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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.607 by mlosch, Fri Feb 10 07:56:43 2006 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o adding precip control xx_precip  o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
8  o moved ptracer ctrl index 17 -> 32    if bulk formulae are used in long integration (especially EmPmR). Turn
9      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
10      if balancePrintMean, the imbalance that is substracted is printed to
11      STDOUT.
12    o fix bug (typo) in obcs_apply_eta.F
13    o add a new package shelfice which enables us to model the circulation
14      underneath shelf-ice with draughts of hundreds of meters.
15     - works
16     - to do: + include improved thermodynamics
17              + check whether kSurfC (from model/inc/SURFACE.h) can be used
18                instead of new field kTopC
19              + can we use topoFile, Ro_surf and existing code in ini_depth.F
20                instead of new field R_shelfIce and new code in ini_depth.F
21                and ini_mask_etc.F?
22    o seaice pkg:
23     - add a cpp-flag to include a simple formula for a salinity dependent
24       freezing point of sea water at the surface
25     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
26       meridional stresses are now different (and hopefully correct)
27    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
28       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
29       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
30    o pkg/diagnostics: add options and parameters for regional-statistics
31       diagnostics ; define regions by reading a region-mask from a file
32       (might add other options later)
33    o pkg/bulk_force:
34     - add option and parameters to use AIM surface-flux formulae.
35     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
36       others forcing fields (defined in PARM05, parameter file "data") are loaded
37       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
38     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
39     - use the right EXCH call for uwind,vwind (to work on CS-grid).
40     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
41       and parameters (note: calcWindStress replaces .NOT.readwindstress).
42     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
43    
44    checkpoint58
45    o add "--embed-source" option to genmake2 which, when the supporting
46      tools can be compiled (as determined by genmake2) will turn on the
47      embed_files package which then embeds the entire MITgcm source code
48      (*.[fFhc] + Makefile) used for the build within the executable
49      - requested by CNH but off by default
50      - adds a paltry <9MB to the mitgcmuv executable in most cases
51      - only writes the output when useEMBEDSRC in eedata is true
52    o clean up 3-dim. relaxation codes:
53      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
54      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
55      * Thanks to Tom Haine for testing!
56    
57    checkpoint57z_post
58    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
59      affects output (@ truncation level) of exp. plume_on_slope ; updated.
60    o fix the pickup behavior for obcs in combination with ptracers
61    o fix a bug in ptracers_external_fields_load
62    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
63      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
64    o transfered surface NH pressure to eta field (if exactConserv).
65    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
66         and update lab_sea output.txt file.
67    o completing 3-dim. relaxation code: additional term
68         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
69      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
70      * At compile time, in "EXF_OPTIONS.h" set
71          #define  ALLOW_CLIMTEMP_RELAXATION
72          #define  ALLOW_CLIMSALT_RELAXATION
73      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
74          tauThetaClimRelax3Dim = 15552000.0,
75          tauSaltClimRelax3Dim  = 15552000.0,
76      * 3 cases:
77          1) Use a constant-in-time 3-dim. field
78          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
79          3) Real-time relax. to time-evolving prescribed field
80    o Adding Laplacian-type smoothness constraint on
81      initial and boundary (forcing) controls (ic, bc)
82      * enable at compile-time via
83        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
84      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
85      * Absolute scale somewhat unclear so far
86      * no area weighting was included since no other cost term does so far
87    
88    checkpoint57y_post
89    First step for a NLFS adjoint
90    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
91    o new init. routines for calc_r_star, calc_surf_dr
92    o still need to deal with ini_masks_etc
93    o testreport seemed happy
94    checkpoint57y_pre
95    
96    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
97    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
98    o add new offset feature to offline pkg (plus minor cleanup)
99    o cfc fixes for final year of integration
100    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
101      be in GCHEM_OPTIONS).
102    
103    checkpoint57x_post
104    o fix testreport Pb in multiple test experiment.
105    o cleanup our namelist syntax in verification:
106      - make it more F95 standards compliant (some work still needed)
107      - allows the vast majority of our tests to work with gfortran
108    o Non-Hydrostatic:
109     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
110     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
111    o Allow to apply AB on T,S rather than on AB(gT,gS):
112     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
113     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
114       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
115     - need a "clever" read_pickup to restart from the other AB formulation
116    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
117    o remove some unused variables (reduces number of compiler warnings)
118    o adjoint
119      * Disable useVariableViscosity for adjoint for time being
120        (there are a number of extensive recomputations)
121      * Initialize certain variables needed for adjoint
122    
123    checkpoint57w_post
124    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
125                 fix the singleCpuIO RS version of MDSWRITEFIELD
126       and add a WARNING if using globalFiles=T with multi-processors.
127    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
128      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
129    o tracer advection scheme:
130      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
131       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
132       was not very convenient).
133      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
134       (further tests needed for the implicit DST & Flux-Limiter schemes).
135    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
136      and sRef for convenience, handy, when you want to initialize
137      ptracers in a large domain with a constant non-zero value. Also,
138      untangle ptracers_init.F a little.
139    
140    checkpoint57v_post
141    o change dome exp. to use variable viscosity in side-drag terms.
142    o remove all the files from the cfc_offline test since they are now
143      incorporated into tutorial_cfc_offline which has been producing
144      identical results for a few days of testing
145    o add new parameter: sideDragFactor to enable half-slip-side BC
146      and change side-drag S/R to use viscosity from mom_calc_visc
147      (can switch back by setting sideDragFactor=0.); affects results at
148      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
149       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
150    o vorticity & strain are now computed without masking, to account for
151      no-slip-side BC in variable viscosity calculation ; mask is applied
152      anyway later on, before computing advection/coriolis terms.
153    o modify exp4 to test new obcs support for reading from external files
154      and for passive tracers
155    o fix behavior of ptracers_monitor when monitor output is written to a
156      netcdf-file; still not independent of monitor.F (writes in the same
157      file).
158    o change default value of tRef (put a uniform, meaningful value for ocean
159      & atmos) and initialize sRef (was missing, as Martin mentioned).
160    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
161      to be proportional to enstrophy dissipation length.  Thus,
162       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
163      This is now consistent with Smagorinsky and with the manual.
164    
165    checkpoint57u_post
166    o OBCS and PTRACERS: add open boundary support for passive tracers
167      - either use homogenous (pseudo) v.Neumann conditions or prescribe
168        OB-values from file; this is not different from the way theta and salinity
169        are treated
170      - however, Orlanski-radiation conditions are not supported, and the model
171        will stop if you use pTracers and Orlanski at the same time.
172      - beefed up the rountine obcs_external_fields_load: now only those open
173        boundary values are overwritten with values from files for which there
174        are really files, otherwise the OB-fields remain untouched. This makes
175        it possible to use different OBs at different ends of the domain (as
176        with EXF)
177    o reduce number of exch calls in shap_filt (s2).
178    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
179      truncation level) 4/5 MLAdjust test results (11&12 digits match).
180    
181    checkpoint57t_post
182    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
183    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
184      same truncation, independent of the face number: affects affects several
185      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
186    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
187      note that biharmonic viscosity + no-slip was not tested in any experiment.
188    o fix bug in non-linear free-surf side-drag ; generate new output for
189      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
190    o make mnc honor the writeBinaryPrec flag for most kinds of output
191    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
192    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
193      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
194    o add brackets in multi-terms sum to get same truncation, independent of
195      the face number (manage to get exactly same value of gU,gV at the cs-edge)
196      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
197    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
198      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
199      a maximum grid-scale Reynolds number.  Also, changes all length calculations
200      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
201      Suggested values of viscosity parameters found in mom_calc_visc.
202      Many new viscosity diagnostics available.
203    
204    checkpoint57s_post
205    o Add clearing-house for viscosity calculations, mom_calc_visc and
206      correct numerous bugs in LeithD and Smagorinsky discretizations.  
207      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
208      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
209      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
210      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
211      The Strain-Tension form is now called with useStrainTensonVisc=.true.
212      ViscAhStrain and viscAhTension are now retired.
213    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
214    o In response to JMC's bug report, genmake2 now ignores any soft-links
215      that it finds in the *current* directory when searching for files.
216      Soft-links found in any other source directories will still work as
217      they did before.
218    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
219      a C routine to unlimit the stack size
220    o mnc-ify pkg/aim snapshot vars
221    o mnc-ify pkg/land as requested by Daniel
222    o various changes to mnc including:
223      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
224      - output can now be grouped so that all files within a group
225          change the ITER portion of their names in lock-step together
226      - can now read ("global") PER-FACE (in addition to PER-TILE) files
227          and works with both EXCH1 and EXCH2 (but needs more testing)
228      - writing works for all verification test cases w/ g77 on Linux
229    
230    checkpoint57r_post
231    o make MNC variable initialization happen earlier
232    o add diagnostics for (almost) each term of the momentum Eq.
233    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
234    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
235    o remove MINIMAL_TAVE_OUTPUT option ;
236      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
237    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
238      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
239    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
240    o add time-dependent SST, SSS control
241    o cost terms in ecco/ modularized (new cost_generic.F)
242    o cost_averages routines are modularized (new cost_averagesgeneric.F)
243    o new infrastructure for seaice model vs. obs misfits in seaice/
244      * driver from the_main_loop.F is seaice_cost_driver.F
245      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
246      * gradient check in Exp. 6a of natl_box_adjoint/
247    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
248      (see README file)
249    
250    checkpoint57q_post
251    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
252    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
253      - bug was reported by Jean-Michel and Ian Fenty
254    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
255      update exp. cpl_aim+ocn output.
256    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
257      Needed for high-res. runs with large global files
258      to be able to limit tapelev size
259    o Changed some tests for adjoint:
260      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
261      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
262      * global_ocean.90x40x15/ back to default 3-level checkpointing
263    o Modifications to enable scripted COMMON to MODULE conversion
264      * verification/OpenAD/code/ has necessary scripts and description;
265      * converts, compiles and runs successfully;
266    
267    checkpoint57p_post
268    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
269    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
270      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
271    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
272    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
273      (was already the case for dissipation with mom_vecinv,
274       and also the case for grad.PhiHyd when staggered-timeStep)
275      This will allow to put dissipation out-off the AB time-stepping.
276     Unfortunately, affects truncation error. Update output of exp. that "fails"
277      (cg2d matching number) and leave the others for later: front_relax(10),
278      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
279      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
280    
281    checkpoint57o_post
282    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
283      (2) its ready to be documented during the 20050801 DocFest
284    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
285      for ideal_2D_oce and lab_sea on linux_ia32_g77
286    o set to #undef CTRL_SET_OLD_MAXCVARS_30
287      in global1x1_tot/code_seaice_adj to access indices 32, 33
288      (worth another tag)
289    
290    checkpoint57n_post
291    o adding precip control xx_precip 32
292    o adding swflux control xx_swflux 33
293    o Replacing 10 forcing penalty cost routines by 1 generic.
294    o Implementing partitioning in time-mean and variable adjustment
295      for atmos. state.
296    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
297  o in natl_box_adjoint:  o in natl_box_adjoint:
298    * updated: results_bulk/    * updated exp 1 to 10
299    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
300    o updated global1x1/*_seaice_adj/
301      to incorporate latest changes
302    o enable useSingleCpuIO for mdsio vector routines
303      (applies in particular to tapelev I/O)
304    o removed inefficient K-loop in all active_file*control*.F
305    
306  checkpoint57m_post  checkpoint57m_post
307  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)

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