| 3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 4 |
============================== |
============================== |
| 5 |
|
|
| 6 |
untagged modifications |
checkpoint46g_post |
| 7 |
o Updated useSingleCpuIO option in mdsio_writefield.F to |
o Include a new diagnostic variable phiHydLow for the ocean model |
| 8 |
work with multi-field files, e.g., for single-file pickup. |
- in z-coordinates, it is the bottom pressure anomaly |
| 9 |
o pkg/seaice: |
- in p-coordinates, it is the sea surface elevation |
| 10 |
- bug fix in growth.F: QNET for no shortwave case |
- in both cases, these variable have global drift, reflecting the mass |
| 11 |
- added HeffFile for specifying initial sea-ice thickness |
drift in z-coordinates and the volume drift in p-coordinates |
| 12 |
|
- included time averaging for phiHydLow, be aware of the drift! |
| 13 |
release1_p11 |
o depth-dependent computation of Bo_surf for pressure coordinates |
| 14 |
o Modifications for using pkg/exf with pkg/seaice |
in the ocean (buoyancyRelation='OCEANICP') |
| 15 |
- improved description of the various forcing configurations |
- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
| 16 |
- added basic radiation bulk formulae to pkg/exf |
Theta, Salinity, and Pressure in the parameter list. This routine is |
| 17 |
- units/sign fix for evap computation in exf_getffields.F |
presently contained in find_rho.F. This routine does not give the |
| 18 |
- updated verification/global_with_exf/results/output.txt |
correct density for 'POLY3', which would be a z-dependent reference |
| 19 |
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
density. |
| 20 |
(SBO) core products, including oceanic mass, center-of-mass, |
o cleaned up find_rho |
| 21 |
angular, and bottom pressure (see pkg/sbo/README.sbo). |
- removed obsolete 'eqn' from the parameter list. |
| 22 |
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
o added two new verification experiments: gop and goz |
| 23 |
to avoid negative values in shallow regions. |
(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
| 24 |
- updated verification/natl_box/results/output.txt |
checkpoint46g_pre |
| 25 |
- updated verification/lab_sea/results/output.txt |
|
| 26 |
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
checkpoint46f_post |
| 27 |
o Added useSingleCpuIO option (see PARAMS.h). |
o Enable tangent linear (forward mode) gradient checks: |
| 28 |
|
- extended active file handling to g_... files |
| 29 |
release1_p10 |
- added TANGENT_SIMULATION to theSimulationMode |
| 30 |
o modifications for using pkg/exf with pkg/seaice |
- extended grdchk package accordingly |
| 31 |
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
o added tangent linear setup in verification/carbon/code_ftl |
| 32 |
and SEAICE_EXTERNAL_FLUXES |
o added adjoint setup in verification/front_relax/code_ad |
| 33 |
- pkg/exf CPP options EXF_READ_EVAP and |
|
| 34 |
EXF_NO_BULK_COMPUTATIONS |
checkpoint46e_post |
| 35 |
- usage examples are Experiments 8 and 9 in |
o Added new equation of state -> MDJWF |
| 36 |
verification/lab_sea/README |
- EOS of McDougall et al., 2002, JAOT, submitted |
| 37 |
- verification/lab_sea default experiment now uses |
- caveat: the equation of state is only valid for a smaller (more |
| 38 |
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf |
realistic?) range of values than JMD95P/Z and UNESCO |
| 39 |
|
- added masks to the calculation of pressure in store_pressure |
| 40 |
release1_p9 |
- added more check values for density in check_eos (ini_eos.F), some of |
| 41 |
o pkg/seaice |
the old check values are out of the range of the MDJWF-eos, so don't |
| 42 |
- removed GOTO's and added taf directives |
expect perfect matches for those |
| 43 |
- double precision constants to reduce the g77 (Linux) |
checkpoint46e_pre |
| 44 |
to F77 (SGI) differences reported in release1_p8 |
|
| 45 |
o tools/genmake |
checkpoint46d_post |
| 46 |
- added SGI options |
o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
| 47 |
o verification/testscript |
'OCEANICP', also initialised field pressure correctly in ini_eos in the |
| 48 |
- updated to that of checkpoint47a_post |
case of pressure coordinates. eosType='JMD95Z' in |
| 49 |
o verification/global_ocean.90x40x15/input/eedata |
combination with buoyancyRelation='OCEANICP' now causes an error. |
| 50 |
- modified for SGI f77 compatibility |
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
| 51 |
o verification/lab_sea |
in find_alpha/beta. |
| 52 |
- added description of sea-ice model |
checkpoint46d_pre |
| 53 |
- added missing matlab routines |
|
| 54 |
- added test of thermodynamics parallelization |
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
| 55 |
|
so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
| 56 |
release1_p8 |
|
| 57 |
o verification/natl_box: |
checkpoint46c_post |
| 58 |
updating new external_fields_load routine |
o Changes necessary for ocean in p-coordinates |
| 59 |
o New package: pkg/seaice |
- Added new buoyancy relation = 'OCEANICP' |
| 60 |
Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). |
- Added new parameters = gravitySign (this used to be contained inside |
| 61 |
The sea-ice code is based on Hibler (1979-1980). |
the factor dRdZ which I added when we first switched to R coordinates). |
| 62 |
Two sea-ice dynamic solvers, ADI and LSR, are included. |
X GM/Redi is not compatible (yet) |
| 63 |
In addition to computing prognostic sea-ice variables and diagnosing |
X bottom drag and no-slip need to be debugged. |
| 64 |
the forcing/external data fields that drive the ocean model, |
checkpoint46c_pre |
| 65 |
SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
|
| 66 |
The implied surface heat flux is then stored in variable |
checkpoint46b_post |
| 67 |
surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and |
o Added new equation of state -> JMD95Z and JMD95P |
| 68 |
kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the |
- EOS of Jackett and McDougall, 1995, JAOT |
| 69 |
non-local transport term. Because this call precedes model |
- moved all EOS parameters into EOS.h |
| 70 |
thermodynamics, temperature under sea-ice may not be "exactly" at |
- new routines ini_eos.F, store_pressure.F |
| 71 |
the freezing point by the time theta is dumped or time-averaged. |
o Added UNESCO EOS, but not recommended because it requires |
| 72 |
N.B.: fairly large differences in accuracy occur across |
in-situ temperature (see JMD95) |
| 73 |
different platforms/compilers; comparison between |
o Modified formatting for knudsen2.f in utils/knudsen2 and added |
| 74 |
g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) |
unesco.f to be used with POLY3 |
| 75 |
generated output gives: |
checkpoint46b_pre |
| 76 |
T S U V |
|
| 77 |
C D M c m s m s m s m s |
checkpoint46a_post |
| 78 |
n p a R g m m e . m m e . m m e . m m e . |
o Added (atmospheric) pressure loading |
| 79 |
f n k u 2 i a a d i a a d i a a d i a a d |
- new field in FFIELDS.h, etc... |
| 80 |
g d e n d n x n . n x n . n x n . n x n . |
- new cpp flag ATMOSPHERIC_LOADING |
| 81 |
|
o Changed hFacC to _hFacC in calc_phi_hyd.F |
| 82 |
Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea |
o Added SHORTWAVE_HEATING to some files for consistency |
| 83 |
|
checkpoint46a_pre |
| 84 |
release1_p7 |
|
| 85 |
o GAD: |
checkpoint46 |
| 86 |
- generated new common blocks to account for call of |
further merges from release1_p5 |
|
same gad routines with differing traceridentities |
|
|
(needed to modify tracerIdentity indices in GAD.h) |
|
|
- generated separate common blocks for case useCubedSphereExchange |
|
|
(Department of Futurology) |
|
|
- parameter lists to gmredi_?transport: added tracerIdentity |
|
|
- added new key indices to tamc.h |
|
|
o external_fields_load: |
|
|
- added this routine to TAF list |
|
|
- needed to make some common blocks global and additional storing |
|
|
along the same lines as exf package (checkpoint_lev?_directives.h) |
|
|
o exf: |
|
|
updated external forcing package |
|
|
- bug fixes carried over from ecco-branch |
|
|
(missing OBCS_OPTIONS.h in two routines) |
|
|
- enable easy to use "no forcing". |
|
|
- added exf I/O for atmospheric loading |
|
|
- added exf I/O for runoff data |
|
|
- transfered scaling between exf <-> MITgcm to exf namelist |
|
|
o Adding new verification experiment global_with_exf. |
|
|
This verification experiment is almost identical to the |
|
|
global_ocean.90x40x15 experiment, except that it uses |
|
|
the exf (and cal) package instead of the |
|
|
external_fields_load routine (cf README file). |
|
|
|
|
|
release1_p6 |
|
|
o fixed the verification/global_ocean.90x40x15 experiment: |
|
|
- new bathymetry (the world according to A., JMC, and M.) |
|
|
- new initial fields and forcing fields (*.bin files) |
|
|
- new POLY3.COEFFS (for the next release one should switch to a full |
|
|
equation of state) |
|
|
- fixed several errors and redundancies in the data file |
|
|
- experiment uses looped cells |
|
|
- added matlab directory with diagnostic scripts for plotting of output |
|
|
|
|
|
release1_p5 |
|
|
o import recent fix from MAIN branch: |
|
|
- use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
|
|
- change phiMin in exp1 (to agree with documentation) |
|
|
from checkpoint45 to checkpoint45a_post: |
|
|
- specific exchange for X-slice domain (case Ny=1) |
|
|
- argument futureIter of S/R obcs_calc missing in |
|
|
exp4 & internal_wave /code |
|
|
- solve_for_pressure : set cg2d_x to zero where OBCS are applied |
|
|
from checkpoint44f_post to checkpoint44g_post: |
|
|
- fix surface correction term in multiDimAdvection |
|
|
(affects plume_on_slope results |
|
|
o bug fix in packages_readparms (missing ALLOW_CALENDAR) |
|
|
o bug fix in CG2D.h (correct array size for LETS_MAKE_JAM |
|
|
o Adjoint-related bug fixes in kpp: |
|
|
- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
|
|
- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
|
|
o added Eliassen-Palm flux hooks (dynamics,ini_fields) |
|
|
o removed unused TAF keys iikey, idkey (dynamics,thermodynamics) |
|
|
o flow directives: |
|
|
- new for S/R do_the_model_io |
|
|
- enhanced for S/R checkpoint |
|
|
o added Eliassen Palm flux controls to gradient check package |
|
| 87 |
o new ctrl package |
o new ctrl package |
| 88 |
- adopted from ECCO environment to enable optimization |
- adopted from ECCO environment to enable optimization |
| 89 |
- added Eliassen Palm fluxes to controls |
- added Eliassen Palm fluxes to controls |
| 90 |
- adjusted global_ocean.90x40x15/ and carbon/ accordingly |
o added Eliassen Palm flux controls to gradient check package |
| 91 |
|
o cost package |
| 92 |
|
- Compatible with new ctrl package |
| 93 |
|
- added Eliassen Palm cost hooks |
| 94 |
|
- modif's of existing cost functions |
| 95 |
|
o Adjoint-related bug fixes in kpp: |
| 96 |
|
- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
| 97 |
|
- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
| 98 |
|
o autodiff package |
| 99 |
|
- flow directives: |
| 100 |
|
+ new for S/R do_the_model_io |
| 101 |
|
+ enhanced for S/R checkpoint |
| 102 |
|
+ new gmredi.flow |
| 103 |
|
- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
| 104 |
|
disable adcommon.h/g_common.h by default. |
| 105 |
|
- fixed problem for adjoint of global_max |
| 106 |
|
o modified verification/carbon/ |
| 107 |
|
o New setup for adjoint of global_ocean |
| 108 |
|
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
| 109 |
|
o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
| 110 |
|
o incorporated hooks for sponge layer code (external_forcing.F) |
| 111 |
|
|
| 112 |
|
checkpoint45d_post |
| 113 |
|
o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
| 114 |
|
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
| 115 |
|
(affects plume_on_slope "cg2d" output) |
| 116 |
|
o add new parameter deltaTfreesurf for free-surface time stepping |
| 117 |
|
o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
| 118 |
|
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
| 119 |
|
o change phiMin in exp1 (to agree with documentation) |
| 120 |
|
o add new flags: |
| 121 |
|
- T,S forcing inside/outside Adams-Bashforth |
| 122 |
|
- turn off temp,salt advection and/or forcing |
| 123 |
|
- for each tracer, define internal flag for multiDimAdvection & A-B |
| 124 |
|
o monitor: change definition of KE to check conservation of Energy |
| 125 |
|
|
| 126 |
release1_p4 |
checkpoint45c_post |
| 127 |
o Removed f90 comments ("!") |
o Removed f90 comments ("!") |
| 128 |
o Modified initialisations to enable exf package for MITgcm |
o Modified initialisations to enable exf package for MITgcm |
| 129 |
(without invoking ECCO_PACKAGE). |
(without invoking ECCO_PACKAGE). |
| 131 |
- enable centered differences |
- enable centered differences |
| 132 |
- modified format of standard output |
- modified format of standard output |
| 133 |
|
|
| 134 |
release1_p3 |
checkpoint45b_post |
| 135 |
o added tangent linear setup to verification/carbon/ |
o cleaned exchange calls in cg2d |
| 136 |
o added adjoint sensitivity setup to verification/global_ocean... |
o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
| 137 |
o moved packages_init_variables before convective_adjustment |
o included CPP option SINGLE_LAYER_MODE in thermodynamics |
| 138 |
o output of verif. which use GMRedi brought up-to-date with |
to configure barotropic setup (Martin Losch) |
| 139 |
MAIN trunk (those were re-created after changes in GMRedi) |
o moved some initialisations within bi,bj loop in dynamics |
| 140 |
o included CPP option SINGLE_LAYER_MODE |
(TAF flow dependency) |
| 141 |
to configure barotropic setup (Martin Losch). |
o in initialise_varia, moved call packages_init_variables |
| 142 |
o Removed auxiliary variable in impldiff |
before convective_adjustment_init |
| 143 |
(caused numerical differences with MAIN trunk routine). |
(corresponding adjustment of TAF tape initialisation). |
| 144 |
o Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
| 145 |
disable adcommon.h/g_common.h by default. |
|
| 146 |
o Cleaned exchange calls in cg2d. |
checkpoint45a_post |
| 147 |
|
o compute Rho over the whole domain (extend iMin,jMin indices) |
| 148 |
release1_p2 |
o specific exchange for X-slice domain (case Ny=1) |
| 149 |
o fixed array boundary problem for adjoint |
o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
| 150 |
(related to partial recomputation within subroutine |
o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
| 151 |
related to dynamics -> calc_viscosity -> mom_... |
|
| 152 |
o fixed recomputation in thermodynamics |
checkpoint44h_post = checkpoint45 |
| 153 |
o prepare (but not complete) recomputation problem in impldiff |
o Fix to restore differentiability: |
| 154 |
o fixed problem for adjoint of global_max |
place at which packages_init_variables is called in |
| 155 |
o switched off sponge layer code in external_forcing |
initialise_varia is crucial for reverse control flow. |
| 156 |
|
o modifications in GMRedi to enable stable adjoint |
| 157 |
release1_p1 |
(corresponding modif's in thermodynamics, dynamics) |
| 158 |
o merged necessary patches: |
o added missing hook for sponge layer code in external_forcing |
| 159 |
- AD-related changes for GMRedi |
o modified test cost functions |
| 160 |
- fixes i KPP (delZ -> drF) |
o storing in gad_advection (plus removal of write(0,*)! |
| 161 |
- hook to OBCS songe layer code in external_forcing |
o missing headers TR1.h added in convective_adjustment routines |
| 162 |
- errorMessageUnit non-zero in eeboot.F |
o errorMessageUnit set non-equal zero in eeboot |
| 163 |
- modified test cost function and carbon verif. |
(conflict on some platforms, e.g. IBM SP3) |
| 164 |
|
o modified carbon verif. |
| 165 |
release1_chkpt44d_post = chkpt44d_post |
|
| 166 |
|
checkpoint44h_pre |
| 167 |
|
o vertical grid option: allow to put the Interface at the middle between |
| 168 |
|
2 cell-centers ; replace delZ in pkg/kpp by drF. |
| 169 |
|
o GM Advective form: Tracers are advected using the residual transport (= |
| 170 |
|
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
| 171 |
|
|
| 172 |
|
checkpoint44g_post |
| 173 |
|
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
| 174 |
|
results) ; ifdef missing in thermodynamics.F |
| 175 |
|
|
| 176 |
|
checkpoint44f_pre,checkpoint44f_post |
| 177 |
|
o added PTRACERS package |
| 178 |
|
This allows an arbitrary number of passive tracers to be integrated |
| 179 |
|
forward simultaneously with the dynamicaly model. |
| 180 |
|
+ Implemented so far: |
| 181 |
|
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
| 182 |
|
- I/O and checkpointing |
| 183 |
|
- GM/Redi *but* using the GM/Redi coefficient of Salt |
| 184 |
|
+ Not implemented so far: |
| 185 |
|
- KPP |
| 186 |
|
- OBCS |
| 187 |
|
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
| 188 |
|
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
| 189 |
|
line in data.pkg. |
| 190 |
|
+ This package is disabled by default since it increases storage. |
| 191 |
|
|
| 192 |
|
|
| 193 |
|
o testscript: added -cleanup option |
| 194 |
|
o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
| 195 |
|
b) enable to filter 2D fields. |
| 196 |
|
|
| 197 |
|
checkpoint44e_pre,post |
| 198 |
|
o re-wrote convective adjustment to use pre-calculated weights |
| 199 |
|
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
| 200 |
|
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
| 201 |
|
Original calls to convect() still in place. |
| 202 |
|
|
| 203 |
chkpt44d_pre,post |
chkpt44d_pre,post |
| 204 |
o added missing EXCLUDE_MONITOR flags |
o added missing EXCLUDE_MONITOR flags |
| 209 |
plus resetting for case SunOS |
plus resetting for case SunOS |
| 210 |
o added timer_stats.c routine for IBM SP3 |
o added timer_stats.c routine for IBM SP3 |
| 211 |
o removed variables in dynamics |
o removed variables in dynamics |
| 212 |
|
!!! I forgot to create tag chkpt44d_pre !!! |
| 213 |
|
!!! But chkpt44d_pre = chkpt44c_post !!! |
| 214 |
|
|
| 215 |
o real fresh water flux implemented with non-linear free-surface. |
o real fresh water flux implemented with non-linear free-surface. |
| 216 |
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|
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