (standard test); |
| 627 |
|
- in global_ocean.cs32x15 exp., postpone output.icedyn.txt update |
| 628 |
|
by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h |
| 629 |
|
o pkg/aim_v23: |
| 630 |
|
- use tiled array for aim_CO2 and surface wind speed for export to coupler; |
| 631 |
|
- use standard pkg/mdsio routines to read & write CO2 pickup file; |
| 632 |
|
- in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F; |
| 633 |
|
- Implement new sequence of calls for seaice advection (with thsice and |
| 634 |
|
seaice diffusion): do ice advection after ice-Thermodynamic (previously |
| 635 |
|
was done before); change aim_do_physics.F (split the bi,bj loops block); |
| 636 |
|
- use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence; |
| 637 |
|
o pkg/thsice: |
| 638 |
|
- add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case |
| 639 |
|
where just seaice diffusion is used without seaice-dynamics. |
| 640 |
|
|
| 641 |
|
checkpoint64c (2013/01/18) |
| 642 |
|
o pkg/seaice: |
| 643 |
|
- add a parameter JFNKres_tFac that can replace JFNKres_t |
| 644 |
|
(= JFNKres_tFac*JFNKresidual before JFNK solver) |
| 645 |
|
- add a line search option to the JFNK solver |
| 646 |
|
- move update of u/vIce and computation of initial residual into a separate |
| 647 |
|
routine (same file); makes the code a little easier to read (?) |
| 648 |
|
- the line search requires computation of the residual and for some reason |
| 649 |
|
I cannot do the update of u/vIce at the beginning of the Newton loop |
| 650 |
|
without changing the results, so we move computation of the new residual |
| 651 |
|
also to the end of the Newton loop, even without the line search |
| 652 |
|
o pkg/mdsio: |
| 653 |
|
- write missing value (corresponding to undefined array value) to meta files; |
| 654 |
|
skip this if missing value is one (UNSET_RL would be a better value for the |
| 655 |
|
case of undefined missing value but it's current the default missing-value); |
| 656 |
|
Also update mdsio_read_meta.F (reading timeInterval & missing-value). |
| 657 |
|
o pkg/exf & thsice: |
| 658 |
|
- for diagnostics purpose, fill-up and update Qsw array (+ fill the |
| 659 |
|
diagnostics) even when SHORTWAVE_HEATING is #undef; |
| 660 |
|
o verification/cfc_example: |
| 661 |
|
- turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to |
| 662 |
|
illustrate how to use it). |
| 663 |
|
o verification/offline_exf_seaice: |
| 664 |
|
in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing |
| 665 |
|
files to only one time-record. |
| 666 |
|
in input.thermo: narrow the 2 bands of low initial ice-concentration near |
| 667 |
|
N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for |
| 668 |
|
snapshot output; same mcPheePiston value as in thsice with |
| 669 |
|
surf-current=0.2m/s. |
| 670 |
|
in input.thsice: similar set-up as in input.thermo (channel with same seaice |
| 671 |
|
initial conditions). |
| 672 |
|
o verification/cfc_example: |
| 673 |
|
- update file "data" with more standard choice (default rotationPeriod, |
| 674 |
|
exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F, |
| 675 |
|
set deltaTFreeSurf to deltaTtracer) and update the output. |
| 676 |
|
o pkg/layers: |
| 677 |
|
- fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC; |
| 678 |
|
- ensure that "layers_bolus" is switched to False when useGMRedi=False. |
| 679 |
|
o verification/offline_exf_seaice: |
| 680 |
|
- set all {field}period to zero for constant-in-time forcing (not tested |
| 681 |
|
anywhere else). |
| 682 |
|
o verification/offline_exf_seaice: |
| 683 |
|
- dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice; |
| 684 |
|
- dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice. |
| 685 |
|
o model/src: |
| 686 |
|
- implement Finite-Volume method for (hydrostatic) presure gradient |
| 687 |
|
from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate. |
| 688 |
|
o pkg/seaice: implement EVP* by Lemieux et al. (2012). |
| 689 |
|
- In order to be compatible with the default EVP code, this requires changing |
| 690 |
|
the EVP code around a little; and because any small change immediately |
| 691 |
|
breaks the lab_sea.hb87 verification experiment, the reference output is |
| 692 |
|
updated two times (each time the remaining aggrement was only 2 digits): |
| 693 |
|
- after replacing 1/dt by 1*recip_dt with a precomputed recip_dt |
| 694 |
|
- after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt |
| 695 |
|
The adjoint test lab_sea.evp also needed to be updated. |
| 696 |
|
- Turn on EVP* by setting SEAICE_deltaTevp as before, and setting |
| 697 |
|
SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be |
| 698 |
|
a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps |
| 699 |
|
explicitly with SEAICEnEVPstarSteps (thereby overriding the default of |
| 700 |
|
INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately |
| 701 |
|
kept obscure, because I need to test it a little more. |
| 702 |
|
o pkg/cheapaml: |
| 703 |
|
- fix few incorrect type (_RL/_RS) in subroutine calls. |
| 704 |
|
o pkg/seaice: |
| 705 |
|
- new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays |
| 706 |
|
to _RL vector; this fixes JFNK code when compiling with "-use_r4" option. |
| 707 |
|
o model/src: |
| 708 |
|
- add a warning if using select_rStar=2 with nonlinFreeSurf <> 4; |
| 709 |
|
change (in input_ad*/data) select_rStar from 2 to 1 for AD verification |
| 710 |
|
experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output) |
| 711 |
|
o pkg/cheapaml: |
| 712 |
|
- replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and |
| 713 |
|
update output of experiment cheapAML_box. |
| 714 |
|
- store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity, |
| 715 |
|
and set them only in one place (cheapaml_readparms.F). |
| 716 |
|
- replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI" |
| 717 |
|
- remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms) |
| 718 |
|
and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia). |
| 719 |
|
o model/src/the_main_loop.F: |
| 720 |
|
- fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION. |
| 721 |
|
o pkg/seaice: |
| 722 |
|
- remove legacy branch code. |
| 723 |
|
- retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly. |
| 724 |
|
o verification/*/code*/SEAICE_OPTIONS.h: |
| 725 |
|
- remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY, |
| 726 |
|
SEAICE_CAP_HEFF). |
| 727 |
|
o pkg/cheapaml: |
| 728 |
|
- use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time |
| 729 |
|
to load new forcing fields. |
| 730 |
|
- add missing "_d 0" where it's needed; + some editing (improve indentation). |
| 731 |
|
- remove switch to "-r8" compiler option (no longer needed) in verification |
| 732 |
|
cheapAML_box, keep same output (small trucation error differences). |
| 733 |
|
o verification/offline_exf_seaice: |
| 734 |
|
- add thermodynamics only test. |
| 735 |
|
o verification/cheapAML_box: |
| 736 |
|
- split the domain in 8 (2x4) tiles; add MPI and multi-threaded test; |
| 737 |
|
keep same output (same 14 digits for cg2d). |
| 738 |
|
- switch on "-r8" compiler option (some numerical values are missing |
| 739 |
|
the "_d 0") and update output (only 6 digits for cg2d were preserved). |
| 740 |
|
|
| 741 |
|
checkpoint64b (2012/12/24) |
| 742 |
|
o pkg/cheapaml: |
| 743 |
|
- remove un-used variables (Qnet,EmPmR) from pickup files. |
| 744 |
|
- store tendency of advected variables into cheapaml pickup file |
| 745 |
|
and fix the AB-2 restart. |
| 746 |
|
o verification/offline_exf_seaice and lab_sea adjoint: |
| 747 |
|
- switch to new code (#undef SEAICE_GROWTH_LEGACY). |
| 748 |
|
- switch to 4 time steps in offline, consistent with lab_sea. |
| 749 |
|
- match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice. |
| 750 |
|
- update results after change of experiment seaice. |
| 751 |
|
o pkg/seaice: |
| 752 |
|
- remove option SEAICE_MULTICATEGORY; has been replaced with run-time |
| 753 |
|
parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is |
| 754 |
|
still defined since SEAICE_multDim needs to be set to MULTDIM value (from |
| 755 |
|
SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default. |
| 756 |
|
o model/src: |
| 757 |
|
- add run-time parameter to select CG2D solver minimum-residual solution |
| 758 |
|
(in case of a poor convergence). |
| 759 |
|
o pkg/seaice/seaice_lsr.F |
| 760 |
|
- move calculation of matrix coefficients into new |
| 761 |
|
S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same |
| 762 |
|
file; the main purpose of this change is to be able to reuse the code |
| 763 |
|
in S/R SEAICE_PRECONDITIONER |
| 764 |
|
- modify the computation of the residual so that the mass of sea-ice |
| 765 |
|
is not used twice; this simplifies the calculations, but since |
| 766 |
|
the residual is never used except when LSR_mixIniGuess.ge.4---and this is |
| 767 |
|
not tested in testreport---this does not affect the testreport results. |
| 768 |
|
o verification/seaice_obcs: |
| 769 |
|
- disable SEAICE_GROWTH_LEGACY; reset input files to match those of |
| 770 |
|
verification/lab_sea/input.salt_plume; changes results/output.txt* |
| 771 |
|
o model/src: |
| 772 |
|
- adapt quasi-hydrostatic formulation to work with p or p* coordinate. |
| 773 |
|
o pkg/seaice: |
| 774 |
|
- improve description of parameters in seaice_fgmres.F and start |
| 775 |
|
cleaning up the code |
| 776 |
|
- change name of SCALPROD to SEAICE_SCALPROD and modify meaning of |
| 777 |
|
second argument |
| 778 |
|
- add a metric based on grid cell area to SEAICE_SCALPROD; update |
| 779 |
|
results of offline_exf_seaice.dyn_jfnk |
| 780 |
|
- compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD |
| 781 |
|
o pkg/aim_v23: |
| 782 |
|
- fix an other bug in dissipation heating (grid-cell area was missing). |
| 783 |
|
o model/src + pkg/seaice: |
| 784 |
|
- add global (multi-tile) linear solver for pair of tri-diagonal system |
| 785 |
|
along X and Y lines, respectively for U and V component. |
| 786 |
|
Note: 1) MPI and cube-exchange not yet coded. |
| 787 |
|
2) probably not accurate for poorly conditioned / large size problem. |
| 788 |
|
- add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver; |
| 789 |
|
default: not compiled and not used. |
| 790 |
|
o pkg/seaice: |
| 791 |
|
- first attempt at a multi-threaded fgmres solver for the JFNK solver: |
| 792 |
|
introduce bi/bj loops and use global_sum_tile_rl instead of |
| 793 |
|
mpi_allreduce in seaice_fgmres.F |
| 794 |
|
- improve diagnostics output for fgmres solver (seaice_fgmres.F) |
| 795 |
|
- replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F) |
| 796 |
|
- add a verification experiment for JFNK in offline_exf_seaice |
| 797 |
|
o verification: |
| 798 |
|
- change (for now, only fwd test) offline_exf_seaice experiment: |
| 799 |
|
use a re-entrant channel with idealized coastline (trapezoidal shape) |
| 800 |
|
at southern boundary to explore seaice dynamics and thermodynamics |
| 801 |
|
with simple forcing. Main set-up has dynamics+thermo and SST relaxation; |
| 802 |
|
secondary test (input.thsice) use thermodynamics only with SST relaxation. |
| 803 |
|
- add seaice-dynamics only secondary test using LSR and pkg/thsice advection. |
| 804 |
|
o pkg/exf: |
| 805 |
|
- disable "sstExtrapol" when Nr=1 |
| 806 |
|
o verification: |
| 807 |
|
- add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble) |
| 808 |
|
to test pkg/cheapaml. |
| 809 |
|
o pkg/aim_v23 & pkg/shap_filt: |
| 810 |
|
- fix dissipation heating (erroneous gravity multiplication factor). |
| 811 |
|
o pkg/seaice: |
| 812 |
|
- remove unused field pressPre from jfnk solver |
| 813 |
|
- rename two subroutines in seaice_preconditioner.F |
| 814 |
|
o eesupp/src: |
| 815 |
|
- S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...) |
| 816 |
|
o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again |
| 817 |
|
- remove wrong parts of the rhs and the lhs (were in there |
| 818 |
|
because I did not understand the concept of this preconditioner) |
| 819 |
|
- add an exchange between u- and v-sweep. This increases communication |
| 820 |
|
by a factor of two but improves the convergence of jfnk. Ideally, |
| 821 |
|
one would like the u- and v-sweep to be independent. So far within |
| 822 |
|
undocumented ifdefs |
| 823 |
|
- reorganize the extra computations for printing the residuals |
| 824 |
|
o tools/genmake2: |
| 825 |
|
- comment out the "mpif.h" include in NetCDF test programm (for MPI built) |
| 826 |
|
since it's not necessary (and was preventing to use MNC in some cases). |
| 827 |
|
|
| 828 |
|
checkpoint64a (2012/11/16) |
| 829 |
|
o pkg/autodiff: |
| 830 |
|
- improve pkg-internal logical parameter switch (inAd/inFwd mode) so that |
| 831 |
|
autodiff_readparms.F no longer depends on calling order (within |
| 832 |
|
packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h): |
| 833 |
|
rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd |
| 834 |
|
and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd. |
| 835 |
|
o pkg/obcs: |
| 836 |
|
- adding tidal velocity forcing capability to obcs |
| 837 |
|
for usage example, see verification/seaice_obcs/input.tides |
| 838 |
|
o pkg/seaice: |
| 839 |
|
- turn the LSR-relaxation parameters WFAU/V into runtime parameters |
| 840 |
|
SEAICE_LSRrelaxU/V |
| 841 |
|
- introduce runtime parameter SEAICEetaZmethod (=0 by default) |
| 842 |
|
o pkg/aim_v23: |
| 843 |
|
- implement heating from friction (bottom friction and stratospheric drag). |
| 844 |
|
o pkg/shap_filt: |
| 845 |
|
- fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from |
| 846 |
|
dissipation but only for Shap_funct=2, active when addFrictionHeating=T. |
| 847 |
|
o model/src: |
| 848 |
|
- move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in |
| 849 |
|
time-constant addMass field from file (addMassFile); |
| 850 |
|
- support for heating due to friction (and Kinetic Energy dissipation): |
| 851 |
|
add option, run-time switch and 3-D field array + support code ; each pkg |
| 852 |
|
or S/R can add heating contribution (if there is a sink of KE); the sum is |
| 853 |
|
accounted for as a Temperature tendency term (EXTERNAL_FORCING_T). |
| 854 |
|
o pkg/seaice: |
| 855 |
|
- complete merge of ITD code into seaice_growth.F |
| 856 |
|
from MITgcm_contrib/torge/itd/code/ |
| 857 |
|
no verification so far, but Torge Martin tested |
| 858 |
|
"1-D test case and Beaufort set up; |
| 859 |
|
deliver okay results after 1 model year." |
| 860 |
|
- complete merge of SEAICE_SIZE.h into all relevant routines |
| 861 |
|
- move computation of eta at Z-points into calc_viscosities |
| 862 |
|
+ introduce global field etaZ |
| 863 |
|
+ add different methods for computing etaZ, for now the old |
| 864 |
|
method (simple averages of eta to Z-points) is hardwired |
| 865 |
|
+ replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual, |
| 866 |
|
seaice_preconditioner |
| 867 |
|
- simplify computations for SEAICE_ZETA_SMOOTHREG |
| 868 |
|
- seaice_preconditioner: |
| 869 |
|
+ replace one remaining press by pressLoc (mistake) |
| 870 |
|
+ adjust printing of residuals |
| 871 |
|
- improve I/O of diagnostics of JFNK in seaice_jfnk.F: |
| 872 |
|
+ add (SEAICE.h) and rename some counters (initiliased in |
| 873 |
|
seaice_init_fixed.F) |
| 874 |
|
+ add _BEGIN/END_MASTER (myThid) around print statements |
| 875 |
|
+ print total number of iterations and failures over SEAICE_monFreq |
| 876 |
|
interval to STDOUT |
| 877 |
|
- move control over output-messages by fgmres to seaice_jfnk to save |
| 878 |
|
some operations |
| 879 |
|
- move resetting initial guess for fgmres outside of seaice_fgmres_driver |
| 880 |
|
in order to make restarts with sol .ne. zero (fgmres with restarts) |
| 881 |
|
(seaice_jfnk.F, seaice_fgmres.F) |
| 882 |
|
- seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes |
| 883 |
|
a serious convergence problem when open boundaries are involved |
| 884 |
|
o pkg/ggl90: fix computation of control volumes for the case of |
| 885 |
|
ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes |
| 886 |
|
up half a grid cell from C-centered to W-centered (pointed out by C. Eden) |
| 887 |
|
o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC |
| 888 |
|
o pkg/autodiff |
| 889 |
|
- Add inAdMode switch for SEAICEuseDYNAMICS: |
| 890 |
|
SEAICEuseDYNAMICSinAdMode |
| 891 |
|
(extend logic in ADAUTODIFF_INADMODE_SET) |
| 892 |
|
o pkg/seaice |
| 893 |
|
- Step 1 of merging ice-thickness distribution (ITD) code from |
| 894 |
|
MITgcm_contrib/torge/itd/ (author: Torge Martin) |
| 895 |
|
The code implements concept laid out in Thorndike et al. (1975); |
| 896 |
|
code is enabled via CPP flag SEAICE_ITD |
| 897 |
|
nITD (in SEAICE_SIZE.h) defines number of ice thickness categories; |
| 898 |
|
code is not complete yet!! |
| 899 |
|
- SEAICE_SIZE.h now included in almost all seaice routines |
| 900 |
|
o verification (using seaice): |
| 901 |
|
- switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp. |
| 902 |
|
global_ocean.cs32x15.seaice ; update results. |
| 903 |
|
- compile B-grid dynamics in FW test exp 1D_ocean_ice_column ; |
| 904 |
|
- compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp |
| 905 |
|
offline_exf_seaice (previously compiling B-grid). |
| 906 |
|
o pkg/exf: |
| 907 |
|
- fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow |
| 908 |
|
to specify neither just 1 comp of wind or wind-stress, nor no surface momentum |
| 909 |
|
forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind. |
| 910 |
|
o pkg/layers (adjust changes from Sept 19): |
| 911 |
|
- do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F) |
| 912 |
|
this allows to remove "layers_maxNum" dimension from all layers arrays. |
| 913 |
|
o pkg/layers (adjust changes from Sept 19): |
| 914 |
|
- remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ; |
| 915 |
|
- snap-shot extended to all type of layers (not just the 1rst type); |
| 916 |
|
- remove layers variables when corresponding CPP option is undef. |
| 917 |
|
o pkg/layers: |
| 918 |
|
- rename pkg/layers variable and add new output (layer exist & un-weighted |
| 919 |
|
velocity in layer) |
| 920 |
|
o pkg/seaice: |
| 921 |
|
- simplify (?) ocean-drag coefficent computations by using |
| 922 |
|
the same routine in all three solvers (saves some code lines) |
| 923 |
|
- remove global fields DRAGA and DRAGS from C-grid code and |
| 924 |
|
declare them locally in lsr.F (the only place where they are |
| 925 |
|
still used) |
| 926 |
|
- update AD output of lab_sea.evp (very sensitive anyway). |
| 927 |
|
o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics |
| 928 |
|
(Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK |
| 929 |
|
and SEAICEuseJFNK=.true. A few things to note: |
| 930 |
|
- involves a FGMRES, that is parallel but very inefficient, |
| 931 |
|
because of many scalar products (global sums) in the Gram-Schmidt |
| 932 |
|
orthogonalization method. Needs to be replaced. Original code |
| 933 |
|
from J.-F. Lemieux |
| 934 |
|
- preconditioner for FGMRES is a stripped down version of LSOR |
| 935 |
|
- SOLV_MAX_ITERS is now used for LSOR as a solver and as a |
| 936 |
|
preconditioner. For the preconditioner, the default is set to 10. |
| 937 |
|
- Jacobian times vector is computed with finite differences |
| 938 |
|
- marginally related to JFNK-solver: add a smooth regularization for |
| 939 |
|
zeta with tanh that will improve convergence (Lemieux and Tremblay, |
| 940 |
|
2009) for any implicit solver (not implemented for EVP because EVP |
| 941 |
|
does not need this regularization in the first place). Define |
| 942 |
|
SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use. |
| 943 |
|
o eesupp/src: |
| 944 |
|
- check in genmake2 that intrinsic S/R flush is available. |
| 945 |
|
- add S/R to flush IO unit (if intrinsic S/R flush is available) |
| 946 |
|
- flush standard & error msg unit before MPI termination |
| 947 |
|
- if debugMode, flush IO unit after printing msg |
| 948 |
|
o pkg/ctrl: |
| 949 |
|
- ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call |
| 950 |
|
to ctrl_set_unpack_xyz. |
| 951 |
|
|
| 952 |
|
checkpoint64 (2012/10/09) |
| 953 |
|
o pkg/shelfice |
| 954 |
|
- in mom_fluxform.F, mom_vecinv.F: |
| 955 |
|
CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid) |
| 956 |
|
Bug fix KappaRU -> KappaRV |
| 957 |
|
does not change verification/isomip but may change other setups |
| 958 |
|
(presumably constant KappaRU=KappaRV) |
| 959 |
|
- fix diagnostics SHIU/Vdrag (thanks to Tom Millgate) |
| 960 |
|
o pkg/obcs: |
| 961 |
|
- fixed some indexing bugs in obcs_seaice_sponge.F |
| 962 |
|
- added obcs relaxation subroutines for HSALT and HSNOW |
| 963 |
|
- changes verification/seaice_obcs/results/obcs_seaice_sponge.F |
| 964 |
|
o pkg/seaice: |
| 965 |
|
- add "multicategory" parameterization for snow in analogy to ice, |
| 966 |
|
default is off for now. |
| 967 |
|
o pkg/obcs: |
| 968 |
|
- added obcs_seaice_sponge.F for obcs relaxation of seaice variables; |
| 969 |
|
see verification/seaice_obcs/input.seaiceSponge for example application. |
| 970 |
|
- remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB |
| 971 |
|
index setting by master-thread. This fix multi-threads Pb in previous modifs. |
| 972 |
|
o pkg/layers : |
| 973 |
|
- add diagnostics to pkg/layers |
| 974 |
|
- move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F |
| 975 |
|
(from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly. |
| 976 |
|
o pkg/generic_advdiff/gad_implicit_r.F : |
| 977 |
|
- fix ADVr diagnostics in case of both implicit vertical advection and diffusion. |
| 978 |
|
o pkg/seaice/seaice_growth.F: |
| 979 |
|
- fix SItflux diagnostics in virtual salt flux + balanceEmpmr case. |
| 980 |
|
o pkg/obcs: |
| 981 |
|
- change default setting of OBCS_UVICE_OLD from defined to undef; |
| 982 |
|
- use new parameter OB_indexNone for null index value (instead of hard-coded 0) |
| 983 |
|
in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F; |
| 984 |
|
- pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z; |
| 985 |
|
- change OB null index value (OB_indexNone) to -99 ; this fix the problem |
| 986 |
|
with Southern & Western OB at a tile edge (at least in a simple set-up). |
| 987 |
|
o pkg/obcs: |
| 988 |
|
- change settings of OB index in case OB coincides with tile edge (shared by |
| 989 |
|
2 tiles), so that common OB location is registered by both tiles (instead of |
| 990 |
|
only 1). However, for Southern and Western OB, index value = 0 is not |
| 991 |
|
recognized as valid OB index (=default null value) and needs to be fixed. |
| 992 |
|
- modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting) |
| 993 |
|
- new parameter "OB_indexNone" for null index value (for now, still zero) |
| 994 |
|
to replace hard-coded null index value of zero. |
| 995 |
|
o pkg/exch2: |
| 996 |
|
- improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON: |
| 997 |
|
always check buffer-size (but outside the loop); move checking for valid |
| 998 |
|
index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON, |
| 999 |
|
print each tile and point connection only if |W2_printMsg|>= 2 and 3. |
| 1000 |
|
o pkg/ctrl (pack & unpack): |
| 1001 |
|
- in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable |
| 1002 |
|
(locally defined) for different variables (+ remove the variable-specific |
| 1003 |
|
file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL |
| 1004 |
|
(to be extended to other local file names in ctrl.h). |
| 1005 |
|
o pkg/flt: |
| 1006 |
|
- add a FLT_Iter0 option (similar to PTRACERS_Iter0). |
| 1007 |
|
o pkg/mdsio: |
| 1008 |
|
- fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing |
| 1009 |
|
o tools/genmake2: |
| 1010 |
|
- add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE |
| 1011 |
|
(added by Alistair in version 1.51 for building without make depend); |
| 1012 |
|
- remove Header files list (H_SRC_FILES) from the dependence of targets |
| 1013 |
|
ad_input_code.f & ftl_input_code.f (not clear why it was added in the first |
| 1014 |
|
place in version 1.23): this save going through staf when unrelated header |
| 1015 |
|
file has been modified. |
| 1016 |
|
Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without |
| 1017 |
|
"make depend" step, still need to do "make links" before "make adtaf". |
| 1018 |
|
o eesupp/src (+ few pkg src files) & genmake2: |
| 1019 |
|
- finish to remove ALWAYS_USE_MPI in source code that TAF does not see; |
| 1020 |
|
- no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2). |
| 1021 |
|
- improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish |
| 1022 |
|
upper/lower case ; account for space between "#" and undef/define) |
| 1023 |
|
o pkg/flt (with exch2): |
| 1024 |
|
- cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F; |
| 1025 |
|
- simplify threads synchronisation; fix (many issues) multi-threaded with MPI. |
| 1026 |
|
|
| 1027 |
|
checkpoint63s (2012/09/05) |
| 1028 |
|
o pkg/ecco: |
| 1029 |
|
- remove #ifdef ALLOW_SMOOTH_CORREL3D brackets. |
| 1030 |
|
- add more relevant #ifdef ALLOW_SMOOTH ones. |
| 1031 |
|
- sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D. |
| 1032 |
|
o pkg/ctrl: |
| 1033 |
|
- CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D, |
| 1034 |
|
ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D. |
| 1035 |
|
- ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag, |
| 1036 |
|
doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and |
| 1037 |
|
ctrlSmoothCorrel3D (new). |
| 1038 |
|
The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP. |
| 1039 |
|
- ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist. |
| 1040 |
|
- ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress |
| 1041 |
|
controls when useAtmWind, and vice versa. |
| 1042 |
|
- ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers. |
| 1043 |
|
- ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with |
| 1044 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH. |
| 1045 |
|
- ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with |
| 1046 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH. |
| 1047 |
|
- ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F: |
| 1048 |
|
replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D. |
| 1049 |
|
o pkg/smooth: |
| 1050 |
|
- remove un-necessary includes. |
| 1051 |
|
- remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets. |
| 1052 |
|
Those CPP options were never defined, and not necessary. |
| 1053 |
|
o model/src: |
| 1054 |
|
- fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi). |
| 1055 |
|
- standard treatment of useSMOOTH. |
| 1056 |
|
o pkg/autodiff: |
| 1057 |
|
- add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode, |
| 1058 |
|
useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint. |
| 1059 |
|
o pkg/exch2: |
| 1060 |
|
- add "if usingMPI" where it was missing (in exch2_rx?_cube*.template) |
| 1061 |
|
+ start to remove ALWAYS_USE_MPI in source code that TAF does not see. |
| 1062 |
|
- make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag |
| 1063 |
|
and tiles to process mapping. |
| 1064 |
|
- re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h) |
| 1065 |
|
moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h; |
| 1066 |
|
rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX |
| 1067 |
|
from w2_eeboot.F to w2_readparms.F. |
| 1068 |
|
o eesupp/src: |
| 1069 |
|
- set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of |
| 1070 |
|
ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F; |
| 1071 |
|
also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F |
| 1072 |
|
- in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI |
| 1073 |
|
is defined (remove condition on usingMPI) to match cases where MPI_INIT |
| 1074 |
|
has been called. |
| 1075 |
|
- fix bug I put in previous modif of exch_sm_3d_rx.template (not much used); |
| 1076 |
|
- change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings |
| 1077 |
|
(so that on 1 proc, get same myPid independently of usingMPI) |
| 1078 |
|
- add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and |
| 1079 |
|
useCubedSphereExchange with EXCH-1 (safer). |
| 1080 |
|
- add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI). |
| 1081 |
|
o pkg/ggl90: |
| 1082 |
|
- fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call) |
| 1083 |
|
used in ALLOW_GGL90_SMOOTH code. |
| 1084 |
|
o pkg/flt: |
| 1085 |
|
- fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping |
| 1086 |
|
floats at the Southern end of the domain). |
| 1087 |
|
o eesupp/inc: |
| 1088 |
|
- add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h); |
| 1089 |
|
but not used (and not to be used) anywhere, just for documentation. |
| 1090 |
|
o pkg/autodiff, exf, ptracers & seaice (AD & TL output): |
| 1091 |
|
- comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since: |
| 1092 |
|
a) can damage previously written records in any other multi-record files. |
| 1093 |
|
b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S. |
| 1094 |
|
o tools/genmake2: |
| 1095 |
|
- define variable MAKE within Makefile and use it in place of 'make'; |
| 1096 |
|
- update AD_CONFIG.h (if needed) before building any of the executable |
| 1097 |
|
(forward, adjoint or tangent-lin); this involves a 2nd invocation of make; |
| 1098 |
|
and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h; |
| 1099 |
|
- always print usual warning comment 'this file is automatically generated' |
| 1100 |
|
from script convert_cpp_cmd2defines (+ remove this warning from genmake2). |
| 1101 |
|
o pkg/cheapaml: |
| 1102 |
|
- updated to correspond to the code used in accepted paper (Nico Wienders). |
| 1103 |
|
o pkg/exf: |
| 1104 |
|
added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch. |
| 1105 |
|
ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F) |
| 1106 |
|
and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h). |
| 1107 |
|
o pkg/exf, autodiff, ctrl, ecco and seaice: |
| 1108 |
|
remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones. |
| 1109 |
|
o pkg/ctrl, ecco: |
| 1110 |
|
allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL. |
| 1111 |
|
Depending on useAtmWind, one is inactive, and the other is active (see |
| 1112 |
|
exf_getffields.F/exf_getsurfacefluxes.F). |
| 1113 |
|
o tools/genmake2: |
| 1114 |
|
- improve error msg when failing in 2nd test of check_for_broken_Ff |
| 1115 |
|
- fix option '-makefile' short-name (-mf according to genmake2 -help) |
| 1116 |
|
- source local config file "genmake_local" just after processing the genmake2 |
| 1117 |
|
command arguments (previously done before processing arg). |
| 1118 |
|
o pkg/grdchk: |
| 1119 |
|
- add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call |
| 1120 |
|
to this routine from cost_final has been dropped in g_cost_final) |
| 1121 |
|
- improve printed information (more explicit msg, no longer using "print *," |
| 1122 |
|
fix fcpertminus printed value). |
| 1123 |
|
o model/src: |
| 1124 |
|
- move call to COST_INIT_VARIA out of packages_init_variables.F directly |
| 1125 |
|
into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES): |
| 1126 |
|
this prevents getting cost-funct reset in adinitialise_varia recomputations. |
| 1127 |
|
o pkg/dic: |
| 1128 |
|
- move initialisation of "freefe" array from from dic_biotic_forcing.F to |
| 1129 |
|
fe_chem.F: this prevents TAF from dropping this initialisation in TLM code. |
| 1130 |
|
o pkg/grdchk: |
| 1131 |
|
- grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid ) |
| 1132 |
|
- grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0 |
| 1133 |
|
o pkg/autodiff/ctrl/grdchk : |
| 1134 |
|
- attempt to sort out what works and what does not, |
| 1135 |
|
with regard to I/O, and to warn/stop accordingly. |
| 1136 |
|
o pkg/grdchk: |
| 1137 |
|
- attempt to fix grdchk in the case of useSingleCpuIO. |
| 1138 |
|
- "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )" |
| 1139 |
|
statements were moved from grdchk_main.F and into |
| 1140 |
|
grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F. |
| 1141 |
|
- a global sum is applied to record numbers icvrec/layer |
| 1142 |
|
out of grdchk_loc so that they be passed to I/O routines. |
| 1143 |
|
o pkg/smooth: |
| 1144 |
|
- fix recomputation that appeared with nlfs : use smooth_recip_hFacC, |
| 1145 |
|
smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case. |
| 1146 |
|
o verification/testreport: |
| 1147 |
|
- add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive); |
| 1148 |
|
- can also use compressed (gzip) reference output file; |
| 1149 |
|
- change format (in pkg/grdchk) of TLM output (+ add forward gradient) |
| 1150 |
|
to be easier to collect by testreport. |
| 1151 |
|
- update existing TLM output (half out-of-date by more than 3 yrs). |
| 1152 |
|
- report NETCDF & LAPACK settings (from genmake2) in output dir. |
| 1153 |
|
- report run-time in each individual summary (previously only for AD test); |
| 1154 |
|
for TLM test, add also TAF version. |
| 1155 |
|
- add daily TLM test on (old) aces cluster + weekly test on baudelaire. |
| 1156 |
|
|
| 1157 |
|
checkpoint63r (2012/08/15) |
| 1158 |
|
o tools/genmake2: |
| 1159 |
|
- fix Makefile for target ftlall (+ update files to clean after make ftlall) |
| 1160 |
|
o pkg/ecco/ecco_cost_final.F : |
| 1161 |
|
- fix fc print statements (to stdout and costfunction0000) so |
| 1162 |
|
that the printed value is always after the global sum. |
| 1163 |
|
o pkg/seaice/seaice_dynsolver.F : |
| 1164 |
|
- fix ice strength assymptote at SEAICE_area_max<1 |
| 1165 |
|
(no change for the standard case of SEAICE_area_max=1) |
| 1166 |
|
o some cleaning: |
| 1167 |
|
- pkg source files: ensure that all *.F files from each pkg included the |
| 1168 |
|
corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which |
| 1169 |
|
only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment |
| 1170 |
|
code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding |
| 1171 |
|
includes; |
| 1172 |
|
- model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used. |
| 1173 |
|
- ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR |
| 1174 |
|
is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when |
| 1175 |
|
ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop. |
| 1176 |
|
- update option-file CPP_OPTIONS.h of all AD experiments: |
| 1177 |
|
* no longer include PACKAGES_CONFIG.h ; |
| 1178 |
|
* includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ; |
| 1179 |
|
* def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before |
| 1180 |
|
including ECCO_CPPOPTIONS.h). |
| 1181 |
|
o pkg/cost, pkg/ctrl, pkg/ecco option-file: |
| 1182 |
|
- clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into |
| 1183 |
|
separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h, |
| 1184 |
|
not necessary accurate). |
| 1185 |
|
- add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in |
| 1186 |
|
pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to |
| 1187 |
|
deliberately break compilation (a remainder that it needs to be customized) |
| 1188 |
|
- in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h |
| 1189 |
|
- rename COST_CPPOPTIONS.h to COST_OPTIONS.h |
| 1190 |
|
- rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h |
| 1191 |
|
o tools/genamke2: |
| 1192 |
|
- check for lapack. |
| 1193 |
|
o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies. |
| 1194 |
|
- pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions |
| 1195 |
|
jointly. The exclusive ifdefs were removed, to add costs terms (when defined) |
| 1196 |
|
from both packages. |
| 1197 |
|
- the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly. |
| 1198 |
|
- for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs. |
| 1199 |
|
- pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes |
| 1200 |
|
of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly. |
| 1201 |
|
o pkg/cost : add comments to explain special and/or untested setups. |
| 1202 |
|
o pkg/exf: |
| 1203 |
|
- use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h |
| 1204 |
|
(previously, ALLOW_AUTODIFF_TAMC was controling this switch). |
| 1205 |
|
o verification/*/code_ad: |
| 1206 |
|
mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file: |
| 1207 |
|
- reccord when this file is included (define ECCO_CPPOPTIONS_H) |
| 1208 |
|
- remove the most obvious obsolete features (e.g., #define ALLOW_COST not |
| 1209 |
|
allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h) |
| 1210 |
|
o pkg/seaice : |
| 1211 |
|
- added possibility to change ice strength/PRESS0 relationship to |
| 1212 |
|
HEFF, according to the following run time parameters |
| 1213 |
|
SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0) |
| 1214 |
|
SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0) |
| 1215 |
|
SEAICEpresH0 :: HEFF threshold for ice strength (m) |
| 1216 |
|
o pkg/ggl90 : |
| 1217 |
|
- added run time flag mxlSurfFlag to include the code that ensure |
| 1218 |
|
mixing between first and second level (previously included as a comment) |
| 1219 |
|
o verification/1D_ocean_ice_column/input_ad/data.autodiff : |
| 1220 |
|
- add test of newly added dumpAdByRec=T option where |
| 1221 |
|
we write all records to one file per variable. |
| 1222 |
|
o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h : |
| 1223 |
|
- switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES |
| 1224 |
|
to check that this code is ok with taf and compiles in adjoint. |
| 1225 |
|
o pkg/autodiff : |
| 1226 |
|
- added run time param dumpAdByRec : ad dump format switch. |
| 1227 |
|
If true then write all records to one file per variable. |
| 1228 |
|
Else write one file per record (remains the default). |
| 1229 |
|
- revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly. |
| 1230 |
|
o pkg/seaice: |
| 1231 |
|
- Added SEAICEuseTILT run time switch : if set to |
| 1232 |
|
false then omit the tilt term in seaice dynamics. |
| 1233 |
|
- Fix free drift calculation. |
| 1234 |
|
o pkg/shelfice: |
| 1235 |
|
When initializing SHELFICEDragQuadratic, set default to be |
| 1236 |
|
consistent with shiCdrag in case SHELFICEuseGammaFrict is used, |
| 1237 |
|
but retain option to set it independently |
| 1238 |
|
(inconsistenty spotted by Veronique Dansereau) |
| 1239 |
|
o eesupp/inc: |
| 1240 |
|
- in EEPARAMS.h, add real-type constant for some frequently used simple number |
| 1241 |
|
(0,1,2,1/2), with name explicitly referring to RS/RL type. |
| 1242 |
|
o model/src: |
| 1243 |
|
- move balancing of relaxation terms to new S/R balance_relax.F. |
| 1244 |
|
o pkg/autodiff: |
| 1245 |
|
re-write active I/O high-level (control) S/R: |
| 1246 |
|
- rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL |
| 1247 |
|
- add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R. |
| 1248 |
|
- use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and |
| 1249 |
|
MDS_READ/WRITE_FIELD); change loops to multi-threads. |
| 1250 |
|
- update and merge active_file_control_slice.flow into active_file_control.flow |
| 1251 |
|
- update the calls in lower level S/R (active_file.F, active_file_g.F and |
| 1252 |
|
active_file_ad.F) keeping the argument list and function unchanged. |
| 1253 |
|
- also update lower-level "_LOC" version (call same S/R with "useCurrentDir |
| 1254 |
|
=.TRUE.") and remove high-level (control) _loc version (not called anymore). |
| 1255 |
|
- new low-level active I/O routines, one for each type (RL/RS), for active var |
| 1256 |
|
of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr); |
| 1257 |
|
fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the |
| 1258 |
|
right type. |
| 1259 |
|
o autodiff and RS=real*4: |
| 1260 |
|
- call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf |
| 1261 |
|
ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ; |
| 1262 |
|
- change argument type of 3-D mask argument to _RS to match type in the call |
| 1263 |
|
(in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued. |
| 1264 |
|
o pkg/thsice: |
| 1265 |
|
- re-anable balanceEmPmR when useSEAICE=T with useThSIce=T. |
| 1266 |
|
- option to correct ocean fresh-water flux for imbalance of Atmos+Land |
| 1267 |
|
fresh-water flux: uniform correction or proportional to local precip. |
| 1268 |
|
o pkg/ctrl: |
| 1269 |
|
- new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D |
| 1270 |
|
- redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to |
| 1271 |
|
ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC |
| 1272 |
|
- verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL |
| 1273 |
|
|
| 1274 |
|
checkpoint63q (2012/07/30) |
| 1275 |
|
o pkg/autodiff: |
| 1276 |
|
note about monitor and snap-shot of ad-variables: |
| 1277 |
|
a) need to apply ADEXCH before monitor or output of ad-vars to include |
| 1278 |
|
overlap contributions (was done for adjDump but missing for monitor). |
| 1279 |
|
b) since ADEXCH implies adding overlap values to interior array, machine |
| 1280 |
|
truncation error is expected when adding an ADEXCH call in the middle of |
| 1281 |
|
the time-stepping (although mathematically identical). |
| 1282 |
|
modifs: |
| 1283 |
|
- fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars |
| 1284 |
|
declaration (adEddyPsiX,adEddyPsiY in adcommon.h). |
| 1285 |
|
- add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to |
| 1286 |
|
apply ADEXCH before monitor or snap-shot of ad-variables: |
| 1287 |
|
=0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy. |
| 1288 |
|
- implement new method (copy+adexch) for snap-shot and monitor of main model |
| 1289 |
|
ad-vars (initially not used by default -> output unchanged). |
| 1290 |
|
- change default (set to 2) to use new method and update few output_adm.txt |
| 1291 |
|
with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo |
| 1292 |
|
and both tutorial_tracer_adjsens tests). |
| 1293 |
|
- switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice) |
| 1294 |
|
and turn off momDissip_In_AB in the 2 other (needed for stable AB-3). |
| 1295 |
|
o pkg/ctrl: |
| 1296 |
|
enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of |
| 1297 |
|
generic control variables via |
| 1298 |
|
#define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL |
| 1299 |
|
Only required customization should be S/R ctrl_map_ini_genarr.F |
| 1300 |
|
(routine in repository contains example) |
| 1301 |
|
o pkg/exf: |
| 1302 |
|
- fix and refine checking of surface-relaxation setting when using EXF |
| 1303 |
|
o verification (adjoint exp): |
| 1304 |
|
- reduce length of simulation by half for experiment global_ocean.cs32x15 |
| 1305 |
|
(std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output. |
| 1306 |
|
o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag) |
| 1307 |
|
- replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers |
| 1308 |
|
of KE that can occur with aggressive optimization |
| 1309 |
|
+ put quadratic bottom drag calculation in separated loops (only done if |
| 1310 |
|
using bottomDragQuadratic) |
| 1311 |
|
o model/src: CG2D_NSA |
| 1312 |
|
- clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF |
| 1313 |
|
and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE. |
| 1314 |
|
- in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens), |
| 1315 |
|
change cg2d residual target to be expressed in Wunits (=> do not normalise |
| 1316 |
|
RHS ; this fix global_max Pb with TAF); update output. |
| 1317 |
|
o verification/tutorial_tracer_adjsens: |
| 1318 |
|
improve parameter consistency (and get rid of warnings): |
| 1319 |
|
- use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf); |
| 1320 |
|
- switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical) |
| 1321 |
|
- use staggerTimeStep (for stability) in som81; use default rotation period. |
| 1322 |
|
o pkg/exch2: |
| 1323 |
|
- with empty facet: fix compact-format (W2_mapIO=1) definition (was previously |
| 1324 |
|
reset to 0 = 1 long line in X) |
| 1325 |
|
o pkg/mdsio: |
| 1326 |
|
- fix reading of dimensions from meta file for large-size domain |
| 1327 |
|
o model/src: |
| 1328 |
|
- fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long); |
| 1329 |
|
- to refine CS-grid check, add logical flag "hasWetCSCorners": true if using |
| 1330 |
|
Cubed-Sphere Exch with CS-corners inside the domain; |
| 1331 |
|
make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate |
| 1332 |
|
globalArea and to set hasWetCSCorners. |
| 1333 |
|
- add warning if usingCurvilinearGrid and momAdvection in flux-form (missing |
| 1334 |
|
metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form. |
| 1335 |
|
- re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if |
| 1336 |
|
useCDscheme and useCubedSphereExchange). |
| 1337 |
|
o pkg/seaice/seaice_growth.F : |
| 1338 |
|
- compute the SEAICE_DISABLE_HEATCONSFIX term accordingly |
| 1339 |
|
for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0) |
| 1340 |
|
when the previous code was not correct. |
| 1341 |
|
- in all cases diagnoze the boundary condition mismatch to SIaaflux |
| 1342 |
|
- in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add |
| 1343 |
|
that term to QNET (essentially to set the melt/freeze water to 0degC). |
| 1344 |
|
when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed. |
| 1345 |
|
o verification/global_ocean.cs32x15/input.seaice : |
| 1346 |
|
- add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget. |
| 1347 |
|
- add diagnostics (commented out) for budget test using my matlab codes (gcmfaces). |
| 1348 |
|
- update results (output.seaice.txt) accordingly. |
| 1349 |
|
o verification/lab_sea/input/data.seaice : |
| 1350 |
|
- remove SEAICEheatConsFix, which is now be tested |
| 1351 |
|
in global_ocean.cs32x15. The presently coded fix |
| 1352 |
|
is only consistent with real fresh water + nlfs. |
| 1353 |
|
- update results (output.txt) accordingly. |
| 1354 |
|
o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd). |
| 1355 |
|
o AD_CONFIG.h file: |
| 1356 |
|
- in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h; |
| 1357 |
|
- remove #include "AD_CONFIG.h" from all included OPTIONS files and |
| 1358 |
|
add it explicitly in each fortran src file where it is needed. |
| 1359 |
|
motivation: header file AD_CONFIG.h is generated/modified after "make depend" |
| 1360 |
|
thus introducing potentially wrong dependency; therefore, better to include |
| 1361 |
|
it only where it's really needed, and after any other included OPTIONS file |
| 1362 |
|
(less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN |
| 1363 |
|
or ALLOW_TANGENTLINEAR_RUN). |
| 1364 |
|
|
| 1365 |
|
checkpoint63p (2012/07/06) |
| 1366 |
|
o pkg/autodiff: |
| 1367 |
|
- rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ; |
| 1368 |
|
- create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters |
| 1369 |
|
which are now read from new parameter file "data.autodiff" (inAdExact |
| 1370 |
|
previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg) |
| 1371 |
|
- add file "data.autodiff" in all verification/*/input_ad/ directories. |
| 1372 |
|
- add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward |
| 1373 |
|
mode (used in global_ocean.cs32x15.seaice_dynmix test exp.) |
| 1374 |
|
o verification/tutorial_tracer_adjsens/ |
| 1375 |
|
- add extra sub-verification which uses "SOM" advection scheme |
| 1376 |
|
(2nd Order-Moment Advection Scheme, Prather Limiter) with |
| 1377 |
|
#define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h |
| 1378 |
|
and in data: |
| 1379 |
|
multiDimAdvection=.TRUE., |
| 1380 |
|
tempAdvScheme=81, |
| 1381 |
|
saltAdvScheme=81, |
| 1382 |
|
o model/src: |
| 1383 |
|
- introduce ALLOW_BALANCE_RELAX which allow the removal |
| 1384 |
|
of the global mean of relaxation terms by setting |
| 1385 |
|
balanceThetaClimRelax and balanceSaltClimRelax |
| 1386 |
|
- disable balanceEmPmR and balanceQnet in the case when useSeaice. |
| 1387 |
|
This case is now treated appropriately in seaice_growth.F |
| 1388 |
|
o pkg/seaice: |
| 1389 |
|
- do balanceEmPmR and balanceQnet based on the net fluxes |
| 1390 |
|
(SItflux) that enter the ocean+ice system rather than QNET |
| 1391 |
|
and EMPMR. Works best in real fresh water. |
| 1392 |
|
- SIatmFW, SIatmQnet, and SItflux computations had to be moved |
| 1393 |
|
out of the diagnotics bloc, and stored in global arrays. |
| 1394 |
|
|
| 1395 |
|
checkpoint63o (2012/06/29) |
| 1396 |
|
o vertical mixing schemes: |
| 1397 |
|
- remove unused S/R CALC_BUOYANCY (left from branch-atmos merging) |
| 1398 |
|
- replace computation of density (in Function STATE1, opps_calc.F) by a call |
| 1399 |
|
to S/R FIND_RHO_SCALAR |
| 1400 |
|
- pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC |
| 1401 |
|
and use it for N^2 calculation in ggl90_calc.F (save 2 density computations); |
| 1402 |
|
affects output (vermix.ggl90) at truncation level. |
| 1403 |
|
o testreport: |
| 1404 |
|
- change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles |
| 1405 |
|
(nSx,nSy) for the number of threads (from eedata.mth) |
| 1406 |
|
o model/src: |
| 1407 |
|
- remove 2nd set of calls at the top of initialise_varia.F (Adjoint part) |
| 1408 |
|
related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary). |
| 1409 |
|
o verification/tutorial_tracer_adjsens/ |
| 1410 |
|
- compile with ALLOW_CG2D_NSA |
| 1411 |
|
- run with nonlinFreeSurf=3 |
| 1412 |
|
- update reference output_adm.txt |
| 1413 |
|
o tools/genmake2: |
| 1414 |
|
- add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ; |
| 1415 |
|
refine usePROFILES switching off (only when NetCDF is not available). |
| 1416 |
|
o verification (atmospheric set-up): |
| 1417 |
|
- change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration |
| 1418 |
|
o pkg/profiles : refine profiles and files handling. |
| 1419 |
|
o model/src and pkg/ecco : introduce run-time switch usePROFILES. |
| 1420 |
|
o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h : |
| 1421 |
|
- changes to use model/src/the_main_loop.F rather than the ecco version |
| 1422 |
|
in ecco type adjoint runs. |
| 1423 |
|
o model/src: |
| 1424 |
|
- move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID |
| 1425 |
|
- move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC |
| 1426 |
|
- update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL) |
| 1427 |
|
o model/src: |
| 1428 |
|
- fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before); |
| 1429 |
|
update output of test experiment bottom_ctrl_5x5. |
| 1430 |
|
o pkg/generic_advdiff: |
| 1431 |
|
- implement vertical bi-harmonic diffusion (for now, only for T & S and |
| 1432 |
|
only explicitly). |
| 1433 |
|
o verification/bottom_ctrl_5x5/ |
| 1434 |
|
update reference output (results changed quite some time ago, |
| 1435 |
|
not sure when; but new reference results look ok in terms of grdchk) |
| 1436 |
|
o verification/1D_ocean_ice_column/ |
| 1437 |
|
For verification purposes, the exact adjoint rather than an approx. |
| 1438 |
|
should be used (e.g., to comare against F.D. or TLM). |
| 1439 |
|
removed autodiff_inadmode*_ad.F routines in code_ad/ |
| 1440 |
|
Update results/ accordingly. |
| 1441 |
|
o pkg/cal: |
| 1442 |
|
- change cal_getdate.F so that output date is function of input time only |
| 1443 |
|
(less ambiguous, not mixed up with input iteration number). |
| 1444 |
|
- fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP). |
| 1445 |
|
o pkg/diagnostics: |
| 1446 |
|
- implement calendarDumps also for stats-diags |
| 1447 |
|
- implement calendarDumps also for snap-shot output (negative freq) |
| 1448 |
|
- for now, ignores calendarDumps if non-zero phase-lag. |
| 1449 |
|
|
| 1450 |
|
checkpoint63n (2012/06/04) |
| 1451 |
|
o model/src: |
| 1452 |
|
- recompute rSurfW & S to ensure consistent column thickness (needed for rStar) |
| 1453 |
|
between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice; |
| 1454 |
|
- use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more |
| 1455 |
|
similar to calc_r_star.F); update results of experiment internal_wave and |
| 1456 |
|
tutorial_global_oce_in_p (affected @ truncation level). |
| 1457 |
|
o pkg/shelfice: |
| 1458 |
|
- add parameterisation of advective-diffusive flux into the ice shelf |
| 1459 |
|
according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd |
| 1460 |
|
- simply eps3/3a computation |
| 1461 |
|
o eesupp: |
| 1462 |
|
- add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange |
| 1463 |
|
between tiles, just fill-in edges assuming locally periodic subdomain) and |
| 1464 |
|
add corresponding exchange subroutines (EXCH0); |
| 1465 |
|
- new CG-solver version (_EX0) for disconnected-tiles special case. |
| 1466 |
|
o model/src (CG-solvers): |
| 1467 |
|
- modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached |
| 1468 |
|
(similar final residual output and max-Iter number as with standard version); |
| 1469 |
|
- allows to store and use lowest-residual solution (standard & _SR versions); |
| 1470 |
|
- cleaning up (remove old, commented out code, LETS_MAKE_JAM ...). |
| 1471 |
|
- by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h) |
| 1472 |
|
o eesup/src: |
| 1473 |
|
- global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef |
| 1474 |
|
ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012) |
| 1475 |
|
o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn |
| 1476 |
|
|
| 1477 |
|
checkpoint63m (2012/04/27) |
| 1478 |
|
o pkg/shelfice: |
| 1479 |
|
- account for partical cells in surface level below ice-shelf for hydrostatic |
| 1480 |
|
pressure calculion (set uniformFreeSurfLev to F); update isomip experiments. |
| 1481 |
|
o ad test experiments: |
| 1482 |
|
- update and rename to "ad_optfile.local" local AD-optfile specific to a |
| 1483 |
|
particular adjoint verification experiment (in verification/*/code_ad/) |
| 1484 |
|
o pkg/seaice & pkg/exf: |
| 1485 |
|
- Part two of ECCO-CLIVAR code merges. |
| 1486 |
|
Completes merge of seaice area relax. code. |
| 1487 |
|
Requires unified CPP option EXF_ALLOW_SEAICE_RELAX |
| 1488 |
|
to be set in EXF_OPTIONS.h since this pkg controls its I/O |
| 1489 |
|
(and avoids second CPP option in SEAICE_OPTIONS.h) |
| 1490 |
|
- change default value of costIceStart & costIceEnd to a valid date. |
| 1491 |
|
- add snowPrecip to HSNOW in seaice_growth |
| 1492 |
|
o pkg/ptracers: |
| 1493 |
|
- move ptracers summary and setup check into separated S/R ; add a check for |
| 1494 |
|
valid PTRACERS_Iter0 value (error+stop or just warning). |
| 1495 |
|
o pkg/cal (+ pkg/ecco): |
| 1496 |
|
- avoid calling a S/R with 2 times the same arg (FWD: unless both are only used |
| 1497 |
|
as input; and for AD, unless both are not differentiable (e.g., k index)). |
| 1498 |
|
o model/src: |
| 1499 |
|
- define internal flag "uniformFreeSurfLev" (=T when free-surface level-index |
| 1500 |
|
is everywhere k=1) to speed-up some calculations (by pass kSurf reference); |
| 1501 |
|
temporary set to usingZCoords value (to be changed to F when using shelfice). |
| 1502 |
|
- hydrostatic pressure: implement partial cell near the surface also for |
| 1503 |
|
Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on |
| 1504 |
|
usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code). |
| 1505 |
|
o pkg/ctrl/ctrl_init.F: |
| 1506 |
|
- add a formal parameter to s/r ctrl_init_rec to print |
| 1507 |
|
xx_$(ctrl_valiable)_file for easier debugging |
| 1508 |
|
- move call of cal_* routines into the if-block where they are really |
| 1509 |
|
needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having |
| 1510 |
|
to specify a startdate |
| 1511 |
|
o pkg/seaice: |
| 1512 |
|
- update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and |
| 1513 |
|
global_ocean.cs32x15/code versions). |
| 1514 |
|
- turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for |
| 1515 |
|
verification experiment global_ocean.cs32x15.seaice and update results. |
| 1516 |
|
o pkg/exf: |
| 1517 |
|
- new S/R EXF_GETFIELD_START to return starting-time of a forcing field |
| 1518 |
|
(according to useExfYearlyFields). |
| 1519 |
|
o pkg/cal: |
| 1520 |
|
- move calendar setting & summary (previously in cal_readparams.F) into new |
| 1521 |
|
S/R CAL_INIT_FIXED to be called later in the initialisation process, once |
| 1522 |
|
length of the simulation is set (after SET_PARMS call); This is an attempt |
| 1523 |
|
to fix Pb when, e.g.: pkg/longstep, modifies the length of the run. |
| 1524 |
|
- For safety: keep a record of pkg/cal parameter settings status |
| 1525 |
|
to allow to STOP if one pkg/cal S/R is called too early. |
| 1526 |
|
- add a stop in all basic pkg/cal subroutines if called before setting is done. |
| 1527 |
|
- modify cal_getdate.F: stop when nothing was returned; |
| 1528 |
|
if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2); |
| 1529 |
|
this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F. |
| 1530 |
|
|
| 1531 |
|
checkpoint63l (2012/04/04) |
| 1532 |
|
o pkg/bbl: |
| 1533 |
|
- fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc); |
| 1534 |
|
update global_with_exf output.yearly.txt file. |
| 1535 |
|
o pkg/cal: |
| 1536 |
|
- start to clean-up cal_set.F ; fix for the case where baseTime is non-zero. |
| 1537 |
|
- remove 2 unsused and very short (1 line only) functions ; |
| 1538 |
|
- remove unsused subroutines from AD-Diff list. |
| 1539 |
|
o model/src: |
| 1540 |
|
- start to implement clean wait to stop in initialization S/R (config_check.F, |
| 1541 |
|
packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage) |
| 1542 |
|
o folowing PRINT_MESSAGE changes: |
| 1543 |
|
- remove reminder multiple print to the same file (STDOUT) when multi-threads. |
| 1544 |
o pkg/bbl: |
o pkg/bbl: |
| 1545 |
- modification so it can work with z* |
- modification so it can work with z* |
| 1546 |
- replace deltaT with dTtracerLev(k) for asynchronous time stepping |
- replace deltaT with dTtracerLev(k) for asynchronous time stepping |
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