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revision 1.665 by mlosch, Mon Jun 5 22:54:54 2006 UTC revision 1.754 by mlosch, Thu Dec 14 08:23:13 2006 UTC
# Line 3  $Name$ Line 3  $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    checkpoint58s_post
7    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
8      changed exf_set_gen.F so that
9        genperiod=0 means input file is one time-constant field and
10        genperiod=-12 means input file contains 12 monthly means
11    o CG2D: use pre-computed solver main-diagonal (stored in common block);
12      this affects truncation error ; generate new output file for exp. which
13      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
14        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
15        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
16        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
17        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
18        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
19    o start implementation of deep-atmosphere and anelastic formulation
20    o verification: remove 2nd copy of input files and use script "prepare_run"
21      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
22    o mom_common/vecinv/fluxform: fix a few initialisation isssues
23    o profiles: fix for multithreaded case
24    
25    o diagnostics: rename few diags:
26      s/'PRESSURE'/'RCENTER '/g
27      s/'TICE    '/'oceFreez'/g
28      s/'TAUX    '/'oceTAUX '/g
29      s/'TAUY    '/'oceTAUY '/g
30      s/'SWFLUX  '/'oceQsw  '/g
31      s/DIFx/DFxE/g
32      s/DIFy/DFyE/g
33      and add few ocean-forcing diagnostics:
34      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
35    o modifications to pkg/seaice/growth.F and budget.F, which change results of
36      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
37      as actual snow thickness.  It now refers everywhere to effective snow
38      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
39    
40    checkpoint58r_post
41    o modifications to pkg/seaice/growth.F, which change results of
42      lab_sea experiment: fixes pertain to melting snow over open water, to
43      masking EVAP under sea ice, and to using the correct AREA variable for
44      computations of EVAP, PRECIP, HSNOW, and GHEFF
45    o add ability to read bathy, salt, and theta using MNC (off by def)
46    o add flooding algorithm and advection of HSNOW for pkg/seaice;
47      both are turned off by default and do no change any results
48    o seaice advection with pkg/thsice: a step toward the use of non-linear
49      advection scheme, but #ifdef or commented out for now (requires more EXCH).
50    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
51      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
52      in natl_box (affects results @ truncation level: update output.txt)
53    o multi-threading and IO:
54      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
55      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
56        (needed to work with SingleCpuIO): tested in all verif. exp.
57    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
58      affects the results (but none of the verification test uses this scheme).
59    o Adding some pkg/diagnostics capability to pkg/seaice
60      (will certainly be subject to changes)
61    o ctrl: adding new control variables:
62      lwflux, lwdown, evap, snowprecip, apressure, runoff
63    
64    checkpoint58q_post
65    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
66      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
67      high_res_cube configuration by 4% on Columbia.
68    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
69      add (in global_with_exf/code) a version of EXF_INTERP_READ without
70      dynamical allocation (seems to work in multi-threaded).
71    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
72      single CPU io) so that TAF does not have to see EESUPPORT.h
73    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
74    
75    checkpoint58p_post
76    o obcs: stop if obcs is used with useCDscheme = .true.
77    o shelfice:
78     - fix a sign error so that no slip at shelfice interface works
79     - remove stop for combination non-hydrostatic code and shelfice. That does
80       not mean, that the results are correct, but at least they are numerically
81       stable
82    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
83    o added adjoint exch routined for all exch*3d* routines
84      and updated flow directives
85    
86    checkpoint58o_post
87    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
88      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
89    o change controling S/R for writing pickup file (new S/R do_write_pickup)
90      and clean-up reading/writing of pickup files.
91    o fix local version of read/write pickup (NH part) in rotating_tank/code
92    o simplify EXCH interface:
93     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
94     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
95    o added the regrid package
96    o shelfice:
97     - add a simple boundary layer scheme to reduce noise
98     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
99    
100    checkpoint58n_post
101    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
102       local variable (not in common block).
103    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
104      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
105      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
106        to work with SingleCpuIO.
107    o add "_d 0" to real constant of pkg/cfc subroutines ;
108       update exp. cfc_exemple & tutorial_cfc_offline output files.
109    o multi-threading and IO:
110      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
111        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
112      - barrier before and after reading.
113      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
114      - avoid using MDS_WRITELOCAL for LAND pkg output.
115      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
116        common-block variables ; Allows multi-threading with master-thread IO.
117    o change default MAX_NO_THREADS from 32 to 4 ;
118      and stop cleanly when MAX_NO_THREADS is too small.
119    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
120    
121    checkpoint58m_post
122    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
123       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
124    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
125       keep global_ocean.90x40x15 (for AD testing) with former secondary test
126       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
127    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
128        add MITgcm_tutorials (= code + all the tutorials)
129    o ecco, option to compute cost for total ssh (mean+anom)
130    o consistent with addition of ptracer and ssh in pkg/profiles
131    o profiles: adding ptracer and ssh
132    o testreport: change multi-test output-file name
133      (from output.txt.{name} to output.{name}.txt)
134    o profiles: now ok for mutli-tiles case
135    o seaice: add 4 parameters for different advection schemes for area,
136      (effective) seaice thickness, enthalphy, and snow height. Their default
137      is the standard parameter SEAICEadvScheme
138    o calc_gw:
139     - add cosFacU in zonal viscous flux (harmonic.visc.).
140     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
141       of tutorial_plume_on_slope.
142    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
143    o calc_gw: true flux-form, account for horizontal grid spacing.
144      update rotating_tank results, but not plume_on_slope (affected at
145      truncation level, 11 digits).
146    
147    checkpoint58l_post
148    o calc_gw:
149     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
150     - remove side-drag for now (need to fix it); update plume_on_slope results.
151     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
152    o commit code to make SST/SSS weights spatially variable
153      (based on either variable in-situ or variable initial T/S weights)
154    o pkg/ecco:
155      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
156        now based on horizontally varying weights wthetaLev, wsaltLev
157      * cost_averagesflags now returns year indices in addition to day, month
158      * sflux balance is performed on annual basis
159        (sflxumm, sfluxmm2, bal_sfluxmm)
160      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
161        including separate counting and multipliers
162    o pkg/rbcs
163      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
164    
165    checkpoint58k_post
166    o testreport:
167     - always build in dir. "build" (if not there, mkdir build instead of building
168       & running in input)
169     - run in dir run (if it exists), in build otherwise.
170     - call prepare_run (if input/prepare_run exists)
171     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
172    o pkg/exf modifications to interpolation and rotation routines for more
173       reasonable treatment of North Pole singularity: for tracers North Pole
174       value is set to northernmost zonal-mean value, for zonal velocity it is
175       set to zero, and for meridional velocity it is set to northernmost value.
176    o pkg/exf/exf_check_range.F
177     - add tile index to diagnostics and move stop statement to the very
178       end of the routine.
179    o pkg/diagnostics: (diagnostics_main_init.F)
180      define title of isomorphic variables according to the current config.
181    o pkg/thsice with pkg/seaice dynamics:
182    - fix domain of computation (interior only, required for exf) and do exchanges
183    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
184    o towards a standard way of dealing with multi-threading in MONITOR
185      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
186    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
187       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
188    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
189    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
190    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
191       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
192    o tracer advection:
193     - clean-up and simplify calc_common_factors.F
194     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
195       advection subroutine (but still not used within DST advection S/R)
196    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
197    
198    checkpoint58j_post
199    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
200      from file (collects calls previously in FORWARD_STEP)
201    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
202    o adjoint store dir. adjusted accordingly
203    o genmake2
204      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
205    
206    checkpoint58i_post
207    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
208      on wind stress (SEAICEstressFactor defaults to 1.)
209    o Total number of Timers is finite (<=40): comment out 2 non-essential one
210      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
211    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
212      on CS-grid: no longer loosing mass.
213    o exf & curvilinear-grid: no longer modify longitude xC & xG.
214    o pkg/ggl90: fix sloppy output and fix a bug
215    o pkg/seaice: added SEAICEuseEVPpickup parameter
216      - Set to false in order to start EVP solver with
217        non-EVP pickup files when using SEAICEuseEVP
218      - fix sign error in diffusion in seaice_calc_rhs
219    
220    checkpoint58h_post
221    * Modifications for bottom topography control
222      o replace hFacC by _hFacC at various places
223      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
224      o add non-self-adjoint cg2d_nsa
225      o update autodiff support routines
226      o re-initialise hfac after ctrl_depth_ini
227      o works for 5x5 box, doesnt work for global_ocean.90x40x15
228    * Adding verification for 5x5 box (4-layer) bottom topography control
229    
230    checkpoint58g_post
231    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
232       used for mean seasonal cycle, mean diurnal cycle); add an example
233       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
234    o pkg/ggl90:
235      - add parameter (minimum surface kinetic energy)
236      - fix bug (avoiding division by zero)
237  o couple pkg/thsice to pkg/seaice:  o couple pkg/thsice to pkg/seaice:
238    - modify advection in seaice to accomodate new scalar fields to be advected    - modify advection in seaice to accomodate new scalar fields to be advected
239    - only muliDimAdection scheme work with seaice/thsice    - only muliDimAdection scheme work with seaice/thsice

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